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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1810.11918 | Le Yan | Le Yan, Richard Neher, and Boris I Shraiman | Phylodynamics of rapidly adapting pathogens: extinction and speciation
of a Red Queen | 15 pages, 9 figures, 1 table | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Rapidly evolving pathogens like influenza viruses can persist by accumulating
antigenic novelty fast enough to evade the adaptive immunity of the host
population, yet without continuous accumulation of genetic diversity. This
dynamical state is often compared to the Red Queen evolving as fast as it can
just to mainta... | [
{
"created": "Mon, 29 Oct 2018 01:29:34 GMT",
"version": "v1"
}
] | 2018-10-30 | [
[
"Yan",
"Le",
""
],
[
"Neher",
"Richard",
""
],
[
"Shraiman",
"Boris I",
""
]
] | Rapidly evolving pathogens like influenza viruses can persist by accumulating antigenic novelty fast enough to evade the adaptive immunity of the host population, yet without continuous accumulation of genetic diversity. This dynamical state is often compared to the Red Queen evolving as fast as it can just to maintain... |
1405.5007 | Igor Goychuk | Igor Goychuk | Stochastic modeling of excitable dynamics: improved Langevin model for
mesoscopic channel noise | V.M. Mladenov and P.C. Ivanov (Eds.): NDES 2014, Communications in
Computer and Information Science, vol. 438 (Springer, Switzerland, 2014), pp.
325-332 | Communications in Computer and Information Science 438, 325 (2014) | 10.1007/978-3-319-08672-9_38 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Influence of mesoscopic channel noise on excitable dynamics of living cells
became a hot subject within the last decade, and the traditional biophysical
models of neuronal dynamics such as Hodgkin-Huxley model have been generalized
to incorporate such effects. There still exists but a controversy on how to do
it in a... | [
{
"created": "Tue, 20 May 2014 09:20:34 GMT",
"version": "v1"
}
] | 2014-09-24 | [
[
"Goychuk",
"Igor",
""
]
] | Influence of mesoscopic channel noise on excitable dynamics of living cells became a hot subject within the last decade, and the traditional biophysical models of neuronal dynamics such as Hodgkin-Huxley model have been generalized to incorporate such effects. There still exists but a controversy on how to do it in a p... |
2112.10989 | Yifei Li | Yifei Li, Pascal R. Buenzli and Matthew J. Simpson | Interpreting how nonlinear diffusion affects the fate of bistable
populations using a discrete modelling framework | 40 pages, 11 figures, 1 supplementary material document | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding whether a population will survive and flourish or become
extinct is a central question in population biology. One way of exploring this
question is to study population dynamics using reaction-diffusion equations,
where migration is usually represented as a linear diffusion term, and
birth-death is repre... | [
{
"created": "Tue, 21 Dec 2021 05:12:48 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Jan 2022 02:56:37 GMT",
"version": "v2"
}
] | 2022-01-10 | [
[
"Li",
"Yifei",
""
],
[
"Buenzli",
"Pascal R.",
""
],
[
"Simpson",
"Matthew J.",
""
]
] | Understanding whether a population will survive and flourish or become extinct is a central question in population biology. One way of exploring this question is to study population dynamics using reaction-diffusion equations, where migration is usually represented as a linear diffusion term, and birth-death is represe... |
0803.2904 | Gabriel Cardona | Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente | A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks | 16 pages, 16 figures | null | null | null | q-bio.PE cs.CE cs.DM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The presence of reticulate evolutionary events in phylogenies turn
phylogenetic trees into phylogenetic networks. These events imply in particular
that there may exist multiple evolutionary paths from a non-extant species to
an extant one, and this multiplicity makes the comparison of phylogenetic
networks much more ... | [
{
"created": "Wed, 19 Mar 2008 22:24:11 GMT",
"version": "v1"
}
] | 2008-03-21 | [
[
"Cardona",
"Gabriel",
""
],
[
"Llabres",
"Merce",
""
],
[
"Rossello",
"Francesc",
""
],
[
"Valiente",
"Gabriel",
""
]
] | The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one, and this multiplicity makes the comparison of phylogenetic networks much more di... |
1903.07317 | Fabian Eitel | Moritz B\"ohle and Fabian Eitel and Martin Weygandt and Kerstin Ritter | Layer-Wise Relevance Propagation for Explaining Deep Neural Network
Decisions in MRI-Based Alzheimer's Disease Classification | null | Front. Aging Neurosci., 31 July 2019 | 10.3389/fnagi.2019.00194 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep neural networks have led to state-of-the-art results in many medical
imaging tasks including Alzheimer's disease (AD) detection based on structural
magnetic resonance imaging (MRI) data. However, the network decisions are often
perceived as being highly non-transparent, making it difficult to apply these
algorit... | [
{
"created": "Mon, 18 Mar 2019 09:18:06 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Aug 2019 15:46:15 GMT",
"version": "v2"
}
] | 2019-08-28 | [
[
"Böhle",
"Moritz",
""
],
[
"Eitel",
"Fabian",
""
],
[
"Weygandt",
"Martin",
""
],
[
"Ritter",
"Kerstin",
""
]
] | Deep neural networks have led to state-of-the-art results in many medical imaging tasks including Alzheimer's disease (AD) detection based on structural magnetic resonance imaging (MRI) data. However, the network decisions are often perceived as being highly non-transparent, making it difficult to apply these algorithm... |
0905.1410 | Yasser Roudi | Yasser Roudi, Erik Aurell, John Hertz | Statistical physics of pairwise probability models | 25 pages, 3 figures | Front. Comput. Neurosci (2009) 3:22 | 10.3389/neuro.10.022.2009 | NORDITA-2009-25 | q-bio.QM cond-mat.dis-nn q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical models for describing the probability distribution over the
states of biological systems are commonly used for dimensional reduction. Among
these models, pairwise models are very attractive in part because they can be
fit using a reasonable amount of data: knowledge of the means and correlations
between p... | [
{
"created": "Sat, 9 May 2009 14:10:37 GMT",
"version": "v1"
}
] | 2009-11-30 | [
[
"Roudi",
"Yasser",
""
],
[
"Aurell",
"Erik",
""
],
[
"Hertz",
"John",
""
]
] | Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of data: knowledge of the means and correlations between pai... |
1603.09195 | Vladimir Boza | Vladim\'ir Bo\v{z}a, Bro\v{n}a Brejov\'a and Tom\'a\v{s} Vina\v{r} | DeepNano: Deep Recurrent Neural Networks for Base Calling in MinION
Nanopore Reads | null | PLoS ONE 12(6): e0178751 | 10.1371/journal.pone.0178751 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: The MinION device by Oxford Nanopore is the first portable
sequencing device. MinION is able to produce very long reads (reads over
100~kBp were reported), however it suffers from high sequencing error rate. In
this paper, we show that the error rate can be reduced by improving the base
calling process.
... | [
{
"created": "Wed, 30 Mar 2016 13:52:59 GMT",
"version": "v1"
}
] | 2017-06-29 | [
[
"Boža",
"Vladimír",
""
],
[
"Brejová",
"Broňa",
""
],
[
"Vinař",
"Tomáš",
""
]
] | Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we show that the error rate can be reduced by improving the base calling process. Res... |
1810.08725 | Sergei Gepshtein | Sergei Gepshtein, Ambarish S. Pawar, Sergey Saveliev, Thomas D.
Albright | Neural wave interference and intrinsic tuning in distributed
excitatory-inhibitory networks | 15 pages, 5 figures, 1 table | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We developed a model of cortical computation that implements key features of
cortical circuitry and is capable of describing propagation of neural signals
between cortical locations in response to spatially distributed stimuli. The
model is based on the canonical neural circuit that consists of excitatory and
inhibit... | [
{
"created": "Sat, 20 Oct 2018 01:20:12 GMT",
"version": "v1"
}
] | 2018-10-23 | [
[
"Gepshtein",
"Sergei",
""
],
[
"Pawar",
"Ambarish S.",
""
],
[
"Saveliev",
"Sergey",
""
],
[
"Albright",
"Thomas D.",
""
]
] | We developed a model of cortical computation that implements key features of cortical circuitry and is capable of describing propagation of neural signals between cortical locations in response to spatially distributed stimuli. The model is based on the canonical neural circuit that consists of excitatory and inhibitor... |
2004.07208 | Sandor D. Katz | Z. Fodor, S.D. Katz, T.G. Kovacs | Why integral equations should be used instead of differential equations
to describe the dynamics of epidemics | 11 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is of vital importance to understand and track the dynamics of rapidly
unfolding epidemics. The health and economic consequences of the current
COVID-19 pandemic provide a poignant case. Here we point out that since they
are based on differential equations, the most widely used models of epidemic
spread are plague... | [
{
"created": "Wed, 15 Apr 2020 17:09:44 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Apr 2020 16:15:56 GMT",
"version": "v2"
}
] | 2020-04-28 | [
[
"Fodor",
"Z.",
""
],
[
"Katz",
"S. D.",
""
],
[
"Kovacs",
"T. G.",
""
]
] | It is of vital importance to understand and track the dynamics of rapidly unfolding epidemics. The health and economic consequences of the current COVID-19 pandemic provide a poignant case. Here we point out that since they are based on differential equations, the most widely used models of epidemic spread are plagued ... |
2004.04768 | Zhibo Yang | Jianyuan Deng, Zhibo Yang, Yao Li, Dimitris Samaras, Fusheng Wang | Towards Better Opioid Antagonists Using Deep Reinforcement Learning | 10 pages, 7 figures | null | null | null | q-bio.BM cs.AI cs.CL cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Naloxone, an opioid antagonist, has been widely used to save lives from
opioid overdose, a leading cause for death in the opioid epidemic. However,
naloxone has short brain retention ability, which limits its therapeutic
efficacy. Developing better opioid antagonists is critical in combating the
opioid epidemic.Inste... | [
{
"created": "Thu, 26 Mar 2020 15:28:50 GMT",
"version": "v1"
}
] | 2020-04-13 | [
[
"Deng",
"Jianyuan",
""
],
[
"Yang",
"Zhibo",
""
],
[
"Li",
"Yao",
""
],
[
"Samaras",
"Dimitris",
""
],
[
"Wang",
"Fusheng",
""
]
] | Naloxone, an opioid antagonist, has been widely used to save lives from opioid overdose, a leading cause for death in the opioid epidemic. However, naloxone has short brain retention ability, which limits its therapeutic efficacy. Developing better opioid antagonists is critical in combating the opioid epidemic.Instead... |
1710.10861 | Caroline Gr\"onwall | Caroline Gronwall, Khaled Amara, Uta Hardt, Akilan Krishnamurthy,
Johanna Steen, Marianne Engstrom, Meng Sun, A. Jimmy Ytterberg, Roman A.
Zubarev, Dagmar Scheel-Toellner, Jeffrey D. Greenberg, Lars Klareskog, Anca
I. Catrina, Vivianne Malmstrom and Gregg J. Silverman | Autoreactivity to malondialdehyde-modifications in rheumatoid arthritis
is linked to disease activity and synovial pathogenesis | null | J Autoimmun. 2017 Nov; 84:29-45 | 10.1016/j.jaut.2017.06.004 | null | q-bio.BM q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Oxidation-associated malondialdehyde (MDA) modification of proteins can
generate immunogenic neo-epitopes that are recognized by autoantibodies. In
health, IgM antibodies to MDA-adducts are part of the natural antibody pool,
while elevated levels of IgG anti-MDA are associated with inflammatory
conditions. Yet, in hu... | [
{
"created": "Mon, 30 Oct 2017 10:50:19 GMT",
"version": "v1"
}
] | 2017-10-31 | [
[
"Gronwall",
"Caroline",
""
],
[
"Amara",
"Khaled",
""
],
[
"Hardt",
"Uta",
""
],
[
"Krishnamurthy",
"Akilan",
""
],
[
"Steen",
"Johanna",
""
],
[
"Engstrom",
"Marianne",
""
],
[
"Sun",
"Meng",
""
],
[
... | Oxidation-associated malondialdehyde (MDA) modification of proteins can generate immunogenic neo-epitopes that are recognized by autoantibodies. In health, IgM antibodies to MDA-adducts are part of the natural antibody pool, while elevated levels of IgG anti-MDA are associated with inflammatory conditions. Yet, in huma... |
1711.01629 | Rakesh Malladi | Rakesh Malladi, Don H Johnson, Giridhar P Kalamangalam, Nitin Tandon
and Behnaam Aazhang | Mutual Information in Frequency and its Application to Measure
Cross-Frequency Coupling in Epilepsy | This paper is accepted for publication in IEEE Transactions on Signal
Processing and contains 15 pages, 9 figures and 1 table | null | 10.1109/TSP.2018.2821627 | null | q-bio.NC cs.IT eess.SP math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We define a metric, mutual information in frequency (MI-in-frequency), to
detect and quantify the statistical dependence between different frequency
components in the data, referred to as cross-frequency coupling and apply it to
electrophysiological recordings from the brain to infer cross-frequency
coupling. The cur... | [
{
"created": "Sun, 5 Nov 2017 18:16:06 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Mar 2018 05:47:37 GMT",
"version": "v2"
}
] | 2018-05-23 | [
[
"Malladi",
"Rakesh",
""
],
[
"Johnson",
"Don H",
""
],
[
"Kalamangalam",
"Giridhar P",
""
],
[
"Tandon",
"Nitin",
""
],
[
"Aazhang",
"Behnaam",
""
]
] | We define a metric, mutual information in frequency (MI-in-frequency), to detect and quantify the statistical dependence between different frequency components in the data, referred to as cross-frequency coupling and apply it to electrophysiological recordings from the brain to infer cross-frequency coupling. The curre... |
1201.3749 | Steffen Waldherr | Steffen Waldherr and Bernard Haasdonk | Efficient parametric analysis of the chemical master equation through
model order reduction | 23 pages, 8 figures, 2 tables | BMC Systems Biology 2012, 6:81 | 10.1186/1752-0509-6-81 | null | q-bio.QM math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Stochastic biochemical reaction networks are commonly modelled by
the chemical master equation, and can be simulated as first order linear
differential equations through a finite state projection. Due to the very high
state space dimension of these equations, numerical simulations are
computationally expe... | [
{
"created": "Wed, 18 Jan 2012 10:41:12 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Jul 2012 15:36:07 GMT",
"version": "v2"
}
] | 2012-07-10 | [
[
"Waldherr",
"Steffen",
""
],
[
"Haasdonk",
"Bernard",
""
]
] | Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state space dimension of these equations, numerical simulations are computationally expens... |
2007.09856 | Bijan Sarkar | Bijan Sarkar | The cooperation-defection evolution on social networks | A scientific explanation can be accomplished through a simple easier
logical procedure. A time consuming trick can also be replaced by an elegant
trick | Physica A: Statistical Mechanics and its Applications, Volume 584,
15 December 2021, 126381 | 10.1016/j.physa.2021.126381 | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Without contributing, defectors take more benefit from social resources than
cooperators which is the reflection of a specific character of individuals.
