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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1308.5826 | Pedro Mendes | Simon Mitchell and Pedro Mendes | A Computational Model of Liver Iron Metabolism | null | null | 10.1371/journal.pcbi.1003299 | null | q-bio.MN | http://creativecommons.org/licenses/by/3.0/ | Iron is essential for all known life due to its redox properties, however
these same properties can also lead to its toxicity in overload through the
production of reactive oxygen species. Robust systemic and cellular control are
required to maintain safe levels of iron and the liver seems to be where this
regulation... | [
{
"created": "Tue, 27 Aug 2013 11:21:39 GMT",
"version": "v1"
}
] | 2014-03-05 | [
[
"Mitchell",
"Simon",
""
],
[
"Mendes",
"Pedro",
""
]
] | Iron is essential for all known life due to its redox properties, however these same properties can also lead to its toxicity in overload through the production of reactive oxygen species. Robust systemic and cellular control are required to maintain safe levels of iron and the liver seems to be where this regulation i... |
1502.06659 | Somwrita Sarkar | Somwrita Sarkar, Sanjay Chawla and Donna Xu | On inferring structural connectivity from brain functional-MRI data | 10 pages, 6 Figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The anatomical structure of the brain can be observed via non-invasive
techniques such as diffusion imaging. However, these are imperfect because they
miss connections that are actually known to exist, especially long range
inter-hemispheric ones. In this paper we formulate the inverse problem of
inferring the struct... | [
{
"created": "Tue, 24 Feb 2015 00:20:14 GMT",
"version": "v1"
}
] | 2015-02-25 | [
[
"Sarkar",
"Somwrita",
""
],
[
"Chawla",
"Sanjay",
""
],
[
"Xu",
"Donna",
""
]
] | The anatomical structure of the brain can be observed via non-invasive techniques such as diffusion imaging. However, these are imperfect because they miss connections that are actually known to exist, especially long range inter-hemispheric ones. In this paper we formulate the inverse problem of inferring the structur... |
2306.13582 | Amin Zia | Amin Zia | Heat shock proteins may be a missing link between febrile infection and
cancer tumor rejection via autoantigen molecular mimicry | 16 pages, 3 figures, one table | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Numerous epidemiological studies suggest febrile infections could confer
long-term immunity to certain types of cancers, though the precise mechanisms
for this phenomenon remain unclear. Systemic heat-shock responses to fever may
be key to understanding the overlapping outcomes of immune responses to
infection and ca... | [
{
"created": "Fri, 23 Jun 2023 16:09:31 GMT",
"version": "v1"
}
] | 2023-06-26 | [
[
"Zia",
"Amin",
""
]
] | Numerous epidemiological studies suggest febrile infections could confer long-term immunity to certain types of cancers, though the precise mechanisms for this phenomenon remain unclear. Systemic heat-shock responses to fever may be key to understanding the overlapping outcomes of immune responses to infection and canc... |
0707.3770 | Tibor Antal | Niko Beerenwinkel, Tibor Antal, David Dingli, Arne Traulsen, Kenneth
W. Kinzler, Victor E. Velculescu, Bert Vogelstein, Martin A. Nowak | Genetic progression and the waiting time to cancer | Details available as supplementary material at
http://www.people.fas.harvard.edu/~antal/publications.html | PLoS Comput Biol 3(11): e225 (2007) | 10.1371/journal.pcbi.0030225 | null | q-bio.PE q-bio.QM | null | Cancer results from genetic alterations that disturb the normal cooperative
behavior of cells. Recent high-throughput genomic studies of cancer cells have
shown that the mutational landscape of cancer is complex and that individual
cancers may evolve through mutations in as many as 20 different
cancer-associated gene... | [
{
"created": "Wed, 25 Jul 2007 15:39:48 GMT",
"version": "v1"
}
] | 2011-11-10 | [
[
"Beerenwinkel",
"Niko",
""
],
[
"Antal",
"Tibor",
""
],
[
"Dingli",
"David",
""
],
[
"Traulsen",
"Arne",
""
],
[
"Kinzler",
"Kenneth W.",
""
],
[
"Velculescu",
"Victor E.",
""
],
[
"Vogelstein",
"Bert",
""
... | Cancer results from genetic alterations that disturb the normal cooperative behavior of cells. Recent high-throughput genomic studies of cancer cells have shown that the mutational landscape of cancer is complex and that individual cancers may evolve through mutations in as many as 20 different cancer-associated genes.... |
2004.03377 | Fabio Miletto Granozio Dr | Fabio Miletto Granozio | On the problem of comparing Covid-19 fatality rates | three pages, one table, three figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding Covid-19 lethality and its variation from country to country is
essential for supporting governments in the choice of appropriate strategies.
Adopting correct indicators to monitor the lethality of the infection in the
course of the outbreak is a crucial issue. This works highlights how far the
time-dep... | [
{
"created": "Mon, 6 Apr 2020 14:32:57 GMT",
"version": "v1"
}
] | 2020-04-08 | [
[
"Granozio",
"Fabio Miletto",
""
]
] | Understanding Covid-19 lethality and its variation from country to country is essential for supporting governments in the choice of appropriate strategies. Adopting correct indicators to monitor the lethality of the infection in the course of the outbreak is a crucial issue. This works highlights how far the time-depen... |
2309.14598 | Li Chen | Guozhong Zheng, Jiqiang Zhang, Jing Zhang, Weiran Cai, and Li Chen | Decoding trust: A reinforcement learning perspective | 12 pages, 11 figures. Comments are appreciated | null | null | null | q-bio.PE cond-mat.dis-nn nlin.AO stat.ML | http://creativecommons.org/licenses/by/4.0/ | Behavioral experiments on the trust game have shown that trust and
trustworthiness are universal among human beings, contradicting the prediction
by assuming \emph{Homo economicus} in orthodox Economics. This means some
mechanism must be at work that favors their emergence. Most previous
explanations however need to ... | [
{
"created": "Tue, 26 Sep 2023 01:06:29 GMT",
"version": "v1"
},
{
"created": "Sun, 26 Nov 2023 11:37:35 GMT",
"version": "v2"
}
] | 2023-11-28 | [
[
"Zheng",
"Guozhong",
""
],
[
"Zhang",
"Jiqiang",
""
],
[
"Zhang",
"Jing",
""
],
[
"Cai",
"Weiran",
""
],
[
"Chen",
"Li",
""
]
] | Behavioral experiments on the trust game have shown that trust and trustworthiness are universal among human beings, contradicting the prediction by assuming \emph{Homo economicus} in orthodox Economics. This means some mechanism must be at work that favors their emergence. Most previous explanations however need to re... |
q-bio/0406018 | Eleonora Alfinito | C. Pennetta, V. Akimov, E. Alfinito, L. Reggiani and G. Gomila | Fluctuations of Complex Networks: Electrical Properties of Single
Protein Nanodevices | 16 Pages and 10 Figures published in SPIE Proceedings of the II
International Symposium on Fluctuation and Noise, Maspalomas,Gran
Canaria,Spain, 25-28 May 2004 | null | 10.1117/12.547636 | null | q-bio.MN cond-mat.other physics.bio-ph q-bio.OT | null | We present for the first time a complex network approach to the study of the
electrical properties of single protein devices. In particular, we consider an
electronic nanobiosensor based on a G-protein coupled receptor. By adopting a
coarse grain description, the protein is modeled as a complex network of
elementary ... | [
{
"created": "Tue, 8 Jun 2004 09:24:54 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Pennetta",
"C.",
""
],
[
"Akimov",
"V.",
""
],
[
"Alfinito",
"E.",
""
],
[
"Reggiani",
"L.",
""
],
[
"Gomila",
"G.",
""
]
] | We present for the first time a complex network approach to the study of the electrical properties of single protein devices. In particular, we consider an electronic nanobiosensor based on a G-protein coupled receptor. By adopting a coarse grain description, the protein is modeled as a complex network of elementary im... |
1103.3294 | Daniel Jost | Daniel Jost, Asif Zubair and Ralf Everaers | Bubble statistics and positioning in superhelically stressed DNA | to be appeared in Physical Review E | null | 10.1103/PhysRevE.84.031912 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a general framework to study the thermodynamic denaturation of
double-stranded DNA under superhelical stress. We report calculations of
position- and size-dependent opening probabilities for bubbles along the
sequence. Our results are obtained from transfer-matrix solutions of the
Zimm-Bragg model for unco... | [
{
"created": "Wed, 16 Mar 2011 20:48:57 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Sep 2011 14:03:20 GMT",
"version": "v2"
}
] | 2013-05-29 | [
[
"Jost",
"Daniel",
""
],
[
"Zubair",
"Asif",
""
],
[
"Everaers",
"Ralf",
""
]
] | We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our results are obtained from transfer-matrix solutions of the Zimm-Bragg model for uncons... |
0812.5114 | Peter Waddell | Peter J Waddell | Fit of Fossils and Mammalian Molecular Trees: Dating Inconsistencies
Revisited | null | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Divergence time estimation requires the reconciliation of two major sources
of data. These are fossil and/or biogeographic evidence that give estimates of
the absolute age of nodes (ancestors) and molecular estimates that give us
estimates of the relative ages of nodes in a molecular evolutionary tree. Both
forms of ... | [
{
"created": "Tue, 30 Dec 2008 20:46:22 GMT",
"version": "v1"
}
] | 2008-12-31 | [
[
"Waddell",
"Peter J",
""
]
] | Divergence time estimation requires the reconciliation of two major sources of data. These are fossil and/or biogeographic evidence that give estimates of the absolute age of nodes (ancestors) and molecular estimates that give us estimates of the relative ages of nodes in a molecular evolutionary tree. Both forms of da... |
2105.06057 | Sang-Yoon Kim | Sang-Yoon Kim and Woochang Lim | Dynamical Origin for Winner-Take-All Competition in A Biological Network
of The Hippocampal Dentate Gyrus | null | null | 10.1103/PhysRevE.105.014418 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a biological network of the hippocampal dentate gyrus (DG). The
DG is a pre-processor for pattern separation which facilitates pattern storage
and retrieval in the CA3 area of the hippocampus. The main encoding cells in
the DG are the granule cells (GCs) which receive the input from the entorhinal
cortex ... | [
{
"created": "Thu, 13 May 2021 03:18:18 GMT",
"version": "v1"
}
] | 2022-02-09 | [
[
"Kim",
"Sang-Yoon",
""
],
[
"Lim",
"Woochang",
""
]
] | We consider a biological network of the hippocampal dentate gyrus (DG). The DG is a pre-processor for pattern separation which facilitates pattern storage and retrieval in the CA3 area of the hippocampus. The main encoding cells in the DG are the granule cells (GCs) which receive the input from the entorhinal cortex (E... |
1505.04432 | Harold P. de Vladar | Harold P. de Vladar and E\"ors Szathm\'ary | Coupled Hebbian learning and evolutionary dynamics in a formal model for
structural synaptic plasticity | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Theoretical models of neuronal function consider different mechanisms through
which networks learn, classify and discern inputs. A central focus of these
models is to understand how associations are established amongst neurons, in
order to predict spiking patterns that are compatible with empirical
observations. Alth... | [
{
"created": "Sun, 17 May 2015 18:34:12 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"de Vladar",
"Harold P.",
""
],
[
"Szathmáry",
"Eörs",
""
]
] | Theoretical models of neuronal function consider different mechanisms through which networks learn, classify and discern inputs. A central focus of these models is to understand how associations are established amongst neurons, in order to predict spiking patterns that are compatible with empirical observations. Althou... |
1607.04469 | Fernando Alcalde Cuesta | Fernando Alcalde Cuesta, Pablo Gonz\'alez Sequeiros, and \'Alvaro
Lozano Rojo | Suppressors of selection | New title, improved presentation, and further examples. Supporting
Information is also included | null | 10.1371/journal.pone.0180549 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inspired by recent works on evolutionary graph theory, an area of growing
interest in mathematical and computational biology, we present the first known
examples of undirected structures acting as suppressors of selection for any
fitness value $r > 1$. This means that the average fixation probability of an
advantageo... | [
{
"created": "Fri, 15 Jul 2016 11:35:39 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Dec 2016 16:06:01 GMT",
"version": "v2"
}
] | 2017-11-01 | [
[
"Cuesta",
"Fernando Alcalde",
""
],
[
"Sequeiros",
"Pablo González",
""
],
[
"Rojo",
"Álvaro Lozano",
""
]
] | Inspired by recent works on evolutionary graph theory, an area of growing interest in mathematical and computational biology, we present the first known examples of undirected structures acting as suppressors of selection for any fitness value $r > 1$. This means that the average fixation probability of an advantageous... |
q-bio/0312014 | Edward R. Abraham | Marcus R. Frean and Edward R. Abraham | Adaptation and enslavement in endosymbiont-host associations | v2: Correction made to equations 5 & 6 v3: Revised version accepted
in Phys. Rev. E; New figure added | null | 10.1103/PhysRevE.69.051913 | null | q-bio.PE | null | The evolutionary persistence of symbiotic associations is a puzzle.
