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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0409019 | Joachim Krug | Joachim Krug and Kavita Jain | Breaking records in the evolutionary race | Proceedings of 8th ICCMSP/Marrakech, to be published in Physica A | Physica A 358, 1 (2005) | 10.1016/j.physa.2005.06.002 | null | q-bio.PE cond-mat.dis-nn | null | We explore some aspects of the relationship between biological evolution
processes and the mathematical theory of records. For Eigen's quasispecies
model with an uncorrelated fitness landscape, we show that the evolutionary
trajectories traced out by a population initially localized at a randomly
chosen point in sequ... | [
{
"created": "Thu, 16 Sep 2004 15:31:25 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Krug",
"Joachim",
""
],
[
"Jain",
"Kavita",
""
]
] | We explore some aspects of the relationship between biological evolution processes and the mathematical theory of records. For Eigen's quasispecies model with an uncorrelated fitness landscape, we show that the evolutionary trajectories traced out by a population initially localized at a randomly chosen point in sequen... |
1511.06754 | Lauren Assour | Lauren A. Assour, Nicholas LaRosa, Scott J. Emrich | Hot RAD: A Tool for Analysis of Next-Gen RAD Tag Data | null | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.)
is an emerging method for analyzing an organism's genome without completely
sequencing it. This can be applied to a non-model organism without a reference
genome, though this creates the problem of how to begin data analysis on
unmapped and u... | [
{
"created": "Fri, 20 Nov 2015 20:56:45 GMT",
"version": "v1"
}
] | 2015-11-23 | [
[
"Assour",
"Lauren A.",
""
],
[
"LaRosa",
"Nicholas",
""
],
[
"Emrich",
"Scott J.",
""
]
] | Restriction site Associated DNA (RAD) tagging (also known as RAD-seq, etc.) is an emerging method for analyzing an organism's genome without completely sequencing it. This can be applied to a non-model organism without a reference genome, though this creates the problem of how to begin data analysis on unmapped and una... |
1703.00698 | Alain Destexhe | Yann Zerlaut and Alain Destexhe | A mean-field model for conductance-based networks of adaptive
exponential integrate-and-fire neurons | 21 pages, 7 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Voltage-sensitive dye imaging (VSDi) has revealed fundamental properties of
neocortical processing at mesoscopic scales. Since VSDi signals report the
average membrane potential, it seems natural to use a mean-field formalism to
model such signals. Here, we investigate a mean-field model of networks of
Adaptive Expon... | [
{
"created": "Thu, 2 Mar 2017 10:19:17 GMT",
"version": "v1"
}
] | 2017-03-03 | [
[
"Zerlaut",
"Yann",
""
],
[
"Destexhe",
"Alain",
""
]
] | Voltage-sensitive dye imaging (VSDi) has revealed fundamental properties of neocortical processing at mesoscopic scales. Since VSDi signals report the average membrane potential, it seems natural to use a mean-field formalism to model such signals. Here, we investigate a mean-field model of networks of Adaptive Exponen... |
1710.04400 | Olha Shchur | A. Vidybida, O. Shchur | Information reduction in a reverberatory neuronal network through
convergence to complex oscillatory firing patterns | 15 pages, 8 figures, 4 tables, manuscript accepted by Biosystems.
Content of this work was presented at the Twelvth International Neural Coding
Workshop in Cologne, Germany | BioSystems (2017) 161, pp. 24-30 | 10.1016/j.biosystems.2017.07.008 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study dynamics of a reverberating neural net by means of computer
simulation. The net, which is composed of 9 leaky integrate-and-fire (LIF)
neurons arranged in a square lattice, is fully connected with interneuronal
communication delay proportional to the corresponding distance. The network is
initially stimulate... | [
{
"created": "Thu, 12 Oct 2017 08:07:14 GMT",
"version": "v1"
}
] | 2023-06-16 | [
[
"Vidybida",
"A.",
""
],
[
"Shchur",
"O.",
""
]
] | We study dynamics of a reverberating neural net by means of computer simulation. The net, which is composed of 9 leaky integrate-and-fire (LIF) neurons arranged in a square lattice, is fully connected with interneuronal communication delay proportional to the corresponding distance. The network is initially stimulated ... |
1905.03972 | Zhongqi Tian | Zhong-Qi Kyle Tian, Douglas Zhou, David Cai | Digital System Reconstruction by Pairwise Transfer Entropy | 10 pages, 4 figures | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transfer entropy (TE) is an attractive model-free method to detect causality
and infer structural connectivity of general digital systems. However it relies
on high dimensions used in its definition to clearly remove the memory effect
and distinguish the direct causality from the indirect ones which makes it
almost i... | [
{
"created": "Fri, 10 May 2019 07:08:33 GMT",
"version": "v1"
}
] | 2019-05-13 | [
[
"Tian",
"Zhong-Qi Kyle",
""
],
[
"Zhou",
"Douglas",
""
],
[
"Cai",
"David",
""
]
] | Transfer entropy (TE) is an attractive model-free method to detect causality and infer structural connectivity of general digital systems. However it relies on high dimensions used in its definition to clearly remove the memory effect and distinguish the direct causality from the indirect ones which makes it almost ino... |
q-bio/0603032 | Olaf Wolkenhauer | Peter Wellstead, Rick Middleton, Olaf Wolkenhauer | Feedback Medicine: Control Systems Concepts in Personalised, Predictive
Medicine and Combinatorial Intervention | 22 pages, 10 figures | null | null | 27-03-06 | q-bio.TO q-bio.QM | null | In its broadest definition, systems biology is the application of a `systems'
way of thinking about and doing cell biology. By implication, this also invites
us to consider a systems approach in the context of medicine and the treatment
of disease. In particular, the idea that systems biology can form the basis of
a ... | [
{
"created": "Mon, 27 Mar 2006 10:25:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Wellstead",
"Peter",
""
],
[
"Middleton",
"Rick",
""
],
[
"Wolkenhauer",
"Olaf",
""
]
] | In its broadest definition, systems biology is the application of a `systems' way of thinking about and doing cell biology. By implication, this also invites us to consider a systems approach in the context of medicine and the treatment of disease. In particular, the idea that systems biology can form the basis of a pe... |
1802.09381 | Jean-Philippe Vert | Beyrem Khalfaoui (CBIO), Jean-Philippe Vert (CBIO, DMA) | DropLasso: A robust variant of Lasso for single cell RNA-seq data | null | null | null | null | q-bio.QM cs.CV q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-cell RNA sequencing (scRNA-seq) is a fast growing approach to measure
the genome-wide transcriptome of many individual cells in parallel, but results
in noisy data with many dropout events. Existing methods to learn molecular
signatures from bulk transcriptomic data may therefore not be adapted to
scRNA-seq da... | [
{
"created": "Mon, 26 Feb 2018 15:10:44 GMT",
"version": "v1"
}
] | 2018-02-27 | [
[
"Khalfaoui",
"Beyrem",
"",
"CBIO"
],
[
"Vert",
"Jean-Philippe",
"",
"CBIO, DMA"
]
] | Single-cell RNA sequencing (scRNA-seq) is a fast growing approach to measure the genome-wide transcriptome of many individual cells in parallel, but results in noisy data with many dropout events. Existing methods to learn molecular signatures from bulk transcriptomic data may therefore not be adapted to scRNA-seq data... |
2009.08491 | Qiong Wang | Qiong Wang, Tengteng Tang, David Cooper, Felipe Eltit, Peter Fratzl,
Pierre Guy and Rizhi Wang | Globular structure of the hypermineralized tissue in human femoral neck | null | Journal of Structural Biology,Volume 212, Issue 2, 1 November
2020, 107606 | 10.1016/j.jsb.2020.107606 | null | q-bio.TO cond-mat.mtrl-sci | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bone becomes more fragile with ageing. Among many structural changes, a thin
layer of highly mineralized and brittle tissue covers part of the external
surface of the thin femoral neck cortex in older people and has been proposed
to increase hip fragility. However, there have been very limited reports on
this hypermi... | [
{
"created": "Thu, 17 Sep 2020 18:26:17 GMT",
"version": "v1"
}
] | 2020-09-21 | [
[
"Wang",
"Qiong",
""
],
[
"Tang",
"Tengteng",
""
],
[
"Cooper",
"David",
""
],
[
"Eltit",
"Felipe",
""
],
[
"Fratzl",
"Peter",
""
],
[
"Guy",
"Pierre",
""
],
[
"Wang",
"Rizhi",
""
]
] | Bone becomes more fragile with ageing. Among many structural changes, a thin layer of highly mineralized and brittle tissue covers part of the external surface of the thin femoral neck cortex in older people and has been proposed to increase hip fragility. However, there have been very limited reports on this hypermine... |
q-bio/0411027 | Jose Vilar | Jose M. G. Vilar and Stanislas Leibler | DNA looping and physical constraints on transcription regulation | null | J. Mol. Biol. 331, 981-989 (2003) | null | null | q-bio.SC cond-mat.soft cond-mat.stat-mech physics.bio-ph | null | DNA looping participates in transcriptional regulation, for instance, by
allowing distal binding sites to act synergistically. Here we study this
process and compare different regulatory mechanisms based on repression with
and without looping. Within a simple mathematical model for the lac operon, we
show that regula... | [
{
"created": "Thu, 11 Nov 2004 23:50:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Vilar",
"Jose M. G.",
""
],
[
"Leibler",
"Stanislas",
""
]
] | DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without looping. Within a simple mathematical model for the lac operon, we show that regulati... |
1707.09908 | Mareike Fischer | Kristina Wicke and Mareike Fischer | On the Shapley value of unrooted phylogenetic trees | null | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Shapley value, a solution concept from cooperative game theory, has
recently been considered for both unrooted and rooted phylogenetic trees. Here,
we focus on the Shapley value of unrooted trees and first revisit the so-called
split counts of a phylogenetic tree and the Shapley transformation matrix that
allows ... | [
{
"created": "Mon, 31 Jul 2017 15:04:38 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Feb 2018 21:45:33 GMT",
"version": "v2"
}
] | 2018-02-07 | [
[
"Wicke",
"Kristina",
""
],
[
"Fischer",
"Mareike",
""
]
] | The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split counts of a phylogenetic tree and the Shapley transformation matrix that allows fo... |
0908.4408 | Rui Vilela-Mendes | R. Vilela Mendes and Carlos Aguirre | Cooperation, punishment, emergence of government and the tragedy of
authorities | 13 pages, 4 figures | Complex Systems 20 (2012) 363-374 | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Under the conditions prevalent in the late Pleistocene (small hunter-gatherer
groups and frequent inter-group conflicts), coevolution of gene-related
behavior and culturally transmitted group-level institutions provides a
plausible explanation for the parochial altruistic and reciprocator traits of
most modern humans... | [
{
"created": "Sun, 30 Aug 2009 17:55:09 GMT",
"version": "v1"
}
] | 2012-11-27 | [
[
"Mendes",
"R. Vilela",
""
],
[
"Aguirre",
"Carlos",
""
]
] | Under the conditions prevalent in the late Pleistocene (small hunter-gatherer groups and frequent inter-group conflicts), coevolution of gene-related behavior and culturally transmitted group-level institutions provides a plausible explanation for the parochial altruistic and reciprocator traits of most modern humans. ... |
1505.06915 | Jean-Philippe Vert | K\'evin Vervier (CBIO), Pierre Mah\'e, Maud Tournoud, Jean-Baptiste
Veyrieras, Jean-Philippe Vert (CBIO) | Large-scale Machine Learning for Metagenomics Sequence Classification | null | null | null | null | q-bio.QM cs.CE cs.LG q-bio.GN stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metagenomics characterizes the taxonomic diversity of microbial communities
by sequencing DNA directly from an environmental sample. One of the main
challenges in metagenomics data analysis is the binning step, where each
sequenced read is assigned to a taxonomic clade. Due to the large volume of
metagenomics dataset... | [
{
"created": "Tue, 26 May 2015 12:02:04 GMT",
"version": "v1"
}
] | 2015-05-27 | [
[
"Vervier",
"Kévin",
"",
"CBIO"
],
[
"Mahé",
"Pierre",
"",
"CBIO"
],
[
"Tournoud",
"Maud",
"",
"CBIO"
],
[
"Veyrieras",
"Jean-Baptiste",
"",
"CBIO"
],
[
"Vert",
"Jean-Philippe",
"",
"CBIO"
]
] | Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,... |
2006.00652 | Areejit Samal | R.P. Vivek-Ananth, Abhijit Rana, Nithin Rajan, Himansu S. Biswal,
Areejit Samal | In silico identification of potential natural product inhibitors of
human proteases key to SARS-CoV-2 infection | 51 pages, 7 Figures, 2 Tables, 4 SI Figures, SI Tables available upon
request from authors | Molecules 2020, 25(17), 3822 | 10.3390/molecules25173822 | null | q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Presently, there are no approved drugs or vaccines to treat COVID-19 which
has spread to over 200 countries and is responsible for over 3,65,000 deaths
worldwide. Recent studies have shown that two human proteases, TMPRSS2 and
cathepsin L, play a key role in host cell entry of SARS-CoV-2. Importantly,
inhibitors of t... | [
{
"created": "Mon, 1 Jun 2020 00:37:13 GMT",
"version": "v1"
}
] | 2020-09-02 | [
[
"Vivek-Ananth",
"R. P.",
""
],
[
"Rana",
"Abhijit",
""
],
[
"Rajan",
"Nithin",
""
],
[
"Biswal",
"Himansu S.",
""
],
[
"Samal",
"Areejit",
""
]
] | Presently, there are no approved drugs or vaccines to treat COVID-19 which has spread to over 200 countries and is responsible for over 3,65,000 deaths worldwide. Recent studies have shown that two human proteases, TMPRSS2 and cathepsin L, play a key role in host cell entry of SARS-CoV-2. Importantly, inhibitors of the... |
2111.08436 | Gholamreza Jafari | Nastaran Allahyari, Amir Kargaran, Ali Hosseiny, G. R. Jafari | The structure of gene-gene networks beyond pairwise interactions | 16 pages, 5 figures, 4 tables | null | 10.1371/journal.pone.0258596 | null | q-bio.MN physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite its high and direct impact on nearly all biological processes, the
underlying structure of gene-gene interaction networks is investigated so far
according to pair connections. To address this, we explore the gene interaction
networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction
using the ... | [
{
"created": "Thu, 14 Oct 2021 14:51:09 GMT",
"version": "v1"
}
] | 2022-05-04 | [
[
"Allahyari",
"Nastaran",
""
],
[
"Kargaran",
"Amir",
""
],
[
"Hosseiny",
"Ali",
""
],
[
"Jafari",
"G. R.",
""
]
] | Despite its high and direct impact on nearly all biological processes, the underlying structure of gene-gene interaction networks is investigated so far according to pair connections. To address this, we explore the gene interaction networks of the yeast Saccharomyces cerevisiae beyond pairwise interaction using the st... |
0809.1479 | Jeferson J. Arenzon | Estrella A. Sicardi, Hugo Fort, Mendeli H. Vainstein, Jeferson J.