However, natural physical mechanisms of our society promote cooperation. Thus,
in the long run, the evolution about genetic variation is something more than
the soci... | [
{
"created": "Mon, 20 Jul 2020 02:58:33 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Sep 2021 14:04:42 GMT",
"version": "v2"
}
] | 2021-09-16 | [
[
"Sarkar",
"Bijan",
""
]
] | Without contributing, defectors take more benefit from social resources than cooperators which is the reflection of a specific character of individuals. However, natural physical mechanisms of our society promote cooperation. Thus, in the long run, the evolution about genetic variation is something more than the social... |
1307.7933 | Aaron Darling | Viraj Deshpande, Eric DK Fung, Son Pham, and Vineet Bafna | Cerulean: A hybrid assembly using high throughput short and long reads | Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013) | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome assembly using high throughput data with short reads, arguably,
remains an unresolvable task in repetitive genomes, since when the length of a
repeat exceeds the read length, it becomes difficult to unambiguously connect
the flanking regions. The emergence of third generation sequencing (Pacific
Biosciences) w... | [
{
"created": "Tue, 30 Jul 2013 12:05:30 GMT",
"version": "v1"
}
] | 2013-07-31 | [
[
"Deshpande",
"Viraj",
""
],
[
"Fung",
"Eric DK",
""
],
[
"Pham",
"Son",
""
],
[
"Bafna",
"Vineet",
""
]
] | Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking regions. The emergence of third generation sequencing (Pacific Biosciences) wit... |
q-bio/0506029 | Moo Young Choi | J. Choi, M.Y. Choi, and B.-G. Yoon | Dynamic model for failures in biological systems | To appear in Europhys. Lett | null | 10.1209/epl/i2004-10544-3 | null | q-bio.CB physics.bio-ph | null | A dynamic model for failures in biological organisms is proposed and studied
both analytically and numerically. Each cell in the organism becomes dead under
sufficiently strong stress, and is then allowed to be healed with some
probability. It is found that unlike the case of no healing, the organism in
general does ... | [
{
"created": "Mon, 20 Jun 2005 20:26:47 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Choi",
"J.",
""
],
[
"Choi",
"M. Y.",
""
],
[
"Yoon",
"B. -G.",
""
]
] | A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability. It is found that unlike the case of no healing, the organism in general does no... |
2405.06377 | Robert Worden | Robert Worden | The Evolution of Language and Human Rationality | 12 pages; presented at the 14th EvoLang conference, 2024 | null | null | null | q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | If language evolved by sexual selection to display superior intelligence,
then we require conversational skills, to impress other people, gain high
social status, and get a mate. Conversational skills include a Theory of Mind,
a sense of self, self esteem and social emotions. To be impressive, we must
converse fluent... | [
{
"created": "Fri, 10 May 2024 10:25:21 GMT",
"version": "v1"
}
] | 2024-05-13 | [
[
"Worden",
"Robert",
""
]
] | If language evolved by sexual selection to display superior intelligence, then we require conversational skills, to impress other people, gain high social status, and get a mate. Conversational skills include a Theory of Mind, a sense of self, self esteem and social emotions. To be impressive, we must converse fluently... |
2101.01548 | Ahlem Karbab | Karbab Ahlem | Extraction, isolation, structure elucidation and evaluation of toxicity,
anti-inflammatory and analgesic activity of Pituranthos scoparius
constituents | null | null | null | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The present work aimed to investigate an ethnobotanical survey about
Pituranthos scoparius and assess the toxicity, anti-inflammatory (in vitro, and
in vivo) potential, in vitro antioxidant, and analgesic effects of stems and
roots of Pituranthos scoparius. Furthermore; to isolate and elucidate the
chemical constitue... | [
{
"created": "Fri, 1 Jan 2021 19:32:47 GMT",
"version": "v1"
}
] | 2021-01-06 | [
[
"Ahlem",
"Karbab",
""
]
] | The present work aimed to investigate an ethnobotanical survey about Pituranthos scoparius and assess the toxicity, anti-inflammatory (in vitro, and in vivo) potential, in vitro antioxidant, and analgesic effects of stems and roots of Pituranthos scoparius. Furthermore; to isolate and elucidate the chemical constituent... |
1408.2474 | Daniele Cappelletti | Daniele Cappelletti and Carsten Wiuf | Elimination of Intermediate Species in Multiscale Stochastic Reaction
Networks | null | null | 10.1214/15-AAP1166 | null | q-bio.MN math.DS math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study networks of biochemical reactions modelled by continuous-time Markov
processes. Such networks typically contain many molecular species and reactions
and are hard to study analytically as well as by simulation. Particularly, we
are interested in reaction networks with intermediate species such as the
substrat... | [
{
"created": "Mon, 11 Aug 2014 17:23:43 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Oct 2015 01:31:46 GMT",
"version": "v2"
},
{
"created": "Mon, 30 Nov 2015 15:40:54 GMT",
"version": "v3"
}
] | 2018-05-22 | [
[
"Cappelletti",
"Daniele",
""
],
[
"Wiuf",
"Carsten",
""
]
] | We study networks of biochemical reactions modelled by continuous-time Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are interested in reaction networks with intermediate species such as the substrate-... |
1606.00821 | Diego Mateos | R. Guevara Erra, D. M. Mateos, R. Wennberg, J.L. Perez Velazquez | Towards a statistical mechanics of consciousness: maximization of number
of connections is associated with conscious awareness | 17 page, 4 figures, 2 tables | null | 10.1103/PhysRevE.94.052402 | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | It has been said that complexity lies between order and disorder. In the case
of brain activity, and physiology in general, complexity issues are being
considered with increased emphasis. We sought to identify features of brain
organization that are optimal for sensory processing, and that may guide the
emergence of ... | [
{
"created": "Wed, 1 Jun 2016 17:45:43 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Jan 2017 19:42:45 GMT",
"version": "v2"
}
] | 2017-01-11 | [
[
"Erra",
"R. Guevara",
""
],
[
"Mateos",
"D. M.",
""
],
[
"Wennberg",
"R.",
""
],
[
"Velazquez",
"J. L. Perez",
""
]
] | It has been said that complexity lies between order and disorder. In the case of brain activity, and physiology in general, complexity issues are being considered with increased emphasis. We sought to identify features of brain organization that are optimal for sensory processing, and that may guide the emergence of co... |
2301.11126 | Yue Wang | Yue Wang | Three facets of mathematical cancer biology research | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Cancer, as the uncontrollable cell growth, is related to many branches of
biology. In this review, we will discuss three mathematical approaches for
studying cancer biology: population dynamics, gene regulation, and
developmental biology. If we understand all biochemical mechanisms of cancer
cells, we can directly ca... | [
{
"created": "Tue, 24 Jan 2023 18:06:52 GMT",
"version": "v1"
}
] | 2023-01-27 | [
[
"Wang",
"Yue",
""
]
] | Cancer, as the uncontrollable cell growth, is related to many branches of biology. In this review, we will discuss three mathematical approaches for studying cancer biology: population dynamics, gene regulation, and developmental biology. If we understand all biochemical mechanisms of cancer cells, we can directly calc... |
1112.5905 | Boris Shraiman | Kevin K. Chiou, Lars Hufnagel and Boris I. Shraiman | Mechanical Stress Inference for Two Dimensional Cell Arrays | null | null | 10.1371/journal.pcbi.1002512 | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many morphogenetic processes involve mechanical rearrangement of epithelial
tissues that is driven by precisely regulated cytoskeletal forces and cell
adhesion. The mechanical state of the cell and intercellular adhesion are not
only the targets of regulation, but are themselves likely signals that
coordinate develop... | [
{
"created": "Tue, 27 Dec 2011 01:15:10 GMT",
"version": "v1"
}
] | 2015-06-03 | [
[
"Chiou",
"Kevin K.",
""
],
[
"Hufnagel",
"Lars",
""
],
[
"Shraiman",
"Boris I.",
""
]
] | Many morphogenetic processes involve mechanical rearrangement of epithelial tissues that is driven by precisely regulated cytoskeletal forces and cell adhesion. The mechanical state of the cell and intercellular adhesion are not only the targets of regulation, but are themselves likely signals that coordinate developme... |
1511.09166 | Benjamin Dickens | Benjamin Dickens, Charles K. Fisher, and Pankaj Mehta | An analytically tractable model for community ecology with many species | 15 pages, 4 figures | Phys. Rev. E 94, 022423 (2016) | 10.1103/PhysRevE.94.022423 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A fundamental problem in community ecology is to understand how ecological
processes such as selection, drift, and immigration give rise to observed
patterns in species composition and diversity. Here, we present a simple,
analytically tractable, presence-absence (PA) model for community assembly and
use it to ask ho... | [
{
"created": "Mon, 30 Nov 2015 05:38:45 GMT",
"version": "v1"
}
] | 2016-09-07 | [
[
"Dickens",
"Benjamin",
""
],
[
"Fisher",
"Charles K.",
""
],
[
"Mehta",
"Pankaj",
""
]
] | A fundamental problem in community ecology is to understand how ecological processes such as selection, drift, and immigration give rise to observed patterns in species composition and diversity. Here, we present a simple, analytically tractable, presence-absence (PA) model for community assembly and use it to ask how ... |
1705.03407 | Ulysse Herbach | Ulysse Herbach, Arnaud Bonnaffoux, Thibault Espinasse, Olivier
Gandrillon | Inferring gene regulatory networks from single-cell data: a mechanistic
approach | null | null | 10.1186/s12918-017-0487-0 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recent development of single-cell transcriptomics has enabled gene
expression to be measured in individual cells instead of being
population-averaged. Despite this considerable precision improvement, inferring
regulatory networks remains challenging because stochasticity now proves to
play a fundamental role in g... | [
{
"created": "Tue, 9 May 2017 16:16:45 GMT",
"version": "v1"
},
{
"created": "Wed, 24 May 2017 18:42:40 GMT",
"version": "v2"
},
{
"created": "Sat, 25 Nov 2017 02:59:55 GMT",
"version": "v3"
}
] | 2017-11-28 | [
[
"Herbach",
"Ulysse",
""
],
[
"Bonnaffoux",
"Arnaud",
""
],
[
"Espinasse",
"Thibault",
""
],
[
"Gandrillon",
"Olivier",
""
]
] | The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks remains challenging because stochasticity now proves to play a fundamental role in gen... |
1912.03949 | Emmanuelle Bayer | Dawei Yan, Shri Yadav (IIT Roorkee), Andrea Paterlini, William Nicolas
(LBM), Ilya Belevich, Magali Grison (LBM), Anne Vaten, Leila Karami, Sedeer
El-Showk, Jung-Youn Lee, Gosia Murawska (LBNL), Jenny Mortimer (LBNL),
Michael Knoblauch, Eija Jokitalo, Jonathan Markham, Emmanuelle Bayer (LBM),
Yk\"a Helariutta | Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and
phloem unloading | Nature Plants, Nature Publishing Group, In press | null | 10.1038/s41477-019-0429-5 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | During phloem unloading, multiple cell-to-cell transport events move organic
substances to the root meristem. Although the primary unloading event from the
sieve elements to the phloem pole pericycle has been characterized to some
extent, little is known about post-sieve element unloading. Here, we report a
novel gen... | [
{
"created": "Mon, 9 Dec 2019 10:22:21 GMT",
"version": "v1"
}
] | 2019-12-10 | [
[
"Yan",
"Dawei",
"",
"IIT Roorkee"
],
[
"Yadav",
"Shri",
"",
"IIT Roorkee"
],
[
"Paterlini",
"Andrea",
"",
"LBM"
],
[
"Nicolas",
"William",
"",
"LBM"
],
[
"Belevich",
"Ilya",
"",
"LBM"
],
[
"Grison",
"Magali... | During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene,... |
1411.4321 | Andrew Kennard | Andrew S. Kennard (1 and 2), Matteo Osella (3), Avelino Javer (1),
Jacopo Grilli (4 and 5), Philippe Nghe (6 and 7), Sander Tans (6), Pietro
Cicuta (1), Marco Cosentino Lagomarsino (8 and 9) ((1) Cavendish Laboratory
University of Cambridge, (2) Biophysics Program Stanford University, (3)
Dipartimento di Fisica... | Individuality and universality in the growth-division laws of single E.
coli cells | 39 pages, 7 main figures, 17 supplementary figures | Phys. Rev. E (2016) 93(1): 012408 | 10.1103/PhysRevE.93.012408 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mean size of exponentially dividing E. coli cells cultured in different
nutrient conditions is known to depend on the mean growth rate only. However,
the joint fluctuations relating cell size, doubling time and individual growth
rate are only starting to be characterized. Recent studies in bacteria (i)
revealed t... | [
{
"created": "Sun, 16 Nov 2014 23:09:52 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Feb 2015 10:08:56 GMT",
"version": "v2"
},
{
"created": "Mon, 22 Jun 2015 07:03:35 GMT",
"version": "v3"
},
{
"created": "Sat, 26 Dec 2015 18:54:18 GMT",
"version": "v4"
}
] | 2016-01-25 | [
[
"Kennard",
"Andrew S.",
"",
"1 and 2"
],
[
"Osella",
"Matteo",
"",
"4 and 5"
],
[
"Javer",
"Avelino",
"",
"4 and 5"
],
[
"Grilli",
"Jacopo",
"",
"4 and 5"
],
[
"Nghe",
"Philippe",
"",
"6 and 7"
],
[
"Tans",
... | The mean size of exponentially dividing E. coli cells cultured in different nutrient conditions is known to depend on the mean growth rate only. However, the joint fluctuations relating cell size, doubling time and individual growth rate are only starting to be characterized. Recent studies in bacteria (i) revealed the... |
2003.13967 | Raphael Wittkowski | Michael te Vrugt, Jens Bickmann, Raphael Wittkowski | Effects of social distancing and isolation on epidemic spreading: a
dynamical density functional theory model | 9 pages, 3 figures | Nature Communications 11, 5576 (2020) | 10.1038/s41467-020-19024-0 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For preventing the spread of epidemics such as the coronavirus disease
COVID-19, social distancing and the isolation of infected persons are crucial.