Adaptation should eliminate cooperative traits if it is possible to enjoy the
advantages of cooperation without reciprocating - a facet of cooperation known
in game theory as the Prisoner's Dilemma. Despite this barrier, symbioses are
widespread, and... | [
{
"created": "Wed, 10 Dec 2003 01:45:54 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Jan 2004 00:44:13 GMT",
"version": "v2"
},
{
"created": "Tue, 24 Feb 2004 04:38:48 GMT",
"version": "v3"
}
] | 2009-11-10 | [
[
"Frean",
"Marcus R.",
""
],
[
"Abraham",
"Edward R.",
""
]
] | The evolutionary persistence of symbiotic associations is a puzzle. Adaptation should eliminate cooperative traits if it is possible to enjoy the advantages of cooperation without reciprocating - a facet of cooperation known in game theory as the Prisoner's Dilemma. Despite this barrier, symbioses are widespread, and m... |
0910.5240 | Mike Steel Prof. | Mike Steel and Arne Mooers | Expected length of pendant and interior edges of a Yule tree | 6 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Yule (pure-birth) model is the simplest null model of speciation; each
lineage gives rise to a new lineage independently with the same rate $\lambda$.
We investigate the expected length of an edge chosen at random from the
resulting evolutionary tree. In particular, we compare the expected length of a
randomly se... | [
{
"created": "Tue, 27 Oct 2009 20:45:45 GMT",
"version": "v1"
}
] | 2009-10-29 | [
[
"Steel",
"Mike",
""
],
[
"Mooers",
"Arne",
""
]
] | The Yule (pure-birth) model is the simplest null model of speciation; each lineage gives rise to a new lineage independently with the same rate $\lambda$. We investigate the expected length of an edge chosen at random from the resulting evolutionary tree. In particular, we compare the expected length of a randomly sele... |
2112.11664 | Victor Vikram Odouard | Victor Vikram Odouard, Diana Smirnova, Shimon Edelman | Polarize, Catalyze, Stabilize: How a minority of norm internalizers
amplify group selection and punishment | 27 pages, 4 pages of references, 14 page appendix | null | null | null | q-bio.PE cs.MA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many mechanisms behind the evolution of cooperation, such as reciprocity,
indirect reciprocity, and altruistic punishment, require group knowledge of
individual actions. But what keeps people cooperating when no one is looking?
Conformist norm internalization, the tendency to abide by the behavior of the
majority of ... | [
{
"created": "Wed, 22 Dec 2021 04:35:23 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Jan 2022 20:27:01 GMT",
"version": "v2"
},
{
"created": "Tue, 12 Apr 2022 21:02:20 GMT",
"version": "v3"
},
{
"created": "Mon, 27 Mar 2023 04:45:10 GMT",
"version": "v4"
},
{
"c... | 2023-09-22 | [
[
"Odouard",
"Victor Vikram",
""
],
[
"Smirnova",
"Diana",
""
],
[
"Edelman",
"Shimon",
""
]
] | Many mechanisms behind the evolution of cooperation, such as reciprocity, indirect reciprocity, and altruistic punishment, require group knowledge of individual actions. But what keeps people cooperating when no one is looking? Conformist norm internalization, the tendency to abide by the behavior of the majority of th... |
1602.08913 | Eugene Rosenfeld | E. V. Rosenfeld | X-ray experiment provides a way to reveal the distinction between
discrete and continuous conformation of myosin head | Anyone who understands the principles of interference can easily
check the results of very simple calculations in this text. However, the
editors of a number of biophysical journals rejected the MS and refused to
discuss details. I believe the result is important and stimulates an
experiment. So, I would be sin... | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The corner stone of the classical model after Huxley and Simmons is
supposition that a myosin head can reside only in several discrete states and
irregularly jumps from one state to another. Until now, it has not been found a
way to experimentally verify this supposition although confirmation or
refutation of the exi... | [
{
"created": "Mon, 29 Feb 2016 11:29:50 GMT",
"version": "v1"
}
] | 2016-03-01 | [
[
"Rosenfeld",
"E. V.",
""
]
] | The corner stone of the classical model after Huxley and Simmons is supposition that a myosin head can reside only in several discrete states and irregularly jumps from one state to another. Until now, it has not been found a way to experimentally verify this supposition although confirmation or refutation of the exist... |
2109.14445 | Yen Ting Lin | Jacob Neumann, Yen Ting Lin, Abhishek Mallela, Ely F. Miller, Joshua
Colvin, Abell T. Duprat1, Ye Chen, William S. Hlavacek and Richard G. Posner | Implementation of a practical Markov chain Monte Carlo sampling
algorithm in PyBioNetFit | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Bayesian inference in biological modeling commonly relies on Markov chain
Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior
distribution that is not analytically tractable. Here, we present the
implementation of a practical MCMC method in the open-source software package
PyBioNetFit (PyBNF)... | [
{
"created": "Wed, 29 Sep 2021 14:27:10 GMT",
"version": "v1"
}
] | 2021-09-30 | [
[
"Neumann",
"Jacob",
""
],
[
"Lin",
"Yen Ting",
""
],
[
"Mallela",
"Abhishek",
""
],
[
"Miller",
"Ely F.",
""
],
[
"Colvin",
"Joshua",
""
],
[
"Duprat1",
"Abell T.",
""
],
[
"Chen",
"Ye",
""
],
[
"Hl... | Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), ... |
2106.05181 | Cheng Qian | Cheng Qian | Condition Integration Memory Network: An Interpretation of the Meaning
of the Neuronal Design | 40 pages, 6 figures; added a section | null | null | null | q-bio.NC cs.NE | http://creativecommons.org/publicdomain/zero/1.0/ | Understanding the basic operational logics of the nervous system is essential
to advancing neuroscientific research. However, theoretical efforts to tackle
this fundamental problem are lacking, despite the abundant empirical data about
the brain that has been collected in the past few decades. To address this
shortco... | [
{
"created": "Fri, 21 May 2021 05:59:27 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Sep 2021 06:27:24 GMT",
"version": "v2"
}
] | 2021-09-07 | [
[
"Qian",
"Cheng",
""
]
] | Understanding the basic operational logics of the nervous system is essential to advancing neuroscientific research. However, theoretical efforts to tackle this fundamental problem are lacking, despite the abundant empirical data about the brain that has been collected in the past few decades. To address this shortcomi... |
1104.0025 | Chris Adami | Christoph Adami, Jifeng Qian, Matthew Rupp, and Arend Hintze | Information content of colored motifs in complex networks | 21 pages, 8 figures, to appear in Artificial Life | Artificial Life 17 (2011) 375-390 | 10.1162/artl_a_00045 | null | q-bio.QM cs.IT math.IT nlin.AO q-bio.MN q-bio.NC q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study complex networks in which the nodes of the network are tagged with
different colors depending on the functionality of the nodes (colored graphs),
using information theory applied to the distribution of motifs in such
networks. We find that colored motifs can be viewed as the building blocks of
the networks (... | [
{
"created": "Thu, 31 Mar 2011 20:35:44 GMT",
"version": "v1"
}
] | 2011-11-08 | [
[
"Adami",
"Christoph",
""
],
[
"Qian",
"Jifeng",
""
],
[
"Rupp",
"Matthew",
""
],
[
"Hintze",
"Arend",
""
]
] | We study complex networks in which the nodes of the network are tagged with different colors depending on the functionality of the nodes (colored graphs), using information theory applied to the distribution of motifs in such networks. We find that colored motifs can be viewed as the building blocks of the networks (mu... |
1210.4511 | Joel Miller | Joel C. Miller | Co-circulation of infectious diseases on networks | null | null | 10.1103/PhysRevE.87.060801 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider multiple diseases spreading in a static Configuration Model
network. We make standard assumptions that infection transmits from neighbor to
neighbor at a disease-specific rate and infected individuals recover at a
disease-specific rate. Infection by one disease confers immediate and permanent
immunity to ... | [
{
"created": "Tue, 16 Oct 2012 17:51:42 GMT",
"version": "v1"
}
] | 2015-06-11 | [
[
"Miller",
"Joel C.",
""
]
] | We consider multiple diseases spreading in a static Configuration Model network. We make standard assumptions that infection transmits from neighbor to neighbor at a disease-specific rate and infected individuals recover at a disease-specific rate. Infection by one disease confers immediate and permanent immunity to in... |
2202.12223 | Diego Ferreiro | Ezequiel A. Galpern, Jacopo Marchi, Thierry Mora, Aleksandra M.
Walczak, Diego U. Ferreiro | From evolution to folding of repeat proteins | 8 pages, 5 figures plus Supplementary text and Figures | null | 10.1073/pnas.2204131119 | null | q-bio.BM cond-mat.stat-mech | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Repeat proteins are made with tandem copies of similar amino acid stretches
that fold into elongated architectures. Due to their symmetry, these proteins
constitute excellent model systems to investigate how evolution relates to
structure, folding and function. Here, we propose a scheme to map evolutionary
informatio... | [
{
"created": "Thu, 24 Feb 2022 17:37:10 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Galpern",
"Ezequiel A.",
""
],
[
"Marchi",
"Jacopo",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
],
[
"Ferreiro",
"Diego U.",
""
]
] | Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure, folding and function. Here, we propose a scheme to map evolutionary information ... |
2002.08433 | Chen Liao | Chen Liao, Tong Wang, Sergei Maslov, Joao B. Xavier | Modeling microbial cross-feeding at intermediate scale portrays
community dynamics and species coexistence | 6 figures | null | 10.1371/journal.pcbi.1008135 | null | q-bio.PE q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Social interaction between microbes can be described at many levels of
details, ranging from the biochemistry of cell-cell interactions to the
ecological dynamics of populations. Choosing the best level to model microbial
communities without losing generality remains a challenge. Here we propose to
model cross-feedin... | [
{
"created": "Wed, 19 Feb 2020 20:37:51 GMT",
"version": "v1"
}
] | 2020-09-09 | [
[
"Liao",
"Chen",
""
],
[
"Wang",
"Tong",
""
],
[
"Maslov",
"Sergei",
""
],
[
"Xavier",
"Joao B.",
""
]
] | Social interaction between microbes can be described at many levels of details, ranging from the biochemistry of cell-cell interactions to the ecological dynamics of populations. Choosing the best level to model microbial communities without losing generality remains a challenge. Here we propose to model cross-feeding ... |
0912.3482 | Luca Ciandrini | L. Ciandrini, I. Stansfield, M. C. Romano | Role of the particle's stepping cycle in an asymmetric exclusion
process: A model of mRNA translation | 9 pages, 9 figures | Phys. Rev. E 81, 051904 (2010) | 10.1103/PhysRevE.81.051904 | null | q-bio.SC cond-mat.stat-mech physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Messenger RNA translation is often studied by means of statistical-mechanical
models based on the Asymmetric Simple Exclusion Process (ASEP), which considers
hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In
this work we extend this class of models and consider the two fundamental steps
of... | [
{
"created": "Thu, 17 Dec 2009 18:34:32 GMT",
"version": "v1"
},
{
"created": "Mon, 3 May 2010 20:56:51 GMT",
"version": "v2"
}
] | 2010-05-06 | [
[
"Ciandrini",
"L.",
""
],
[
"Stansfield",
"I.",
""
],
[
"Romano",
"M. C.",
""
]
] | Messenger RNA translation is often studied by means of statistical-mechanical models based on the Asymmetric Simple Exclusion Process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this work we extend this class of models and consider the two fundamental steps of t... |
2107.14073 | Mark Leake | Sarah Lecinski, Jack W Shepherd, Lewis Frame, Imogen Hayton, Chris
MacDonald, Mark C Leake | Investigating molecular crowding during cell division in budding yeast
with FRET | null | null | null | null | q-bio.CB physics.bio-ph q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell division, aging, and stress recovery triggers spatial reorganization of
cellular components in the cytoplasm, including membrane bound organelles, with
molecular changes in their compositions and structures. However, it is not
clear how these events are coordinated and how they integrate with regulation
of molec... | [
{
"created": "Thu, 29 Jul 2021 15:05:04 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Sep 2021 22:41:38 GMT",
"version": "v2"
}
] | 2021-09-06 | [
[
"Lecinski",
"Sarah",
""
],
[
"Shepherd",
"Jack W",
""
],
[
"Frame",
"Lewis",
""
],
[
"Hayton",
"Imogen",
""
],
[
"MacDonald",
"Chris",
""
],
[
"Leake",
"Mark C",
""
]
] | Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecul... |
1412.3800 | Lior Pachter | Akshay Tambe, Jennifer Doudna and Lior Pachter | Identifying RNA contacts from SHAPE-MaP by partial correlation analysis | null | null | null | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a recent paper Siegfried et al. published a new sequence-based structural
RNA assay that utilizes mutational profiling to detect base pairing (MaP).