Arenzon | Random mobility and spatial structure often enhance cooperation | Submitted to J. Theor. Biol | J. Theor. Biol. 256 (2009) 240 | 10.1016/j.jtbi.2008.09.022 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The effects of an unconditional move rule in the spatial Prisoner's Dilemma,
Snowdrift and Stag Hunt games are studied. Spatial structure by itself is known
to modify the outcome of many games when compared with a randomly mixed
population, sometimes promoting, sometimes inhibiting cooperation. Here we show
that rand... | [
{
"created": "Tue, 9 Sep 2008 12:53:37 GMT",
"version": "v1"
}
] | 2009-02-25 | [
[
"Sicardi",
"Estrella A.",
""
],
[
"Fort",
"Hugo",
""
],
[
"Vainstein",
"Mendeli H.",
""
],
[
"Arenzon",
"Jeferson J.",
""
]
] | The effects of an unconditional move rule in the spatial Prisoner's Dilemma, Snowdrift and Stag Hunt games are studied. Spatial structure by itself is known to modify the outcome of many games when compared with a randomly mixed population, sometimes promoting, sometimes inhibiting cooperation. Here we show that random... |
2006.01171 | Austin Clyde | Austin Clyde, Xiaotian Duan, Rick Stevens | Regression Enrichment Surfaces: a Simple Analysis Technique for Virtual
Drug Screening Models | null | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a new method for understanding the performance of a model in
virtual drug screening tasks. While most virtual screening problems present as
a mix between ranking and classification, the models are typically trained as
regression models presenting a problem requiring either a choice of a cutoff or
ranking m... | [
{
"created": "Mon, 1 Jun 2020 18:03:25 GMT",
"version": "v1"
}
] | 2020-06-03 | [
[
"Clyde",
"Austin",
""
],
[
"Duan",
"Xiaotian",
""
],
[
"Stevens",
"Rick",
""
]
] | We present a new method for understanding the performance of a model in virtual drug screening tasks. While most virtual screening problems present as a mix between ranking and classification, the models are typically trained as regression models presenting a problem requiring either a choice of a cutoff or ranking mea... |
2403.16933 | Paul Haider | Benjamin Ellenberger, Paul Haider, Jakob Jordan, Kevin Max, Ismael
Jaras, Laura Kriener, Federico Benitez, Mihai A. Petrovici | Backpropagation through space, time, and the brain | First authorship shared by Benjamin Ellenberger and Paul Haider | null | null | null | q-bio.NC cs.AI cs.LG cs.NE eess.SP | http://creativecommons.org/licenses/by-nc-sa/4.0/ | How physical networks of neurons, bound by spatio-temporal locality
constraints, can perform efficient credit assignment, remains, to a large
extent, an open question. In machine learning, the answer is almost universally
given by the error backpropagation algorithm, through both space and time.
However, this algorit... | [
{
"created": "Mon, 25 Mar 2024 16:57:02 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Jul 2024 17:37:05 GMT",
"version": "v2"
}
] | 2024-07-17 | [
[
"Ellenberger",
"Benjamin",
""
],
[
"Haider",
"Paul",
""
],
[
"Jordan",
"Jakob",
""
],
[
"Max",
"Kevin",
""
],
[
"Jaras",
"Ismael",
""
],
[
"Kriener",
"Laura",
""
],
[
"Benitez",
"Federico",
""
],
[
... | How physical networks of neurons, bound by spatio-temporal locality constraints, can perform efficient credit assignment, remains, to a large extent, an open question. In machine learning, the answer is almost universally given by the error backpropagation algorithm, through both space and time. However, this algorithm... |
1902.06122 | Daniel Baker | Daniel H. Baker, Greta Vilidaite, Freya A. Lygo, Anika K. Smith, Tessa
R. Flack, Andre D. Gouws and Timothy J. Andrews | Power contours: optimising sample size and precision in experimental
psychology and human neuroscience | null | Psychological Methods (2021), 26(3): 295-314 | 10.1037/met0000337 | null | q-bio.NC stat.ME | http://creativecommons.org/licenses/by/4.0/ | When designing experimental studies with human participants, experimenters
must decide how many trials each participant will complete, as well as how many
participants to test. Most discussion of statistical power (the ability of a
study design to detect an effect) has focussed on sample size, and assumed
sufficient ... | [
{
"created": "Sat, 16 Feb 2019 16:30:59 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Feb 2019 06:43:51 GMT",
"version": "v2"
},
{
"created": "Wed, 3 Jul 2019 15:24:19 GMT",
"version": "v3"
},
{
"created": "Sat, 2 Nov 2019 10:02:27 GMT",
"version": "v4"
},
{
"cre... | 2021-08-30 | [
[
"Baker",
"Daniel H.",
""
],
[
"Vilidaite",
"Greta",
""
],
[
"Lygo",
"Freya A.",
""
],
[
"Smith",
"Anika K.",
""
],
[
"Flack",
"Tessa R.",
""
],
[
"Gouws",
"Andre D.",
""
],
[
"Andrews",
"Timothy J.",
""
]... | When designing experimental studies with human participants, experimenters must decide how many trials each participant will complete, as well as how many participants to test. Most discussion of statistical power (the ability of a study design to detect an effect) has focussed on sample size, and assumed sufficient tr... |
2208.11233 | Carlos Hernandez-Suarez M | Carlos Hernandez-Suarez and Osval Montesinos Lopez | Revised calculation of the coefficient of parentage in plant breeding | The pdf version is 23 pages long, with 6 figures and 5 tables | Plant breeding, 2022 | 10.1111/pbr.13071 | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The Coefficient of Parentage (COP) between two individuals is the expected
inbreeding of their offspring. Originally exploited by animal breeders, is now
a routine calculation among plant breeders as part of crop improvement
programs. Here we show that the COP between strains requires a different
calculation than the... | [
{
"created": "Tue, 23 Aug 2022 23:42:19 GMT",
"version": "v1"
}
] | 2022-12-01 | [
[
"Hernandez-Suarez",
"Carlos",
""
],
[
"Lopez",
"Osval Montesinos",
""
]
] | The Coefficient of Parentage (COP) between two individuals is the expected inbreeding of their offspring. Originally exploited by animal breeders, is now a routine calculation among plant breeders as part of crop improvement programs. Here we show that the COP between strains requires a different calculation than the u... |
q-bio/0702005 | Mikl\'os Cs\H{u}r\"os | Mikl\'os Cs\H{u}r\"os, J. Andrew Holey, Igor B. Rogozin | In search of lost introns | null | null | null | null | q-bio.PE q-bio.GN | null | Many fundamental questions concerning the emergence and subsequent evolution
of eukaryotic exon-intron organization are still unsettled. Genome-scale
comparative studies, which can shed light on crucial aspects of eukaryotic
evolution, require adequate computational tools.
We describe novel computational methods fo... | [
{
"created": "Sat, 3 Feb 2007 21:26:02 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Csűrös",
"Miklós",
""
],
[
"Holey",
"J. Andrew",
""
],
[
"Rogozin",
"Igor B.",
""
]
] | Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools. We describe novel computational methods for st... |
2210.13323 | Samuel W.K. Wong | Yuxuan Zhao, Samuel W.K. Wong | A Comparative Study of Compartmental Models for COVID-19 Transmission in
Ontario, Canada | 26 pages, 8 figures | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The number of confirmed COVID-19 cases reached over 1.3 million in Ontario,
Canada by June 4, 2022. The continued spread of the virus underlying COVID-19
has been spurred by the emergence of variants since the initial outbreak in
December, 2019. Much attention has thus been devoted to tracking and modelling
the trans... | [
{
"created": "Mon, 24 Oct 2022 15:24:54 GMT",
"version": "v1"
}
] | 2022-10-25 | [
[
"Zhao",
"Yuxuan",
""
],
[
"Wong",
"Samuel W. K.",
""
]
] | The number of confirmed COVID-19 cases reached over 1.3 million in Ontario, Canada by June 4, 2022. The continued spread of the virus underlying COVID-19 has been spurred by the emergence of variants since the initial outbreak in December, 2019. Much attention has thus been devoted to tracking and modelling the transmi... |
1605.00748 | Hemachander Subramanian | Hemachander Subramanian, Robert A. Gatenby | Evolutionary advantage of a broken symmetry in autocatalytic polymers
explains fundamental properties of DNA | 41 pages, 7 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The macromolecules that encode and translate information in living systems,
DNA and RNA, exhibit distinctive structural asymmetries, including
homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are
invariant across all life forms. The evolutionary advantages of these broken
symmetries remain u... | [
{
"created": "Tue, 3 May 2016 03:34:36 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Oct 2016 16:41:17 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Mar 2017 03:27:46 GMT",
"version": "v3"
}
] | 2017-03-10 | [
[
"Subramanian",
"Hemachander",
""
],
[
"Gatenby",
"Robert A.",
""
]
] | The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and $3' - 5'$ directionality, that are invariant across all life forms. The evolutionary advantages of these broken symmetries remain unk... |
0705.2092 | Erik Volz | Erik Volz | SIR dynamics in random networks with heterogeneous connectivity | 25 pages, 6 figures. Greatly revised version of arXiv:physics/0508160 | null | null | null | q-bio.PE q-bio.QM | null | Random networks with specified degree distributions have been proposed as
realistic models of population structure, yet the problem of dynamically
modeling SIR-type epidemics in random networks remains complex. I resolve this
dilemma by showing how the SIR dynamics can be modeled with a system of three
nonlinear ODE'... | [
{
"created": "Tue, 15 May 2007 08:16:56 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Volz",
"Erik",
""
]
] | Random networks with specified degree distributions have been proposed as realistic models of population structure, yet the problem of dynamically modeling SIR-type epidemics in random networks remains complex. I resolve this dilemma by showing how the SIR dynamics can be modeled with a system of three nonlinear ODE's.... |
1005.4301 | Amit Lakhanpal | Amit Lakhanpal, David Sprinzak, Michael B. Elowitz | Mutual inactivation of Notch and Delta permits a simple mechanism for
lateral inhibition patterning | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lateral inhibition patterns mediated by the Notch-Delta signaling system
occur in diverse developmental contexts. These systems are based on an
intercellular feedback loop in which Notch activation leads to down-regulation
of Delta. However, even in relatively well-characterized systems, the pathway
leading from Notc... | [
{
"created": "Mon, 24 May 2010 10:40:38 GMT",
"version": "v1"
}
] | 2010-05-25 | [
[
"Lakhanpal",
"Amit",
""
],
[
"Sprinzak",
"David",
""
],
[
"Elowitz",
"Michael B.",
""
]
] | Lateral inhibition patterns mediated by the Notch-Delta signaling system occur in diverse developmental contexts. These systems are based on an intercellular feedback loop in which Notch activation leads to down-regulation of Delta. However, even in relatively well-characterized systems, the pathway leading from Notch ... |
q-bio/0601021 | Le Zhang | Thomas S. Deisboeck, Caterina Guiot, Pier Paolo Delsanto, Nicola Pugno | Does Cancer Growth Depend on Surface Extension? | 11 pages, 1 figure | null | null | null | q-bio.TO | null | We argue that volumetric growth dynamics of a solid cancer depend on the
tumor system's overall surface extension. While this at first may seem evident,
to our knowledge, so far no theoretical argument has been presented explaining
this relationship explicitly. In here, we therefore develop a conceptual
framework bas... | [
{
"created": "Sat, 14 Jan 2006 16:28:51 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Deisboeck",
"Thomas S.",
""
],
[
"Guiot",
"Caterina",
""
],
[
"Delsanto",
"Pier Paolo",
""
],
[
"Pugno",
"Nicola",
""
]
] | We argue that volumetric growth dynamics of a solid cancer depend on the tumor system's overall surface extension. While this at first may seem evident, to our knowledge, so far no theoretical argument has been presented explaining this relationship explicitly. In here, we therefore develop a conceptual framework based... |
1906.04590 | Gerardo Chowell | G. Chowell, A. Tariq, M. Kiskowski | Vaccination strategies to control Ebola epidemics in the context of
variable household inaccessibility levels | 36 pages; 9 figures | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | In the context of the ongoing Ebola epidemic in DRC, active conflict and
community distrust are undermining control efforts, including vaccination
strategies. In this paper, we employed an individual-level stochastic
structured transmission model to assess the impact of vaccination strategies on
epidemic control in t... | [
{
"created": "Tue, 11 Jun 2019 13:42:32 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jun 2019 18:46:16 GMT",
"version": "v2"
},
{
"created": "Thu, 22 Aug 2019 23:35:33 GMT",
"version": "v3"
}
] | 2019-08-26 | [
[
"Chowell",
"G.",
""
],
[
"Tariq",
"A.",
""
],
[
"Kiskowski",
"M.",
""
]
] | In the context of the ongoing Ebola epidemic in DRC, active conflict and community distrust are undermining control efforts, including vaccination strategies. In this paper, we employed an individual-level stochastic structured transmission model to assess the impact of vaccination strategies on epidemic control in the... |
1204.6231 | Carl Boettiger | Carl Boettiger and Alan Hastings | Quantifying Limits to Detection of Early Warning for Critical
Transitions | Accepted to Journal of the Royal Society Interface. 29 pages, 8
figures | null | null | null | q-bio.OT physics.data-an q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | Catastrophic regime shifts in complex natural systems may be averted through
advanced detection. Recent work has provided a proof-of-principle that many
systems approaching a catastrophic transition may be identified through the
lens of early warning indicators such as rising variance or increased return
times. Despi... | [
{
"created": "Thu, 26 Apr 2012 19:22:31 GMT",
"version": "v1"
}
] | 2012-04-30 | [
[
"Boettiger",
"Carl",
""
],
[
"Hastings",
"Alan",
""
]
] | Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite... |
1311.2789 | Stian Soiland-Reyes | Kristina M. Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft,
Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don
Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure, Oscar
Corcho, Graham Klyne, Reinout van Schouwen, Peter A. C. 't Hoen, Sean
Bechhofer, Carole Goble... | Structuring research methods and data with the Research Object model:
genomics workflows as a case study | 35 pages, 10 figures, 1 table. Submitted to Journal of Biomedical
Semantics on 2013-05-13, resubmitted after reviews 2013-11-09, 2014-06-27.