However, existing reaction-diffusion equations for epidemic spreading are
incapable of describing these effects. We present an extended model for disease
spread based o... | [
{
"created": "Tue, 31 Mar 2020 06:17:01 GMT",
"version": "v1"
},
{
"created": "Fri, 8 May 2020 16:55:26 GMT",
"version": "v2"
}
] | 2020-11-18 | [
[
"Vrugt",
"Michael te",
""
],
[
"Bickmann",
"Jens",
""
],
[
"Wittkowski",
"Raphael",
""
]
] | For preventing the spread of epidemics such as the coronavirus disease COVID-19, social distancing and the isolation of infected persons are crucial. However, existing reaction-diffusion equations for epidemic spreading are incapable of describing these effects. We present an extended model for disease spread based on ... |
2212.08826 | Xin Xia | Xin Xia, Yansen Su, Chunhou Zheng, Xiangxiang Zeng | Molecule optimization via multi-objective evolutionary in implicit
chemical space | 38 pages, 6 figures, 74 conferences | null | null | null | q-bio.BM cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine learning methods have been used to accelerate the molecule
optimization process. However, efficient search for optimized molecules
satisfying several properties with scarce labeled data remains a challenge for
machine learning molecule optimization. In this study, we propose MOMO, a
multi-objective molecule o... | [
{
"created": "Sat, 17 Dec 2022 09:09:23 GMT",
"version": "v1"
}
] | 2022-12-20 | [
[
"Xia",
"Xin",
""
],
[
"Su",
"Yansen",
""
],
[
"Zheng",
"Chunhou",
""
],
[
"Zeng",
"Xiangxiang",
""
]
] | Machine learning methods have been used to accelerate the molecule optimization process. However, efficient search for optimized molecules satisfying several properties with scarce labeled data remains a challenge for machine learning molecule optimization. In this study, we propose MOMO, a multi-objective molecule opt... |
1104.5216 | Michael Courtney | Simeon Cole-Fletcher, Lucas Marin-Salcedo, Ajaya Rana, and Michael
Courtney | Errors in Length-weight Parameters at FishBase.org | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To investigate possible errors, length-weight parameters from FishBase.org
were used to graph length-weight curves for six different species: channel
catfish, black crappie, largemouth bass, rainbow trout, flathead catfish, and
lake trout along with the standard weight curves (Anderson and Neumann 1996,
Bister et al.... | [
{
"created": "Wed, 27 Apr 2011 19:01:41 GMT",
"version": "v1"
}
] | 2011-04-28 | [
[
"Cole-Fletcher",
"Simeon",
""
],
[
"Marin-Salcedo",
"Lucas",
""
],
[
"Rana",
"Ajaya",
""
],
[
"Courtney",
"Michael",
""
]
] | To investigate possible errors, length-weight parameters from FishBase.org were used to graph length-weight curves for six different species: channel catfish, black crappie, largemouth bass, rainbow trout, flathead catfish, and lake trout along with the standard weight curves (Anderson and Neumann 1996, Bister et al. 2... |
1805.10827 | Yanlong Sun | Yanlong Sun, Hongbin Wang | Learning Temporal Structures of Random Patterns | 15 pages, 5 figures | null | null | null | q-bio.NC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A cornerstone of human statistical learning is the ability to extract
temporal regularities / patterns from random sequences. Here we present a
method of computing pattern time statistics with generating functions for
first-order Markov trials and independent Bernoulli trials. We show that the
pattern time statistics... | [
{
"created": "Mon, 28 May 2018 09:12:49 GMT",
"version": "v1"
}
] | 2018-06-29 | [
[
"Sun",
"Yanlong",
""
],
[
"Wang",
"Hongbin",
""
]
] | A cornerstone of human statistical learning is the ability to extract temporal regularities / patterns from random sequences. Here we present a method of computing pattern time statistics with generating functions for first-order Markov trials and independent Bernoulli trials. We show that the pattern time statistics c... |
q-bio/0611046 | Michael Meyer-Hermann | Michael Meyer-Hermann, Philip K. Maini, Dagmar Iber | An analysis of B cell selection mechanisms in germinal centers | 25 pages, 1 table, 6 figures, supplementary material not included | Math Med Biol 23 (2006) 255 | null | null | q-bio.CB physics.bio-ph q-bio.TO | null | Affinity maturation of antibodies during immune responses is achieved by
multiple rounds of somatic hypermutation and subsequent preferential selection
of those B cells that express B cell receptors with improved binding
characteristics for the antigen. The mechanism underlying B cell selection has
not yet been defin... | [
{
"created": "Wed, 15 Nov 2006 17:06:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Meyer-Hermann",
"Michael",
""
],
[
"Maini",
"Philip K.",
""
],
[
"Iber",
"Dagmar",
""
]
] | Affinity maturation of antibodies during immune responses is achieved by multiple rounds of somatic hypermutation and subsequent preferential selection of those B cells that express B cell receptors with improved binding characteristics for the antigen. The mechanism underlying B cell selection has not yet been defined... |
1911.05479 | Asim Iqbal | Asim Iqbal, Phil Dong, Christopher M Kim, Heeun Jang | Decoding Neural Responses in Mouse Visual Cortex through a Deep Neural
Network | null | 2019 International Joint Conference on Neural Networks (IJCNN).
IEEE, 2019 | 10.1109/IJCNN.2019.8852121 | null | q-bio.NC cs.AI cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Finding a code to unravel the population of neural responses that leads to a
distinct animal behavior has been a long-standing question in the field of
neuroscience. With the recent advances in machine learning, it is shown that
the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding
unique featu... | [
{
"created": "Sat, 26 Oct 2019 05:02:33 GMT",
"version": "v1"
}
] | 2019-11-14 | [
[
"Iqbal",
"Asim",
""
],
[
"Dong",
"Phil",
""
],
[
"Kim",
"Christopher M",
""
],
[
"Jang",
"Heeun",
""
]
] | Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the hierarchically Deep Neural Networks (DNNs) perform optimally in decoding unique feature... |
1310.8598 | Onur Varol | Onur Varol, Deniz Yuret, Burak Erman, Alkan Kabak\c{c}{\i}o\u{g}lu | Mode-coupling points to functionally important residues in Myosin II | 17 pages, 6 figures, 1 table | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Relevance of mode coupling to energy/information transfer during protein
function, particularly in the context of allosteric interactions is widely
accepted. However, existing evidence in favor of this hypothesis comes
essentially from model systems. We here report a novel formal analysis of the
near-native dynamics ... | [
{
"created": "Thu, 31 Oct 2013 17:14:34 GMT",
"version": "v1"
}
] | 2013-11-01 | [
[
"Varol",
"Onur",
""
],
[
"Yuret",
"Deniz",
""
],
[
"Erman",
"Burak",
""
],
[
"Kabakçıoğlu",
"Alkan",
""
]
] | Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of... |
1108.3464 | Richard A Neher | Richard A. Neher, Boris I. Shraiman, and Daniel S. Fisher | Rate of Adaptation in Large Sexual Populations | null | null | null | NSF-ITP-09-219 | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adaptation often involves the acquisition of a large number of genomic
changes which arise as mutations in single individuals. In asexual populations,
combinations of mutations can fix only when they arise in the same lineage, but
for populations in which genetic information is exchanged, beneficial mutations
can ari... | [
{
"created": "Wed, 17 Aug 2011 12:18:40 GMT",
"version": "v1"
}
] | 2011-08-18 | [
[
"Neher",
"Richard A.",
""
],
[
"Shraiman",
"Boris I.",
""
],
[
"Fisher",
"Daniel S.",
""
]
] | Adaptation often involves the acquisition of a large number of genomic changes which arise as mutations in single individuals. In asexual populations, combinations of mutations can fix only when they arise in the same lineage, but for populations in which genetic information is exchanged, beneficial mutations can arise... |
2404.17329 | Paul Eisenhuth | Paul Eisenhuth, Fabian Liessmann, Rocco Moretti, Jens Meiler | REvoLd: Ultra-Large Library Screening with an Evolutionary Algorithm in
Rosetta | 29 pages, 9 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ultra-large make-on-demand compound libraries now contain billions of readily
available compounds. This represents a golden opportunity for in-silico drug
discovery. One challenge, however, is the time and computational cost of an
exhaustive screen of such large libraries when receptor flexibility is taken
into accou... | [
{
"created": "Fri, 26 Apr 2024 11:22:57 GMT",
"version": "v1"
}
] | 2024-04-29 | [
[
"Eisenhuth",
"Paul",
""
],
[
"Liessmann",
"Fabian",
""
],
[
"Moretti",
"Rocco",
""
],
[
"Meiler",
"Jens",
""
]
] | Ultra-large make-on-demand compound libraries now contain billions of readily available compounds. This represents a golden opportunity for in-silico drug discovery. One challenge, however, is the time and computational cost of an exhaustive screen of such large libraries when receptor flexibility is taken into account... |
2009.01445 | Ernest Montbrio | Ernest Montbri\'o and Diego Paz\'o | Exact mean-field theory explains the dual role of electrical synapses in
collective synchronization | null | Phys. Rev. Lett. 125, 248101 (2020) | 10.1103/PhysRevLett.125.248101 | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Electrical synapses play a major role in setting up neuronal synchronization,
but the precise mechanisms whereby these synapses contribute to synchrony are
subtle and remain elusive. To investigate these mechanisms mean-field theories
for quadratic integrate-and-fire neurons with electrical synapses have been
recentl... | [
{
"created": "Thu, 3 Sep 2020 04:27:19 GMT",
"version": "v1"
}
] | 2020-12-15 | [
[
"Montbrió",
"Ernest",
""
],
[
"Pazó",
"Diego",
""
]
] | Electrical synapses play a major role in setting up neuronal synchronization, but the precise mechanisms whereby these synapses contribute to synchrony are subtle and remain elusive. To investigate these mechanisms mean-field theories for quadratic integrate-and-fire neurons with electrical synapses have been recently ... |
2308.07413 | Charles Harris | Charles Harris, Kieran Didi, Arian R. Jamasb, Chaitanya K. Joshi,
Simon V. Mathis, Pietro Lio, Tom Blundell | Benchmarking Generated Poses: How Rational is Structure-based Drug
Design with Generative Models? | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Deep generative models for structure-based drug design (SBDD), where molecule
generation is conditioned on a 3D protein pocket, have received considerable
interest in recent years. These methods offer the promise of higher-quality
molecule generation by explicitly modelling the 3D interaction between a
potential drug... | [
{
"created": "Mon, 14 Aug 2023 19:01:21 GMT",
"version": "v1"
}
] | 2023-08-16 | [
[
"Harris",
"Charles",
""
],
[
"Didi",
"Kieran",
""
],
[
"Jamasb",
"Arian R.",
""
],
[
"Joshi",
"Chaitanya K.",
""
],
[
"Mathis",
"Simon V.",
""
],
[
"Lio",
"Pietro",
""
],
[
"Blundell",
"Tom",
""
]
] | Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years. These methods offer the promise of higher-quality molecule generation by explicitly modelling the 3D interaction between a potential drug a... |
2011.08713 | Glyn Nelson Dr | Glyn Nelson, Laurent Gelman, Orestis Faklaris, Roland Nitschke, Alex
Laude | Interpretation of Confocal ISO 21073: 2019 confocal microscopes: Optical
data of fluorescence confocal microscopes for biological imaging- Recommended
Methodology for Quality Control | When drawing up this document, it became apparent that further work
was required to determine best methodology and further minimal QC tests, as
well as extend to other common imaging modalities. As a consequence,
QUAREP-LiMi (https://quarep.org) was established to produce a more definitive
and expansive QC Meth... | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The performance of a confocal imaging system may be no better than a
general-purpose widefield system if it is not properly maintained or quality
controlled. The publication of ISO 21073, 'Confocal microscopes- Optical data
of fluorescence confocal microscopes for biological imaging', set a standard
for the minimal Q... | [
{
"created": "Tue, 17 Nov 2020 15:38:41 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Nov 2020 08:19:33 GMT",
"version": "v2"
}
] | 2020-11-20 | [
[
"Nelson",
"Glyn",
""
],
[
"Gelman",
"Laurent",
""
],
[
"Faklaris",
"Orestis",
""
],
[
"Nitschke",
"Roland",
""
],
[
"Laude",
"Alex",
""
]
] | The performance of a confocal imaging system may be no better than a general-purpose widefield system if it is not properly maintained or quality controlled. The publication of ISO 21073, 'Confocal microscopes- Optical data of fluorescence confocal microscopes for biological imaging', set a standard for the minimal Qua... |
1705.02336 | Sergei Shedko | Sergei V. Shedko | Revision of nucleotide substitution rate in mtDNA control region of
white sturgeon Acipenser transmontanus (Acipenseridae) | 8 pages, in Russian, 1 figure | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The raw data from study of variation of D-loop mtDNA of white sturgeon
Acipenser transmontanus (Mol. Biol. Evol. 1993. 10: 326-341) was re-analyzed.