Output from MaP provides information about both pairing (via reactivities) and
contact (via correlations). Reactivities can be coupled to partition function
folding m... | [
{
"created": "Mon, 8 Dec 2014 19:04:51 GMT",
"version": "v1"
}
] | 2014-12-12 | [
[
"Tambe",
"Akshay",
""
],
[
"Doudna",
"Jennifer",
""
],
[
"Pachter",
"Lior",
""
]
] | In a recent paper Siegfried et al. published a new sequence-based structural RNA assay that utilizes mutational profiling to detect base pairing (MaP). Output from MaP provides information about both pairing (via reactivities) and contact (via correlations). Reactivities can be coupled to partition function folding mod... |
1504.02816 | Greg Gloor Dr | Amy McMillan, Stephen Rulisa, Mark Sumarah, Jean M. Macklaim, Justin
Renaud, Jordan Bisanz, Gregory B. Gloor, and Gregor Reid | A multi-platform metabolomics approach identifies novel biomarkers
associated with bacterial diversity in the human vagina | null | null | 10.1038/srep14174 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of
preterm labour, and its associated malodour impacts the quality of life for
many women. Clinical diagnosis primarily relies on microscopy to presumptively
detect a loss of lactobacilli and acquisition of anaerobes. This diagnostic
does not r... | [
{
"created": "Fri, 10 Apr 2015 23:40:14 GMT",
"version": "v1"
}
] | 2017-04-06 | [
[
"McMillan",
"Amy",
""
],
[
"Rulisa",
"Stephen",
""
],
[
"Sumarah",
"Mark",
""
],
[
"Macklaim",
"Jean M.",
""
],
[
"Renaud",
"Justin",
""
],
[
"Bisanz",
"Jordan",
""
],
[
"Gloor",
"Gregory B.",
""
],
[
... | Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour, and its associated malodour impacts the quality of life for many women. Clinical diagnosis primarily relies on microscopy to presumptively detect a loss of lactobacilli and acquisition of anaerobes. This diagnostic does not ref... |
1407.8247 | John Vandermeer | John Vandermeer, Pejman Rohani | The interaction of regional and local in the dynamics of the coffee rust
disease | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A simple mean field model is proposed that captures the two scales of dynamic
processes involved in the spread of the coffee rust disease. At a local level
the state variable is the fraction of coffee plants on an average farm that are
infested with the disease and at the regional level the state variable is the
frac... | [
{
"created": "Thu, 31 Jul 2014 00:44:25 GMT",
"version": "v1"
}
] | 2014-08-01 | [
[
"Vandermeer",
"John",
""
],
[
"Rohani",
"Pejman",
""
]
] | A simple mean field model is proposed that captures the two scales of dynamic processes involved in the spread of the coffee rust disease. At a local level the state variable is the fraction of coffee plants on an average farm that are infested with the disease and at the regional level the state variable is the fracti... |
2102.03746 | Jiayu Shang | Jiayu Shang and Jingzhe Jiang and Yanni Sun | Bacteriophage classification for assembled contigs using Graph
Convolutional Network | 15 pages, 10 figures | Bioinformatics, Volume 37, Issue Supplement1, July 2021, Pages
25-33 | 10.1093/bioinformatics/btab293 | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play
key roles in the biology of microbes. As the most abundant biological entities
on the planet, the number of discovered phages is only the tip of the iceberg.
Recently, many new phages have been revealed using high throughput sequencing,
parti... | [
{
"created": "Sun, 7 Feb 2021 08:58:35 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Sep 2021 10:08:25 GMT",
"version": "v2"
}
] | 2021-09-07 | [
[
"Shang",
"Jiayu",
""
],
[
"Jiang",
"Jingzhe",
""
],
[
"Sun",
"Yanni",
""
]
] | Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg. Recently, many new phages have been revealed using high throughput sequencing, particu... |
1005.0311 | Favard Cyril | C. Favard, J. Ehrig, J. Wenger, P.-F. Lenne and H. Rigneault | FCS diffusion laws on two-phases lipid membranes : experimental and
Monte-carlo simulation determination of domain size | 20 pages, 10 figures | null | null | null | q-bio.QM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For more than ten years now, many efforts have been done to identify and
characterize nature of obstructed diffusion in model and cellular lipid
membranes. Amongst all the techniques developed for this purpose, FCS, by means
of determination of FCS diffusion laws, has been shown to be a very efficient
approach. In th... | [
{
"created": "Mon, 3 May 2010 14:36:46 GMT",
"version": "v1"
}
] | 2010-05-04 | [
[
"Favard",
"C.",
""
],
[
"Ehrig",
"J.",
""
],
[
"Wenger",
"J.",
""
],
[
"Lenne",
"P. -F.",
""
],
[
"Rigneault",
"H.",
""
]
] | For more than ten years now, many efforts have been done to identify and characterize nature of obstructed diffusion in model and cellular lipid membranes. Amongst all the techniques developed for this purpose, FCS, by means of determination of FCS diffusion laws, has been shown to be a very efficient approach. In this... |
1705.09868 | Andrei Khrennikov Yu | Ichiro Yamato, Takeshi Murata and Andrei Khrennikov | Energy flow in biological system: Bioenergy transduction of V1-ATPase
molecular rotary motor from E. hirae | Progress in Biophysics and Molecular Biology, 2017 | Progress in Biophysics and Molecular Biology 130, Part A, 33-38
(2017) | null | null | q-bio.BM quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We classify research fields in biology into those on flows of materials,
energy, and information. As a representative energy transducing machinery in
biology, our research target, V1-ATPase from a bacterium Enterococcus hirae, a
typical molecular rotary motor is introduced. Structures of several
intermediates of the ... | [
{
"created": "Sat, 27 May 2017 21:31:53 GMT",
"version": "v1"
}
] | 2018-07-18 | [
[
"Yamato",
"Ichiro",
""
],
[
"Murata",
"Takeshi",
""
],
[
"Khrennikov",
"Andrei",
""
]
] | We classify research fields in biology into those on flows of materials, energy, and information. As a representative energy transducing machinery in biology, our research target, V1-ATPase from a bacterium Enterococcus hirae, a typical molecular rotary motor is introduced. Structures of several intermediates of the ro... |
1510.09035 | Jose A. Reinoso | Jose A. Reinoso, M. C. Torrent, Cristina Masoller | Emergence of spike correlations in periodically forced excitable systems | null | null | 10.1103/PhysRevE.94.032218 | null | q-bio.NC nlin.CD physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In sensory neurons the presence of noise can facilitate the detection of weak
information-carrying signals, which are encoded and transmitted via correlated
sequences of spikes. Here we investigate relative temporal order in spike
sequences induced by a subthreshold periodic input, in the presence of white
Gaussian n... | [
{
"created": "Fri, 30 Oct 2015 10:07:59 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Mar 2016 12:51:15 GMT",
"version": "v2"
}
] | 2016-10-12 | [
[
"Reinoso",
"Jose A.",
""
],
[
"Torrent",
"M. C.",
""
],
[
"Masoller",
"Cristina",
""
]
] | In sensory neurons the presence of noise can facilitate the detection of weak information-carrying signals, which are encoded and transmitted via correlated sequences of spikes. Here we investigate relative temporal order in spike sequences induced by a subthreshold periodic input, in the presence of white Gaussian noi... |
2110.05478 | Yi Zhang | Yi Zhang | An In-depth Summary of Recent Artificial Intelligence Applications in
Drug Design | 26 pages, 6 figures, 3 tables, 253 references | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | As a promising tool to navigate in the vast chemical space, artificial
intelligence (AI) is leveraged for drug design. From the year 2017 to 2021, the
number of applications of several recent AI models (i.e. graph neural network
(GNN), recurrent neural network (RNN), variation autoencoder (VAE), generative
adversaria... | [
{
"created": "Sun, 10 Oct 2021 00:40:53 GMT",
"version": "v1"
}
] | 2021-10-13 | [
[
"Zhang",
"Yi",
""
]
] | As a promising tool to navigate in the vast chemical space, artificial intelligence (AI) is leveraged for drug design. From the year 2017 to 2021, the number of applications of several recent AI models (i.e. graph neural network (GNN), recurrent neural network (RNN), variation autoencoder (VAE), generative adversarial ... |
1409.4607 | Caitlin Rivers | Caitlin M. Rivers, Eric T. Lofgren, Madhav Marathe, Stephen Eubank,
Bryan L. Lewis | Modeling the Impact of Interventions on an Epidemic of Ebola in Sierra
Leone and Liberia | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An Ebola outbreak of unparalleled size is currently affecting several
countries in West Africa, and international efforts to control the outbreak are
underway. However, the efficacy of these interventions, and their likely impact
on an Ebola epidemic of this size, is unknown. Forecasting and simulation of
these inter... | [
{
"created": "Tue, 16 Sep 2014 12:29:28 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Sep 2014 20:35:02 GMT",
"version": "v2"
}
] | 2014-09-23 | [
[
"Rivers",
"Caitlin M.",
""
],
[
"Lofgren",
"Eric T.",
""
],
[
"Marathe",
"Madhav",
""
],
[
"Eubank",
"Stephen",
""
],
[
"Lewis",
"Bryan L.",
""
]
] | An Ebola outbreak of unparalleled size is currently affecting several countries in West Africa, and international efforts to control the outbreak are underway. However, the efficacy of these interventions, and their likely impact on an Ebola epidemic of this size, is unknown. Forecasting and simulation of these interve... |
q-bio/0701049 | Christian Hagendorf | Francois David, Christian Hagendorf, Kay Joerg Wiese | Random RNA under tension | 6 pages, 10 figures. v2: corrected typos, discussion on locking
argument improved | Europhys. Lett., 78 (2007) 68003 | 10.1209/0295-5075/78/68003 | LPTENS 07/04 | q-bio.BM cond-mat.dis-nn | null | The Laessig-Wiese (LW) field theory for the freezing transition of random RNA
secondary structures is generalized to the situation of an external force. We
find a second-order phase transition at a critical applied force f = f_c. For f
< f_c forces are irrelevant. For f > f_c, the extension L as a function of
pulling... | [
{
"created": "Mon, 29 Jan 2007 19:41:49 GMT",
"version": "v1"
},
{
"created": "Tue, 8 May 2007 16:19:32 GMT",
"version": "v2"
}
] | 2007-06-13 | [
[
"David",
"Francois",
""
],
[
"Hagendorf",
"Christian",
""
],
[
"Wiese",
"Kay Joerg",
""
]
] | The Laessig-Wiese (LW) field theory for the freezing transition of random RNA secondary structures is generalized to the situation of an external force. We find a second-order phase transition at a critical applied force f = f_c. For f < f_c forces are irrelevant. For f > f_c, the extension L as a function of pulling f... |
1905.11640 | Wenzhi Mao | Wenzhi Mao, Wenze Ding and Haipeng Gong | AmoebaContact and GDFold: a new pipeline for rapid prediction of protein
structures | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Native contacts between residues could be predicted from the amino acid
sequence of proteins, and the predicted contact information could assist the de
novo protein structure prediction. Here, we present a novel pipeline of a
residue contact predictor AmoebaContact and a contact-assisted folder GDFold
for rapid prote... | [
{
"created": "Tue, 28 May 2019 06:54:24 GMT",
"version": "v1"
}
] | 2019-05-29 | [
[
"Mao",
"Wenzhi",
""
],
[
"Ding",
"Wenze",
""
],
[
"Gong",
"Haipeng",
""
]
] | Native contacts between residues could be predicted from the amino acid sequence of proteins, and the predicted contact information could assist the de novo protein structure prediction. Here, we present a novel pipeline of a residue contact predictor AmoebaContact and a contact-assisted folder GDFold for rapid protein... |
1504.07303 | Monique Tirion | Monique M. Tirion | On the Sensitivity of Protein Data Bank Normal Mode Analysis: An
Application to GH10 Xylanases | null | Phys. Biol. 12 (2015) 066013 | 10.1088/1478-3975/12/6/066013 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein data bank entries obtain distinct, reproducible flexibility
characteristics determined by normal mode analyses of their three dimensional
coordinate files. We study the effectiveness and sensitivity of this technique
by analyzing the results on one class of glycosidases: family 10 xylanases. A
conserved trypt... | [
{
"created": "Mon, 27 Apr 2015 23:18:55 GMT",
"version": "v1"
},
{
"created": "Thu, 20 Aug 2015 16:58:02 GMT",
"version": "v2"
}
] | 2015-12-01 | [
[
"Tirion",
"Monique M.",
""
]
] | Protein data bank entries obtain distinct, reproducible flexibility characteristics determined by normal mode analyses of their three dimensional coordinate files. We study the effectiveness and sensitivity of this technique by analyzing the results on one class of glycosidases: family 10 xylanases. A conserved tryptop... |
2406.19969 | Kaiqi Zhang | Guanzhou Chen, Kaiqi Zhang, Xiaodong Zhang, Hong Xie, Haobo Yang,
Xiaoliang Tan, Tong Wang, Yule Ma, Qing Wang, Jinzhou Cao and Weihong Cui | Enhancing Terrestrial Net Primary Productivity Estimation with EXP-CASA:
A Novel Light Use Efficiency Model Approach | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Light Use Efficiency model, epitomized by the CASA model, is extensively
applied in the quantitative estimation of vegetation Net Primary Productivity.