Accepted in principle 2014-07-29. Published: 2014-09-18
http://www.jbiomedsem.com/content/5/1/41. Research Object homepage:
http://www.researchobject.org/ | null | 10.1186/2041-1480-5-41 | uk-ac-man-scw:212837 | q-bio.GN cs.DL | http://creativecommons.org/licenses/by/3.0/ | One of the main challenges for biomedical research lies in the
computer-assisted integrative study of large and increasingly complex
combinations of data in order to understand molecular mechanisms. The
preservation of the materials and methods of such computational experiments
with clear annotations is essential for... | [
{
"created": "Tue, 12 Nov 2013 14:23:33 GMT",
"version": "v1"
},
{
"created": "Mon, 18 Aug 2014 13:28:07 GMT",
"version": "v2"
},
{
"created": "Fri, 19 Sep 2014 10:37:56 GMT",
"version": "v3"
}
] | 2014-09-22 | [
[
"Hettne",
"Kristina M.",
""
],
[
"Dharuri",
"Harish",
""
],
[
"Zhao",
"Jun",
""
],
[
"Wolstencroft",
"Katherine",
""
],
[
"Belhajjame",
"Khalid",
""
],
[
"Soiland-Reyes",
"Stian",
""
],
[
"Mina",
"Eleni",
"... | One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for u... |
1508.02408 | Michael Margaliot | Alon Raveh and Michael Margaliot and Eduardo D. Sontag and Tamir
Tuller | A Model for Competition for Ribosomes in the Cell | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Large-scale simultaneous mRNA translation and the resulting competition for
the available ribosomes has important implications to the cell's functioning
and evolution. Developing a better understanding of the intricate correlations
between these simultaneous processes, rather than focusing on the translation
of a sin... | [
{
"created": "Mon, 10 Aug 2015 20:11:06 GMT",
"version": "v1"
}
] | 2015-08-12 | [
[
"Raveh",
"Alon",
""
],
[
"Margaliot",
"Michael",
""
],
[
"Sontag",
"Eduardo D.",
""
],
[
"Tuller",
"Tamir",
""
]
] | Large-scale simultaneous mRNA translation and the resulting competition for the available ribosomes has important implications to the cell's functioning and evolution. Developing a better understanding of the intricate correlations between these simultaneous processes, rather than focusing on the translation of a singl... |
2104.13146 | Zheng Zhao | Zheng Zhao and Philip E. Bourne | Using the structural kinome to systematize kinase drug discovery | 22 pages, 2 figures, 3 tables | null | null | null | q-bio.BM q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Kinase-targeted drug design is challenging. It requires designing inhibitors
that can bind to specific kinases when all kinase catalytic domains share a
common folding scaffold that binds ATP. Thus, obtaining the desired
selectivity, given the whole human kinome, is a fundamental task during
early-stage drug discover... | [
{
"created": "Tue, 27 Apr 2021 12:47:33 GMT",
"version": "v1"
}
] | 2021-04-28 | [
[
"Zhao",
"Zheng",
""
],
[
"Bourne",
"Philip E.",
""
]
] | Kinase-targeted drug design is challenging. It requires designing inhibitors that can bind to specific kinases when all kinase catalytic domains share a common folding scaffold that binds ATP. Thus, obtaining the desired selectivity, given the whole human kinome, is a fundamental task during early-stage drug discovery.... |
q-bio/0403032 | Tzipe Govezensky | Jose A Garcia, Samantha Alvarez, Alejandro Flores, Tzipe Govezensky,
Juan R. Bobadilla, Marco V. Jose | Statistical analysis of the distribution of amino acids in Borrelia
burgdorferi genome under different genetic codes | 7 pages,1 figure | null | 10.1016/j.physa.2004.04.090 | null | q-bio.GN | null | The genetic code is considered to be universal. In order to test if some
statistical properties of the coding bacterial genome were due to inherent
properties of the genetic code, we compared the autocorrelation function, the
scaling properties and the maximum entropy of the distribution of distances of
amino acids i... | [
{
"created": "Mon, 22 Mar 2004 22:52:01 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Garcia",
"Jose A",
""
],
[
"Alvarez",
"Samantha",
""
],
[
"Flores",
"Alejandro",
""
],
[
"Govezensky",
"Tzipe",
""
],
[
"Bobadilla",
"Juan R.",
""
],
[
"Jose",
"Marco V.",
""
]
] | The genetic code is considered to be universal. In order to test if some statistical properties of the coding bacterial genome were due to inherent properties of the genetic code, we compared the autocorrelation function, the scaling properties and the maximum entropy of the distribution of distances of amino acids in ... |
1812.06186 | Felix Meister | Felix Meister, Tiziano Passerini, Viorel Mihalef, Ahmet Tuysuzoglu,
Andreas Maier and Tommaso Mansi | Towards Fast Biomechanical Modeling of Soft Tissue Using Neural Networks | Accepted in Medical Imaging meets NeurIPS Workshop, NeurIPS 2018 | null | null | null | q-bio.QM physics.med-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To date, the simulation of organ deformations for applications like therapy
planning or image-guided interventions is calculated by solving the
elastodynamics equations. While efficient solvers have been proposed for fast
simulations, methods that are both real-time and accurate are still an open
challenge. An ideal,... | [
{
"created": "Thu, 13 Dec 2018 18:57:53 GMT",
"version": "v1"
}
] | 2018-12-18 | [
[
"Meister",
"Felix",
""
],
[
"Passerini",
"Tiziano",
""
],
[
"Mihalef",
"Viorel",
""
],
[
"Tuysuzoglu",
"Ahmet",
""
],
[
"Maier",
"Andreas",
""
],
[
"Mansi",
"Tommaso",
""
]
] | To date, the simulation of organ deformations for applications like therapy planning or image-guided interventions is calculated by solving the elastodynamics equations. While efficient solvers have been proposed for fast simulations, methods that are both real-time and accurate are still an open challenge. An ideal, i... |
1511.03963 | Alexandre Ferreira Ramos | Guilherme N. Prata, Jos\'e Eduardo M. Hornos, Alexandre F. Ramos | A stochastic model for gene transcription on Drosophila melanogaster
embryos | 27 pages, 6 figures in Phys. Rev. E 2015 | Phys. Rev. E 93, 022403 (2016) | 10.1103/PhysRevE.93.022403 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We examine immunostaining experimental data for the formation of the strip 2
of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An
estimate of the factor converting immunofluorescence intensity units into
molecular numbers is given. The analysis of the $eve$ mRNA's dynamics at the
region of the str... | [
{
"created": "Thu, 12 Nov 2015 16:55:53 GMT",
"version": "v1"
}
] | 2016-02-10 | [
[
"Prata",
"Guilherme N.",
""
],
[
"Hornos",
"José Eduardo M.",
""
],
[
"Ramos",
"Alexandre F.",
""
]
] | We examine immunostaining experimental data for the formation of the strip 2 of $even-skipped$ ($eve$) transcripts on $D.$ $melanogaster$ embryos. An estimate of the factor converting immunofluorescence intensity units into molecular numbers is given. The analysis of the $eve$ mRNA's dynamics at the region of the strip... |
1610.04962 | Omid Sadat Rezai | Omid Rezai, Pinar Boyraz Jentsch, Bryan Tripp | A Rich Source of Labels for Deep Network Models of the Primate Dorsal
Visual Stream | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deep convolutional neural networks (CNNs) have structures that are loosely
related to that of the primate visual cortex. Surprisingly, when these networks
are trained for object classification, the activity of their early,
intermediate, and later layers becomes closely related to activity patterns in
corresponding pa... | [
{
"created": "Mon, 17 Oct 2016 03:16:58 GMT",
"version": "v1"
}
] | 2016-10-18 | [
[
"Rezai",
"Omid",
""
],
[
"Jentsch",
"Pinar Boyraz",
""
],
[
"Tripp",
"Bryan",
""
]
] | Deep convolutional neural networks (CNNs) have structures that are loosely related to that of the primate visual cortex. Surprisingly, when these networks are trained for object classification, the activity of their early, intermediate, and later layers becomes closely related to activity patterns in corresponding part... |
0905.4092 | Pankaj Mehta | Pankaj Mehta, Sidhartha Goyal, Tao Long, Bonnie Bassler, Ned S.
Wingreen | Information processing and signal integration in bacterial quorum
sensing | Supporting information is in appendix | null | null | null | q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacteria communicate using secreted chemical signaling molecules called
autoinducers in a process known as quorum sensing. The quorum-sensing network
of the marine bacterium {\it Vibrio harveyi} employs three autoinducers, each
known to encode distinct ecological information. Yet how cells integrate and
interpret the... | [
{
"created": "Mon, 25 May 2009 22:50:20 GMT",
"version": "v1"
}
] | 2009-05-27 | [
[
"Mehta",
"Pankaj",
""
],
[
"Goyal",
"Sidhartha",
""
],
[
"Long",
"Tao",
""
],
[
"Bassler",
"Bonnie",
""
],
[
"Wingreen",
"Ned S.",
""
]
] | Bacteria communicate using secreted chemical signaling molecules called autoinducers in a process known as quorum sensing. The quorum-sensing network of the marine bacterium {\it Vibrio harveyi} employs three autoinducers, each known to encode distinct ecological information. Yet how cells integrate and interpret the i... |
2209.09971 | Luciano Stucchi | Luciano Stucchi, Javier Galeano, Juan Manuel Pastor, Jos\'e Mar\'ia
Iriondo, Jos\'e A. Cuesta | Prevalence of mutualism in a simple model of microbial co-evolution | 13 pages, 11 figures, 2 tables, includes Supplementary Material | Physical Review E 106, 054401 (2022) | 10.1103/PhysRevE.106.054401 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Evolutionary transitions among ecological interactions are widely known,
although their detailed dynamics remain absent for most population models.