Re-calculated nucleotide substitution rate ({\mu}) was 0.782-0.939 x 10-7
substitutions/site/year/lineage, which was 1.4 times less than the estimate
given in above-ment... | [
{
"created": "Fri, 5 May 2017 02:41:28 GMT",
"version": "v1"
}
] | 2017-05-09 | [
[
"Shedko",
"Sergei V.",
""
]
] | The raw data from study of variation of D-loop mtDNA of white sturgeon Acipenser transmontanus (Mol. Biol. Evol. 1993. 10: 326-341) was re-analyzed. Re-calculated nucleotide substitution rate ({\mu}) was 0.782-0.939 x 10-7 substitutions/site/year/lineage, which was 1.4 times less than the estimate given in above-mentio... |
1312.2041 | John Storey | Wei Hao, Minsun Song, and John D. Storey | Probabilistic models of genetic variation in structured populations
applied to global human studies | Wei Hao and Minsun Song contributed equally to this work | null | 10.1093/bioinformatics/btv641 | null | q-bio.PE q-bio.GN q-bio.QM stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern population genetics studies typically involve genome-wide genotyping
of individuals from a diverse network of ancestries. An important, unsolved
problem is how to formulate and estimate probabilistic models of observed
genotypes that allow for complex population structure. We formulate two general
probabilisti... | [
{
"created": "Sat, 7 Dec 2013 00:14:17 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Mar 2015 03:41:05 GMT",
"version": "v2"
}
] | 2017-01-10 | [
[
"Hao",
"Wei",
""
],
[
"Song",
"Minsun",
""
],
[
"Storey",
"John D.",
""
]
] | Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that allow for complex population structure. We formulate two general probabilistic ... |
2311.17103 | Hu Dayu | Dayu Hu, Zhibin Dong, Ke Liang, Jun Wang, Siwei Wang and Xinwang Liu | Single-cell Multi-view Clustering via Community Detection with Unknown
Number of Clusters | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-cell multi-view clustering enables the exploration of cellular
heterogeneity within the same cell from different views. Despite the
development of several multi-view clustering methods, two primary challenges
persist. Firstly, most existing methods treat the information from both
single-cell RNA (scRNA) and si... | [
{
"created": "Tue, 28 Nov 2023 08:34:58 GMT",
"version": "v1"
}
] | 2023-11-30 | [
[
"Hu",
"Dayu",
""
],
[
"Dong",
"Zhibin",
""
],
[
"Liang",
"Ke",
""
],
[
"Wang",
"Jun",
""
],
[
"Wang",
"Siwei",
""
],
[
"Liu",
"Xinwang",
""
]
] | Single-cell multi-view clustering enables the exploration of cellular heterogeneity within the same cell from different views. Despite the development of several multi-view clustering methods, two primary challenges persist. Firstly, most existing methods treat the information from both single-cell RNA (scRNA) and sing... |
2209.05728 | Guy Florian Draenert | Guy Florian Draenert, Gergo Mitov | Lack of corundum, carbon residues and revealing gaps on dental implants | further information available on request | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Surface modification is an important topic to improve dental implants.
Corundum residues, which are part of current dental implant blasting,
disappeared on Straumann dental implants in recent publications. In our
investigations of the surface of 4 different Straumann implants using scanning
electron microscopy (SEM) ... | [
{
"created": "Tue, 13 Sep 2022 04:45:44 GMT",
"version": "v1"
}
] | 2022-09-14 | [
[
"Draenert",
"Guy Florian",
""
],
[
"Mitov",
"Gergo",
""
]
] | Surface modification is an important topic to improve dental implants. Corundum residues, which are part of current dental implant blasting, disappeared on Straumann dental implants in recent publications. In our investigations of the surface of 4 different Straumann implants using scanning electron microscopy (SEM) an... |
2112.08366 | Ruiwei Feng | Ruiwei Feng, Yufeng Xie, Minshan Lai, Danny Z. Chen, Ji Cao, Jian Wu | AGMI: Attention-Guided Multi-omics Integration for Drug Response
Prediction with Graph Neural Networks | null | null | 10.1109/BIBM52615.2021.9669314 | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate drug response prediction (DRP) is a crucial yet challenging task in
precision medicine. This paper presents a novel Attention-Guided Multi-omics
Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph
(MeG) for each cell line, and then aggregates multi-omics features to predict
drug re... | [
{
"created": "Wed, 15 Dec 2021 07:42:46 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Jan 2022 02:46:36 GMT",
"version": "v2"
}
] | 2022-01-20 | [
[
"Feng",
"Ruiwei",
""
],
[
"Xie",
"Yufeng",
""
],
[
"Lai",
"Minshan",
""
],
[
"Chen",
"Danny Z.",
""
],
[
"Cao",
"Ji",
""
],
[
"Wu",
"Jian",
""
]
] | Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG) for each cell line, and then aggregates multi-omics features to predict drug resp... |
1209.5559 | Alex Susemihl | Alex Susemihl, Ron Meir, Manfred Opper | Dynamic State Estimation Based on Poisson Spike Trains: Towards a Theory
of Optimal Encoding | 26 pages, 9 figures | J. Stat. Mech. (2013) P03009 | 10.1088/1742-5468/2013/03/P03009 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons in the nervous system convey information to higher brain regions by
the generation of spike trains. An important question in the field of
computational neuroscience is how these sensory neurons encode environmental
information in a way which may be simply analyzed by subsequent systems. Many
aspects of the fo... | [
{
"created": "Tue, 25 Sep 2012 09:51:33 GMT",
"version": "v1"
}
] | 2013-09-13 | [
[
"Susemihl",
"Alex",
""
],
[
"Meir",
"Ron",
""
],
[
"Opper",
"Manfred",
""
]
] | Neurons in the nervous system convey information to higher brain regions by the generation of spike trains. An important question in the field of computational neuroscience is how these sensory neurons encode environmental information in a way which may be simply analyzed by subsequent systems. Many aspects of the form... |
1001.4212 | Nikolai Sinitsyn | N. A. Sinitsyn and I. Nemenman | Time-dependent corrections to effective rate and event statistics in
Michaelis-Menten kinetics | 11 pages | IET Syst Biol 4, 409, 2010 | 10.1049/iet-syb.2010.0064 | Technical report: LA-UR-08-04425 | q-bio.QM cond-mat.stat-mech physics.chem-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We generalize the concept of the geometric phase in stochastic kinetics to a
noncyclic evolution. Its application is demonstrated on kinetics of the
Michaelis-Menten reaction. It is shown that the nonperiodic geometric phase is
responsible for the correction to the Michaelis-Menten law when parameters,
such as a subs... | [
{
"created": "Sun, 24 Jan 2010 00:13:16 GMT",
"version": "v1"
}
] | 2010-11-24 | [
[
"Sinitsyn",
"N. A.",
""
],
[
"Nemenman",
"I.",
""
]
] | We generalize the concept of the geometric phase in stochastic kinetics to a noncyclic evolution. Its application is demonstrated on kinetics of the Michaelis-Menten reaction. It is shown that the nonperiodic geometric phase is responsible for the correction to the Michaelis-Menten law when parameters, such as a substr... |
2405.02674 | Josinaldo Menezes Da Silva | R. Barbalho, S. Rodrigues, M. Tenorio, J. Menezes | Ambush strategy enhances organisms' performance in rock-paper-scissors
games | 8 pages, 5 figures | BioSystems 240, 105229 (2024) | 10.1016/j.biosystems.2024.105229 | null | q-bio.PE nlin.AO nlin.PS physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study a five-species cyclic system wherein individuals of one species
strategically adapt their movements to enhance their performance in the spatial
rock-paper-scissors game. Environmental cues enable the awareness of the
presence of organisms targeted for elimination in the cyclic game. If the local
density of t... | [
{
"created": "Sat, 4 May 2024 14:23:59 GMT",
"version": "v1"
}
] | 2024-06-05 | [
[
"Barbalho",
"R.",
""
],
[
"Rodrigues",
"S.",
""
],
[
"Tenorio",
"M.",
""
],
[
"Menezes",
"J.",
""
]
] | We study a five-species cyclic system wherein individuals of one species strategically adapt their movements to enhance their performance in the spatial rock-paper-scissors game. Environmental cues enable the awareness of the presence of organisms targeted for elimination in the cyclic game. If the local density of tar... |
1502.00155 | Ulrich S. Schwarz | Marvin A. Boettcher, Heinrich C. R. Klein and Ulrich S. Schwarz
(Heidelberg University) | Role of dynamic capsomere supply for viral capsid self-assembly | Revtex, 26 pages, 7 EPS figures | Phys. Biol. 12:016014 (2015) | 10.1088/1478-3975/12/1/016014 | null | q-bio.SC physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many viruses rely on the self-assembly of their capsids to protect and
transport their genomic material. For many viral systems, in particular for
human viruses like hepatitis B, adeno or human immunodeficiency virus, that
lead to persistent infections, capsomeres are continuously produced in the
cytoplasm of the hos... | [
{
"created": "Sat, 31 Jan 2015 19:43:07 GMT",
"version": "v1"
}
] | 2015-02-03 | [
[
"Boettcher",
"Marvin A.",
"",
"Heidelberg University"
],
[
"Klein",
"Heinrich C. R.",
"",
"Heidelberg University"
],
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg University"
]
] | Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host ... |
1703.08792 | Burkhard Morgenstern | Chris-Andre Leimeister, Thomas Dencker, Burkhard Morgenstern | Anchor points for genome alignment based on Filtered Spaced Word Matches | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alignment of large genomic sequences is a fundamental task in computational
genome analysis. Most methods for genomic alignment use high-scoring local
alignments as {\em anchor points} to reduce the search space of the alignment
procedure. Speed and quality of these methods therefore depend on the
underlying anchor p... | [
{
"created": "Sun, 26 Mar 2017 09:21:07 GMT",
"version": "v1"
}
] | 2017-03-28 | [
[
"Leimeister",
"Chris-Andre",
""
],
[
"Dencker",
"Thomas",
""
],
[
"Morgenstern",
"Burkhard",
""
]
] | Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure. Speed and quality of these methods therefore depend on the underlying anchor poi... |
1902.04851 | Edmund Crampin | Hilary Hunt, Agne Tilunaite, Greg Bass, Christian Soeller, H. Llewelyn
Roderick, Vijay Rajagopal, Edmund J. Crampin | Ca2+ release via IP3 receptors shapes the cytosolic Ca2+ transient for
hypertrophic signalling in ventricular cardiomyocytes | Biophysical Journal, in press | null | 10.1016/j.bpj.2020.08.001 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calcium (Ca2+) plays a central role in mediating both contractile function
and hypertrophic signalling in ventricular cardiomyocytes. L-type Ca2+ channels
trigger release of Ca2+ from ryanodine receptors (RyRs) for cellular
contraction, while signalling downstream of Gq coupled receptors stimulates
Ca2+ release via i... | [
{
"created": "Wed, 13 Feb 2019 10:51:18 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Mar 2019 04:48:58 GMT",
"version": "v2"
},
{
"created": "Fri, 17 Jan 2020 04:38:12 GMT",
"version": "v3"
},
{
"created": "Mon, 17 Aug 2020 06:30:01 GMT",
"version": "v4"
}
] | 2020-08-18 | [
[
"Hunt",
"Hilary",
""
],
[
"Tilunaite",
"Agne",
""
],
[
"Bass",
"Greg",
""
],
[
"Soeller",
"Christian",
""
],
[
"Roderick",
"H. Llewelyn",
""
],
[
"Rajagopal",
"Vijay",
""
],
[
"Crampin",
"Edmund J.",
""
]... | Calcium (Ca2+) plays a central role in mediating both contractile function and hypertrophic signalling in ventricular cardiomyocytes. L-type Ca2+ channels trigger release of Ca2+ from ryanodine receptors (RyRs) for cellular contraction, while signalling downstream of Gq coupled receptors stimulates Ca2+ release via ino... |
2102.05236 | Pan Wang | Pan Wang, Rui Zhou, Shuo Wang, Ling Li, Wenjia Bai, Jialu Fan, Chunlin
Li, Peter Childs, and Yike Guo | A General Framework for Revealing Human Mind with auto-encoding GANs | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Addressing the question of visualising human mind could help us to find
regions that are associated with observed cognition and responsible for
expressing the elusive mental image, leading to a better understanding of
cognitive function. The traditional approach treats brain decoding as a
classification problem, read... | [
{
"created": "Wed, 10 Feb 2021 03:18:46 GMT",
"version": "v1"
}
] | 2021-02-11 | [
[
"Wang",
"Pan",
""
],
[
"Zhou",
"Rui",
""
],
[
"Wang",
"Shuo",
""
],
[
"Li",
"Ling",
""
],
[
"Bai",
"Wenjia",
""
],
[
"Fan",
"Jialu",
""
],
[
"Li",
"Chunlin",
""
],
[
"Childs",
"Peter",
""
... | Addressing the question of visualising human mind could help us to find regions that are associated with observed cognition and responsible for expressing the elusive mental image, leading to a better understanding of cognitive function. The traditional approach treats brain decoding as a classification problem, readin... |
2405.04557 | Da Zhou Prof. | Yuman Wang, Shuli Chen, Jie Hu, and Da Zhou | Determining cell population size from cell fraction in cell plasticity
models | null | null | null | null | q-bio.QM q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Quantifying the size of cell populations is crucial for understanding
biological processes such as growth, injury repair, and disease progression.