However, the classic CASA model is marked by significant complexity: the
estimation of environmental stress parameters, in particular, necessitates
multi-source o... | [
{
"created": "Fri, 28 Jun 2024 14:57:40 GMT",
"version": "v1"
}
] | 2024-07-01 | [
[
"Chen",
"Guanzhou",
""
],
[
"Zhang",
"Kaiqi",
""
],
[
"Zhang",
"Xiaodong",
""
],
[
"Xie",
"Hong",
""
],
[
"Yang",
"Haobo",
""
],
[
"Tan",
"Xiaoliang",
""
],
[
"Wang",
"Tong",
""
],
[
"Ma",
"Yule... | The Light Use Efficiency model, epitomized by the CASA model, is extensively applied in the quantitative estimation of vegetation Net Primary Productivity. However, the classic CASA model is marked by significant complexity: the estimation of environmental stress parameters, in particular, necessitates multi-source obs... |
q-bio/0511046 | David Stockwell PhD | David R.B. Stockwell | Improving ecological niche models by data mining large environmental
datasets for surrogate models | 16 pages, 4 figures, to appear in Ecological Modelling | null | null | null | q-bio.QM cs.AI | null | WhyWhere is a new ecological niche modeling (ENM) algorithm for mapping and
explaining the distribution of species. The algorithm uses image processing
methods to efficiently sift through large amounts of data to find the few
variables that best predict species occurrence. The purpose of this paper is to
describe and... | [
{
"created": "Mon, 28 Nov 2005 19:47:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Stockwell",
"David R. B.",
""
]
] | WhyWhere is a new ecological niche modeling (ENM) algorithm for mapping and explaining the distribution of species. The algorithm uses image processing methods to efficiently sift through large amounts of data to find the few variables that best predict species occurrence. The purpose of this paper is to describe and j... |
q-bio/0503039 | Toshio Fukumi | Toshio Fukumi | Free energy adopted stochastic optimization protein folding | AMS-LaTeX 3 pages, no figure | null | null | null | q-bio.BM | null | Optimal structure of proteins is described by linear stochastic differential
equation with mean decrease of free energy and volatility. Structure
determining strategy is given by a twin of stochastic variables for which
empirical conditions are not postulated. Optimal structure determination will
be deformed to be ad... | [
{
"created": "Tue, 29 Mar 2005 04:17:27 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Fukumi",
"Toshio",
""
]
] | Optimal structure of proteins is described by linear stochastic differential equation with mean decrease of free energy and volatility. Structure determining strategy is given by a twin of stochastic variables for which empirical conditions are not postulated. Optimal structure determination will be deformed to be adop... |
q-bio/0503003 | Tomoshiro Ochiai | T. Ochiai, J.C. Nacher, T. Akutsu | Symmetry and Dynamics in living organisms: The self-similarity principle
governs gene expression dynamics | 27 pages, 14 figures, Latex | null | null | null | q-bio.BM | null | The ambitious and ultimate research purpose in Systems Biology is the
understanding and modelling of the cell's system. Although a vast number of
models have been developed in order to extract biological knowledge from
complex systems composed of basic elements as proteins, genes and chemical
compounds, a need remain... | [
{
"created": "Tue, 1 Mar 2005 14:02:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ochiai",
"T.",
""
],
[
"Nacher",
"J. C.",
""
],
[
"Akutsu",
"T.",
""
]
] | The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems composed of basic elements as proteins, genes and chemical compounds, a need remains ... |
1101.2170 | Simone Linz | Maria Luisa Bonet, Simone Linz, and Katherine St. John | The Complexity of Finding Multiple Solutions to Betweenness and Quartet
Compatibility | 25 pages, 7 figures | null | null | null | q-bio.PE cs.CC cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that two important problems that have applications in computational
biology are ASP-complete, which implies that, given a solution to a problem, it
is NP-complete to decide if another solution exists. We show first that a
variation of Betweenness, which is the underlying problem of questions related
to radiat... | [
{
"created": "Tue, 11 Jan 2011 17:48:54 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Mar 2011 07:57:11 GMT",
"version": "v2"
}
] | 2015-03-17 | [
[
"Bonet",
"Maria Luisa",
""
],
[
"Linz",
"Simone",
""
],
[
"John",
"Katherine St.",
""
]
] | We show that two important problems that have applications in computational biology are ASP-complete, which implies that, given a solution to a problem, it is NP-complete to decide if another solution exists. We show first that a variation of Betweenness, which is the underlying problem of questions related to radiatio... |
2009.06313 | Minghan Chen | Minghan Chen, Mansooreh Ahmadian, Layne Watson, Yang Cao | Finding Acceptable Parameter Regions of Stochastic Hill functions for
Multisite Phosphorylation Mechanism | null | The Journal of Chemical Physics 152.12 (2020): 124108 | 10.1063/1.5143004 | null | q-bio.MN math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multisite phosphorylation plays an important role in regulating switchlike
protein activity and has been used widely in mathematical models. With the
development of new experimental techniques and more molecular data, molecular
phosphorylation processes emerge in many systems with increasing complexity and
sizes. The... | [
{
"created": "Mon, 14 Sep 2020 10:27:33 GMT",
"version": "v1"
}
] | 2020-09-15 | [
[
"Chen",
"Minghan",
""
],
[
"Ahmadian",
"Mansooreh",
""
],
[
"Watson",
"Layne",
""
],
[
"Cao",
"Yang",
""
]
] | Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular phosphorylation processes emerge in many systems with increasing complexity and sizes. These... |
1412.0207 | Surojit Biswas | Surojit Biswas, Meredith McDonald, Derek S. Lundberg, Jeffery L.
Dangl, Vladimir Jojic | Learning microbial interaction networks from metagenomic count data | Submitted to RECOMB 2015 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many microbes associate with higher eukaryotes and impact their vitality. In
order to engineer microbiomes for host benefit, we must understand the rules of
community assembly and maintenence, which in large part, demands an
understanding of the direct interactions between community members. Toward this
end, we've de... | [
{
"created": "Sun, 30 Nov 2014 11:19:59 GMT",
"version": "v1"
}
] | 2014-12-02 | [
[
"Biswas",
"Surojit",
""
],
[
"McDonald",
"Meredith",
""
],
[
"Lundberg",
"Derek S.",
""
],
[
"Dangl",
"Jeffery L.",
""
],
[
"Jojic",
"Vladimir",
""
]
] | Many microbes associate with higher eukaryotes and impact their vitality. In order to engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenence, which in large part, demands an understanding of the direct interactions between community members. Toward this end, we've deve... |
2202.07218 | Susanna Gordleeva | Susanna Gordleeva, Yuliya A. Tsybina, Mikhail I. Krivonosov, Ivan Y.
Tyukin, Victor B. Kazantsev, Alexey A. Zaikin, Alexander N. Gorban | Situation-based memory in spiking neuron-astrocyte network | 38 pages, 11 figures, 4 tables | IEEE Transactions on Neural Networks and Learning Systems, 04
December 2023, Early Access | 10.1109/TNNLS.2023.33354 | null | q-bio.NC q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Mammalian brains operate in a very special surrounding: to survive they have
to react quickly and effectively to the pool of stimuli patterns previously
recognized as danger. Many learning tasks often encountered by living organisms
involve a specific set-up centered around a relatively small set of patterns
presente... | [
{
"created": "Tue, 15 Feb 2022 06:16:30 GMT",
"version": "v1"
}
] | 2023-12-07 | [
[
"Gordleeva",
"Susanna",
""
],
[
"Tsybina",
"Yuliya A.",
""
],
[
"Krivonosov",
"Mikhail I.",
""
],
[
"Tyukin",
"Ivan Y.",
""
],
[
"Kazantsev",
"Victor B.",
""
],
[
"Zaikin",
"Alexey A.",
""
],
[
"Gorban",
"Alexa... | Mammalian brains operate in a very special surrounding: to survive they have to react quickly and effectively to the pool of stimuli patterns previously recognized as danger. Many learning tasks often encountered by living organisms involve a specific set-up centered around a relatively small set of patterns presented ... |
2204.00007 | Joseph Whittaker Mr | Joseph Whittaker and Kexin Wu | Low-fat diets and testosterone in men: Systematic review and
meta-analysis of intervention studies | null | The Journal of steroid biochemistry and molecular biology (2021)
210: 105878 | 10.1016/j.jsbmb.2021.105878 | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Background: Higher endogenous testosterone levels are associated with reduced
chronic disease risk and mortality. Since the mid-20th century, there have been
significant changes in dietary patterns, and men's testosterone levels have
declined in western countries. Cross-sectional studies show inconsistent
association... | [
{
"created": "Thu, 31 Mar 2022 13:20:22 GMT",
"version": "v1"
}
] | 2022-04-04 | [
[
"Whittaker",
"Joseph",
""
],
[
"Wu",
"Kexin",
""
]
] | Background: Higher endogenous testosterone levels are associated with reduced chronic disease risk and mortality. Since the mid-20th century, there have been significant changes in dietary patterns, and men's testosterone levels have declined in western countries. Cross-sectional studies show inconsistent associations ... |
2301.09097 | Angelo D'Ambrosio | Angelo D'Ambrosio, Raisa Kociurzynski, Alexis Papathanassopoulos,
Fabian B\"urkin, Hajo Grundmann, Tjibbe Donker | Forecasting local hospital bed demand for COVID-19 using on-request
simulations | 23 pages, 3 figures. Code available at
https://github.com/QUPI-IUK/Bed-demand-forecast | null | null | null | q-bio.QM stat.AP | http://creativecommons.org/licenses/by/4.0/ | For hospitals, realistic forecasting of bed demand during impending epidemics
of infectious diseases is essential to avoid being overwhelmed by a potential
sudden increase in the number of admitted patients. Short-term forecasting can
aid hospitals in adjusting their planning and freeing up beds in time. We
created a... | [
{
"created": "Sun, 22 Jan 2023 10:37:01 GMT",
"version": "v1"
}
] | 2023-01-24 | [
[
"D'Ambrosio",
"Angelo",
""
],
[
"Kociurzynski",
"Raisa",
""
],
[
"Papathanassopoulos",
"Alexis",
""
],
[
"Bürkin",
"Fabian",
""
],
[
"Grundmann",
"Hajo",
""
],
[
"Donker",
"Tjibbe",
""
]
] | For hospitals, realistic forecasting of bed demand during impending epidemics of infectious diseases is essential to avoid being overwhelmed by a potential sudden increase in the number of admitted patients. Short-term forecasting can aid hospitals in adjusting their planning and freeing up beds in time. We created an ... |
0902.3784 | Emma Jin | Emma Y. Jin and Christian M. Reidys | Irreducibility in RNA structures | 17 figures 28 pages | null | null | null | q-bio.BM math.CO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we study irreducibility in RNA structures. By RNA structure we
mean RNA secondary as well as RNA pseudoknot structures. In our analysis we
shall contrast random and minimum free energy (mfe) configurations. We compute
various distributions: of the numbers of irreducible substructures, their
locations an... | [
{
"created": "Sun, 22 Feb 2009 10:09:10 GMT",
"version": "v1"
}
] | 2009-02-24 | [
[
"Jin",
"Emma Y.",
""
],
[
"Reidys",
"Christian M.",
""
]
] | In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various distributions: of the numbers of irreducible substructures, their locations and ... |
0905.0375 | Michael Hagan | Michael F. Hagan | Understanding the Concentration Dependence of Viral Capsid Assembly
Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus
Size | Submitted to Biophysical Journal | null | 10.1016/j.bpj.2009.11.023 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The kinetics for the assembly of viral proteins into a population of capsids
can be measured in vitro with size exclusion chromatography or dynamic light
scattering, but extracting mechanistic information from these studies is
challenging. For example, it is not straightforward to determine the critical
nucleus size ... | [
{
"created": "Mon, 4 May 2009 12:51:25 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Hagan",
"Michael F.",
""
]
] | The kinetics for the assembly of viral proteins into a population of capsids can be measured in vitro with size exclusion chromatography or dynamic light scattering, but extracting mechanistic information from these studies is challenging. For example, it is not straightforward to determine the critical nucleus size or... |
2005.13282 | \v{Z}iga Zaplotnik | Ziga Zaplotnik, Aleksandar Gavric, Luka Medic | Simulation of the COVID-19 pandemic on the social network of Slovenia:
estimating the intrinsic forecast uncertainty | null | null | 10.1371/journal.pone.0238090 | null | q-bio.PE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the article a virus transmission model is constructed on a simplified
social network. The social network consists of more than 2 million nodes, each
representing an inhabitant of Slovenia. The nodes are organised and
interconnected according to the real household and elderly-care center
distribution, while their c... | [
{
"created": "Wed, 27 May 2020 11:18:02 GMT",
"version": "v1"
}
] | 2021-01-27 | [
[
"Zaplotnik",
"Ziga",
""
],
[
"Gavric",
"Aleksandar",
""
],
[
"Medic",
"Luka",
""
]
] | In the article a virus transmission model is constructed on a simplified social network. The social network consists of more than 2 million nodes, each representing an inhabitant of Slovenia. The nodes are organised and interconnected according to the real household and elderly-care center distribution, while their con... |
1910.12007 | Anastasios Matzavinos | Karen Larson, Sarah Olson, Anastasios Matzavinos | Bayesian uncertainty quantification for micro-swimmers with fully
resolved hydrodynamics | null | null | null | null | q-bio.QM cs.NA math.NA physics.bio-ph physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Due to the computational complexity of micro-swimmer models with fully
resolved hydrodynamics, parameter estimation has been prohibitively expensive.
Here, we describe a Bayesian uncertainty quantification framework that is
highly parallelizable, making parameter estimation for complex forward models
tractable. Using... | [
{
"created": "Sat, 26 Oct 2019 06:15:37 GMT",
"version": "v1"
}
] | 2019-10-29 | [
[
"Larson",
"Karen",
""
],
[
"Olson",
"Sarah",
""
],
[
"Matzavinos",
"Anastasios",
""
]
] | Due to the computational complexity of micro-swimmer models with fully resolved hydrodynamics, parameter estimation has been prohibitively expensive. Here, we describe a Bayesian uncertainty quantification framework that is highly parallelizable, making parameter estimation for complex forward models tractable. Using n... |
1112.4952 | Tobias Pl\"oger | Tobias A. Pl\"oger and G\"unter von Kiedrowski | A Self-Replicating Peptide Nucleic Acid | 36 pages | null | null | null | q-bio.MN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We report on a case of autocatalytic feedback in a template directed
synthesis of a self-complementary hexa-PNA from two trimeric building blocks.