Adaptive dynamics has been used to illustrate how the parameters of population
models might shift through evolution, but within an ecological regime. Here we
use adaptive... | [
{
"created": "Tue, 20 Sep 2022 20:00:34 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Sep 2022 04:41:55 GMT",
"version": "v2"
}
] | 2022-11-14 | [
[
"Stucchi",
"Luciano",
""
],
[
"Galeano",
"Javier",
""
],
[
"Pastor",
"Juan Manuel",
""
],
[
"Iriondo",
"José María",
""
],
[
"Cuesta",
"José A.",
""
]
] | Evolutionary transitions among ecological interactions are widely known, although their detailed dynamics remain absent for most population models. Adaptive dynamics has been used to illustrate how the parameters of population models might shift through evolution, but within an ecological regime. Here we use adaptive d... |
q-bio/0410028 | Binder Hans | Hans Binder and Stephan Preibisch | Specific and non specific hybridization of oligonucleotide probes on
microarrays | null | null | 10.1529/biophysj.104.055343 | null | q-bio.BM | null | Gene expression analysis by means of microarrays is based on the sequence
specific binding of mRNA to DNA oligonucleotide probes and its measurement
using fluorescent labels. The binding of RNA fragments involving other
sequences than the intended target is problematic because it adds a "chemical
background" to the s... | [
{
"created": "Mon, 25 Oct 2004 09:15:36 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Apr 2005 15:57:06 GMT",
"version": "v2"
}
] | 2009-11-10 | [
[
"Binder",
"Hans",
""
],
[
"Preibisch",
"Stephan",
""
]
] | Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the intended target is problematic because it adds a "chemical background" to the sig... |
1703.05428 | Yu Takagi | Yu Takagi, Yuki Sakai, Giuseppe Lisi, Noriaki Yahata, Yoshinari Abe,
Seiji Nishida, Takashi Nakamae, Jun Morimoto, Mitsuo Kawato, Jin Narumoto and
Saori C. Tanaka | A neural marker of obsessive-compulsive disorder from whole-brain
functional connectivity | 47 pages, 3 figures | Sci Rep. 2017 Aug 8;7(1):7538 | 10.1038/s41598-017-07792-7 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Obsessive-compulsive disorder (OCD) is a common psychiatric disorder with a
lifetime prevalence of 2-3 percent. Recently, brain activity in the resting
state is gathering attention as a new means of exploring altered functional
connectivity in psychiatric disorders. Although previous resting-state
functional magnetic... | [
{
"created": "Wed, 15 Mar 2017 23:54:37 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Sep 2017 16:53:09 GMT",
"version": "v2"
}
] | 2017-09-07 | [
[
"Takagi",
"Yu",
""
],
[
"Sakai",
"Yuki",
""
],
[
"Lisi",
"Giuseppe",
""
],
[
"Yahata",
"Noriaki",
""
],
[
"Abe",
"Yoshinari",
""
],
[
"Nishida",
"Seiji",
""
],
[
"Nakamae",
"Takashi",
""
],
[
"Morim... | Obsessive-compulsive disorder (OCD) is a common psychiatric disorder with a lifetime prevalence of 2-3 percent. Recently, brain activity in the resting state is gathering attention as a new means of exploring altered functional connectivity in psychiatric disorders. Although previous resting-state functional magnetic r... |
2302.12381 | Md Nurul Anwar | Md Nurul Anwar, Roslyn I. Hickson, Somya Mehra, David J. Price, James
M. McCaw, Mark B. Flegg, and Jennifer A. Flegg | Optimal interruption of P. vivax malaria transmission using mass drug
administration | 39 pages, 14 figures | null | 10.1007/s11538-023-01153-4 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | \textit{Plasmodium vivax} is the most geographically widespread
malaria-causing parasite resulting in significant associated global morbidity
and mortality. One of the factors driving this widespread phenomenon is the
ability of the parasites to remain dormant in the liver. Known as hypnozoites,
they reside in the li... | [
{
"created": "Fri, 24 Feb 2023 00:59:14 GMT",
"version": "v1"
}
] | 2023-09-18 | [
[
"Anwar",
"Md Nurul",
""
],
[
"Hickson",
"Roslyn I.",
""
],
[
"Mehra",
"Somya",
""
],
[
"Price",
"David J.",
""
],
[
"McCaw",
"James M.",
""
],
[
"Flegg",
"Mark B.",
""
],
[
"Flegg",
"Jennifer A.",
""
]
] | \textit{Plasmodium vivax} is the most geographically widespread malaria-causing parasite resulting in significant associated global morbidity and mortality. One of the factors driving this widespread phenomenon is the ability of the parasites to remain dormant in the liver. Known as hypnozoites, they reside in the live... |
2007.13028 | Aubain Nzokem PhD | Aubain Nzokem and Neal Madras | epidemic dynamics and adaptive vaccination strategy: renewal equation
approach | null | Bull Math Biol 82, 122 (2020) | 10.1007/s11538-020-00802-2 | null | q-bio.PE math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use analytical methods to investigate a continuous vaccination strategy
effects on the infectious disease dynamics in a closed population and a
demographically open population. The methodology and key assumptions are based
on Breda et al (2012). We show that the cumulative force of infection for the
closed populat... | [
{
"created": "Sat, 25 Jul 2020 22:56:42 GMT",
"version": "v1"
}
] | 2020-09-24 | [
[
"Nzokem",
"Aubain",
""
],
[
"Madras",
"Neal",
""
]
] | We use analytical methods to investigate a continuous vaccination strategy effects on the infectious disease dynamics in a closed population and a demographically open population. The methodology and key assumptions are based on Breda et al (2012). We show that the cumulative force of infection for the closed populatio... |
1005.3244 | Valmir Barbosa | Valmir C. Barbosa, Raul Donangelo, Sergio R. Souza | Early appraisal of the fixation probability in directed networks | null | Physical Review E 82 (2010), 046114 | 10.1103/PhysRevE.82.046114 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In evolutionary dynamics, the probability that a mutation spreads through the
whole population, having arisen in a single individual, is known as the
fixation probability. In general, it is not possible to find the fixation
probability analytically given the mutant's fitness and the topological
constraints that gover... | [
{
"created": "Tue, 18 May 2010 16:20:30 GMT",
"version": "v1"
}
] | 2010-10-26 | [
[
"Barbosa",
"Valmir C.",
""
],
[
"Donangelo",
"Raul",
""
],
[
"Souza",
"Sergio R.",
""
]
] | In evolutionary dynamics, the probability that a mutation spreads through the whole population, having arisen in a single individual, is known as the fixation probability. In general, it is not possible to find the fixation probability analytically given the mutant's fitness and the topological constraints that govern ... |
0710.3784 | Carlos Gershenson | Carlos Gershenson and Tom Lenaerts | Evolution of Complexity | Introduction to Special Issue | Artificial Life 14(3): 241-243. 2008 | 10.1162/artl.2008.14.3.14300 | null | q-bio.PE | null | The evolution of complexity has been a central theme for Biology [2] and
Artificial Life research [1]. It is generally agreed that complexity has
increased in our universe, giving way to life, multi-cellularity, societies,
and systems of higher complexities. However, the mechanisms behind the
complexification and its... | [
{
"created": "Fri, 19 Oct 2007 20:46:09 GMT",
"version": "v1"
}
] | 2011-09-06 | [
[
"Gershenson",
"Carlos",
""
],
[
"Lenaerts",
"Tom",
""
]
] | The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of higher complexities. However, the mechanisms behind the complexification and its r... |
2306.03162 | A. David Redish | Ugurcan Mugan, Seiichiro Amemiya, Paul S. Regier, A. David Redish | Navigation through the complex world -- the neurophysiology of
decision-making processes | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Current theories suggest that adaptive decision-making necessitates the
interaction between multiple decision-making systems. The computational
definitions of different models of decision-making suggest interactions with
task demands and complexity. We review these computational theories and derive
experimental predi... | [
{
"created": "Mon, 5 Jun 2023 18:16:49 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Jul 2023 13:38:16 GMT",
"version": "v2"
}
] | 2023-07-28 | [
[
"Mugan",
"Ugurcan",
""
],
[
"Amemiya",
"Seiichiro",
""
],
[
"Regier",
"Paul S.",
""
],
[
"Redish",
"A. David",
""
]
] | Current theories suggest that adaptive decision-making necessitates the interaction between multiple decision-making systems. The computational definitions of different models of decision-making suggest interactions with task demands and complexity. We review these computational theories and derive experimental predict... |
2212.06995 | Maximilian Nguyen | Sinan A. Ozbay, Bjarke F. Nielsen, Maximilian M. Nguyen | Bifurcations in the Herd Immunity Threshold for Discrete-Time Models of
Epidemic Spread | null | null | null | null | q-bio.PE cs.SI physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We performed a thorough sensitivity analysis of the herd immunity threshold
for discrete-time SIR compartmental models with a static network structure. We
find unexpectedly that these models violate classical intuition which holds
that the herd immunity threshold should monotonically increase with the
transmission pa... | [
{
"created": "Wed, 14 Dec 2022 03:04:46 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Dec 2022 00:25:35 GMT",
"version": "v2"
},
{
"created": "Fri, 24 Feb 2023 15:47:21 GMT",
"version": "v3"
}
] | 2023-02-27 | [
[
"Ozbay",
"Sinan A.",
""
],
[
"Nielsen",
"Bjarke F.",
""
],
[
"Nguyen",
"Maximilian M.",
""
]
] | We performed a thorough sensitivity analysis of the herd immunity threshold for discrete-time SIR compartmental models with a static network structure. We find unexpectedly that these models violate classical intuition which holds that the herd immunity threshold should monotonically increase with the transmission para... |
1009.3697 | Changbong Hyeon | Changbong Hyeon | Exploring the energy landscape of biopolymers using single molecule
force spectroscopy and molecular simulations | 32 pages, 4 figures, Book Chapter in "Simulations in
Nanobiotechnology" | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, single molecule force techniques have opened a new avenue to
decipher the folding landscapes of biopolymers by allowing us to watch and
manipulate the dynamics of individual proteins and nucleic acids. In single
molecule force experiments, quantitative analyses of measurements employing
sound theoret... | [
{
"created": "Mon, 20 Sep 2010 05:50:06 GMT",
"version": "v1"
}
] | 2016-11-25 | [
[
"Hyeon",
"Changbong",
""
]
] | In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretic... |
0904.1637 | Timothy Saunders | Timothy E Saunders and Martin Howard | Morphogen Profiles Can Be Optimised to Buffer Against Noise | 5 pages, 3 figures | Physical Review E: 80, 041902 (October 2009) | 10.1103/PhysRevE.80.041902 | null | q-bio.MN cond-mat.soft cond-mat.stat-mech physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Morphogen profiles play a vital role in biology by specifying position in
embryonic development. However, the factors that influence the shape of a
morphogen profile remain poorly understood. Since morphogens should provide
precise positional information, one significant factor is the robustness of the
profile to noi... | [
{
"created": "Fri, 10 Apr 2009 13:26:56 GMT",
"version": "v1"
}
] | 2009-11-27 | [
[
"Saunders",
"Timothy E",
""
],
[
"Howard",
"Martin",
""
]
] | Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise positional information, one significant factor is the robustness of the profile to noise... |
2001.11589 | Gurcan Comert | Nurullah Arslan, Kazim Besirli, Gurcan Comert, Omer F Beyca | Computational Fluid Dynamic Simulations In a Model of a Carotid
Bifurcation Under Steady Flow Conditions | 4 Pages, 7 figures, 4th International Advanced Technologies Symposium
September 28 30, 2005, Konya, Turkey | null | null | null | q-bio.TO physics.flu-dyn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Strokes are still one of the leading causes for death after heart diseases
and cancer in all over the world. Most strokes happen because an artery that
carries blood uphill from the heart to the head gets clogged. Most of the time,
as with heart attacks, the problem is atherosclerosis, hardening of the
arteries, calc... | [
{
"created": "Thu, 16 Jan 2020 15:00:06 GMT",
"version": "v1"
}
] | 2020-02-03 | [
[
"Arslan",
"Nurullah",
""
],
[
"Besirli",
"Kazim",
""
],
[
"Comert",
"Gurcan",
""
],
[
"Beyca",
"Omer F",
""
]
] | Strokes are still one of the leading causes for death after heart diseases and cancer in all over the world. Most strokes happen because an artery that carries blood uphill from the heart to the head gets clogged. Most of the time, as with heart attacks, the problem is atherosclerosis, hardening of the arteries, calcif... |
2311.13000 | Reza Bozorgpour | Reza Bozorgpour | Computational Explorations in Biomedicine: Unraveling Molecular Dynamics
for Cancer, Drug Delivery, and Biomolecular Insights using LAMMPS Simulations | 16 pages- 11 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | With the rapid advancement of computational techniques, Molecular Dynamics
(MD) simulations have emerged as powerful tools in biomedical research,
enabling in-depth investigations of biological systems at the atomic level.
Among the diverse range of simulation software available, LAMMPS (Large-scale
Atomic/Molecular ... | [
{
"created": "Tue, 21 Nov 2023 21:21:23 GMT",
"version": "v1"
},
{
"created": "Sun, 30 Jun 2024 20:46:02 GMT",
"version": "v2"
},
{
"created": "Tue, 9 Jul 2024 05:30:42 GMT",
"version": "v3"
}
] | 2024-07-10 | [
[
"Bozorgpour",
"Reza",
""
]
] | With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse range of simulation software available, LAMMPS (Large-scale Atomic/Molecular Ma... |
2110.01806 | Teresa Head-Gordon | Jie Li, Oufan Zhang, Yingze Wang, Kunyang Sun, Xingyi Guan, Dorian
Bagni, Mojtaba Haghighatlari, Fiona L. Kearns, Conor Parks, Rommie E.Amaro,
Teresa Head-Gordon | Mining for Potent Inhibitors through Artificial Intelligence and
Physics: A Unified Methodology for Ligand Based and Structure Based Drug
Design | null | null | null | null | q-bio.BM physics.bio-ph physics.chem-ph physics.data-an | http://creativecommons.org/licenses/by/4.0/ | The viability of a new drug molecule is a time and resource intensive task
that makes computer-aided assessments a vital approach to rapid drug discovery.
Here we develop a machine learning algorithm, iMiner, that generates novel
inhibitor molecules for target proteins by combining deep reinforcement
learning with re... | [
{
"created": "Tue, 5 Oct 2021 03:45:15 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Jan 2024 18:14:37 GMT",
"version": "v2"
}
] | 2024-01-11 | [
[
"Li",
"Jie",
""
],
[
"Zhang",
"Oufan",
""
],
[
"Wang",
"Yingze",
""
],
[
"Sun",
"Kunyang",
""
],
[
"Guan",
"Xingyi",
""
],
[
"Bagni",
"Dorian",
""
],
[
"Haghighatlari",
"Mojtaba",
""
],
[
"Kearns",
... | The viability of a new drug molecule is a time and resource intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibitor molecules for target proteins by combining deep reinforcement learning with real... |
2405.10035 | Alessio Perinelli | Alessio Perinelli, Leonardo Ricci | A quality control analysis of the resting state hypothesis via
permutation entropy on EEG recordings | 17 pages, 6 figures. Submitted to: Chaos | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The analysis of electrophysiological recordings of the human brain in resting
state is a key experimental technique in neuroscience. Resting state is indeed
the default condition to characterize brain dynamics. Its successful
implementation relies both on the capacity of subjects to comply with the
requirement of sta... | [
{
"created": "Thu, 16 May 2024 12:16:03 GMT",
"version": "v1"
}
] | 2024-05-17 | [
[
"Perinelli",
"Alessio",
""
],
[
"Ricci",
"Leonardo",
""
]
] | The analysis of electrophysiological recordings of the human brain in resting state is a key experimental technique in neuroscience. Resting state is indeed the default condition to characterize brain dynamics. Its successful implementation relies both on the capacity of subjects to comply with the requirement of stayi... |
2406.02623 | Sabrina Toro | Kathleen R. Mullen (1), Imke Tammen (2), Nicolas A. Matentzoglu (3),
Marius Mather (2), Christopher J. Mungall (4), Melissa A. Haendel (5), Frank
W. Nicholas (2), Sabrina Toro (5), the Vertebrate Breed Ontology Consortium
((1) University of Colorado Anschutz Medical Campus, (2) University of
Sydney, (3) Semanti... | The Vertebrate Breed Ontology: Towards Effective Breed Data
Standardization | null | null | null | null | q-bio.OT cs.DL | http://creativecommons.org/licenses/by/4.0/ | Background: Limited universally adopted data standards in veterinary science
hinders data interoperability and therefore integration and comparison; this
ultimately impedes application of existing information-based tools to support
advancement in veterinary diagnostics, treatments, and precision medicine.