Often, experimental data offer information in the form of relative frequencies
of distinct cell types, rather than absolute cell counts. This emphasizes the
need to devise... | [
{
"created": "Tue, 7 May 2024 08:44:18 GMT",
"version": "v1"
}
] | 2024-05-09 | [
[
"Wang",
"Yuman",
""
],
[
"Chen",
"Shuli",
""
],
[
"Hu",
"Jie",
""
],
[
"Zhou",
"Da",
""
]
] | Quantifying the size of cell populations is crucial for understanding biological processes such as growth, injury repair, and disease progression. Often, experimental data offer information in the form of relative frequencies of distinct cell types, rather than absolute cell counts. This emphasizes the need to devise e... |
1912.00270 | Gerrit Hilgen | Gerrit Hilgen (Biosciences Institute, Faculty of Medical Sciences,
Newcastle University, Newcastle, NE2 4HH, United Kingdom) | Challenges for automated spike sorting: beware of pharmacological
manipulations | mini review, 1 figure, 7 pages | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The advent of large-scale and high-density extracellular recording devices
allows simultaneous recording from thousands of neurons. However, the
complexity and size of the data makes it mandatory to develop robust algorithms
for fully automated spike sorting. Here it is shown that limitations imposed by
biological co... | [
{
"created": "Sat, 30 Nov 2019 21:51:28 GMT",
"version": "v1"
}
] | 2019-12-03 | [
[
"Hilgen",
"Gerrit",
"",
"Biosciences Institute, Faculty of Medical Sciences,\n Newcastle University, Newcastle, NE2 4HH, United Kingdom"
]
] | The advent of large-scale and high-density extracellular recording devices allows simultaneous recording from thousands of neurons. However, the complexity and size of the data makes it mandatory to develop robust algorithms for fully automated spike sorting. Here it is shown that limitations imposed by biological cons... |
1309.3436 | David Holcman | N. Hoze, D. Holcman | Potential wells for AMPA receptors organized in ring nanodomains | 4 figures extension of Hoze et al, PNAS 2012 | null | null | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | By combining high-density super-resolution imaging with a novel stochastic
analysis, we report here a peculiar nano-structure organization revealed by the
density function of individual AMPA receptors moving on the surface of cultured
hippocampal dendrites. High density regions of hundreds of nanometers for the
traje... | [
{
"created": "Fri, 13 Sep 2013 12:27:24 GMT",
"version": "v1"
},
{
"created": "Tue, 24 Sep 2013 17:58:42 GMT",
"version": "v2"
}
] | 2014-07-01 | [
[
"Hoze",
"N.",
""
],
[
"Holcman",
"D.",
""
]
] | By combining high-density super-resolution imaging with a novel stochastic analysis, we report here a peculiar nano-structure organization revealed by the density function of individual AMPA receptors moving on the surface of cultured hippocampal dendrites. High density regions of hundreds of nanometers for the traject... |
2006.02359 | Simon DeDeo | Zachary Wojtowicz and Simon DeDeo | From Probability to Consilience: How Explanatory Values Implement
Bayesian Reasoning | 19 pages, 1 figure, comments welcome | Trends in Cognitive Sciences (2020) | 10.1016/j.tics.2020.09.013 | null | q-bio.NC cs.AI stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent work in cognitive science has uncovered a diversity of explanatory
values, or dimensions along which we judge explanations as better or worse. We
propose a Bayesian account of how these values fit together to guide
explanation. The resulting taxonomy provides a set of predictors for which
explanations people p... | [
{
"created": "Wed, 3 Jun 2020 16:11:45 GMT",
"version": "v1"
}
] | 2020-10-29 | [
[
"Wojtowicz",
"Zachary",
""
],
[
"DeDeo",
"Simon",
""
]
] | Recent work in cognitive science has uncovered a diversity of explanatory values, or dimensions along which we judge explanations as better or worse. We propose a Bayesian account of how these values fit together to guide explanation. The resulting taxonomy provides a set of predictors for which explanations people pre... |
0809.1630 | Alexei Koulakov | Alexei Koulakov, Tomas Hromadka, and Anthony M. Zador | Correlated connectivity and the distribution of firing rates in the
neocortex | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two recent experimental observations pose a challenge to many cortical
models. First, the activity in the auditory cortex is sparse, and firing rates
can be described by a lognormal distribution. Second, the distribution of
non-zero synaptic strengths between nearby cortical neurons can also be
described by a lognorm... | [
{
"created": "Tue, 9 Sep 2008 18:44:58 GMT",
"version": "v1"
}
] | 2008-09-10 | [
[
"Koulakov",
"Alexei",
""
],
[
"Hromadka",
"Tomas",
""
],
[
"Zador",
"Anthony M.",
""
]
] | Two recent experimental observations pose a challenge to many cortical models. First, the activity in the auditory cortex is sparse, and firing rates can be described by a lognormal distribution. Second, the distribution of non-zero synaptic strengths between nearby cortical neurons can also be described by a lognormal... |
1811.08718 | Yunming Xiao | Yunming Xiao, Bin Wu | Close spatial arrangement of mutants favors and disfavors fixation | 23 pages, 8 figures | null | 10.1371/journal.pcbi.1007212 | null | q-bio.PE cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperation is ubiquitous across all levels of biological systems ranging
from microbial communities to human societies. It, however, seemingly
contradicts the evolutionary theory, since cooperators are exploited by
free-riders and thus are disfavored by natural selection. Many studies based on
evolutionary game theo... | [
{
"created": "Wed, 21 Nov 2018 13:32:29 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Aug 2019 02:17:39 GMT",
"version": "v2"
}
] | 2019-09-23 | [
[
"Xiao",
"Yunming",
""
],
[
"Wu",
"Bin",
""
]
] | Cooperation is ubiquitous across all levels of biological systems ranging from microbial communities to human societies. It, however, seemingly contradicts the evolutionary theory, since cooperators are exploited by free-riders and thus are disfavored by natural selection. Many studies based on evolutionary game theory... |
1507.07580 | Stefano Fusi | Marcus K. Benna and Stefano Fusi | Computational principles of biological memory | 21 pages + 46 pages of suppl. info | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Memories are stored, retained, and recollected through complex, coupled
processes operating on multiple timescales. To understand the computational
principles behind these intricate networks of interactions we construct a broad
class of synaptic models that efficiently harnesses biological complexity to
preserve nume... | [
{
"created": "Mon, 27 Jul 2015 20:29:33 GMT",
"version": "v1"
}
] | 2015-07-29 | [
[
"Benna",
"Marcus K.",
""
],
[
"Fusi",
"Stefano",
""
]
] | Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of synaptic models that efficiently harnesses biological complexity to preserve numero... |
2004.05069 | Gianluca Calcagni | Gianluca Calcagni, Justin A. Harris, Ricardo Pell\'on | Beyond Rescorla-Wagner: the ups and downs of learning | 39 pages, 11 figures, 8 tables. v2: discussion improved, figures
added, some parts shortened, conclusions unchanged, matches published version | Comput. Brain Behav. (2021) | 10.1007/s42113-021-00103-4 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We check the robustness of a recently proposed dynamical model of associative
Pavlovian learning that extends the Rescorla-Wagner (RW) model in a natural way
and predicts progressively damped oscillations in the response of the subjects.
Using the data of two experiments, we compare the dynamical oscillatory model
(D... | [
{
"created": "Fri, 10 Apr 2020 15:16:18 GMT",
"version": "v1"
},
{
"created": "Sun, 18 Apr 2021 20:13:59 GMT",
"version": "v2"
}
] | 2021-04-20 | [
[
"Calcagni",
"Gianluca",
""
],
[
"Harris",
"Justin A.",
""
],
[
"Pellón",
"Ricardo",
""
]
] | We check the robustness of a recently proposed dynamical model of associative Pavlovian learning that extends the Rescorla-Wagner (RW) model in a natural way and predicts progressively damped oscillations in the response of the subjects. Using the data of two experiments, we compare the dynamical oscillatory model (DOM... |
1607.00104 | Conrad Burden | Conrad J. Burden and Yurong Tang | An approximate stationary solution for multi-allele neutral diffusion
with low mutation rates | 34 pages, 7 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We address the problem of determining the stationary distribution of the
multi-allelic, neutral-evolution Wright-Fisher model in the diffusion limit. A
full solution to this problem for an arbitrary K x K mutation rate matrix
involves solving for the stationary solution of a forward Kolmogorov equation
over a (K - 1)... | [
{
"created": "Fri, 1 Jul 2016 03:46:34 GMT",
"version": "v1"
}
] | 2016-07-04 | [
[
"Burden",
"Conrad J.",
""
],
[
"Tang",
"Yurong",
""
]
] | We address the problem of determining the stationary distribution of the multi-allelic, neutral-evolution Wright-Fisher model in the diffusion limit. A full solution to this problem for an arbitrary K x K mutation rate matrix involves solving for the stationary solution of a forward Kolmogorov equation over a (K - 1)-d... |
0906.2872 | Thierry Rabilloud | Christian Villiers (U823), Mireille Chevallet (BBSI), H\'el\`ene
Diemer (IPHC), Rachel Couderc (U823), Heidi Freitas (U823), Alain Van
Dorsselaer (IPHC), Patrice N Marche (U823), Thierry Rabilloud (BBSI) | From secretome analysis to immunology: chitosan induces major
alterations in the activation of dendritic cells via a TLR4-dependent
mechanism | null | Mol Cell Proteomics 8, 6 (2009) 1252-64 | 10.1074/mcp.M800589-MCP200 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dendritic cells are known to be activated by a wide range of microbial
products, leading to cytokine production and increased levels of membrane
markers such as major histocompatibility complex class II molecules. Such
activated dendritic cells possess the capacity to activate na\"ive T cells. In
the present study we... | [
{
"created": "Tue, 16 Jun 2009 08:48:57 GMT",
"version": "v1"
}
] | 2009-06-17 | [
[
"Villiers",
"Christian",
"",
"U823"
],
[
"Chevallet",
"Mireille",
"",
"BBSI"
],
[
"Diemer",
"Hélène",
"",
"IPHC"
],
[
"Couderc",
"Rachel",
"",
"U823"
],
[
"Freitas",
"Heidi",
"",
"U823"
],
[
"Van Dorsselaer",
... | Dendritic cells are known to be activated by a wide range of microbial products, leading to cytokine production and increased levels of membrane markers such as major histocompatibility complex class II molecules. Such activated dendritic cells possess the capacity to activate na\"ive T cells. In the present study we d... |
2011.11638 | Cristina Postigo | Kaidi Hu, Josefina Toran, Ester Lopez-Garcia, Maria Vittoria Barbieri,
Cristina Postigo, Miren Lopez de Alda, Gloria Caminal, Montserrat Sarra,
Paqui Blanquez | Fungal bioremediation of diuron-contaminated waters: evaluation of its
degradation and the effect of amendable factors on its removal in a
trickle-bed reactor under non-sterile conditions | Published in Science of the Total Environment | Science of The Total Environment Volume 743, 15 November 2020,
140628 | 10.1016/j.scitotenv.2020.140628 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The occurrence of the extensively used herbicide diuron in the environment
poses a severe threat to the ecosystem and human health. Four different
ligninolytic fungi were studied as biodegradation candidates for the removal of
diuron. Among them, T. versicolor was the most effective species, degrading
rapidly not onl... | [
{
"created": "Mon, 23 Nov 2020 17:08:49 GMT",
"version": "v1"
}
] | 2020-11-25 | [
[
"Hu",
"Kaidi",
""
],
[
"Toran",
"Josefina",
""
],
[
"Lopez-Garcia",
"Ester",
""
],
[
"Barbieri",
"Maria Vittoria",
""
],
[
"Postigo",
"Cristina",
""
],
[
"de Alda",
"Miren Lopez",
""
],
[
"Caminal",
"Gloria",
... | The occurrence of the extensively used herbicide diuron in the environment poses a severe threat to the ecosystem and human health. Four different ligninolytic fungi were studied as biodegradation candidates for the removal of diuron. Among them, T. versicolor was the most effective species, degrading rapidly not only ... |
2005.11186 | Constantinos Siettos | Evangelos Galaris, Ioannis Gallos, Ivan Myatchin, Lieven Lagae,
Constantinos Siettos | EEG source localization analysis in epileptic children during a visual
working-memory task | null | International Journal of Numerical Methods in Biomedical
Engineering, 36:e3404, 2020 | 10.1002/cnm.3404 | null | q-bio.NC cs.NA math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We localize the sources of brain activity of children with epilepsy based on
EEG recordings acquired during a visual discrimination working memory task. For
the numerical solution of the inverse problem, with the aid of age-specific MRI
scans processed from a publicly available database, we use and compare three
regu... | [
{
"created": "Fri, 22 May 2020 13:43:23 GMT",
"version": "v1"
}
] | 2023-03-16 | [
[
"Galaris",
"Evangelos",
""
],
[
"Gallos",
"Ioannis",
""
],
[
"Myatchin",
"Ivan",
""
],
[
"Lagae",
"Lieven",
""
],
[
"Siettos",
"Constantinos",
""
]
] | We localize the sources of brain activity of children with epilepsy based on EEG recordings acquired during a visual discrimination working memory task. For the numerical solution of the inverse problem, with the aid of age-specific MRI scans processed from a publicly available database, we use and compare three regula... |
1404.6932 | Kunihiko Goto | Kunihiko Goto and Toshio Nakaye | Dynamic and integrated mechanical movements of a rat brain associated
with evoked potentials | 7 pages,and 3 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/publicdomain/ | By using a piezoelectric sensor, it was demonstrated that the visual evoked
potential of a rat brain was accompanied by mechanical movements of the brain
when it was excited. A phase of upward movement was found to be followed by a
phase of downward movement. The largest upward movement was a rise in swelling
pressur... | [
{
"created": "Mon, 28 Apr 2014 11:09:46 GMT",
"version": "v1"
}
] | 2014-04-29 | [
[
"Goto",
"Kunihiko",
""
],
[
"Nakaye",
"Toshio",
""
]
] | By using a piezoelectric sensor, it was demonstrated that the visual evoked potential of a rat brain was accompanied by mechanical movements of the brain when it was excited. A phase of upward movement was found to be followed by a phase of downward movement. The largest upward movement was a rise in swelling pressure ... |
2307.13079 | Siavash Ahrar | Brian T. Le, Katherine M. Auer, David A. Lopez, Justin P. Shum, Brian
Suarsana, Ga-Young Kelly Suh, Per Niklas Hedde, Siavash Ahrar | Orthogonal-view Microscope for the Biomechanics Investigations of
Aquatic Organisms | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | Microscopes are essential for biomechanics and hydrodynamical investigation
of small aquatic organisms. We report a DIY microscope (GLUBscope) that enables
the visualization of organisms from two orthogonal imaging planes (top and side
views). Compared to conventional imaging systems, this approach provides a
compreh... | [
{
"created": "Mon, 24 Jul 2023 19:06:00 GMT",
"version": "v1"
}
] | 2023-07-26 | [
[
"Le",
"Brian T.",
""
],
[
"Auer",
"Katherine M.",
""
],
[
"Lopez",
"David A.",
""
],
[
"Shum",
"Justin P.",
""
],
[
"Suarsana",
"Brian",
""
],
[
"Suh",
"Ga-Young Kelly",
""
],
[
"Hedde",
"Per Niklas",
""
... | Microscopes are essential for biomechanics and hydrodynamical investigation of small aquatic organisms. We report a DIY microscope (GLUBscope) that enables the visualization of organisms from two orthogonal imaging planes (top and side views). Compared to conventional imaging systems, this approach provides a comprehen... |
1609.01664 | Olga Vsevolozhskaya | Olga A. Vsevolozhskaya, Gabriel Ruiz, Dmitri V. Zaykin | Assessment of P-value variability in the current replicability crisis | Corrected typos | null | null | null | q-bio.GN stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Increased availability of data and accessibility of computational tools in
recent years have created unprecedented opportunities for scientific research
driven by statistical analysis. Inherent limitations of statistics impose
constrains on reliability of conclusions drawn from data but misuse of
statistical methods ... | [
{
"created": "Tue, 6 Sep 2016 17:35:29 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Sep 2016 21:10:42 GMT",
"version": "v2"
},
{
"created": "Sat, 10 Sep 2016 15:28:19 GMT",
"version": "v3"
}
] | 2016-09-13 | [
[
"Vsevolozhskaya",
"Olga A.",
""
],
[
"Ruiz",
"Gabriel",
""
],
[
"Zaykin",
"Dmitri V.",
""
]
] | Increased availability of data and accessibility of computational tools in recent years have created unprecedented opportunities for scientific research driven by statistical analysis. Inherent limitations of statistics impose constrains on reliability of conclusions drawn from data but misuse of statistical methods is... |
0901.1657 | Thu-Hien To | Thu-Hien To and Michel Habib | Level-k Phylogenetic Network can be Constructed from a Dense Triplet Set
in Polynomial Time | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Given a dense triplet set $\mathcal{T}$, there arise two interesting
questions: Does there exists any phylogenetic network consistent with
$\mathcal{T}$? And if so, can we find an effective algorithm to construct one?