The course of the reaction was monitored in the presence of increasing initial
concentrations of product by means of RP-HPLC. Kinetic modeling with the SimFit
program reve... | [
{
"created": "Wed, 21 Dec 2011 08:50:52 GMT",
"version": "v1"
}
] | 2011-12-22 | [
[
"Plöger",
"Tobias A.",
""
],
[
"von Kiedrowski",
"Günter",
""
]
] | We report on a case of autocatalytic feedback in a template directed synthesis of a self-complementary hexa-PNA from two trimeric building blocks. The course of the reaction was monitored in the presence of increasing initial concentrations of product by means of RP-HPLC. Kinetic modeling with the SimFit program reveal... |
2006.01586 | Hisashi Kobayashi | Hisashi Kobayashi | Stochastic Modeling of an Infectious Disease, Part I: Understand the
Negative Binomial Distribution and Predict an Epidemic More Reliably | 28 pages, 14 figures | null | null | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Why are the epidemic patterns of COVID-19 so different among different cities
or countries which are similar in their populations, medical infrastructures,
and people's behavior? Why are forecasts or predictions made by so-called
experts often grossly wrong, concerning the numbers of people who get infected
or die? T... | [
{
"created": "Tue, 2 Jun 2020 13:25:36 GMT",
"version": "v1"
}
] | 2020-06-03 | [
[
"Kobayashi",
"Hisashi",
""
]
] | Why are the epidemic patterns of COVID-19 so different among different cities or countries which are similar in their populations, medical infrastructures, and people's behavior? Why are forecasts or predictions made by so-called experts often grossly wrong, concerning the numbers of people who get infected or die? The... |
q-bio/0605033 | Mathias Kuhnt | Mathias Kuhnt, Ingmar Glauche and Martin Greiner | Impact of observational incompleteness on the structural properties of
protein interaction networks | 17 pages, 7 figures, accepted by Physica A | null | 10.1016/j.physa.2006.04.120 | null | q-bio.MN | null | The observed structure of protein interaction networks is corrupted by many
false positive/negative links. This observational incompleteness is abstracted
as random link removal and a specific, experimentally motivated (spoke) link
rearrangement. Their impact on the structural properties of
gene-duplication-and-mutat... | [
{
"created": "Fri, 19 May 2006 20:24:26 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Kuhnt",
"Mathias",
""
],
[
"Glauche",
"Ingmar",
""
],
[
"Greiner",
"Martin",
""
]
] | The observed structure of protein interaction networks is corrupted by many false positive/negative links. This observational incompleteness is abstracted as random link removal and a specific, experimentally motivated (spoke) link rearrangement. Their impact on the structural properties of gene-duplication-and-mutatio... |
2012.05501 | Bruno. Cessac | Bruno Cessac | The Retina as a Dynamical System | Review paper, submitted as a chapter of the "Book in honour of Prof.
Miguel A.F. Sanju\'an on his 60th Birthday" | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Considering the retina as a high dimensional, non autonomous, dynamical
system, layered and structured, with non stationary and spatially inhomogeneous
entries (visual scenes), we present several examples where dynamical systems-,
bifurcations-, and ergodic-theory provide useful insights on retinal behaviour
and dyna... | [
{
"created": "Thu, 10 Dec 2020 08:03:29 GMT",
"version": "v1"
}
] | 2020-12-11 | [
[
"Cessac",
"Bruno",
""
]
] | Considering the retina as a high dimensional, non autonomous, dynamical system, layered and structured, with non stationary and spatially inhomogeneous entries (visual scenes), we present several examples where dynamical systems-, bifurcations-, and ergodic-theory provide useful insights on retinal behaviour and dynami... |
q-bio/0611064 | Yong Chen | L. C. Yu, Yong Chen, and Pan Zhang | Frequency and phase synchronization of two coupled neurons with channel
noise | 8 pages, 10 figures | Eur. Phys. J. B 59, 249-257(2007) | 10.1140/epjb/e2007-00278-0 | null | q-bio.NC q-bio.OT | null | We study the frequency and phase synchronization in two coupled identical and
nonidentical neurons with channel noise. The occupation number method is used
to model the neurons in the context of stochastic Hodgkin-Huxley model in which
the strength of of channel noise is represented by ion channel cluster size of
the... | [
{
"created": "Mon, 20 Nov 2006 09:08:40 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Nov 2007 01:50:31 GMT",
"version": "v2"
}
] | 2007-11-07 | [
[
"Yu",
"L. C.",
""
],
[
"Chen",
"Yong",
""
],
[
"Zhang",
"Pan",
""
]
] | We study the frequency and phase synchronization in two coupled identical and nonidentical neurons with channel noise. The occupation number method is used to model the neurons in the context of stochastic Hodgkin-Huxley model in which the strength of of channel noise is represented by ion channel cluster size of the i... |
1401.1490 | Bahman Afsari | Bahman Afsari, Ulisses M. Braga-Neto, Donald Geman | Rank discriminants for predicting phenotypes from RNA expression | Published in at http://dx.doi.org/10.1214/14-AOAS738 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org) | Annals of Applied Statistics 2014, Vol. 8, No. 3, 1469-1491 | 10.1214/14-AOAS738 | IMS-AOAS-AOAS738 | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical methods for analyzing large-scale biomolecular data are
commonplace in computational biology. A notable example is phenotype prediction
from gene expression data, for instance, detecting human cancers,
differentiating subtypes and predicting clinical outcomes. Still, clinical
applications remain scarce. O... | [
{
"created": "Tue, 7 Jan 2014 20:26:59 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Apr 2014 22:58:29 GMT",
"version": "v2"
},
{
"created": "Fri, 21 Nov 2014 08:18:00 GMT",
"version": "v3"
}
] | 2014-11-24 | [
[
"Afsari",
"Bahman",
""
],
[
"Braga-Neto",
"Ulisses M.",
""
],
[
"Geman",
"Donald",
""
]
] | Statistical methods for analyzing large-scale biomolecular data are commonplace in computational biology. A notable example is phenotype prediction from gene expression data, for instance, detecting human cancers, differentiating subtypes and predicting clinical outcomes. Still, clinical applications remain scarce. One... |
2102.08471 | Hrithwik Shalu | Joseph Stember, Parvathy Jayan, Hrithwik Shalu | Deep Neural Network Based Differential Equation Solver for HIV Enzyme
Kinetics | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Purpose: We seek to use neural networks (NNs) to solve a well-known system of
differential equations describing the balance between T cells and HIV viral
burden.
Materials and Methods: In this paper, we employ a 3-input parallel NN to
approximate solutions for the system of first-order ordinary differential
equatio... | [
{
"created": "Tue, 16 Feb 2021 22:16:57 GMT",
"version": "v1"
}
] | 2021-02-18 | [
[
"Stember",
"Joseph",
""
],
[
"Jayan",
"Parvathy",
""
],
[
"Shalu",
"Hrithwik",
""
]
] | Purpose: We seek to use neural networks (NNs) to solve a well-known system of differential equations describing the balance between T cells and HIV viral burden. Materials and Methods: In this paper, we employ a 3-input parallel NN to approximate solutions for the system of first-order ordinary differential equations d... |
1812.08569 | Louxin Zhang | Andreas DM Gunawan and Jeyaram Rathin and Louxin Zhang | Counting and Enumerating Galled Networks | 7 figures, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Galled trees are widely studied as a recombination model in population
genetics. This class of phylogenetic networks is generalized into galled
networks by relaxing a structural condition. In this work, a linear recurrence
formula is given for counting 1-galled networks, which are galled networks
satisfying the condi... | [
{
"created": "Thu, 20 Dec 2018 14:00:04 GMT",
"version": "v1"
}
] | 2018-12-21 | [
[
"Gunawan",
"Andreas DM",
""
],
[
"Rathin",
"Jeyaram",
""
],
[
"Zhang",
"Louxin",
""
]
] | Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given for counting 1-galled networks, which are galled networks satisfying the conditi... |
1610.09431 | Omar Claflin | Omar Claflin | Attention acts to suppress goal-based conflict under high competition | 25 pages, 3 figures, 3 tables | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is known that when multiple stimuli are present, top-down attention
selectively enhances the neural signal in the visual cortex for task-relevant
stimuli, but this has been tested only under conditions of minimal competition
of visual attention. Here we show during high competition, that is, two stimuli
in a share... | [
{
"created": "Sat, 29 Oct 2016 00:21:31 GMT",
"version": "v1"
}
] | 2016-11-01 | [
[
"Claflin",
"Omar",
""
]
] | It is known that when multiple stimuli are present, top-down attention selectively enhances the neural signal in the visual cortex for task-relevant stimuli, but this has been tested only under conditions of minimal competition of visual attention. Here we show during high competition, that is, two stimuli in a shared ... |
0807.3638 | Moritz Gerstung | Moritz Gerstung and Niko Beerenwinkel | Waiting time models of cancer progression | null | null | 10.1080/08898480.2010.490994 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer progression is an evolutionary process that is driven by mutation and
selection in a population of tumor cells. We discuss mathematical models of
cancer progression, starting from traditional multistage theory. Each stage is
associated with the occurrence of genetic alterations and their fixation in the
popula... | [
{
"created": "Wed, 23 Jul 2008 14:23:52 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Feb 2009 19:07:23 GMT",
"version": "v2"
}
] | 2011-08-31 | [
[
"Gerstung",
"Moritz",
""
],
[
"Beerenwinkel",
"Niko",
""
]
] | Cancer progression is an evolutionary process that is driven by mutation and selection in a population of tumor cells. We discuss mathematical models of cancer progression, starting from traditional multistage theory. Each stage is associated with the occurrence of genetic alterations and their fixation in the populati... |
1202.1358 | Yi Fang | Yi Fang | Protein Folding: The Gibbs Free Energy | 18 pages, 2 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The fundamental law for protein folding is the Thermodynamic Principle: the
amino acid sequence of a protein determines its native structure and the native
structure has the minimum Gibbs free energy. If all chemical problems can be
answered by quantum mechanics, there should be a quantum mechanics derivation
of Gibb... | [
{
"created": "Tue, 7 Feb 2012 07:11:31 GMT",
"version": "v1"
},
{
"created": "Sun, 8 Apr 2012 04:13:59 GMT",
"version": "v2"
}
] | 2012-04-10 | [
[
"Fang",
"Yi",
""
]
] | The fundamental law for protein folding is the Thermodynamic Principle: the amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy. If all chemical problems can be answered by quantum mechanics, there should be a quantum mechanics derivation of Gibbs ... |
1301.2885 | Asha Gopinathan | Asha Gopinathan | Solving the Cable Equation Using a Compact Difference Scheme -- Passive
Soma Dendrite | 24 pages, 11 figures, 6 tables | null | null | null | q-bio.NC q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dendrites are extensions to the neuronal cell body in the brain which are
posited in several functions ranging from electrical and chemical
compartmentalization to coincident detection. Dendrites vary across cell types
but one common feature they share is a branched structure. The cable equation
is a partial differen... | [
{
"created": "Mon, 14 Jan 2013 08:41:40 GMT",
"version": "v1"
}
] | 2013-01-15 | [
[
"Gopinathan",
"Asha",
""
]
] | Dendrites are extensions to the neuronal cell body in the brain which are posited in several functions ranging from electrical and chemical compartmentalization to coincident detection. Dendrites vary across cell types but one common feature they share is a branched structure. The cable equation is a partial differenti... |
2012.04077 | Molly Schumer | Benjamin M Moran, Cheyenne Payne, Quinn Langdon, Daniel L Powell,
Yaniv Brandvain, Molly Schumer | The genomic consequences of hybridization | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In the past decade, advances in genome sequencing have allowed researchers to
uncover the history of hybridization in diverse groups of species, including
our own. Although the field has made impressive progress in documenting the
extent of natural hybridization, both historical and recent, there are still
many unans... | [
{
"created": "Mon, 7 Dec 2020 21:46:49 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Mar 2021 20:53:40 GMT",
"version": "v2"
}
] | 2021-03-23 | [
[
"Moran",
"Benjamin M",
""
],
[
"Payne",
"Cheyenne",
""
],
[
"Langdon",
"Quinn",
""
],
[
"Powell",
"Daniel L",
""
],
[
"Brandvain",
"Yaniv",
""
],
[
"Schumer",
"Molly",
""
]
] | In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswe... |
1406.2926 | Nadav M. Shnerb | Michael Kalyuzhny, Ronen Kadmon and Nadav M. Shnerb | A generalized neutral theory explains static and dynamic properties of
biotic communities | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the forces shaping ecological communities is crucially
important to basic science and conservation. In recent years, considerable
progress was made in explaining communities using simple and general models,
with neutral theory as a prominent example. However, while successful in
explaining static patter... | [
{
"created": "Wed, 11 Jun 2014 14:57:16 GMT",
"version": "v1"
}
] | 2014-06-12 | [
[
"Kalyuzhny",
"Michael",
""
],
[
"Kadmon",
"Ronen",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | Understanding the forces shaping ecological communities is crucially important to basic science and conservation. In recent years, considerable progress was made in explaining communities using simple and general models, with neutral theory as a prominent example. However, while successful in explaining static patterns... |
1911.06105 | Aaron Vose | Aaron D. Vose, Jacob Balma, Damon Farnsworth, Kaylie Anderson, and
Yuri K. Peterson | PharML.Bind: Pharmacologic Machine Learning for Protein-Ligand
Interactions | null | null | null | null | q-bio.BM cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Is it feasible to create an analysis paradigm that can analyze and then
accurately and quickly predict known drugs from experimental data? PharML.Bind
is a machine learning toolkit which is able to accomplish this feat. Utilizing
deep neural networks and big data, PharML.Bind correlates
experimentally-derived drug af... | [
{
"created": "Wed, 23 Oct 2019 23:32:44 GMT",
"version": "v1"
}
] | 2019-11-15 | [
[
"Vose",
"Aaron D.",
""
],
[
"Balma",
"Jacob",
""
],
[
"Farnsworth",
"Damon",
""
],
[
"Anderson",
"Kaylie",
""
],
[
"Peterson",
"Yuri K.",
""
]
] | Is it feasible to create an analysis paradigm that can analyze and then accurately and quickly predict known drugs from experimental data? PharML.Bind is a machine learning toolkit which is able to accomplish this feat. Utilizing deep neural networks and big data, PharML.Bind correlates experimentally-derived drug affi... |