Objective... | [
{
"created": "Mon, 3 Jun 2024 20:06:41 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Mullen",
"Kathleen R.",
""
],
[
"Tammen",
"Imke",
""
],
[
"Matentzoglu",
"Nicolas A.",
""
],
[
"Mather",
"Marius",
""
],
[
"Mungall",
"Christopher J.",
""
],
[
"Haendel",
"Melissa A.",
""
],
[
"Nicholas",
"Fra... | Background: Limited universally adopted data standards in veterinary science hinders data interoperability and therefore integration and comparison; this ultimately impedes application of existing information-based tools to support advancement in veterinary diagnostics, treatments, and precision medicine. Objectives: C... |
1605.07789 | Mark Leake | Helen Miller, Adam J. M. Wollman, Mark C. Leake | Designing a single-molecule biophysics tool for characterizing DNA
damage for techniques that kill infectious pathogens through DNA damage
effects | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antibiotics such as the quinolones and fluoroquinolones kill bacterial
pathogens ultimately through DNA damage. They target the essential type IIA
topoisomerases in bacteria by stabilising the normally transient double strand
break state which is created to modify the supercoiling state of the DNA. Here
we discuss th... | [
{
"created": "Wed, 25 May 2016 09:17:38 GMT",
"version": "v1"
}
] | 2016-05-26 | [
[
"Miller",
"Helen",
""
],
[
"Wollman",
"Adam J. M.",
""
],
[
"Leake",
"Mark C.",
""
]
] | Antibiotics such as the quinolones and fluoroquinolones kill bacterial pathogens ultimately through DNA damage. They target the essential type IIA topoisomerases in bacteria by stabilising the normally transient double strand break state which is created to modify the supercoiling state of the DNA. Here we discuss the ... |
2108.02315 | Scott Greenhalgh | Alisha Kumari, Elijah Reece, Kursad Tosun, Scott Greenhalgh | On the origin of zombies: a modeling approach | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A zombie apocalypse is one pandemic that would likely be worse than anything
humanity has ever seen. However, despite the mechanisms for zombie uprisings in
pop culture, it is unknown whether zombies, from an evolutionary point of view,
can actually rise from the dead. To provide insight into this unknown, we
created... | [
{
"created": "Wed, 4 Aug 2021 23:36:06 GMT",
"version": "v1"
}
] | 2021-08-06 | [
[
"Kumari",
"Alisha",
""
],
[
"Reece",
"Elijah",
""
],
[
"Tosun",
"Kursad",
""
],
[
"Greenhalgh",
"Scott",
""
]
] | A zombie apocalypse is one pandemic that would likely be worse than anything humanity has ever seen. However, despite the mechanisms for zombie uprisings in pop culture, it is unknown whether zombies, from an evolutionary point of view, can actually rise from the dead. To provide insight into this unknown, we created a... |
1512.00844 | Soumya Banerjee | Soumya Banerjee | Optimal Strategies for Virus Propagation | 10 pages, 3 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper explores a number of questions regarding optimal strategies
evolved by viruses upon entry into a vertebrate host. The infected cell life
cycle consists of a non-productively infected stage in which it is producing
virions but not releasing them and of a productively infected stage in which it
is just relea... | [
{
"created": "Wed, 2 Dec 2015 10:25:33 GMT",
"version": "v1"
},
{
"created": "Sat, 6 Feb 2016 23:05:55 GMT",
"version": "v2"
}
] | 2016-02-09 | [
[
"Banerjee",
"Soumya",
""
]
] | This paper explores a number of questions regarding optimal strategies evolved by viruses upon entry into a vertebrate host. The infected cell life cycle consists of a non-productively infected stage in which it is producing virions but not releasing them and of a productively infected stage in which it is just releasi... |
2311.03421 | Arnau Marin-Llobet | Arnau Marin-Llobet and Arnau Manasanch and Maria V. Sanchez-Vives | Hopfield-Enhanced Deep Neural Networks for Artifact-Resilient Brain
State Decoding | null | null | null | null | q-bio.NC cs.LG | http://creativecommons.org/licenses/by/4.0/ | The study of brain states, ranging from highly synchronous to asynchronous
neuronal patterns like the sleep-wake cycle, is fundamental for assessing the
brain's spatiotemporal dynamics and their close connection to behavior.
However, the development of new techniques to accurately identify them still
remains a challe... | [
{
"created": "Mon, 6 Nov 2023 15:08:13 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Nov 2023 17:39:47 GMT",
"version": "v2"
},
{
"created": "Fri, 10 Nov 2023 16:52:26 GMT",
"version": "v3"
}
] | 2023-11-13 | [
[
"Marin-Llobet",
"Arnau",
""
],
[
"Manasanch",
"Arnau",
""
],
[
"Sanchez-Vives",
"Maria V.",
""
]
] | The study of brain states, ranging from highly synchronous to asynchronous neuronal patterns like the sleep-wake cycle, is fundamental for assessing the brain's spatiotemporal dynamics and their close connection to behavior. However, the development of new techniques to accurately identify them still remains a challeng... |
2310.01743 | Rebekah Rogers | James E. Titus-McQuillan, Brandon A. Turner, Rebekah L. Rogers | Sex-specific ultraviolet radiation tolerance across Drosophila | 18 pages text. 5 figures. 4 tables | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The genetic basis of phenotypic differences between species is among the most
longstanding questions in evolutionary biology. How new genes form and the
processes selection acts to produce differences across species are fundamental
to understand how species persist and evolve in an ever-changing environment.
Adaptati... | [
{
"created": "Tue, 3 Oct 2023 02:10:08 GMT",
"version": "v1"
}
] | 2023-10-04 | [
[
"Titus-McQuillan",
"James E.",
""
],
[
"Turner",
"Brandon A.",
""
],
[
"Rogers",
"Rebekah L.",
""
]
] | The genetic basis of phenotypic differences between species is among the most longstanding questions in evolutionary biology. How new genes form and the processes selection acts to produce differences across species are fundamental to understand how species persist and evolve in an ever-changing environment. Adaptation... |
2303.14448 | Trevor McCourt | Trevor McCourt, Ila R. Fiete, Isaac L. Chuang | Noisy dynamical systems evolve error correcting codes and modularity | 7 pages 4 figures | null | null | null | q-bio.PE nlin.AO q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Noise is a ubiquitous feature of the physical world. As a result, the first
prerequisite of life is fault tolerance: maintaining integrity of state despite
external bombardment. Recent experimental advances have revealed that
biological systems achieve fault tolerance by implementing mathematically
intricate error-co... | [
{
"created": "Sat, 25 Mar 2023 11:54:18 GMT",
"version": "v1"
},
{
"created": "Wed, 12 Apr 2023 22:16:35 GMT",
"version": "v2"
}
] | 2023-04-14 | [
[
"McCourt",
"Trevor",
""
],
[
"Fiete",
"Ila R.",
""
],
[
"Chuang",
"Isaac L.",
""
]
] | Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-corr... |
1512.03094 | Pedro Jeferson Miranda | Pedro Jeferson Miranda, Sandro Ely de Souza Pinto, Murilo da Silva
Baptista and Giuliano Gadioli La Guardia | Theoretical knock-outs on biological networks | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we formalize a method to compute the degree of importance of
biological agents that participates on the dynamics of a biological phenomenon
build upon a complex network. We call this new procedure by theoretical
knock-out (KO). To devise this method, we make two approaches: algebraically
and algorithmica... | [
{
"created": "Tue, 1 Dec 2015 04:01:01 GMT",
"version": "v1"
}
] | 2015-12-11 | [
[
"Miranda",
"Pedro Jeferson",
""
],
[
"Pinto",
"Sandro Ely de Souza",
""
],
[
"Baptista",
"Murilo da Silva",
""
],
[
"La Guardia",
"Giuliano Gadioli",
""
]
] | In this work we formalize a method to compute the degree of importance of biological agents that participates on the dynamics of a biological phenomenon build upon a complex network. We call this new procedure by theoretical knock-out (KO). To devise this method, we make two approaches: algebraically and algorithmicall... |
2203.11402 | Eleanor Dunlop Mrs | Eleanor Dunlop, Jette Jakobsen, Marie Bagge Jensen, Jayashree Arcot,
Liang Qiao, Judy Cunningham and Lucinda J Black | Vitamin K content of cheese, yoghurt and meat products in Australia | 23 pages, 2 tables | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vitamin K is vital for normal blood coagulation, and may influence bone,
neurological and vascular health. Data on the vitamin K content of Australian
foods are limited, preventing estimation of vitamin K intakes in the Australian
population. We measured phylloquinone (PK) and menaquinone (MK) -4 to -10 in
cheese, yo... | [
{
"created": "Tue, 22 Mar 2022 00:50:11 GMT",
"version": "v1"
}
] | 2022-03-23 | [
[
"Dunlop",
"Eleanor",
""
],
[
"Jakobsen",
"Jette",
""
],
[
"Jensen",
"Marie Bagge",
""
],
[
"Arcot",
"Jayashree",
""
],
[
"Qiao",
"Liang",
""
],
[
"Cunningham",
"Judy",
""
],
[
"Black",
"Lucinda J",
""
]
] | Vitamin K is vital for normal blood coagulation, and may influence bone, neurological and vascular health. Data on the vitamin K content of Australian foods are limited, preventing estimation of vitamin K intakes in the Australian population. We measured phylloquinone (PK) and menaquinone (MK) -4 to -10 in cheese, yogh... |
2309.00694 | William Cuello | William S. Cuello, Marcio Gameiro, Juan A. Bonachela, and Konstantin
Mischaikow | Inferring Long-term Dynamics of Ecological Communities Using
Combinatorics | 25 pages, 9 figures | null | null | null | q-bio.PE math.CO math.DS q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In an increasingly changing world, predicting the fate of species across the
globe has become a major concern. Understanding how the population dynamics of
various species and communities will unfold requires predictive tools that
experimental data alone can not capture. Here, we introduce our combinatorial
framework... | [
{
"created": "Fri, 1 Sep 2023 18:27:54 GMT",
"version": "v1"
}
] | 2023-09-06 | [
[
"Cuello",
"William S.",
""
],
[
"Gameiro",
"Marcio",
""
],
[
"Bonachela",
"Juan A.",
""
],
[
"Mischaikow",
"Konstantin",
""
]
] | In an increasingly changing world, predicting the fate of species across the globe has become a major concern. Understanding how the population dynamics of various species and communities will unfold requires predictive tools that experimental data alone can not capture. Here, we introduce our combinatorial framework, ... |
1503.07518 | Sadie Ryan | Sadie J. Ryan, Tal Ben-Horin, Leah R. Johnson | Malaria control and senescence: the importance of accounting for the
pace and shape of aging in wild mosquitoes | 35 + 214 pages, 4 figures, 1 table, 1 supplemental figure, 1
supplemental table, +1 appendix [Ecological Archives] | Ecosphere 6(9):170 (2015) | 10.1890/ES15-00094.1 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The assumption that vector mortality remains constant with age is used widely
to assess malaria transmission risk and predict the public health consequences
of vector control strategies. However, laboratory studies commonly demonstrate
clear evidence of senescence, or a decrease in physiological function and
increase... | [
{
"created": "Wed, 25 Mar 2015 17:44:54 GMT",
"version": "v1"
},
{
"created": "Wed, 27 May 2015 20:03:28 GMT",
"version": "v2"
},
{
"created": "Wed, 30 Sep 2015 01:16:55 GMT",
"version": "v3"
}
] | 2015-10-01 | [
[
"Ryan",
"Sadie J.",
""
],
[
"Ben-Horin",
"Tal",
""
],
[
"Johnson",
"Leah R.",
""
]
] | The assumption that vector mortality remains constant with age is used widely to assess malaria transmission risk and predict the public health consequences of vector control strategies. However, laboratory studies commonly demonstrate clear evidence of senescence, or a decrease in physiological function and increase i... |
2202.07290 | Pierre Orhan | Pierre Orhan, Yves Boubenec, Jean-R\'emi King | Don't stop the training: continuously-updating self-supervised
algorithms best account for auditory responses in the cortex | null | null | null | null | q-bio.NC cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Over the last decade, numerous studies have shown that deep neural networks
exhibit sensory representations similar to those of the mammalian brain, in
that their activations linearly map onto cortical responses to the same sensory
inputs. However, it remains unknown whether these artificial networks also
learn like ... | [
{
"created": "Tue, 15 Feb 2022 10:12:56 GMT",
"version": "v1"
}
] | 2022-02-16 | [
[
"Orhan",
"Pierre",
""
],
[
"Boubenec",
"Yves",
""
],
[
"King",
"Jean-Rémi",
""
]
] | Over the last decade, numerous studies have shown that deep neural networks exhibit sensory representations similar to those of the mammalian brain, in that their activations linearly map onto cortical responses to the same sensory inputs. However, it remains unknown whether these artificial networks also learn like th... |
1204.3126 | Mustafa Barasa | Barasa Mustafa, Gicheru Muita MichaeL, Kagasi Ambogo Esther, Ozwara
Suba Hastings | Characterisation of placental malaria in olive baboons (Papio anubis)
infected with Plasmodium knowlesi H strain | Five pages, four figures: This reserch was supported by the research
capability strengthening World Health Organisation (WHO Grant Number: A
50075) for malaria research in Africa under the Multilateral Initiative on
Malaria / Special Programme for Research and Training in Tropical Diseases
(WHO-MIM/TDR). The In... | Int. J. Integ. Biol: Year 2012 Volume 9, Issue No. 2: 54 - 58 | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pregnant women have increased susceptibility to malaria infection. In these
women, malaria parasites are frequently found sequestered in the placental
intervillous spaces, a condition referred to as placental malaria (PM).