For cases of networks of levels $k=0$ or 1 or 2, these questions were answered
with effective polyno... | [
{
"created": "Mon, 12 Jan 2009 20:54:44 GMT",
"version": "v1"
}
] | 2009-01-13 | [
[
"To",
"Thu-Hien",
""
],
[
"Habib",
"Michel",
""
]
] | Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks of levels $k=0$ or 1 or 2, these questions were answered with effective polynomi... |
2211.05661 | Fanwang Meng | Wenwen Liu, Cheng Luo, Hecheng Wang, Fanwang Meng | A Benchmarking Dataset with 2440 Organic Molecules for Volume
Distribution at Steady State | null | null | null | null | q-bio.QM physics.bio-ph physics.chem-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: The volume of distribution at steady state (VDss) is a
fundamental pharmacokinetics (PK) property of drugs, which measures how
effectively a drug molecule is distributed throughout the body. Along with the
clearance (CL), it determines the half-life and, therefore, the drug dosing
interval. However, the m... | [
{
"created": "Thu, 10 Nov 2022 15:46:17 GMT",
"version": "v1"
}
] | 2022-11-11 | [
[
"Liu",
"Wenwen",
""
],
[
"Luo",
"Cheng",
""
],
[
"Wang",
"Hecheng",
""
],
[
"Meng",
"Fanwang",
""
]
] | Background: The volume of distribution at steady state (VDss) is a fundamental pharmacokinetics (PK) property of drugs, which measures how effectively a drug molecule is distributed throughout the body. Along with the clearance (CL), it determines the half-life and, therefore, the drug dosing interval. However, the mol... |
1311.3717 | Amin Emad | Jonathan G. Ligo, Minji Kim, Amin Emad, Olgica Milenkovic and
Venugopal V. Veeravalli | MCUIUC -- A New Framework for Metagenomic Read Compression | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metagenomics is an emerging field of molecular biology concerned with
analyzing the genomes of environmental samples comprising many different
diverse organisms. Given the nature of metagenomic data, one usually has to
sequence the genomic material of all organisms in a batch, leading to a mix of
reads coming from di... | [
{
"created": "Fri, 15 Nov 2013 03:57:05 GMT",
"version": "v1"
}
] | 2013-11-20 | [
[
"Ligo",
"Jonathan G.",
""
],
[
"Kim",
"Minji",
""
],
[
"Emad",
"Amin",
""
],
[
"Milenkovic",
"Olgica",
""
],
[
"Veeravalli",
"Venugopal V.",
""
]
] | Metagenomics is an emerging field of molecular biology concerned with analyzing the genomes of environmental samples comprising many different diverse organisms. Given the nature of metagenomic data, one usually has to sequence the genomic material of all organisms in a batch, leading to a mix of reads coming from diff... |
2007.03245 | Oleksandr Oliynyk | Keke Hu, Yan-Ling Liu, Alexander Oleinick (PASTEUR), Michael Mirkin,
Wei-Hua Huang, Christian Amatore (PASTEUR) | Nanoelectrodes for intracellular measurements of reactive oxygen and
nitrogen species in single living cells | null | Current Opinion in Electrochemistry, Elsevier, 2020, 22, pp.44-50 | 10.1016/j.coelec.2020.04.003 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reactive oxygen and nitrogen species (ROS and RNS) play important roles in
various physiological processes (e.g., phagocytosis) and pathological
conditions (e.g., cancer). The primary ROS/RNS, viz., hydrogen peroxide,
peroxynitrite ion, nitric oxide, and nitrite ion, can be oxidized at different
electrode potentials ... | [
{
"created": "Tue, 7 Jul 2020 07:29:23 GMT",
"version": "v1"
}
] | 2020-07-08 | [
[
"Hu",
"Keke",
"",
"PASTEUR"
],
[
"Liu",
"Yan-Ling",
"",
"PASTEUR"
],
[
"Oleinick",
"Alexander",
"",
"PASTEUR"
],
[
"Mirkin",
"Michael",
"",
"PASTEUR"
],
[
"Huang",
"Wei-Hua",
"",
"PASTEUR"
],
[
"Amatore",
"... | Reactive oxygen and nitrogen species (ROS and RNS) play important roles in various physiological processes (e.g., phagocytosis) and pathological conditions (e.g., cancer). The primary ROS/RNS, viz., hydrogen peroxide, peroxynitrite ion, nitric oxide, and nitrite ion, can be oxidized at different electrode potentials an... |
1903.04866 | Donald Forsdyke Dr. | Donald R. Forsdyke | Success of Alignment-Free Oligonucleotide (k-mer) Analysis Confirms
Relative Importance of Genomes not Genes in Speciation and Phylogeny | A 25 page review | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The utility of DNA sequence substrings (k-mers) in alignment-free
phylogenetic classification, including that of bacteria and viruses, is
increasingly recognized. However, its biological basis eludes many twenty-first
century practitioners. A path from the nineteenth century recognition of the
informational basis of ... | [
{
"created": "Tue, 12 Mar 2019 12:21:36 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Apr 2019 19:37:06 GMT",
"version": "v2"
}
] | 2019-04-29 | [
[
"Forsdyke",
"Donald R.",
""
]
] | The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners. A path from the nineteenth century recognition of the informational basis of he... |
2110.04913 | Diederik Aerts | Diederik Aerts and Lester Beltran | Are Words the Quanta of Human Language? Extending the Domain of Quantum
Cognition | 27 pages, 3 figures | Entropy 24, 6 (2022) | 10.3390/e24010006 | null | q-bio.NC cs.CL quant-ph | http://creativecommons.org/licenses/by/4.0/ | In previous research, we showed that 'texts that tell a story' exhibit a
statistical structure that is not Maxwell-Boltzmann but Bose-Einstein. Our
explanation is that this is due to the presence of 'indistinguishability' in
human language as a result of the same words in different parts of the story
being indistingu... | [
{
"created": "Sun, 10 Oct 2021 22:02:06 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Dec 2021 03:59:22 GMT",
"version": "v2"
}
] | 2023-02-27 | [
[
"Aerts",
"Diederik",
""
],
[
"Beltran",
"Lester",
""
]
] | In previous research, we showed that 'texts that tell a story' exhibit a statistical structure that is not Maxwell-Boltzmann but Bose-Einstein. Our explanation is that this is due to the presence of 'indistinguishability' in human language as a result of the same words in different parts of the story being indistinguis... |
2206.00455 | Bangwei Guo | Bangwei Guo, Xingyu Li, Miaomiao Yang, Hong Zhang, Xu Steven Xu | A robust and lightweight deep attention multiple instance learning
algorithm for predicting genetic alterations | null | null | null | null | q-bio.QM cs.AI cs.CV cs.LG q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep-learning models based on whole-slide digital pathology images (WSIs)
become increasingly popular for predicting molecular biomarkers. Instance-based
models has been the mainstream strategy for predicting genetic alterations
using WSIs although bag-based models along with self-attention mechanism-based
algorithms... | [
{
"created": "Tue, 31 May 2022 15:45:29 GMT",
"version": "v1"
}
] | 2022-06-02 | [
[
"Guo",
"Bangwei",
""
],
[
"Li",
"Xingyu",
""
],
[
"Yang",
"Miaomiao",
""
],
[
"Zhang",
"Hong",
""
],
[
"Xu",
"Xu Steven",
""
]
] | Deep-learning models based on whole-slide digital pathology images (WSIs) become increasingly popular for predicting molecular biomarkers. Instance-based models has been the mainstream strategy for predicting genetic alterations using WSIs although bag-based models along with self-attention mechanism-based algorithms h... |
2307.14099 | Jeremi K. Ochab | Jakub Janarek, Zbigniew Drogosz, Jacek Grela, Jeremi K. Ochab,
Pawe{\l} O\'swi\k{e}cimka | Investigating structural and functional aspects of the brain's
criticality in stroke | 24 pages, 11 figures | Scientific Reports 13: 12341 (2023) | 10.1038/s41598-023-39467-x | null | q-bio.NC cond-mat.dis-nn q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper addresses the question of the brain's critical dynamics after an
injury such as a stroke. It is hypothesized that the healthy brain operates
near a phase transition (critical point), which provides optimal conditions for
information transmission and responses to inputs. If structural damage could
cause the... | [
{
"created": "Wed, 26 Jul 2023 10:58:53 GMT",
"version": "v1"
}
] | 2023-08-01 | [
[
"Janarek",
"Jakub",
""
],
[
"Drogosz",
"Zbigniew",
""
],
[
"Grela",
"Jacek",
""
],
[
"Ochab",
"Jeremi K.",
""
],
[
"Oświęcimka",
"Paweł",
""
]
] | This paper addresses the question of the brain's critical dynamics after an injury such as a stroke. It is hypothesized that the healthy brain operates near a phase transition (critical point), which provides optimal conditions for information transmission and responses to inputs. If structural damage could cause the c... |
1811.07140 | Xi Han | X. Han, L. Zhang, K. Zhou, X. Wang | Deep learning framework DNN with conditional WGAN for protein solubility
prediction | 7 pages, 4 figures, 3 tables, journal Bioinformatics(submitted) | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein solubility plays a critical role in improving production yield of
recombinant proteins in biocatalyst and pharmaceutical field. To some extent,
protein solubility can represent the function and activity of biocatalysts
which are mainly composed of recombinant proteins. Highly soluble proteins are
more effecti... | [
{
"created": "Sat, 17 Nov 2018 10:34:24 GMT",
"version": "v1"
}
] | 2018-11-20 | [
[
"Han",
"X.",
""
],
[
"Zhang",
"L.",
""
],
[
"Zhou",
"K.",
""
],
[
"Wang",
"X.",
""
]
] | Protein solubility plays a critical role in improving production yield of recombinant proteins in biocatalyst and pharmaceutical field. To some extent, protein solubility can represent the function and activity of biocatalysts which are mainly composed of recombinant proteins. Highly soluble proteins are more effective... |
2107.11856 | Amine Amor | Amine Amor (1), Pietro Lio' (1), Vikash Singh (1), Ramon Vi\~nas
Torn\'e (1), Helena Andres Terre (1) | Graph Representation Learning on Tissue-Specific Multi-Omics | This paper was accepted at the 2021 ICML Workshop on Computational
Biology | null | null | null | q-bio.GN cs.LG stat.AP | http://creativecommons.org/licenses/by/4.0/ | Combining different modalities of data from human tissues has been critical
in advancing biomedical research and personalised medical care. In this study,
we leverage a graph embedding model (i.e VGAE) to perform link prediction on
tissue-specific Gene-Gene Interaction (GGI) networks. Through ablation
experiments, we... | [
{
"created": "Sun, 25 Jul 2021 17:38:45 GMT",
"version": "v1"
}
] | 2021-07-27 | [
[
"Amor",
"Amine",
""
],
[
"Lio'",
"Pietro",
""
],
[
"Singh",
"Vikash",
""
],
[
"Torné",
"Ramon Viñas",
""
],
[
"Terre",
"Helena Andres",
""
]
] | Combining different modalities of data from human tissues has been critical in advancing biomedical research and personalised medical care. In this study, we leverage a graph embedding model (i.e VGAE) to perform link prediction on tissue-specific Gene-Gene Interaction (GGI) networks. Through ablation experiments, we p... |
1307.4922 | Kazuhiro Takemoto | Kazuhiro Takemoto, Takeyuki Tamura, Tatsuya Akutsu | Theoretical estimation of metabolic network robustness against multiple
reaction knockouts using branching process approximation | 20 pages, 6 figures, 2 tables | Physica A 392, 5525 (2013) | 10.1016/j.physa.2013.07.003 | null | q-bio.MN physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In our previous study, we showed that the branching process approximation is
useful for estimating metabolic robustness, measured using the impact degree.