2005.14669 | Guo-Wei Wei | Jiahui Chen, Rui Wang, Menglun Wang, and Guo-Wei Wei | Mutations strengthened SARS-CoV-2 infectivity | 24 pages, 2 tables and 19 figures | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a
major concern in coronavirus disease 2019 (COVID-19) prevention and economic
reopening. However, rigorous determination of SARS-COV-2 infectivity is
essentially impossible owing to its continuous evolution with over 13752 single
nucleotide ... | [
{
"created": "Wed, 27 May 2020 20:55:24 GMT",
"version": "v1"
}
] | 2020-06-01 | [
[
"Chen",
"Jiahui",
""
],
[
"Wang",
"Rui",
""
],
[
"Wang",
"Menglun",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is essentially impossible owing to its continuous evolution with over 13752 single nucleotide po... |
2106.05180 | Jiajia Li | JiaJia Li, Peihua Feng, Liang Zhao, Junying Chen, Mengmeng Du,
Yangyang Yu, Jian Song, Ying Wu | Transition behavior of the seizure dynamics modulated by the astrocyte
inositol triphosphate noise | 26 pages, 8 figures | null | 10.1063/5.0124123 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epilepsy is a neurological disorder with recurrent seizures of complexity and
randomness. Until now, the mechanism of epileptic randomness has not been fully
elucidated. Inspired by the recent finding that astrocyte GTPase-activating
protein (G-protein)-coupled receptors could be involved in stochastic epileptic
seiz... | [
{
"created": "Wed, 26 May 2021 15:42:06 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Jun 2022 12:58:42 GMT",
"version": "v2"
},
{
"created": "Thu, 11 Aug 2022 16:54:33 GMT",
"version": "v3"
},
{
"created": "Mon, 31 Oct 2022 09:23:57 GMT",
"version": "v4"
}
] | 2024-06-19 | [
[
"Li",
"JiaJia",
""
],
[
"Feng",
"Peihua",
""
],
[
"Zhao",
"Liang",
""
],
[
"Chen",
"Junying",
""
],
[
"Du",
"Mengmeng",
""
],
[
"Yu",
"Yangyang",
""
],
[
"Song",
"Jian",
""
],
[
"Wu",
"Ying",
... | Epilepsy is a neurological disorder with recurrent seizures of complexity and randomness. Until now, the mechanism of epileptic randomness has not been fully elucidated. Inspired by the recent finding that astrocyte GTPase-activating protein (G-protein)-coupled receptors could be involved in stochastic epileptic seizur... |
2110.12286 | Kevin Lin | Zhuo-Cheng Xiao, Kevin K. Lin, Lai-Sang Young | A data-informed mean-field approach to mapping of cortical parameter
landscapes | null | PLoS Computat. Biol. 17 (2021) | 10.1371/journal.pcbi.1009718 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Constraining the many biological parameters that govern cortical dynamics is
computationally and conceptually difficult because of the curse of
dimensionality. This paper addresses these challenges by proposing (1) a novel
data-informed mean-field (MF) approach to efficiently map the parameter space
of network models... | [
{
"created": "Sat, 23 Oct 2021 19:42:14 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Nov 2021 02:25:42 GMT",
"version": "v2"
}
] | 2021-12-30 | [
[
"Xiao",
"Zhuo-Cheng",
""
],
[
"Lin",
"Kevin K.",
""
],
[
"Young",
"Lai-Sang",
""
]
] | Constraining the many biological parameters that govern cortical dynamics is computationally and conceptually difficult because of the curse of dimensionality. This paper addresses these challenges by proposing (1) a novel data-informed mean-field (MF) approach to efficiently map the parameter space of network models; ... |
2004.09912 | V. K. Jindal | V. K. Jindal | COVID 19, a realistic model for saturation, growth and decay of the
India specific disease | 10 pages, 7 figures, 15 references, 1 table. COVID-19 by the Numbers,
Modes, Big Data, and Reality April 24th, 2020 | vvoip-theoretical-geography-debates.org COVID-19 by the Numbers,
Modes, Big Data, and Reality April 24th, 2020 | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work presents a simple and realistic approach to handle the available
data of COVID-19 patients in India and to forecast the scenario. The model
proposed is based on the available facts like the onset of lockdown (as
announced by the Government on 25th day, {\tau}0 and the recovery pattern
dictated by a mean lif... | [
{
"created": "Tue, 21 Apr 2020 11:29:15 GMT",
"version": "v1"
}
] | 2020-05-07 | [
[
"Jindal",
"V. K.",
""
]
] | This work presents a simple and realistic approach to handle the available data of COVID-19 patients in India and to forecast the scenario. The model proposed is based on the available facts like the onset of lockdown (as announced by the Government on 25th day, {\tau}0 and the recovery pattern dictated by a mean life ... |
2308.14300 | Bryan Briney | Sarah M. Burbach and Bryan Briney | Improving antibody language models with native pairing | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Current antibody language models are limited by their use of unpaired
antibody sequence data and the biases in publicly available antibody sequence
datasets, which are skewed toward antibodies against a relatively small number
of pathogens. A recently published dataset (by Jaffe, et al) of approximately
1.6 x 10^6 na... | [
{
"created": "Mon, 28 Aug 2023 04:35:14 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Nov 2023 18:36:11 GMT",
"version": "v2"
}
] | 2023-11-08 | [
[
"Burbach",
"Sarah M.",
""
],
[
"Briney",
"Bryan",
""
]
] | Current antibody language models are limited by their use of unpaired antibody sequence data and the biases in publicly available antibody sequence datasets, which are skewed toward antibodies against a relatively small number of pathogens. A recently published dataset (by Jaffe, et al) of approximately 1.6 x 10^6 nati... |
2211.08618 | Nikola Mili\'cevi\'c | Nikola Mili\'cevi\'c and Vladimir Itskov | The combinatorial code and the graph rules of Dale networks | 24 pages, changes that improved the presentation of results based on
referee comments | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe the combinatorics of equilibria and steady states of neurons in
threshold-linear networks that satisfy Dale's law. The combinatorial code of a
Dale network is characterized in terms of two conditions: (i) a condition on
the network connectivity graph, and (ii) a spectral condition on the synaptic
matrix. ... | [
{
"created": "Wed, 16 Nov 2022 02:08:59 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2023 00:43:02 GMT",
"version": "v2"
},
{
"created": "Wed, 5 Jun 2024 19:04:16 GMT",
"version": "v3"
}
] | 2024-06-07 | [
[
"Milićević",
"Nikola",
""
],
[
"Itskov",
"Vladimir",
""
]
] | We describe the combinatorics of equilibria and steady states of neurons in threshold-linear networks that satisfy Dale's law. The combinatorial code of a Dale network is characterized in terms of two conditions: (i) a condition on the network connectivity graph, and (ii) a spectral condition on the synaptic matrix. We... |
2107.13247 | Sigve Nakken | Sigve Nakken (1 and 2 and 3), Sveinung Gundersen (3), Fabian L. M.
Bernal (4), Dimitris Polychronopoulos (5), Eivind Hovig (1 and 3), J{\o}rgen
Wesche (1 and 2) ((1) Department of Tumor Biology, Institute for Cancer
Research, Oslo University Hospital, Norway, (2) Centre for Cancer Cell
Reprogramming, Institute ... | OncoEnrichR: cancer-dedicated gene set interpretation | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Genome-scale screening experiments in cancer produce long lists of candidate
genes that require extensive interpretation for biological insight and
prioritization for follow-up studies. Interrogation of gene lists frequently
represents a significant and time-consuming undertaking, in which experimental
biologists typ... | [
{
"created": "Wed, 28 Jul 2021 10:07:51 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Aug 2021 08:40:00 GMT",
"version": "v2"
},
{
"created": "Tue, 27 Sep 2022 21:14:23 GMT",
"version": "v3"
}
] | 2022-09-29 | [
[
"Nakken",
"Sigve",
"",
"1 and 2 and 3"
],
[
"Gundersen",
"Sveinung",
"",
"1 and 3"
],
[
"Bernal",
"Fabian L. M.",
"",
"1 and 3"
],
[
"Polychronopoulos",
"Dimitris",
"",
"1 and 3"
],
[
"Hovig",
"Eivind",
"",
"1 and 3"
... | Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typic... |
2010.11765 | Aran Nayebi | Aran Nayebi, Sanjana Srivastava, Surya Ganguli, Daniel L.K. Yamins | Identifying Learning Rules From Neural Network Observables | NeurIPS 2020 Camera Ready Version, 21 pages including supplementary
information, 13 figures | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain modifies its synaptic strengths during learning in order to better
adapt to its environment. However, the underlying plasticity rules that govern
learning are unknown. Many proposals have been suggested, including Hebbian
mechanisms, explicit error backpropagation, and a variety of alternatives. It
is an op... | [
{
"created": "Thu, 22 Oct 2020 14:36:54 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Dec 2020 18:48:02 GMT",
"version": "v2"
}
] | 2020-12-09 | [
[
"Nayebi",
"Aran",
""
],
[
"Srivastava",
"Sanjana",
""
],
[
"Ganguli",
"Surya",
""
],
[
"Yamins",
"Daniel L. K.",
""
]
] | The brain modifies its synaptic strengths during learning in order to better adapt to its environment. However, the underlying plasticity rules that govern learning are unknown. Many proposals have been suggested, including Hebbian mechanisms, explicit error backpropagation, and a variety of alternatives. It is an open... |
2003.13901 | HongGuang Sun | Yong Zhang, Xiangnan Yu, HongGuang Sun, Geoffrey R. Tick, Wei Wei, Bin
Jin | COVID-19 infection and recovery in various countries: Modeling the
dynamics and evaluating the non-pharmaceutical mitigation scenarios | 29 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The coronavirus disease 2019 (COVID-19) pandemic radically impacts our lives,
while the transmission/infection and recovery dynamics of COVID-19 remain
obscure. A time-dependent Susceptible, Exposed, Infectious, and Recovered
(SEIR) model was proposed and applied to fit and then predict the time series
of COVID-19 ev... | [
{
"created": "Tue, 31 Mar 2020 01:30:55 GMT",
"version": "v1"
}
] | 2020-04-01 | [
[
"Zhang",
"Yong",
""
],
[
"Yu",
"Xiangnan",
""
],
[
"Sun",
"HongGuang",
""
],
[
"Tick",
"Geoffrey R.",
""
],
[
"Wei",
"Wei",
""
],
[
"Jin",
"Bin",
""
]
] | The coronavirus disease 2019 (COVID-19) pandemic radically impacts our lives, while the transmission/infection and recovery dynamics of COVID-19 remain obscure. A time-dependent Susceptible, Exposed, Infectious, and Recovered (SEIR) model was proposed and applied to fit and then predict the time series of COVID-19 evol... |
1908.05517 | Tom Britton | Tom Britton | Epidemic models on social networks -- with inference | 20 pages, 4 figures | null | null | null | q-bio.PE math.PR stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Consider stochastic models for the spread of an infection in a structured
community, where this structured community is itself described by a random
network model. Some common network models and transmission models are defined
and large population proporties of them are presented. Focus is then shifted to
statistical... | [
{
"created": "Thu, 15 Aug 2019 12:44:37 GMT",
"version": "v1"
}
] | 2019-08-16 | [
[
"Britton",
"Tom",
""
]
] | Consider stochastic models for the spread of an infection in a structured community, where this structured community is itself described by a random network model. Some common network models and transmission models are defined and large population proporties of them are presented. Focus is then shifted to statistical m... |
q-bio/0402040 | Dorjsuren Battogtokh | Dorjsuren Battogtokh and John J. Tyson | Turbulence near cyclic fold bifurcations in birhythmic media | 14 pages 10 figures | null | 10.1103/PhysRevE.70.026212 | null | q-bio.SC | null | We show that at the onset of a cyclic fold bifurcation, a birhythmic medium
composed of glycolytic oscillators displays turbulent dynamics. By computing
the largest Lyapunov exponent, the spatial correlation function, and the
average transient lifetime, we classify it as a weak turbulence with transient
nature. Virtu... | [
{
"created": "Tue, 24 Feb 2004 21:04:46 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Battogtokh",
"Dorjsuren",
""
],
[
"Tyson",
"John J.",
""
]
] | We show that at the onset of a cyclic fold bifurcation, a birhythmic medium composed of glycolytic oscillators displays turbulent dynamics. By computing the largest Lyapunov exponent, the spatial correlation function, and the average transient lifetime, we classify it as a weak turbulence with transient nature. Virtual... |
1109.4085 | Ovidiu Radulescu | Vincent Noel, Dima Grigoriev, Sergei Vakulenko and Ovidiu Radulescu | Tropical geometries and dynamics of biochemical networks. Application to
hybrid cell cycle models | conference SASB 2011, to be published in Electronic Notes in
Theoretical Computer Science | null | null | null | q-bio.MN math.AG | http://creativecommons.org/licenses/publicdomain/ | We use the Litvinov-Maslov correspondence principle to reduce and hybridize
networks of biochemical reactions. We apply this method to a cell cycle
oscillator model. The reduced and hybridized model can be used as a hybrid
model for the cell cycle. We also propose a practical recipe for detecting
quasi-equilibrium QE... | [
{
"created": "Mon, 19 Sep 2011 16:41:36 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Sep 2011 05:45:49 GMT",
"version": "v2"
}
] | 2011-09-21 | [
[
"Noel",
"Vincent",
""
],
[
"Grigoriev",
"Dima",
""
],
[
"Vakulenko",
"Sergei",
""
],
[
"Radulescu",
"Ovidiu",
""
]
] | We use the Litvinov-Maslov correspondence principle to reduce and hybridize networks of biochemical reactions. We apply this method to a cell cycle oscillator model. The reduced and hybridized model can be used as a hybrid model for the cell cycle. We also propose a practical recipe for detecting quasi-equilibrium QE r... |
1308.4102 | Inti Pedroso | Inti Pedroso | Gene and Gene-Set Analysis for Genome-Wide Association Studies | null | null | null | null | q-bio.GN q-bio.MN q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | Genome-wide association studies (GWAS) have identified hundreds of loci at
very stringent levels of statistical significance across many different human
traits. However, it is now clear that very large samples (n~10^4-10^5) are
needed to find the majority of genetic variants underlying risk for most human
diseases. T... | [
{
"created": "Mon, 19 Aug 2013 19:20:12 GMT",
"version": "v1"
}
] | 2013-08-20 | [
[
"Pedroso",
"Inti",
""
]
] | Genome-wide association studies (GWAS) have identified hundreds of loci at very stringent levels of statistical significance across many different human traits. However, it is now clear that very large samples (n~10^4-10^5) are needed to find the majority of genetic variants underlying risk for most human diseases. The... |
1610.04123 | Bob Eisenberg | Bob Eisenberg | Ionic channels in biological membranes. Electrostatic analysis of a
natural nanotube | Spelling errors corrected | Contemporary Physics (1998) 39(6):447- 466 | 10.1080/001075198181775 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A simple theory of ion permeation through a channel is presented, in which
diffusion occurs according to Fick's law and drift according to Ohm's law, in
the electric field determined by all the charges present. This theory accounts
for permeation in the channels studied to date in a wide range of solutions.