Placental malaria threatens the health of the mother and the child's life by
causing still birt... | [
{
"created": "Sat, 14 Apr 2012 00:41:42 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Apr 2012 08:10:37 GMT",
"version": "v2"
}
] | 2012-04-18 | [
[
"Mustafa",
"Barasa",
""
],
[
"MichaeL",
"Gicheru Muita",
""
],
[
"Esther",
"Kagasi Ambogo",
""
],
[
"Hastings",
"Ozwara Suba",
""
]
] | Pregnant women have increased susceptibility to malaria infection. In these women, malaria parasites are frequently found sequestered in the placental intervillous spaces, a condition referred to as placental malaria (PM). Placental malaria threatens the health of the mother and the child's life by causing still births... |
1703.01818 | Daniele De Martino | Daniele De Martino, Anna MC Andersson, Tobias Bergmiller, C\u{a}lin C
Guet, Ga\v{s}per Tka\v{c}ik | Statistical mechanics for metabolic networks during steady-state growth | 12 pages, 4 figures | null | 10.1038/s41467-018-05417-9 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Which properties of metabolic networks can be derived solely from
stoichiometric information about the network's constituent reactions?
Predictive results have been obtained by Flux Balance Analysis (FBA), by
postulating that cells set metabolic fluxes within the allowed stoichiometry so
as to maximize their growth. ... | [
{
"created": "Mon, 6 Mar 2017 11:34:45 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"De Martino",
"Daniele",
""
],
[
"Andersson",
"Anna MC",
""
],
[
"Bergmiller",
"Tobias",
""
],
[
"Guet",
"Călin C",
""
],
[
"Tkačik",
"Gašper",
""
]
] | Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set metabolic fluxes within the allowed stoichiometry so as to maximize their growth. He... |
2312.11338 | Matthias Schott | Lucas Heger, Kerem Akdogan, Matthias Schott | On the Impact of School Closures on COVID-19 Transmission in Germany
using an agent-based Simulation | 5 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The effect of school closures on the spread of COVID-19 has been discussed
among experts and the general public since those measures have been taken only
a few months after the start of the pandemic in 2020. Within this study, the
JuneGermany framework, is used to quantify the impact of school closures in the
German ... | [
{
"created": "Mon, 18 Dec 2023 16:41:34 GMT",
"version": "v1"
}
] | 2023-12-19 | [
[
"Heger",
"Lucas",
""
],
[
"Akdogan",
"Kerem",
""
],
[
"Schott",
"Matthias",
""
]
] | The effect of school closures on the spread of COVID-19 has been discussed among experts and the general public since those measures have been taken only a few months after the start of the pandemic in 2020. Within this study, the JuneGermany framework, is used to quantify the impact of school closures in the German st... |
1804.06507 | Michael Plank | Michael J Plank | How should fishing mortality be distributed under balanced harvesting? | null | Fisheries Research, Volume 207, November 2018, Pages 171-174 | 10.1016/j.fishres.2018.06.003 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Zhou and Smith (2017) investigate different multi-species harvesting
scenarios using a simple Holling-Tanner model. Among these scenarios are two
methods for implementing balanced harvesting, where fishing is distributed
across trophic levels in accordance with their productivity. This note examines
the effects of a ... | [
{
"created": "Tue, 17 Apr 2018 23:55:29 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Oct 2019 02:42:24 GMT",
"version": "v2"
}
] | 2019-10-23 | [
[
"Plank",
"Michael J",
""
]
] | Zhou and Smith (2017) investigate different multi-species harvesting scenarios using a simple Holling-Tanner model. Among these scenarios are two methods for implementing balanced harvesting, where fishing is distributed across trophic levels in accordance with their productivity. This note examines the effects of a di... |
1308.2278 | Simon Childs | S. J. Childs | A Model of Teneral Dehydration in Glossina | 28 pages, 9 figures, 3 tables | Acta Tropica, 131: 79-91, 2014 | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The results of a long-established investigation into teneral transpiration
are used as a rudimentary data set. These data are not complete in that all are
at 25 $^\circ\mathrm{C}$ and the temperature-dependence cannot, therefore be
resolved. An allowance is, nonetheless, made for the outstanding
temperature-dependent... | [
{
"created": "Sat, 10 Aug 2013 05:14:49 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Jun 2014 12:53:01 GMT",
"version": "v2"
},
{
"created": "Wed, 28 Oct 2015 09:04:17 GMT",
"version": "v3"
}
] | 2015-10-29 | [
[
"Childs",
"S. J.",
""
]
] | The results of a long-established investigation into teneral transpiration are used as a rudimentary data set. These data are not complete in that all are at 25 $^\circ\mathrm{C}$ and the temperature-dependence cannot, therefore be resolved. An allowance is, nonetheless, made for the outstanding temperature-dependent d... |
q-bio/0508021 | Eli Eisenberg | Shai Carmi, Erez Y. Levanon, Shlomo Havlin, Eli Eisenberg | Connectivity and expression in protein networks: Proteins in a complex
are uniformly expressed | revised version; accepted for publication in PRE | Phys. Rev. E 73, 031909 (2006) | 10.1103/PhysRevE.73.031909 | null | q-bio.MN cond-mat.other q-bio.OT | null | We explore the interplay between the protein-protein interactions network and
the expression of the interacting proteins. It is shown that interacting
proteins are expressed in significantly more similar cellular concentrations.
This is largely due to interacting pairs which are part of protein complexes.
We solve a ... | [
{
"created": "Wed, 17 Aug 2005 14:35:43 GMT",
"version": "v1"
},
{
"created": "Thu, 26 Jan 2006 17:17:40 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Carmi",
"Shai",
""
],
[
"Levanon",
"Erez Y.",
""
],
[
"Havlin",
"Shlomo",
""
],
[
"Eisenberg",
"Eli",
""
]
] | We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is largely due to interacting pairs which are part of protein complexes. We solve a ge... |
1508.02980 | Susan Khor | Susan Khor | Comparing local search paths with global search paths on protein residue
networks: allosteric communication | 32 pages | J Complex Netw (2017) 5 (3): 409-432 | 10.1093/comnet/cnw020 | null | q-bio.MN q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Although proteins have been recognized as small-world networks and their
small-world network properties of clustering and short paths have been
exploited computationally to produce biologically relevant information, they
have not been truly explored as such, i.e. as navigable small-world networks in
the original spir... | [
{
"created": "Wed, 12 Aug 2015 16:29:54 GMT",
"version": "v1"
},
{
"created": "Sun, 25 Oct 2015 02:46:43 GMT",
"version": "v2"
},
{
"created": "Tue, 19 Jan 2016 18:52:41 GMT",
"version": "v3"
},
{
"created": "Thu, 12 May 2016 21:52:09 GMT",
"version": "v4"
},
{
"c... | 2017-06-20 | [
[
"Khor",
"Susan",
""
]
] | Although proteins have been recognized as small-world networks and their small-world network properties of clustering and short paths have been exploited computationally to produce biologically relevant information, they have not been truly explored as such, i.e. as navigable small-world networks in the original spirit... |
1012.3607 | Jose Vilar | Jose M. G. Vilar | Accurate prediction of gene expression by integration of DNA sequence
statistics with detailed modeling of transcription regulation | 15 pages, 5 figures | Biophys. J. 99, 2408-2413 (2010) | 10.1016/j.bpj.2010.08.006 | null | q-bio.MN cond-mat.stat-mech cs.CE physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene regulation involves a hierarchy of events that extend from specific
protein-DNA interactions to the combinatorial assembly of nucleoprotein
complexes. The effects of DNA sequence on these processes have typically been
studied based either on its quantitative connection with single-domain binding
free energies or... | [
{
"created": "Thu, 16 Dec 2010 14:06:26 GMT",
"version": "v1"
}
] | 2015-05-20 | [
[
"Vilar",
"Jose M. G.",
""
]
] | Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based either on its quantitative connection with single-domain binding free energies or o... |
1505.06898 | Mareike Fischer | Christopher Bryant and Mareike Fischer and Simone Linz and Charles
Semple | On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic
Networks | 28 pages, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Maximum parsimony is one of the most frequently-discussed tree reconstruction
methods in phylogenetic estimation. However, in recent years it has become more
and more apparent that phylogenetic trees are often not sufficient to describe
evolution accurately. For instance, processes like hybridization or lateral
gene ... | [
{
"created": "Tue, 26 May 2015 11:03:32 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Jun 2015 20:45:38 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Nov 2015 14:50:41 GMT",
"version": "v3"
},
{
"created": "Thu, 15 Sep 2016 19:33:40 GMT",
"version": "v4"
},
{
"cr... | 2016-10-25 | [
[
"Bryant",
"Christopher",
""
],
[
"Fischer",
"Mareike",
""
],
[
"Linz",
"Simone",
""
],
[
"Semple",
"Charles",
""
]
] | Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe evolution accurately. For instance, processes like hybridization or lateral gene tr... |
0909.2676 | Serguey Mayburov NN | S.Mayburov | Coherent and Noncoherent Photonic Communications in Biological Systems | 9 pages, talk given at PIERS-2009 conference, Moscow, august 2009, to
appear in Proceedings | null | null | null | q-bio.OT physics.bio-ph q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The possible mechanisms of communications between distant bio-systems by
means of optical and UV photons are studied. It is argued that their main
production mechanism is owed to the biochemical reactions, occurring during the
cell division.. In the proposed model the bio-systems perform such
communications, radiatin... | [
{
"created": "Mon, 14 Sep 2009 10:10:13 GMT",
"version": "v1"
}
] | 2009-11-17 | [
[
"Mayburov",
"S.",
""
]
] | The possible mechanisms of communications between distant bio-systems by means of optical and UV photons are studied. It is argued that their main production mechanism is owed to the biochemical reactions, occurring during the cell division.. In the proposed model the bio-systems perform such communications, radiating ... |
1607.01706 | Shi Gu | Shi Gu, Richard F. Betzel, Matthew Cieslak, Philip R. Delio, Scott T.