By applying a theory of random family forests, we here extend the branching
process approximation to consider the knockout of {\it multiple} reactions,
inspired by... | [
{
"created": "Thu, 18 Jul 2013 12:30:48 GMT",
"version": "v1"
}
] | 2013-08-21 | [
[
"Takemoto",
"Kazuhiro",
""
],
[
"Tamura",
"Takeyuki",
""
],
[
"Akutsu",
"Tatsuya",
""
]
] | In our previous study, we showed that the branching process approximation is useful for estimating metabolic robustness, measured using the impact degree. By applying a theory of random family forests, we here extend the branching process approximation to consider the knockout of {\it multiple} reactions, inspired by t... |
2112.12290 | Alan S. R. Fermin | Alan S. R. Fermin, Karl Friston, Shigeto Yamawaki | Insula Interoception, Active Inference and Feeling Representation | 22 pages, 3 figures, opinion | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The body sends interoceptive visceral information through deep brain
structures to the cerebral cortex. The insula cortex, organized in hierarchical
modules, is the major cortical region receiving interoceptive afferents and
contains visceral topographic maps. Yet, the biological significance of the
insula's modular ... | [
{
"created": "Thu, 23 Dec 2021 00:51:40 GMT",
"version": "v1"
}
] | 2021-12-24 | [
[
"Fermin",
"Alan S. R.",
""
],
[
"Friston",
"Karl",
""
],
[
"Yamawaki",
"Shigeto",
""
]
] | The body sends interoceptive visceral information through deep brain structures to the cerebral cortex. The insula cortex, organized in hierarchical modules, is the major cortical region receiving interoceptive afferents and contains visceral topographic maps. Yet, the biological significance of the insula's modular ar... |
1011.5240 | Ben Vanderlei | Ben Vanderlei, James J. Feng, and Leah Edelstein-Keshet | A computational model of cell polarization and motility coupling
mechanics and biochemistry | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The motion of a eukaryotic cell presents a variety of interesting and
challenging problems from both a modeling and a computational perspective. The
processes span many spatial scales (from molecular to tissue) as well as
disparate time scales, with reaction kinetics on the order of seconds, and the
deformation and m... | [
{
"created": "Tue, 23 Nov 2010 21:24:07 GMT",
"version": "v1"
}
] | 2010-11-25 | [
[
"Vanderlei",
"Ben",
""
],
[
"Feng",
"James J.",
""
],
[
"Edelstein-Keshet",
"Leah",
""
]
] | The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time scales, with reaction kinetics on the order of seconds, and the deformation and mot... |
2106.08067 | Jaroslav Albert | Jaroslav Albert | Stochastic fluctuations in protein interaction networks are nearly
Poissonian | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Gene regulatory networks are comprised of biochemical reactions, which are
inherently stochastic. Each reaction channel contributes to this stochasticity
in different measure. In this paper we study the stochastic dynamics of protein
interaction networks (PIN) that are made up of monomers and dimers. The network
is d... | [
{
"created": "Tue, 15 Jun 2021 11:47:37 GMT",
"version": "v1"
}
] | 2021-06-16 | [
[
"Albert",
"Jaroslav",
""
]
] | Gene regulatory networks are comprised of biochemical reactions, which are inherently stochastic. Each reaction channel contributes to this stochasticity in different measure. In this paper we study the stochastic dynamics of protein interaction networks (PIN) that are made up of monomers and dimers. The network is def... |
1810.03766 | Daniel Hurley G | Daniel G. Hurley, Joseph Cursons, Matthew Faria, David M. Budden,
Vijay Rajagopal, Edmund J. Crampin | Reference environments: A universal tool for reproducibility in
computational biology | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The drive for reproducibility in the computational sciences has provoked
discussion and effort across a broad range of perspectives: technological,
legislative/policy, education, and publishing. Discussion on these topics is
not new, but the need to adopt standards for reproducibility of claims made
based on computat... | [
{
"created": "Tue, 9 Oct 2018 01:20:21 GMT",
"version": "v1"
}
] | 2018-10-10 | [
[
"Hurley",
"Daniel G.",
""
],
[
"Cursons",
"Joseph",
""
],
[
"Faria",
"Matthew",
""
],
[
"Budden",
"David M.",
""
],
[
"Rajagopal",
"Vijay",
""
],
[
"Crampin",
"Edmund J.",
""
]
] | The drive for reproducibility in the computational sciences has provoked discussion and effort across a broad range of perspectives: technological, legislative/policy, education, and publishing. Discussion on these topics is not new, but the need to adopt standards for reproducibility of claims made based on computatio... |
0801.0796 | Wang Weiming | Weiming Wang, Lei Zhang, Hailing Wang, Zhenqing Li | Pattern formation of a predator-prey system with Ivlev-type functional
response | null | null | null | null | q-bio.PE | null | In this paper, we investigate the emergence of a predator-prey system with
Ivlev-type functional response and reaction-diffusion. We study how diffusion
affects the stability of predator-prey coexistence equilibrium and derive the
conditions for Hopf and Turing bifurcation in the spatial domain. Based on the
bifurcat... | [
{
"created": "Sat, 5 Jan 2008 09:08:50 GMT",
"version": "v1"
}
] | 2008-01-08 | [
[
"Wang",
"Weiming",
""
],
[
"Zhang",
"Lei",
""
],
[
"Wang",
"Hailing",
""
],
[
"Li",
"Zhenqing",
""
]
] | In this paper, we investigate the emergence of a predator-prey system with Ivlev-type functional response and reaction-diffusion. We study how diffusion affects the stability of predator-prey coexistence equilibrium and derive the conditions for Hopf and Turing bifurcation in the spatial domain. Based on the bifurcatio... |
1302.2666 | Michael B\"orsch | Thomas Heitkamp, Hendrik Sielaff, Anja Korn, Marc Renz, Nawid Zarrabi,
Michael Boersch | Monitoring subunit rotation in single FRET-labeled FoF1-ATP synthase in
an anti-Brownian electrokinetic trap | 12 pages, 4 figures | null | 10.1117/12.2002966 | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | FoF1-ATP synthase is the membrane protein catalyzing the synthesis of the
'biological energy currency' adenosine triphosphate (ATP). The enzyme uses
internal subunit rotation for the mechanochemical conversion of a proton motive
force to the chemical bond. We apply single-molecule F\"orster resonance energy
transfer ... | [
{
"created": "Mon, 11 Feb 2013 23:15:07 GMT",
"version": "v1"
}
] | 2015-06-15 | [
[
"Heitkamp",
"Thomas",
""
],
[
"Sielaff",
"Hendrik",
""
],
[
"Korn",
"Anja",
""
],
[
"Renz",
"Marc",
""
],
[
"Zarrabi",
"Nawid",
""
],
[
"Boersch",
"Michael",
""
]
] | FoF1-ATP synthase is the membrane protein catalyzing the synthesis of the 'biological energy currency' adenosine triphosphate (ATP). The enzyme uses internal subunit rotation for the mechanochemical conversion of a proton motive force to the chemical bond. We apply single-molecule F\"orster resonance energy transfer (F... |
2007.13815 | Anjalika Nande | Anjalika Nande, Andrew Ferdowsian, Eric Lubin, Erez Yoeli and Martin
Nowak | DyPy: A Python Library for Simulating Matrix-Form Games | null | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Evolutionary Game Theory (EGT) simulations are used to model populations
undergoing biological and cultural evolution in a range of fields, from biology
to economics to linguistics. In this paper we present DyPy, an open source
Python package that can perform evolutionary simulations for any matrix form
game for thre... | [
{
"created": "Mon, 27 Jul 2020 19:04:39 GMT",
"version": "v1"
}
] | 2020-07-29 | [
[
"Nande",
"Anjalika",
""
],
[
"Ferdowsian",
"Andrew",
""
],
[
"Lubin",
"Eric",
""
],
[
"Yoeli",
"Erez",
""
],
[
"Nowak",
"Martin",
""
]
] | Evolutionary Game Theory (EGT) simulations are used to model populations undergoing biological and cultural evolution in a range of fields, from biology to economics to linguistics. In this paper we present DyPy, an open source Python package that can perform evolutionary simulations for any matrix form game for three ... |
2112.13283 | Judit Aizpuru | Judit Aizpuru and Annina Karolin Kemmer and Jong Woo Kim and Stefan
Born and Peter Neubauer and Mariano N. Cruz Bournazou and Tilman Barz | Fitting nonlinear models to continuous oxygen data with oscillatory
signal variations via a loss based on DynamicTime Warping | null | null | null | null | q-bio.QM cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High throughput experimental systems play an important role in bioprocess
development, as they provide an efficient way of analysing different
experimental conditions and perform strain discrimination in previous phases to
the industrial scale production. In the millilitre scale, these systems are
combinations of par... | [
{
"created": "Sat, 25 Dec 2021 20:31:27 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Aizpuru",
"Judit",
""
],
[
"Kemmer",
"Annina Karolin",
""
],
[
"Kim",
"Jong Woo",
""
],
[
"Born",
"Stefan",
""
],
[
"Neubauer",
"Peter",
""
],
[
"Bournazou",
"Mariano N. Cruz",
""
],
[
"Barz",
"Tilman",
""... | High throughput experimental systems play an important role in bioprocess development, as they provide an efficient way of analysing different experimental conditions and perform strain discrimination in previous phases to the industrial scale production. In the millilitre scale, these systems are combinations of paral... |
1504.06290 | Zachary Kilpatrick PhD | Zachary McCleney and Zachary P. Kilpatrick | Entrainment in up and down states of neural populations: non-smooth and
stochastic models | 23 pages, 7 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the impact of noise on a neural population rate model of up and down
states. Up and down states are typically observed in neuronal networks as a
slow oscillation, where the population switches between high and low firing
rates (Sanchez-Vivez and McCormick, 2000). A neural population model with spike
rate ada... | [
{
"created": "Thu, 23 Apr 2015 18:36:01 GMT",
"version": "v1"
}
] | 2015-04-24 | [
[
"McCleney",
"Zachary",
""
],
[
"Kilpatrick",
"Zachary P.",
""
]
] | We study the impact of noise on a neural population rate model of up and down states. Up and down states are typically observed in neuronal networks as a slow oscillation, where the population switches between high and low firing rates (Sanchez-Vivez and McCormick, 2000). A neural population model with spike rate adapt... |
1208.4027 | Edgardo Brigatti | E. Brigatti, M. N\'u\~nez-L\'opez and M. Oliva | Analysis of a spatial Lotka-Volterra model with a finite range
predator-prey interaction | 7 pages, 7 figures | Eur. Phys. J. B 81, 321--326 (2011) | 10.1140/epjb/e2011-10826-6 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We perform an analysis of a recent spatial version of the classical
Lotka-Volterra model, where a finite scale controls individuals' interaction.