Interesti... | [
{
"created": "Thu, 13 Oct 2016 15:18:26 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Oct 2016 08:43:51 GMT",
"version": "v2"
}
] | 2016-10-17 | [
[
"Eisenberg",
"Bob",
""
]
] | A simple theory of ion permeation through a channel is presented, in which diffusion occurs according to Fick's law and drift according to Ohm's law, in the electric field determined by all the charges present. This theory accounts for permeation in the channels studied to date in a wide range of solutions. Interesting... |
2201.05669 | Nan Xi | Nan Miles Xi and Dalong Patrick Huang | Prediction of Drug-Induced TdP Risks Using Machine Learning and Rabbit
Ventricular Wedge Assay | arXiv admin note: text overlap with arXiv:2108.00543 | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | The evaluation of drug-induced Torsades de pointes (TdP) risks is crucial in
drug safety assessment. In this study, we discuss machine learning approaches
in the prediction of drug-induced TdP risks using preclinical data.
Specifically, the random forest model was trained on the dataset generated by
the rabbit ventri... | [
{
"created": "Fri, 14 Jan 2022 21:03:20 GMT",
"version": "v1"
}
] | 2022-01-19 | [
[
"Xi",
"Nan Miles",
""
],
[
"Huang",
"Dalong Patrick",
""
]
] | The evaluation of drug-induced Torsades de pointes (TdP) risks is crucial in drug safety assessment. In this study, we discuss machine learning approaches in the prediction of drug-induced TdP risks using preclinical data. Specifically, the random forest model was trained on the dataset generated by the rabbit ventricu... |
1608.01912 | Toan T. Nguyen | Nguyen Viet Duc, Toan T. Nguyen, and Paolo Carloni | DNA like$-$charge attraction and overcharging by divalent counterions in
the presence of divalent co$-$ions | 10 pages, 6 figures | J. Biol. Phys. (2017) | 10.1007/s10867-017-9443-x | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Strongly correlated electrostatics of DNA systems has drawn the interest of
many groups, especially the condensation and overcharging of DNA by multivalent
counterions. By adding counterions of different valencies and shapes, one can
enhance or reduce DNA overcharging. In this papers, we focus on the effect of
multiv... | [
{
"created": "Fri, 5 Aug 2016 15:17:43 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Aug 2016 04:40:44 GMT",
"version": "v2"
},
{
"created": "Wed, 24 May 2017 16:20:57 GMT",
"version": "v3"
}
] | 2017-05-25 | [
[
"Duc",
"Nguyen Viet",
""
],
[
"Nguyen",
"Toan T.",
""
],
[
"Carloni",
"Paolo",
""
]
] | Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduce DNA overcharging. In this papers, we focus on the effect of multival... |
q-bio/0508005 | Antonia Kropfinger | Marie-Anne F\'elix (IJM) | An inversion in the wiring of an intercellular signal: evolution of Wnt
signaling in the nematode vulva | null | BioEssays 27 (2005) 765-769 | 10.1002/bies.20275 | null | q-bio.PE q-bio.MN | null | Signal transduction pathways are largely conserved throughout the animal
kingdom. The repertoire of pathways is limited and each pathway is used in
different intercellular signaling events during the development of a given
animal. For example, Wnt signaling is recruited, sometimes redundantly with
other molecular pat... | [
{
"created": "Tue, 2 Aug 2005 07:24:56 GMT",
"version": "v1"
}
] | 2016-08-16 | [
[
"Félix",
"Marie-Anne",
"",
"IJM"
]
] | Signal transduction pathways are largely conserved throughout the animal kingdom. The repertoire of pathways is limited and each pathway is used in different intercellular signaling events during the development of a given animal. For example, Wnt signaling is recruited, sometimes redundantly with other molecular pathw... |
1104.2252 | Antti Niemi | Andrei Krokhotine and Antti J. Niemi | Solitons and Physics of the Lysogenic to Lytic Transition in
Enterobacteria Lambda Phage | 5 pages 3 figures | null | null | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The lambda phage is a paradigm temperate bacteriophage. Its lysogenic and
lytic life cycles echo competition between the DNA binding CI and CRO proteins.
Here we address the Physics of this transition in terms of an energy function
that portrays the backbone as a multi-soliton configuration. The precision of
the indi... | [
{
"created": "Tue, 12 Apr 2011 15:53:13 GMT",
"version": "v1"
}
] | 2011-04-13 | [
[
"Krokhotine",
"Andrei",
""
],
[
"Niemi",
"Antti J.",
""
]
] | The lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding CI and CRO proteins. Here we address the Physics of this transition in terms of an energy function that portrays the backbone as a multi-soliton configuration. The precision of the indivi... |
q-bio/0603012 | Richard Yamada | Yujiro Richard Yamada, Charles S. Peskin | A Chemical Kinetic Model of Transcriptional Elongation | 9 pages, 3 figures, 1 table. Corrected typos; condensed size of
manuscript to meet PRL submission guidelines. Details in previous edition | null | null | null | q-bio.BM q-bio.SC | null | A chemical kinetic model of the elongation dynamics of RNA polymerase along a
DNA sequence is introduced. The proposed model governs the discrete movement of
the RNA polymerase along a DNA template, with no consideration given to elastic
effects. The model's novel concept is a ``look-ahead'' feature, in which
nucleot... | [
{
"created": "Sun, 12 Mar 2006 02:50:18 GMT",
"version": "v1"
},
{
"created": "Tue, 23 May 2006 20:39:49 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Yamada",
"Yujiro Richard",
""
],
[
"Peskin",
"Charles S.",
""
]
] | A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic effects. The model's novel concept is a ``look-ahead'' feature, in which nucleotid... |
2002.07810 | Kritika Singhal | Sarah Tymochko, Kritika Singhal, and Giseon Heo | Classifying sleep states using persistent homology and Markov chain: a
Pilot Study | null | null | null | null | q-bio.QM eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Obstructive sleep Apnea (OSA) is a form of sleep disordered breathing
characterized by frequent episodes of upper airway collapse during sleep.
Pediatric OSA occurs in 1-5% of children and can related to other serious
health conditions such as high blood pressure, behavioral issues, or altered
growth. OSA is often di... | [
{
"created": "Mon, 17 Feb 2020 22:24:14 GMT",
"version": "v1"
}
] | 2020-02-20 | [
[
"Tymochko",
"Sarah",
""
],
[
"Singhal",
"Kritika",
""
],
[
"Heo",
"Giseon",
""
]
] | Obstructive sleep Apnea (OSA) is a form of sleep disordered breathing characterized by frequent episodes of upper airway collapse during sleep. Pediatric OSA occurs in 1-5% of children and can related to other serious health conditions such as high blood pressure, behavioral issues, or altered growth. OSA is often diag... |
1504.02751 | Michael Famulare | Michael Famulare | Has wild poliovirus been eliminated from Nigeria? | Added model validation section and updated cVDPV2 forecast in
response to new case data; expanded material on surveillance sensitivity;
additional minor edits; and references added. 24 pages, 4 figures | null | 10.1371/journal.pone.0135765 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Wild poliovirus type 3 (WPV3) has not been seen anywhere since the last case
of WPV3-associated paralysis in Nigeria in November 2012. At the time of
writing, the most recent case of wild poliovirus type 1 (WPV1) in Nigeria
occurred in July 2014, and WPV1 has not been seen in Africa since a case in
Somalia in August ... | [
{
"created": "Fri, 10 Apr 2015 18:12:55 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Jul 2015 21:42:47 GMT",
"version": "v2"
}
] | 2016-02-17 | [
[
"Famulare",
"Michael",
""
]
] | Wild poliovirus type 3 (WPV3) has not been seen anywhere since the last case of WPV3-associated paralysis in Nigeria in November 2012. At the time of writing, the most recent case of wild poliovirus type 1 (WPV1) in Nigeria occurred in July 2014, and WPV1 has not been seen in Africa since a case in Somalia in August 20... |
1807.01491 | David Gall | David Gall and Genevi\`eve Dupont | Tonic activation of extrasynaptic NMDA receptors decreases intrinsic
excitability and promotes bistability in a model of neuronal activity | 20 pages, 5 figures | Int J Mol Sci. 2019 Dec 27;21(1). pii: E206 | 10.3390/ijms21010206 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | NMDA receptors (NMDA-R) typically contribute to excitatory synaptic
transmission in the central nervous system. While calcium influx through NMDA-R
plays a critical role in synaptic plasticity, experimental evidence indicates
that NMDAR-mediated calcium influx also modifies neuronal excitability through
the activatio... | [
{
"created": "Wed, 4 Jul 2018 09:17:50 GMT",
"version": "v1"
},
{
"created": "Fri, 31 Jan 2020 10:21:54 GMT",
"version": "v2"
}
] | 2020-02-03 | [
[
"Gall",
"David",
""
],
[
"Dupont",
"Geneviève",
""
]
] | NMDA receptors (NMDA-R) typically contribute to excitatory synaptic transmission in the central nervous system. While calcium influx through NMDA-R plays a critical role in synaptic plasticity, experimental evidence indicates that NMDAR-mediated calcium influx also modifies neuronal excitability through the activation ... |
2111.03565 | Cl\'audia Arag\~ao | Rita Teod\'osio, Cl\'audia Arag\~ao, Rita Colen, Raquel Carrilho,
Jorge Dias, Sofia Engrola | A nutritional strategy to promote gilthead seabream performance under
low temperatures | null | Aquaculture 537: 736494 (2021) | 10.1016/j.aquaculture.2021.736494 | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Gilthead seabream (Sparus aurata) is vulnerable to low water temperature,
which may occur in the Southern Europe and Mediterranean region during Winter.