Grafton, Fabio Pasqualetti, Danielle S. Bassett | Optimal Trajectories of Brain State Transitions | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The complexity of neural dynamics stems in part from the complexity of the
underlying anatomy. Yet how the organization of white matter architecture
constrains how the brain transitions from one cognitive state to another
remains unknown. Here we address this question from a computational perspective
by defining a br... | [
{
"created": "Wed, 6 Jul 2016 16:57:46 GMT",
"version": "v1"
},
{
"created": "Mon, 9 Jan 2017 02:33:35 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Jan 2017 04:18:23 GMT",
"version": "v3"
}
] | 2017-01-11 | [
[
"Gu",
"Shi",
""
],
[
"Betzel",
"Richard F.",
""
],
[
"Cieslak",
"Matthew",
""
],
[
"Delio",
"Philip R.",
""
],
[
"Grafton",
"Scott T.",
""
],
[
"Pasqualetti",
"Fabio",
""
],
[
"Bassett",
"Danielle S.",
""
... | The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how the organization of white matter architecture constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question from a computational perspective by defining a brai... |
2407.19349 | Tengyao Tu | Tengyao Tu, Wei Zeng, Kun Zhao, Zhenyu Zhang | Predicting T-Cell Receptor Specificity | null | null | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by/4.0/ | Researching the specificity of TCR contributes to the development of
immunotherapy and provides new opportunities and strategies for personalized
cancer immunotherapy. Therefore, we established a TCR generative specificity
detection framework consisting of an antigen selector and a TCR classifier
based on the Random ... | [
{
"created": "Sat, 27 Jul 2024 23:21:07 GMT",
"version": "v1"
}
] | 2024-07-30 | [
[
"Tu",
"Tengyao",
""
],
[
"Zeng",
"Wei",
""
],
[
"Zhao",
"Kun",
""
],
[
"Zhang",
"Zhenyu",
""
]
] | Researching the specificity of TCR contributes to the development of immunotherapy and provides new opportunities and strategies for personalized cancer immunotherapy. Therefore, we established a TCR generative specificity detection framework consisting of an antigen selector and a TCR classifier based on the Random Fo... |
1610.01507 | Areejit Samal | R.P. Sreejith, J\"urgen Jost, Emil Saucan, Areejit Samal | Systematic evaluation of a new combinatorial curvature for complex
networks | 29 pages, 14 figures, 1 table. Accepted for publication in Chaos,
Solitons and Fractals | Chaos, Solitons & Fractals, 101:50-67 (2017) | 10.1016/j.chaos.2017.05.021 | null | q-bio.MN physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have recently introduced Forman's discretization of Ricci curvature to the
realm of complex networks. Forman curvature is an edge-based measure whose
mathematical definition elegantly encapsulates the weights of nodes and edges
in a complex network. In this contribution, we perform a comparative analysis
of Forman... | [
{
"created": "Wed, 5 Oct 2016 16:27:00 GMT",
"version": "v1"
},
{
"created": "Mon, 15 May 2017 21:55:11 GMT",
"version": "v2"
}
] | 2017-06-01 | [
[
"Sreejith",
"R. P.",
""
],
[
"Jost",
"Jürgen",
""
],
[
"Saucan",
"Emil",
""
],
[
"Samal",
"Areejit",
""
]
] | We have recently introduced Forman's discretization of Ricci curvature to the realm of complex networks. Forman curvature is an edge-based measure whose mathematical definition elegantly encapsulates the weights of nodes and edges in a complex network. In this contribution, we perform a comparative analysis of Forman c... |
1111.6493 | Taiki Takahashi | Taiki Takahashi (1), Hidemi Oono (2), Takeshi Inoue (3), Shuken Boku
(3), Yuki Kako (3), Yuji Kitaichi (3), Ichiro Kusumi (3), Takuya Masui (3),
Shin Nakagawa (3), Katsuji Suzuki (3), Teruaki Tanaka (3), Tsukasa Koyama
(3), and Mark H. B. Radford (4) ((1) Direct all correspondence to Taiki
Takahashi, Unit of Co... | Depressive patients are more impulsive and inconsistent in intertemporal
choice behavior for monetary gain and loss than healthy subjects- an analysis
based on Tsallis' statistics | null | Neuro Endocrinol Lett. 2008, 29(3):351-358 | null | null | q-bio.NC q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Depression has been associated with impaired neural processing of reward and
punishment. However, to date, little is known regarding the relationship
between depression and intertemporal choice for gain and loss. We compared
impulsivity and inconsistency in intertemporal choice for monetary gain and
loss (quantified ... | [
{
"created": "Tue, 22 Nov 2011 15:38:02 GMT",
"version": "v1"
}
] | 2012-12-04 | [
[
"Takahashi",
"Taiki",
""
],
[
"Oono",
"Hidemi",
""
],
[
"Inoue",
"Takeshi",
""
],
[
"Boku",
"Shuken",
""
],
[
"Kako",
"Yuki",
""
],
[
"Kitaichi",
"Yuji",
""
],
[
"Kusumi",
"Ichiro",
""
],
[
"Masui",... | Depression has been associated with impaired neural processing of reward and punishment. However, to date, little is known regarding the relationship between depression and intertemporal choice for gain and loss. We compared impulsivity and inconsistency in intertemporal choice for monetary gain and loss (quantified wi... |
1907.00070 | Rostislav Serota | M. Dashti Moghaddam, Jiong Liu, John G. Holden and R. A. Serota | Modeling Response Time Distributions with Generalized Beta Prime | 15 pages, 11 figure, 5 tables | Discontinuity, Nonlinearity, and Complexity, 9 (3), 477 - 488
(2020) | 10.5890/DNC.2020.09.009 | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use Generalized Beta Prime distribution, also known as GB2, for fitting
response time distributions. This distribution, characterized by one scale and
three shape parameters, is incredibly flexible in that it can mimic behavior of
many other distributions. GB2 exhibits power-law behavior at both front and
tail end... | [
{
"created": "Fri, 28 Jun 2019 20:46:21 GMT",
"version": "v1"
}
] | 2024-04-15 | [
[
"Moghaddam",
"M. Dashti",
""
],
[
"Liu",
"Jiong",
""
],
[
"Holden",
"John G.",
""
],
[
"Serota",
"R. A.",
""
]
] | We use Generalized Beta Prime distribution, also known as GB2, for fitting response time distributions. This distribution, characterized by one scale and three shape parameters, is incredibly flexible in that it can mimic behavior of many other distributions. GB2 exhibits power-law behavior at both front and tail ends ... |
1609.02956 | Steven Frank | Steven A. Frank | Puzzles in modern biology. I. Male sterility, failure reveals design | null | F1000Research 5:2088 (2016) | 10.12688/f1000research.9567.1 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Many human males produce dysfunctional sperm. Various plants frequently abort
pollen. Hybrid matings often produce sterile males. Widespread male sterility
is puzzling. Natural selection prunes reproductive failure. Puzzling failure
implies something that we do not understand about how organisms are designed.
Solving... | [
{
"created": "Fri, 9 Sep 2016 22:07:27 GMT",
"version": "v1"
}
] | 2016-09-13 | [
[
"Frank",
"Steven A.",
""
]
] | Many human males produce dysfunctional sperm. Various plants frequently abort pollen. Hybrid matings often produce sterile males. Widespread male sterility is puzzling. Natural selection prunes reproductive failure. Puzzling failure implies something that we do not understand about how organisms are designed. Solving t... |
1112.4808 | Christoph Adami | Evan D. Dorn and Christoph Adami | Robust monomer-distribution biosignatures in evolving digital biota | 22 pages, 4 figures, 1 table. Supplementary Material available from
CA | Astrobiology 11 (2011) 959-968 | 10.1089/ast.2010.0556 | null | q-bio.BM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Because organisms synthesize component molecules at rates that reflect those
molecules' adaptive utility, we expect a population of biota to leave a
distinctive chemical signature on their environment that is anomalous given the
local (abiotic) chemistry. We observe the same effect in the distribution of
computer ins... | [
{
"created": "Tue, 20 Dec 2011 19:45:31 GMT",
"version": "v1"
}
] | 2011-12-21 | [
[
"Dorn",
"Evan D.",
""
],
[
"Adami",
"Christoph",
""
]
] | Because organisms synthesize component molecules at rates that reflect those molecules' adaptive utility, we expect a population of biota to leave a distinctive chemical signature on their environment that is anomalous given the local (abiotic) chemistry. We observe the same effect in the distribution of computer instr... |
1705.06132 | Eslam Abbas | Eslam Abbas | Mathematical Analysis of the Probability of Spontaneous Mutations in
HIV-1 Genome and Their Role in the Emergence of Resistance to Anti-Retroviral
Therapy | null | null | 10.4236/aim.2019.911057 | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | $\textbf{Background:}$ High mutability of HIV is the driving force of
antiretroviral drug resistance, which represents a medical care challenge.
$\textbf{Method and Model Equation:}$ To detect the mutability of each gene
in the HIV-1 genome; a mathematical analysis of HIV-1 genome is performed,
depending on a linea... | [
{
"created": "Mon, 15 May 2017 14:53:45 GMT",
"version": "v1"
}
] | 2019-11-11 | [
[
"Abbas",
"Eslam",
""
]
] | $\textbf{Background:}$ High mutability of HIV is the driving force of antiretroviral drug resistance, which represents a medical care challenge. $\textbf{Method and Model Equation:}$ To detect the mutability of each gene in the HIV-1 genome; a mathematical analysis of HIV-1 genome is performed, depending on a linear re... |
1101.2175 | Tao Jia | Tao Jia and Rahul V. Kulkarni | Intrinsic noise in stochastic models of gene expression with molecular
memory and bursting | Accepted by Physical Review Letters | Phys. Rev. Lett. 106, 058102, 2011 | 10.1103/PhysRevLett.106.058102 | null | q-bio.MN cond-mat.soft cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Regulation of intrinsic noise in gene expression is essential for many
cellular functions. Correspondingly, there is considerable interest in
understanding how different molecular mechanisms of gene expression impact
variations in protein levels across a population of cells. In this work, we
analyze a stochastic mode... | [
{
"created": "Tue, 11 Jan 2011 18:19:27 GMT",
"version": "v1"
}
] | 2011-03-02 | [
[
"Jia",
"Tao",
""
],
[
"Kulkarni",
"Rahul V.",
""
]
] | Regulation of intrinsic noise in gene expression is essential for many cellular functions. Correspondingly, there is considerable interest in understanding how different molecular mechanisms of gene expression impact variations in protein levels across a population of cells. In this work, we analyze a stochastic model ... |
1710.08542 | Yen Ting Lin | Yen Ting Lin, Peter G. Hufton, Esther J. Lee, Davit A. Potoyan | A stochastic and dynamical view of pluripotency in mouse embryonic stem
cells | 11 pages, 7 figures | null | 10.1371/journal.pcbi.1006000 | null | q-bio.MN cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Pluripotent embryonic stem cells are of paramount importance for biomedical
research thanks to their innate ability for self-renewal and differentiation
into all major cell lines. The fateful decision to exit or remain in the
pluripotent state is regulated by complex genetic regulatory network. Latest
advances in tra... | [
{
"created": "Mon, 23 Oct 2017 22:56:44 GMT",
"version": "v1"
}
] | 2018-07-04 | [
[
"Lin",
"Yen Ting",
""
],
[
"Hufton",
"Peter G.",
""
],
[
"Lee",
"Esther J.",
""
],
[
"Potoyan",
"Davit A.",
""
]
] | Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory network. Latest advances in trans... |
q-bio/0703042 | Jeroen van Zon | Jeroen S. van Zon, David K. Lubensky, Pim R.H. Altena and Pieter Rein
ten Wolde | An allosteric model for circadian KaiC phosphorylation - Supporting
Information | Supporting Information for q-bio.MN/0703009 | null | null | null | q-bio.MN q-bio.CB | null | In this Supporting Information, we provide background information on our
model of the in vitro Kai system and the calculations that we have performed.
We will closely follow the outline of the main text.
| [
{
"created": "Mon, 19 Mar 2007 14:25:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"van Zon",
"Jeroen S.",
""
],
[
"Lubensky",
"David K.",
""
],
[
"Altena",
"Pim R. H.",
""
],
[
"Wolde",
"Pieter Rein ten",
""
]
] | In this Supporting Information, we provide background information on our model of the in vitro Kai system and the calculations that we have performed. We will closely follow the outline of the main text. |
1910.03577 | Jin Ming | Suprateek Kundu, Jin Ming, and Jennifer Stevens | Dynamic Brain Functional Networks Guided By Anatomical Knowledge | 45 pages, 5 figures | null | null | null | q-bio.NC stat.AP stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, the potential of dynamic brain networks as a neuroimaging
biomarkers for mental illnesses is being increasingly recognized. However,
there are several unmet challenges in developing such biomarkers, including the
need for methods to model rapidly changing network states. In one of the first
such efforts, we... | [
{
"created": "Mon, 7 Oct 2019 21:48:27 GMT",
"version": "v1"
}
] | 2019-10-10 | [
[
"Kundu",
"Suprateek",
""
],
[
"Ming",
"Jin",
""
],
[
"Stevens",
"Jennifer",
""
]
] | Recently, the potential of dynamic brain networks as a neuroimaging biomarkers for mental illnesses is being increasingly recognized. However, there are several unmet challenges in developing such biomarkers, including the need for methods to model rapidly changing network states. In one of the first such efforts, we d... |
2110.03796 | Pedro Mendes | Abhishekh Gupta and Pedro Mendes | ShinyCOPASI: a web-based exploratory interface for COPASI models | null | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | COPASI is a popular application for simulation and analysis of biochemical
networks and their dynamics. While this software is widely used, it works as a
standalone application and until now it was not possible for users to interact
with its models through the web. We built ShinyCOPASI, a web-based application
that a... | [
{
"created": "Thu, 7 Oct 2021 21:16:03 GMT",
"version": "v1"
}
] | 2021-10-11 | [
[
"Gupta",
"Abhishekh",
""
],
[
"Mendes",
"Pedro",
""
]
] | COPASI is a popular application for simulation and analysis of biochemical networks and their dynamics. While this software is widely used, it works as a standalone application and until now it was not possible for users to interact with its models through the web. We built ShinyCOPASI, a web-based application that all... |
1301.4567 | Marcin Zag\'orski | M. Zagorski, A. Krzywicki, O.C. Martin | Edge usage, motifs and regulatory logic for cell cycling genetic
networks | 9 pages, 9 figures, to be published in Phys. Rev. E | Phys. Rev. E 87, 012727 (2013) | 10.1103/PhysRevE.87.012727 | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The cell cycle is a tightly controlled process, yet its underlying genetic
network shows marked differences across species. Which of the associated
structural features follow solely from the ability to impose the appropriate
gene expression patterns? We tackle this question in silico by examining the
ensemble of all ... | [
{
"created": "Sat, 19 Jan 2013 14:51:52 GMT",
"version": "v1"
}
] | 2015-06-12 | [
[
"Zagorski",
"M.",
""
],
[
"Krzywicki",
"A.",
""
],
[
"Martin",
"O. C.",
""
]
] | The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression patterns? We tackle this question in silico by examining the ensemble of all re... |
2001.10035 | Darius Vasco K\"oster | Lewis Mosby, Marco Polin, Darius V. K\"oster | A Python based automated tracking routine for myosin II filaments | 14 pages, 5 figures | null | 10.1088/1361-6463/ab87bf | null | q-bio.SC physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of motor protein dynamics within cytoskeletal networks is of high
interest to physicists and biologists to understand how the dynamics and
properties of individual motors lead to cooperative effects and control of
overall network behaviour. Here, we report a method to detect and track
muscular myosin II fil... | [
{
"created": "Mon, 27 Jan 2020 19:43:58 GMT",
"version": "v1"
}
] | 2020-06-24 | [
[
"Mosby",
"Lewis",
""
],
[
"Polin",
"Marco",
""
],
[
"Köster",
"Darius V.",
""
]
] | The study of motor protein dynamics within cytoskeletal networks is of high interest to physicists and biologists to understand how the dynamics and properties of individual motors lead to cooperative effects and control of overall network behaviour. Here, we report a method to detect and track muscular myosin II filam... |
1601.03334 | Lior Pachter | Audrey Fu and Lior Pachter | Estimating intrinsic and extrinsic noise from single-cell gene
expression measurements | null | null | null | null | q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression is stochastic and displays variation ("noise") both within
and between cells. Intracellular (intrinsic) variance can be distinguished from
extracellular (extrinsic) variance by applying the law of total variance to
data from two-reporter assays that probe expression of identical gene pairs in
single-c... | [
{
"created": "Wed, 13 Jan 2016 18:08:51 GMT",
"version": "v1"
}
] | 2016-01-14 | [
[
"Fu",
"Audrey",
""
],
[
"Pachter",
"Lior",
""
]
] | Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from two-reporter assays that probe expression of identical gene pairs in single-cel... |
1202.1007 | Michael B\"orsch | Eva Hammann, Andrea Zappe, Stefanie Keis, Stefan Ernst, Doreen
Matthies, Thomas Meier, Gregory M. Cook, Michael Boersch | Step size of the rotary proton motor in single FoF1-ATP synthase from a
thermoalkaliphilic bacterium by DCO-ALEX FRET | 14 pages, 7 figures | null | 10.1117/12.907242 | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thermophilic enzymes can operate at higher temperatures but show reduced
activities at room temperature. They are in general more stable during
preparation and, accordingly, are considered to be more rigid in structure.