We study the behavior of the predator-prey dynamics in physical spaces higher
than one, showing how spatial patterns can emerge for some values of the
interaction range and... | [
{
"created": "Mon, 20 Aug 2012 14:48:41 GMT",
"version": "v1"
}
] | 2012-08-21 | [
[
"Brigatti",
"E.",
""
],
[
"Núñez-López",
"M.",
""
],
[
"Oliva",
"M.",
""
]
] | We perform an analysis of a recent spatial version of the classical Lotka-Volterra model, where a finite scale controls individuals' interaction. We study the behavior of the predator-prey dynamics in physical spaces higher than one, showing how spatial patterns can emerge for some values of the interaction range and o... |
1604.00069 | Thomas Gorochowski | Thomas E. Gorochowski, Rafal Bogacz, Matthew Jones | Cross-Frequency Coupling of Neuronal Oscillations During Cognition | null | null | null | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How the brain co-ordinates the actions of distant regions in an efficient
manner is an open problem. Many believe that cross-frequency coupling between
the amplitude of high frequency local field potential oscillations in one
region and the phase of lower frequency signals in another may form a possible
mechanism. Th... | [
{
"created": "Thu, 31 Mar 2016 22:26:05 GMT",
"version": "v1"
}
] | 2016-04-04 | [
[
"Gorochowski",
"Thomas E.",
""
],
[
"Bogacz",
"Rafal",
""
],
[
"Jones",
"Matthew",
""
]
] | How the brain co-ordinates the actions of distant regions in an efficient manner is an open problem. Many believe that cross-frequency coupling between the amplitude of high frequency local field potential oscillations in one region and the phase of lower frequency signals in another may form a possible mechanism. This... |
1907.00816 | David Hansel | Alexandre Mahrach, Guang Chen, Nuo Li, Carl van Vreeswijk, David
Hansel | Mechanisms underlying the response of mouse cortical networks to
optogenetic manipulation | null | null | null | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | GABAergic interneurons can be subdivided into three subclasses: parvalbumin
positive (PV), somatostatin positive (SOM) and serotonin positive neurons. With
principal cells (PCs) they form complex networks. We examine PCs and PV
responses in mouse anterior lateral motor cortex (ALM) and barrel cortex (S1)
upon PV phot... | [
{
"created": "Mon, 1 Jul 2019 14:22:03 GMT",
"version": "v1"
}
] | 2019-07-02 | [
[
"Mahrach",
"Alexandre",
""
],
[
"Chen",
"Guang",
""
],
[
"Li",
"Nuo",
""
],
[
"van Vreeswijk",
"Carl",
""
],
[
"Hansel",
"David",
""
]
] | GABAergic interneurons can be subdivided into three subclasses: parvalbumin positive (PV), somatostatin positive (SOM) and serotonin positive neurons. With principal cells (PCs) they form complex networks. We examine PCs and PV responses in mouse anterior lateral motor cortex (ALM) and barrel cortex (S1) upon PV photos... |
2205.09548 | Lixue Cheng | Lixue Cheng, Ziyi Yang, Changyu Hsieh, Benben Liao, Shengyu Zhang | ODBO: Bayesian Optimization with Search Space Prescreening for Directed
Protein Evolution | 27 pages, 13 figures | null | null | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Directed evolution is a versatile technique in protein engineering that
mimics the process of natural selection by iteratively alternating between
mutagenesis and screening in order to search for sequences that optimize a
given property of interest, such as catalytic activity and binding affinity to
a specified targe... | [
{
"created": "Thu, 19 May 2022 13:21:31 GMT",
"version": "v1"
},
{
"created": "Fri, 20 May 2022 13:52:17 GMT",
"version": "v2"
},
{
"created": "Fri, 14 Oct 2022 09:58:09 GMT",
"version": "v3"
},
{
"created": "Mon, 24 Oct 2022 09:20:44 GMT",
"version": "v4"
},
{
"c... | 2024-05-02 | [
[
"Cheng",
"Lixue",
""
],
[
"Yang",
"Ziyi",
""
],
[
"Hsieh",
"Changyu",
""
],
[
"Liao",
"Benben",
""
],
[
"Zhang",
"Shengyu",
""
]
] | Directed evolution is a versatile technique in protein engineering that mimics the process of natural selection by iteratively alternating between mutagenesis and screening in order to search for sequences that optimize a given property of interest, such as catalytic activity and binding affinity to a specified target.... |
0901.3067 | Anastasia Deckard | Anastasia C. Deckard, Frank T. Bergmann, and Herbert M. Sauro | Enumeration and Online Library of Mass-Action Reaction Networks | 17 pages, 6 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/3.0/ | The aim of this work is to make available to the community a large collection
of mass-action reaction networks of a given size for further research. The set
is limited to what can be computed on a modern multi-core desktop in reasonable
time (< 20 days). We have currently generated over 47 million unique reaction
net... | [
{
"created": "Mon, 19 Jan 2009 21:35:36 GMT",
"version": "v1"
}
] | 2009-01-21 | [
[
"Deckard",
"Anastasia C.",
""
],
[
"Bergmann",
"Frank T.",
""
],
[
"Sauro",
"Herbert M.",
""
]
] | The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable time (< 20 days). We have currently generated over 47 million unique reaction netwo... |
2304.02729 | Giulia Bernardini | Giulia Bernardini and Leo van Iersel and Esther Julien and Leen
Stougie | Constructing Phylogenetic Networks via Cherry Picking and Machine
Learning | 42 pages, 20 figures, submitted to Algorithms for Molecular Biology
(special issue of WABI 2022) | null | null | null | q-bio.PE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Combining a set of phylogenetic trees into a single phylogenetic network that
explains all of them is a fundamental challenge in evolutionary studies.
Existing methods are computationally expensive and can either handle only small
numbers of phylogenetic trees or are limited to severely restricted classes of
networks... | [
{
"created": "Fri, 31 Mar 2023 15:04:42 GMT",
"version": "v1"
}
] | 2023-04-07 | [
[
"Bernardini",
"Giulia",
""
],
[
"van Iersel",
"Leo",
""
],
[
"Julien",
"Esther",
""
],
[
"Stougie",
"Leen",
""
]
] | Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks. ... |
1309.3535 | Luc Berthouze | Caroline Hartley and Timothy J Taylor and Istvan Z Kiss and Simon F
Farmer and Luc Berthouze | Identification of criticality in neuronal avalanches: II. A theoretical
and empirical investigation of the driven case | 48 pages, 18 figures | The Journal of Mathematical Neuroscience 2014, 4:9 | 10.1186/2190-8567-4-9 | null | q-bio.NC math-ph math.MP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The observation of apparent power-laws in neuronal systems has led to the
suggestion that the brain is at, or close to, a critical state and may be a
self-organised critical system. Within the framework of self-organised
criticality a separation of timescales is thought to be crucial for the
observation of power-law ... | [
{
"created": "Fri, 13 Sep 2013 18:33:55 GMT",
"version": "v1"
}
] | 2014-10-22 | [
[
"Hartley",
"Caroline",
""
],
[
"Taylor",
"Timothy J",
""
],
[
"Kiss",
"Istvan Z",
""
],
[
"Farmer",
"Simon F",
""
],
[
"Berthouze",
"Luc",
""
]
] | The observation of apparent power-laws in neuronal systems has led to the suggestion that the brain is at, or close to, a critical state and may be a self-organised critical system. Within the framework of self-organised criticality a separation of timescales is thought to be crucial for the observation of power-law dy... |
1403.1957 | Joel Miller | Joel C Miller and Istvan Z Kiss | Epidemic spread in networks: Existing methods and current challenges | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the spread of infectious disease through contact networks of
Configuration Model type. We assume that the disease spreads through contacts
and infected individuals recover into an immune state. We discuss a number of
existing mathematical models used to investigate this system, and show
relations between ... | [
{
"created": "Sat, 8 Mar 2014 10:11:58 GMT",
"version": "v1"
}
] | 2014-03-11 | [
[
"Miller",
"Joel C",
""
],
[
"Kiss",
"Istvan Z",
""
]
] | We consider the spread of infectious disease through contact networks of Configuration Model type. We assume that the disease spreads through contacts and infected individuals recover into an immune state. We discuss a number of existing mathematical models used to investigate this system, and show relations between th... |
2308.02589 | Dan Gorbonos | Dan Gorbonos, Felix Oberhauser, Luke L. Costello, Yannick G\"unzel,
Einat Couzin-Fuchs, Benjamin Koger, Iain D. Couzin | An Effective Hydrodynamic Description of Marching Locusts | 21 pages, 13 figures | null | null | null | q-bio.QM cond-mat.stat-mech physics.bio-ph physics.flu-dyn q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A fundamental question in complex systems is how to relate interactions
between individual components ("microscopic description") to the global
properties of the system ("macroscopic description"). Another fundamental
question is whether such a macroscopic description exists at all and how well
it describes the large... | [
{
"created": "Thu, 3 Aug 2023 18:56:58 GMT",
"version": "v1"
}
] | 2023-08-08 | [
[
"Gorbonos",
"Dan",
""
],
[
"Oberhauser",
"Felix",
""
],
[
"Costello",
"Luke L.",
""
],
[
"Günzel",
"Yannick",
""
],
[
"Couzin-Fuchs",
"Einat",
""
],
[
"Koger",
"Benjamin",
""
],
[
"Couzin",
"Iain D.",
""
... | A fundamental question in complex systems is how to relate interactions between individual components ("microscopic description") to the global properties of the system ("macroscopic description"). Another fundamental question is whether such a macroscopic description exists at all and how well it describes the large-s... |
1610.09536 | Osman Kahraman | Osman Kahraman, Yiwei Li and Christoph A. Haselwandter | Stochastic single-molecule dynamics of synaptic membrane protein domains | Main text (7 pages, 4 figures, 1 table) and supplementary material (3
pages, 3 figures) | EPL, 115 (2016) 68006 | 10.1209/0295-5075/115/68006 | null | q-bio.SC physics.bio-ph q-bio.BM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivated by single-molecule experiments on synaptic membrane protein
domains, we use a stochastic lattice model to study protein reaction and
diffusion processes in crowded membranes. We find that the stochastic
reaction-diffusion dynamics of synaptic proteins provide a simple physical
mechanism for collective fluct... | [
{
"created": "Sat, 29 Oct 2016 16:09:18 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Nov 2016 19:25:07 GMT",
"version": "v2"
}
] | 2016-11-08 | [
[
"Kahraman",
"Osman",
""
],
[
"Li",
"Yiwei",
""
],
[
"Haselwandter",
"Christoph A.",
""
]
] | Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctua... |
2109.05545 | Grace Hwang | Elise Buckley, Joseph D. Monaco, Kevin M. Schultz, Robert Chalmers,
Armin Hadzic, Kechen Zhang, Grace M. Hwang, M. Dwight Carr | An interdisciplinary approach to high school curriculum development:
Swarming Powered by Neuroscience | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This article discusses how to create an interactive virtual training program
at the intersection of neuroscience, robotics, and computer science for high
school students. A four-day microseminar, titled Swarming Powered by
Neuroscience (SPN), was conducted virtually through a combination of
presentations and interact... | [
{
"created": "Sun, 12 Sep 2021 16:00:00 GMT",
"version": "v1"
}
] | 2021-09-14 | [
[
"Buckley",
"Elise",
""
],
[
"Monaco",
"Joseph D.",
""
],
[
"Schultz",
"Kevin M.",
""
],
[
"Chalmers",
"Robert",
""
],
[
"Hadzic",
"Armin",
""
],
[
"Zhang",
"Kechen",
""
],
[
"Hwang",
"Grace M.",
""
],
[... | This article discusses how to create an interactive virtual training program at the intersection of neuroscience, robotics, and computer science for high school students. A four-day microseminar, titled Swarming Powered by Neuroscience (SPN), was conducted virtually through a combination of presentations and interactiv... |
2308.13877 | Suraj Rajendran | Akshay Bhalla, Suraj Rajendran | Applications of machine Learning to improve the efficiency and range of
microbial biosynthesis: a review of state-of-art techniques | null | null | null | null | q-bio.SC cs.LG q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | In the modern world, technology is at its peak. Different avenues in
programming and technology have been explored for data analysis, automation,
and robotics. Machine learning is key to optimize data analysis, make accurate
predictions, and hasten/improve existing functions. Thus, presently, the field
of machine lea... | [
{
"created": "Sat, 26 Aug 2023 13:27:40 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Oct 2023 23:27:42 GMT",
"version": "v2"
}
] | 2023-10-18 | [
[
"Bhalla",
"Akshay",
""
],
[
"Rajendran",
"Suraj",
""
]
] | In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions, and hasten/improve existing functions. Thus, presently, the field of machine learn... |
2305.08238 | David Graff | David E. Graff, Edward O. Pyzer-Knapp, Kirk E. Jordan, Eugene I.
Shakhnovich, Connor W. Coley | Evaluating the roughness of structure-property relationships using
pretrained molecular representations | 18 pages, 13 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantitative structure-property relationships (QSPRs) aid in understanding
molecular properties as a function of molecular structure. When the correlation
between structure and property weakens, a dataset is described as "rough," but
this characteristic is partly a function of the chosen representation. Among
possibl... | [
{
"created": "Sun, 14 May 2023 20:10:10 GMT",
"version": "v1"
}
] | 2023-05-16 | [
[
"Graff",
"David E.",
""
],
[
"Pyzer-Knapp",
"Edward O.",
""
],
[
"Jordan",
"Kirk E.",
""
],
[
"Shakhnovich",
"Eugene I.",
""
],
[
"Coley",
"Connor W.",
""
]
] | Quantitative structure-property relationships (QSPRs) aid in understanding molecular properties as a function of molecular structure. When the correlation between structure and property weakens, a dataset is described as "rough," but this characteristic is partly a function of the chosen representation. Among possible ... |
1712.03594 | Hwai-Ray Tung | H. Tung | Precluding Oscillations in Michaelis-Menten Approximations of Dual-site
Phosphorylation Systems | null | Mathematical Biosciences, Volume 306, 2018, Pages 56-59 | 10.1016/j.mbs.2018.10.008 | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oscillations play a major role in a number of biological systems, from
predator-prey models of ecology to circadian clocks. In this paper we focus on
the question of whether oscillations exist within dual-site phosphorylation
systems. Previously, Wang and Sontag showed, using monotone systems theory,
that the Michael... | [
{
"created": "Sun, 10 Dec 2017 21:17:03 GMT",
"version": "v1"
},
{
"created": "Wed, 31 Oct 2018 02:38:39 GMT",
"version": "v2"
}
] | 2020-08-03 | [
[
"Tung",
"H.",
""
]
] | Oscillations play a major role in a number of biological systems, from predator-prey models of ecology to circadian clocks. In this paper we focus on the question of whether oscillations exist within dual-site phosphorylation systems. Previously, Wang and Sontag showed, using monotone systems theory, that the Michaelis... |
1506.00288 | Vijay Singh | Vijay Singh, Ilya Nemenman | Accurate sensing of multiple ligands with a single receptor | 6 pages, 4 figures | null | null | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cells use surface receptors to estimate the concentration of external
ligands. Limits on the accuracy of such estimations have been well studied for
pairs of ligand and receptor species. However, the environment typically
contains many ligands, which can bind to the same receptors with different
affinities, resulting... | [
{
"created": "Sun, 31 May 2015 20:43:24 GMT",
"version": "v1"
}
] | 2015-06-02 | [
[
"Singh",
"Vijay",
""
],
[
"Nemenman",
"Ilya",
""
]
] | Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many ligands, which can bind to the same receptors with different affinities, resulting i... |
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