Fish are poikilothermic animals, so feed intake, digestion, metabolism and
ultimately growth are affected by water temperature. This study aimed to
evaluate growth p... | [
{
"created": "Fri, 5 Nov 2021 15:41:59 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Nov 2021 15:26:59 GMT",
"version": "v2"
}
] | 2021-11-11 | [
[
"Teodósio",
"Rita",
""
],
[
"Aragão",
"Cláudia",
""
],
[
"Colen",
"Rita",
""
],
[
"Carrilho",
"Raquel",
""
],
[
"Dias",
"Jorge",
""
],
[
"Engrola",
"Sofia",
""
]
] | Gilthead seabream (Sparus aurata) is vulnerable to low water temperature, which may occur in the Southern Europe and Mediterranean region during Winter. Fish are poikilothermic animals, so feed intake, digestion, metabolism and ultimately growth are affected by water temperature. This study aimed to evaluate growth per... |
1506.06717 | Dante Chialvo | Dante R. Chialvo, Ana Maria Gonzalez Torrado, Ewa Gudowska-Nowak,
Jeremi K. Ochab, Pedro Montoya, Maciej A. Nowak and Enzo Tagliazucchi | How we move is universal: scaling in the average shape of human activity | Communicated to the Granada Seminar, "Physics Meets the Social
Sciences: Emergent cooperative phenomena, from bacterial to human group
behavior". June 14-19, 2015. La Herradura, Spain | Papers in Physics, vol. 7, art. 070017 (2015) | 10.4279/PIP.070017 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human motor activity is constrained by the rhythmicity of the 24 hours
circadian cycle, including the usual 12-15 hours sleep-wake cycle. However,
activity fluctuations also appear over a wide range of temporal scales, from
days to a few seconds, resulting from the concatenation of a myriad of
individual smaller moto... | [
{
"created": "Mon, 22 Jun 2015 18:58:01 GMT",
"version": "v1"
},
{
"created": "Sun, 22 Nov 2015 11:50:07 GMT",
"version": "v2"
}
] | 2015-11-24 | [
[
"Chialvo",
"Dante R.",
""
],
[
"Torrado",
"Ana Maria Gonzalez",
""
],
[
"Gudowska-Nowak",
"Ewa",
""
],
[
"Ochab",
"Jeremi K.",
""
],
[
"Montoya",
"Pedro",
""
],
[
"Nowak",
"Maciej A.",
""
],
[
"Tagliazucchi",
"... | Human motor activity is constrained by the rhythmicity of the 24 hours circadian cycle, including the usual 12-15 hours sleep-wake cycle. However, activity fluctuations also appear over a wide range of temporal scales, from days to a few seconds, resulting from the concatenation of a myriad of individual smaller motor ... |
2307.00858 | Zijian Dong | Zijian Dong, Yilei Wu, Yu Xiao, Joanna Su Xian Chong, Yueming Jin,
Juan Helen Zhou | Beyond the Snapshot: Brain Tokenized Graph Transformer for Longitudinal
Brain Functional Connectome Embedding | MICCAI 2023 | null | null | null | q-bio.NC cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Under the framework of network-based neurodegeneration, brain functional
connectome (FC)-based Graph Neural Networks (GNN) have emerged as a valuable
tool for the diagnosis and prognosis of neurodegenerative diseases such as
Alzheimer's disease (AD). However, these models are tailored for brain FC at a
single time po... | [
{
"created": "Mon, 3 Jul 2023 08:57:30 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Jul 2023 03:29:05 GMT",
"version": "v2"
}
] | 2023-07-14 | [
[
"Dong",
"Zijian",
""
],
[
"Wu",
"Yilei",
""
],
[
"Xiao",
"Yu",
""
],
[
"Chong",
"Joanna Su Xian",
""
],
[
"Jin",
"Yueming",
""
],
[
"Zhou",
"Juan Helen",
""
]
] | Under the framework of network-based neurodegeneration, brain functional connectome (FC)-based Graph Neural Networks (GNN) have emerged as a valuable tool for the diagnosis and prognosis of neurodegenerative diseases such as Alzheimer's disease (AD). However, these models are tailored for brain FC at a single time poin... |
1901.05051 | Pierre-Philippe Dechant | Pierre-Philippe Dechant and Yang-Hui He | Machine-learning a virus assembly fitness landscape | 13 pages, 4 figures | PLoS ONE 16(5): e0250227 (2021) | 10.1371/journal.pone.0250227 | null | q-bio.BM cs.LG q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Realistic evolutionary fitness landscapes are notoriously difficult to
construct. A recent cutting-edge model of virus assembly consists of a
dodecahedral capsid with $12$ corresponding packaging signals in three affinity
bands. This whole genome/phenotype space consisting of $3^{12}$ genomes has
been explored via co... | [
{
"created": "Sun, 13 Jan 2019 12:17:02 GMT",
"version": "v1"
}
] | 2021-06-22 | [
[
"Dechant",
"Pierre-Philippe",
""
],
[
"He",
"Yang-Hui",
""
]
] | Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole genome/phenotype space consisting of $3^{12}$ genomes has been explored via comp... |
2103.06578 | Weifeng Li | Yanmei Yang, Yunju Zhang, Yuanyuan Qu, Xuewei Liu, Mingwen Zhao,
Yuguang Mu, Weifeng Li | Quantitative Interpretations of Energetic Features and Key Residues at
SARS Coronavirus Spike Receptor-Binding Domain and ACE2 Receptor Interface | 12 pages, 4 figures, 1 table | Nanoscale, 2021 | 10.1039/D1NR01672E | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The wide spread of coronavirus disease 2019 (COVID-19) has declared a global
health emergency. As one of the most important targets for antibody and drug
developments, Spike RBD-ACE2 interface has received extensive attention. Here,
using molecular dynamics simulations, we explicitly evaluated the binding
energetic f... | [
{
"created": "Thu, 11 Mar 2021 10:06:34 GMT",
"version": "v1"
}
] | 2021-05-14 | [
[
"Yang",
"Yanmei",
""
],
[
"Zhang",
"Yunju",
""
],
[
"Qu",
"Yuanyuan",
""
],
[
"Liu",
"Xuewei",
""
],
[
"Zhao",
"Mingwen",
""
],
[
"Mu",
"Yuguang",
""
],
[
"Li",
"Weifeng",
""
]
] | The wide spread of coronavirus disease 2019 (COVID-19) has declared a global health emergency. As one of the most important targets for antibody and drug developments, Spike RBD-ACE2 interface has received extensive attention. Here, using molecular dynamics simulations, we explicitly evaluated the binding energetic fea... |
2308.05131 | Rosalia Ferraro | Rosalia Ferraro, Sergio Caserta, Stefano Guido | A low-cost, user-friendly rheo-optical compression assay to measure
mechanical properties of cell spheroids in standard cell culture plates | 32 pages, 7 figures | null | null | null | q-bio.QM physics.bio-ph q-bio.CB | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The mechanical characterization of cell spheroids, one of the most widely
used 3D biology models in vitro, is a hotspot of current research on the role
played by the mechanical response of cells and tissues. The techniques proposed
so far in the literature, while providing important scientific insights,
require a spe... | [
{
"created": "Wed, 9 Aug 2023 12:40:58 GMT",
"version": "v1"
}
] | 2023-08-11 | [
[
"Ferraro",
"Rosalia",
""
],
[
"Caserta",
"Sergio",
""
],
[
"Guido",
"Stefano",
""
]
] | The mechanical characterization of cell spheroids, one of the most widely used 3D biology models in vitro, is a hotspot of current research on the role played by the mechanical response of cells and tissues. The techniques proposed so far in the literature, while providing important scientific insights, require a speci... |
2308.03532 | Ioannis Karafyllidis G. | G. D. Varsamis, I. G. Karafyllidis, K. M. Gilkes, U. Arranz, R.
Martin-Cuevas, G. Calleja, J. Wong, H. C. Jessen, P. Dimitrakis, P. Kolovos,
R. Sandaltzopoulos | Quantum algorithm for de novo DNA sequence assembly based on quantum
walks on graphs | 13 pages, 7 figures | null | null | null | q-bio.BM quant-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | De novo DNA sequence assembly is based on finding paths in overlap graphs,
which is a NP-hard problem. We developed a quantum algorithm for de novo
assembly based on quantum walks in graphs. The overlap graph is partitioned
repeatedly to smaller graphs that form a hierarchical structure. We use quantum
walks to find ... | [
{
"created": "Mon, 7 Aug 2023 12:30:25 GMT",
"version": "v1"
}
] | 2023-08-08 | [
[
"Varsamis",
"G. D.",
""
],
[
"Karafyllidis",
"I. G.",
""
],
[
"Gilkes",
"K. M.",
""
],
[
"Arranz",
"U.",
""
],
[
"Martin-Cuevas",
"R.",
""
],
[
"Calleja",
"G.",
""
],
[
"Wong",
"J.",
""
],
[
"Jessen... | De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to smaller graphs that form a hierarchical structure. We use quantum walks to find pa... |
0811.3538 | Arne Traulsen | Arne Traulsen and Christoph Hauert | Stochastic evolutionary game dynamics | To appear in "Reviews of Nonlinear Dynamics and Complexity" Vol. II,
Wiley-VCH, 2009, edited by H.-G. Schuster | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this review, we summarize recent developments in stochastic evolutionary
game dynamics of finite populations.
| [
{
"created": "Fri, 21 Nov 2008 13:57:52 GMT",
"version": "v1"
}
] | 2008-11-24 | [
[
"Traulsen",
"Arne",
""
],
[
"Hauert",
"Christoph",
""
]
] | In this review, we summarize recent developments in stochastic evolutionary game dynamics of finite populations. |
2308.14135 | Ilya Timofeyev | Yingxue Su, Brett Geiger, Ilya Timofeyev, Andreas Mang, Robert
Azencott | Rare Events Analysis and Computation for Stochastic Evolution of
Bacterial Populations | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we develop a computational approach for computing most likely
trajectories describing rare events that correspond to the emergence of
non-dominant genotypes. This work is based on the large deviations approach for
discrete Markov chains describing the genetic evolution of large bacterial
populations. W... | [
{
"created": "Sun, 27 Aug 2023 15:29:30 GMT",
"version": "v1"
}
] | 2023-08-29 | [
[
"Su",
"Yingxue",
""
],
[
"Geiger",
"Brett",
""
],
[
"Timofeyev",
"Ilya",
""
],
[
"Mang",
"Andreas",
""
],
[
"Azencott",
"Robert",
""
]
] | In this paper, we develop a computational approach for computing most likely trajectories describing rare events that correspond to the emergence of non-dominant genotypes. This work is based on the large deviations approach for discrete Markov chains describing the genetic evolution of large bacterial populations. We ... |
2304.01975 | Paterne Gahungu | Steve Sibomanaa, Kelly Joelle Gatore Sinigirira, Paterne Gahungu,
David Niyukuri | Mathematical Model for Transmission Dynamics of Tuberculosis in Burundi | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Tuberculosis (TB) is among the main public health challenges in Burundi. The
literature lacks mathematical models for key parameter estimates of TB
transmission dynamics in Burundi. In this paper, the
supectible-exposed-infected-recovered (SEIR) model is used to investigate the
transmission dynamics of tuberculosis i... | [
{
"created": "Tue, 4 Apr 2023 17:32:01 GMT",
"version": "v1"
}
] | 2023-04-05 | [
[
"Sibomanaa",
"Steve",
""
],
[
"Sinigirira",
"Kelly Joelle Gatore",
""
],
[
"Gahungu",
"Paterne",
""
],
[
"Niyukuri",
"David",
""
]
] | Tuberculosis (TB) is among the main public health challenges in Burundi. The literature lacks mathematical models for key parameter estimates of TB transmission dynamics in Burundi. In this paper, the supectible-exposed-infected-recovered (SEIR) model is used to investigate the transmission dynamics of tuberculosis in ... |
0705.3759 | Alain Destexhe | Claude Bedard and Alain Destexhe | A modified cable formalism for modeling neuronal membranes at high
frequencies | To appear in Biophysical Journal; Submitted on May 25, 2007; accepted
on Sept 11th, 2007 | Biophysical Journal 2008 Feb 15;94(4):1133-43. Epub 2007 Oct 5 | 10.1529/biophysj.107.113571 | null | q-bio.NC | null | Intracellular recordings of cortical neurons in vivo display intense
subthreshold membrane potential (Vm) activity. The power spectral density (PSD)
of the Vm displays a power-law structure at high frequencies (>50 Hz) with a
slope of about -2.5. This type of frequency scaling cannot be accounted for by
traditional m... | [
{
"created": "Fri, 25 May 2007 12:34:43 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Aug 2007 08:30:58 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Sep 2007 18:57:14 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Bedard",
"Claude",
""
],
[
"Destexhe",
"Alain",
""
]
] | Intracellular recordings of cortical neurons in vivo display intense subthreshold membrane potential (Vm) activity. The power spectral density (PSD) of the Vm displays a power-law structure at high frequencies (>50 Hz) with a slope of about -2.5. This type of frequency scaling cannot be accounted for by traditional mod... |
1105.2823 | Dhagash Mehta | Esteban A. Hernandez-Vargas, Dhagash Mehta, Richard H. Middleton | Towards Modeling HIV Long Term Behavior | Accepted in proceedings of 18th IFAC World Congress, Milan, August 28
- September 2, 2011 (Invited Contribution: Modeling methods and clinical
applications in medical and biological systems I). 6 pages, 7 figures | null | null | null | q-bio.CB math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The precise mechanism that causes HIV infection to progress to AIDS is still
unknown. This paper presents a mathematical model which is able to predict the
entire trajectory of the HIV/AIDS dynamics, then a possible explanation for
this progression is examined. A dynamical analysis of this model reveals a set
of para... | [
{
"created": "Fri, 13 May 2011 20:00:11 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Hernandez-Vargas",
"Esteban A.",
""
],
[
"Mehta",
"Dhagash",
""
],
[
"Middleton",
"Richard H.",
""
]
] | The precise mechanism that causes HIV infection to progress to AIDS is still unknown. This paper presents a mathematical model which is able to predict the entire trajectory of the HIV/AIDS dynamics, then a possible explanation for this progression is examined. A dynamical analysis of this model reveals a set of parame... |
2101.03147 | Enrico Borriello Dr. | William Bains, Enrico Borriello, Dirk Schulze-Makuch | Evolution of default genetic control mechanisms | 25 pages, 8 figures, 1 table | null | 10.1371/journal.pone.0251568 | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | We present a model of the evolution of control systems in a genome under
environmental constraints. The model conceptually follows the Jacob and Monod
model of gene control. Genes contain control elements which respond to the
internal state of the cell as well as the environment to control expression of
a coding regi... | [
{
"created": "Fri, 8 Jan 2021 18:23:13 GMT",
"version": "v1"
}
] | 2021-06-09 | [
[
"Bains",
"William",
""
],
[
"Borriello",
"Enrico",
""
],
[
"Schulze-Makuch",
"Dirk",
""
]
] | We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region... |
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