Crystallization is often easier compared to proteins from bacteria growing at
ambient temperatures... | [
{
"created": "Sun, 5 Feb 2012 21:50:45 GMT",
"version": "v1"
}
] | 2015-06-04 | [
[
"Hammann",
"Eva",
""
],
[
"Zappe",
"Andrea",
""
],
[
"Keis",
"Stefanie",
""
],
[
"Ernst",
"Stefan",
""
],
[
"Matthies",
"Doreen",
""
],
[
"Meier",
"Thomas",
""
],
[
"Cook",
"Gregory M.",
""
],
[
"Bo... | Thermophilic enzymes can operate at higher temperatures but show reduced activities at room temperature. They are in general more stable during preparation and, accordingly, are considered to be more rigid in structure. Crystallization is often easier compared to proteins from bacteria growing at ambient temperatures, ... |
0901.2378 | Georgy Karev | Georgiy P. Karev | Replicator equations and the principle of minimal production of
information | 27 pages; submitted to Bulletin of Mathematical Biology | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many complex systems in mathematical biology and other areas can be described
by the replicator equation. We show that solutions of a wide class of
replicator equations minimize the production of information under
time-dependent constraints, which, in their turn, can be computed explicitly at
every instant due to the... | [
{
"created": "Fri, 16 Jan 2009 01:10:22 GMT",
"version": "v1"
}
] | 2009-01-19 | [
[
"Karev",
"Georgiy P.",
""
]
] | Many complex systems in mathematical biology and other areas can be described by the replicator equation. We show that solutions of a wide class of replicator equations minimize the production of information under time-dependent constraints, which, in their turn, can be computed explicitly at every instant due to the s... |
1803.01056 | Thierry Mora | Yuval Elhanati, Zachary Sethna, Curtis G. Callan Jr., Thierry Mora,
Aleksandra M. Walczak | Predicting the spectrum of TCR repertoire sharing with a data-driven
model of recombination | null | Immunol Rev. 2018;284:167-179 | 10.1111/imr.12665 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the extreme diversity of T cell repertoires, many identical T-cell
receptor (TCR) sequences are found in a large number of individual mice and
humans. These widely-shared sequences, often referred to as `public', have been
suggested to be over-represented due to their potential immune functionality or
their e... | [
{
"created": "Fri, 2 Mar 2018 21:53:03 GMT",
"version": "v1"
}
] | 2019-01-24 | [
[
"Elhanati",
"Yuval",
""
],
[
"Sethna",
"Zachary",
""
],
[
"Callan",
"Curtis G.",
"Jr."
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | Despite the extreme diversity of T cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely-shared sequences, often referred to as `public', have been suggested to be over-represented due to their potential immune functionality or their eas... |
0912.1277 | Kyung Myriam Kroll | K. Myriam Kroll, Gerard T. Barkema, Enrico Carlon | Linear model for fast background subtraction in oligonucleotide
microarrays | 21 pages, 5 figures | Algorithms for Molecular Biology 2009, 4:15 | 10.1186/1748-7188-4-15 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One important preprocessing step in the analysis of microarray data is
background subtraction. In high-density oligonucleotide arrays this is
recognized as a crucial step for the global performance of the data analysis
from raw intensities to expression values.
We propose here an algorithm for background estimation... | [
{
"created": "Mon, 7 Dec 2009 15:53:13 GMT",
"version": "v1"
}
] | 2009-12-08 | [
[
"Kroll",
"K. Myriam",
""
],
[
"Barkema",
"Gerard T.",
""
],
[
"Carlon",
"Enrico",
""
]
] | One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. We propose here an algorithm for background estimation bas... |
2302.06281 | Philipp Kellmeyer | Sjors Ligthart, Marcello Ienca, Gerben Meynen, Fruzsina Molnar-Gabor,
Roberto Andorno, Christoph Bublitz, Paul Catley, Lisa Claydon, Thomas
Douglas, Nita Farahany, Joseph J. Fins, Sara Goering, Pim Haselager, Fabrice
Jotterand, Andrea Lavazza, Allan McCay, Abel Wajnerman Paz, Stephen Rainey,
Jesper Ryberg, Phil... | Minding rights: Mapping ethical and legal foundations of 'neurorights' | null | null | null | null | q-bio.NC cs.CY | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The rise of neurotechnologies, especially in combination with AI-based
methods for brain data analytics, has given rise to concerns around the
protection of mental privacy, mental integrity and cognitive liberty - often
framed as 'neurorights' in ethical, legal and policy discussions. Several
states are now looking a... | [
{
"created": "Mon, 13 Feb 2023 11:36:23 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Mar 2023 19:52:39 GMT",
"version": "v2"
}
] | 2023-03-22 | [
[
"Ligthart",
"Sjors",
""
],
[
"Ienca",
"Marcello",
""
],
[
"Meynen",
"Gerben",
""
],
[
"Molnar-Gabor",
"Fruzsina",
""
],
[
"Andorno",
"Roberto",
""
],
[
"Bublitz",
"Christoph",
""
],
[
"Catley",
"Paul",
""
... | The rise of neurotechnologies, especially in combination with AI-based methods for brain data analytics, has given rise to concerns around the protection of mental privacy, mental integrity and cognitive liberty - often framed as 'neurorights' in ethical, legal and policy discussions. Several states are now looking at ... |
1812.00052 | Sylvestre Aureliano Carvalho | Sylvestre Aureliano Carvalho and Marcelo Lobato Martins | Community structures in allelopathic interaction networks: an
eco-evolutionary approach | null | Phys. Rev. E 102, 042305 (2020) | 10.1103/PhysRevE.102.042305 | null | q-bio.PE physics.bio-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nowadays, evidence is mounting that the race of living organisms for
adaptation to the chemicals synthesized by their neighbours may drive community
structures. Particularly, some bacterial infections and plant invasions
disruptive of the native community rely on the release of allelochemicals that
inhibit or kill se... | [
{
"created": "Fri, 30 Nov 2018 20:48:29 GMT",
"version": "v1"
}
] | 2020-10-14 | [
[
"Carvalho",
"Sylvestre Aureliano",
""
],
[
"Martins",
"Marcelo Lobato",
""
]
] | Nowadays, evidence is mounting that the race of living organisms for adaptation to the chemicals synthesized by their neighbours may drive community structures. Particularly, some bacterial infections and plant invasions disruptive of the native community rely on the release of allelochemicals that inhibit or kill sens... |
2310.04730 | Juan Li | Juan Li and Claudia Bank | Dominance and multi-locus interaction | 26 pages, 3 figures, 2 tables | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Dominance is usually considered a constant value that describes the relative
difference in fitness or phenotype between heterozygotes and the average of
homozygotes at a focal polymorphic locus. However, the observed dominance can
vary with the genetic background of the focal locus. Here, alleles at other
loci modify... | [
{
"created": "Sat, 7 Oct 2023 08:10:11 GMT",
"version": "v1"
},
{
"created": "Sun, 3 Dec 2023 00:04:57 GMT",
"version": "v2"
}
] | 2023-12-05 | [
[
"Li",
"Juan",
""
],
[
"Bank",
"Claudia",
""
]
] | Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify t... |
2203.06128 | Ashish B. George | Ashish B. George, Tong Wang, Sergei Maslov | Functional universality in slow-growing microbial communities arises
from thermodynamic constraints | null | null | null | null | q-bio.PE cond-mat.stat-mech nlin.AO physics.bio-ph q-bio.MN | http://creativecommons.org/licenses/by-sa/4.0/ | The dynamics of microbial communities is incredibly complex, determined by
competition for metabolic substrates and cross-feeding of byproducts. Species
in the community grow by harvesting energy from chemical reactions that
transform substrates to products. In many anoxic environments, these reactions
are close to t... | [
{
"created": "Fri, 11 Mar 2022 17:56:10 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Mar 2022 19:08:43 GMT",
"version": "v2"
}
] | 2022-03-22 | [
[
"George",
"Ashish B.",
""
],
[
"Wang",
"Tong",
""
],
[
"Maslov",
"Sergei",
""
]
] | The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to the... |
2001.03560 | Justin Kinney | Ammar Tareen, Justin B. Kinney | Biophysical models of cis-regulation as interpretable neural networks | Presented at the 14th conference on Machine Learning in Computational
Biology (MLCB 2019), Vancouver, Canada. Revised to add a link to code and to
correct a typo in the King-Altman diagrams shown in Figure 3 | null | null | null | q-bio.MN cs.LG physics.bio-ph q-bio.QM stat.ML | http://creativecommons.org/licenses/by-sa/4.0/ | The adoption of deep learning techniques in genomics has been hindered by the
difficulty of mechanistically interpreting the models that these techniques
produce. In recent years, a variety of post-hoc attribution methods have been
proposed for addressing this neural network interpretability problem in the
context of... | [
{
"created": "Mon, 30 Dec 2019 14:45:58 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Feb 2020 22:07:08 GMT",
"version": "v2"
}
] | 2020-02-11 | [
[
"Tareen",
"Ammar",
""
],
[
"Kinney",
"Justin B.",
""
]
] | The adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years, a variety of post-hoc attribution methods have been proposed for addressing this neural network interpretability problem in the context of g... |
q-bio/0509019 | Guido Tiana | R. A. Broglia, D. Provasi, F. Vasile, G. Ottolina, R.Longhi and G.
Tiana | A folding inhibitor of the HIV-1 Protease | null | null | null | null | q-bio.BM | null | Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life
cycle, its inhibition can control AIDS. The folding of single domain proteins,
like each of the monomers forming the HIV-1-PR homodimer, is controlled by
local elementary structures (LES, folding units stabilized by strongly
interacting, highly... | [
{
"created": "Thu, 15 Sep 2005 08:10:04 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Broglia",
"R. A.",
""
],
[
"Provasi",
"D.",
""
],
[
"Vasile",
"F.",
""
],
[
"Ottolina",
"G.",
""
],
[
"Longhi",
"R.",
""
],
[
"Tiana",
"G.",
""
]
] | Being the HIV-1 Protease (HIV-1-PR) an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly c... |
2006.13012 | Robin Thompson | Robin N Thompson, T Deirdre Hollingsworth, Valerie Isham, Daniel
Arribas-Bel, Ben Ashby, Tom Britton, Peter Challoner, Lauren H K Chappell,
Hannah Clapham, Nik J Cunniffe, A Philip Dawid, Christl A Donnelly, Rosalind
Eggo, Sebastian Funk, Nigel Gilbert, Julia R Gog, Paul Glendinning, William S
Hart, Hans Heeste... | Key Questions for Modelling COVID-19 Exit Strategies | null | Proc. Roy. Soc. B, 2020 | 10.1098/rspb.2020.1405 | null | q-bio.OT q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Combinations of intense non-pharmaceutical interventions ('lockdowns') were
introduced in countries worldwide to reduce SARS-CoV-2 transmission. Many
governments have begun to implement lockdown exit strategies that allow
restrictions to be relaxed while attempting to control the risk of a surge in
cases. Mathematica... | [
{
"created": "Sun, 21 Jun 2020 17:06:13 GMT",
"version": "v1"
},
{
"created": "Wed, 24 Jun 2020 15:09:13 GMT",
"version": "v2"
},
{
"created": "Thu, 25 Jun 2020 14:09:15 GMT",
"version": "v3"
},
{
"created": "Tue, 21 Jul 2020 13:08:34 GMT",
"version": "v4"
}
] | 2020-08-17 | [
[
"Thompson",
"Robin N",
""
],
[
"Hollingsworth",
"T Deirdre",
""
],
[
"Isham",
"Valerie",
""
],
[
"Arribas-Bel",
"Daniel",
""
],
[
"Ashby",
"Ben",
""
],
[
"Britton",
"Tom",
""
],
[
"Challoner",
"Peter",
""
... | Combinations of intense non-pharmaceutical interventions ('lockdowns') were introduced in countries worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement lockdown exit strategies that allow restrictions to be relaxed while attempting to control the risk of a surge in cases. Mathematical ... |
1611.07272 | Ines Samengo | Maria da Fonseca and Ines Samengo | Derivation of human chromatic discrimination ability from an
information-theoretical notion of distance in color space | 23 pages, 10 figures | Neural Computation doi:10.1162/NECO_a_00903 pp 1-18 (2016) | 10.1162/NECO_a_00903 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The accuracy with which humans can detect small chromatic differences varies
throughout color space. For example, we are far more precise when
discriminating two similar orange stimuli than two similar green stimuli. In
order for two colors to be perceived as different, the neurons representing
chromatic information ... | [
{
"created": "Tue, 22 Nov 2016 12:27:04 GMT",
"version": "v1"
}
] | 2016-11-23 | [
[
"da Fonseca",
"Maria",
""
],
[
"Samengo",
"Ines",
""
]
] | The accuracy with which humans can detect small chromatic differences varies throughout color space. For example, we are far more precise when discriminating two similar orange stimuli than two similar green stimuli. In order for two colors to be perceived as different, the neurons representing chromatic information mu... |
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