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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0312030 | Francois Coppex | Francois Coppex, Michel Droz, Adam Lipowski | Extinction dynamics of Lotka-Volterra ecosystems on evolving networks | 8 pages, 6 eps figures included | Phys. Rev. E 69, 061901 (2004) | 10.1103/PhysRevE.69.061901 | null | q-bio.PE cond-mat.stat-mech | null | We study a model of a multi-species ecosystem described by
Lotka-Volterra-like equations. Interactions among species form a network whose
evolution is determined by the dynamics of the model. Numerical simulations
show power-law distribution of intervals between extinctions, but only for
ecosystems with sufficient va... | [
{
"created": "Fri, 19 Dec 2003 09:40:19 GMT",
"version": "v1"
},
{
"created": "Wed, 2 Jun 2004 08:18:17 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Coppex",
"Francois",
""
],
[
"Droz",
"Michel",
""
],
[
"Lipowski",
"Adam",
""
]
] | We study a model of a multi-species ecosystem described by Lotka-Volterra-like equations. Interactions among species form a network whose evolution is determined by the dynamics of the model. Numerical simulations show power-law distribution of intervals between extinctions, but only for ecosystems with sufficient vari... |
2306.03399 | Haoyu Cheng | Haoyu Cheng, Mobin Asri, Julian Lucas, Sergey Koren, and Heng Li | Scalable telomere-to-telomere assembly for diploid and polyploid genomes
with double graph | 14 pages, 4 fuhires | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Despite recent advances in the length and the accuracy of long-read data,
building haplotype-resolved genome assemblies from telomere to telomere still
requires considerable computational resources. In this study, we present an
efficient de novo assembly algorithm that combines multiple sequencing
technologies to sca... | [
{
"created": "Tue, 6 Jun 2023 04:29:12 GMT",
"version": "v1"
}
] | 2023-06-07 | [
[
"Cheng",
"Haoyu",
""
],
[
"Asri",
"Mobin",
""
],
[
"Lucas",
"Julian",
""
],
[
"Koren",
"Sergey",
""
],
[
"Li",
"Heng",
""
]
] | Despite recent advances in the length and the accuracy of long-read data, building haplotype-resolved genome assemblies from telomere to telomere still requires considerable computational resources. In this study, we present an efficient de novo assembly algorithm that combines multiple sequencing technologies to scale... |
1608.02375 | Dan Wang | Dan Wang, Shuaicheng Li, Fei Guo, Lusheng Wang | Core-genome scaffold comparison reveals the prevalence that inversion
events are associated with pairs of inverted repeats | 8 pages, 11 figures | null | null | null | q-bio.GN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Genome rearrangement plays an important role in evolutionary
biology and has profound impacts on phenotype in organisms ranging from
microbes to humans. The mechanisms for genome rearrangement events remain
unclear. Lots of comparisons have been conducted among different species. To
reveal the mechanisms ... | [
{
"created": "Mon, 8 Aug 2016 10:36:36 GMT",
"version": "v1"
}
] | 2016-08-09 | [
[
"Wang",
"Dan",
""
],
[
"Li",
"Shuaicheng",
""
],
[
"Guo",
"Fei",
""
],
[
"Wang",
"Lusheng",
""
]
] | Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of comparisons have been conducted among different species. To reveal the mechanisms fo... |
1902.03216 | Gaoxiang Zhou | Gaoxiang Zhou, Kai-Wen Liang, Natasa Miskov-Zivanov | Intervention Pathway Discovery via Context-Dependent Dynamic Sensitivity
Analysis | null | null | null | null | q-bio.MN q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | The sensitivity analysis of biological system models can significantly
contribute to identifying and explaining influences of internal or external
changes on model and its elements. We propose here a comprehensive framework to
study sensitivity of intra-cellular networks and to identify key intervention
pathways, by ... | [
{
"created": "Fri, 8 Feb 2019 18:27:24 GMT",
"version": "v1"
}
] | 2019-02-11 | [
[
"Zhou",
"Gaoxiang",
""
],
[
"Liang",
"Kai-Wen",
""
],
[
"Miskov-Zivanov",
"Natasa",
""
]
] | The sensitivity analysis of biological system models can significantly contribute to identifying and explaining influences of internal or external changes on model and its elements. We propose here a comprehensive framework to study sensitivity of intra-cellular networks and to identify key intervention pathways, by pe... |
q-bio/0401042 | Thomas R. Weikl | Thomas R. Weikl and Reinhard Lipowsky | Mechanisms of pattern formation during T cell adhesion | 12 pages, 8 figures | null | 10.1529/biophysj.104.045609 | null | q-bio.SC cond-mat.stat-mech q-bio.CB | null | T cells form intriguing patterns during adhesion to antigen-presenting cells.
The patterns at the cell-cell contact zone are composed of two types of
domains, which either contain short TCR/MHCp receptor-ligand complexes or the
longer LFA-1/ICAM-1 complexes. The final pattern consists of a central TCR/MHCp
domain sur... | [
{
"created": "Wed, 28 Jan 2004 15:51:43 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Weikl",
"Thomas R.",
""
],
[
"Lipowsky",
"Reinhard",
""
]
] | T cells form intriguing patterns during adhesion to antigen-presenting cells. The patterns at the cell-cell contact zone are composed of two types of domains, which either contain short TCR/MHCp receptor-ligand complexes or the longer LFA-1/ICAM-1 complexes. The final pattern consists of a central TCR/MHCp domain surro... |
1203.0222 | Carsten Lemmen | Carsten Lemmen and Kai W. Wirtz | On the sensitivity of the simulated European Neolithic transition to
climate extremes | Revised version submitted to the Journal of Archaeological Science,
special issue on The World Reshaped: impacts of the Neolithic transition. 10
pages, 4 figures, 1 table + supplementary material | null | 10.1016/j.jas.2012.10.023 | null | q-bio.PE cs.MA math.DS physics.geo-ph | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Was the spread of agropastoralism from the Fertile Crescent throughout Europe
influenced by extreme climate events, or was it independent of climate? We here
generate idealized climate events using palaeoclimate records. In a
mathematical model of regional sociocultural development, these events disturb
the subsisten... | [
{
"created": "Thu, 1 Mar 2012 15:48:59 GMT",
"version": "v1"
},
{
"created": "Sat, 11 Aug 2012 06:02:18 GMT",
"version": "v2"
}
] | 2012-11-01 | [
[
"Lemmen",
"Carsten",
""
],
[
"Wirtz",
"Kai W.",
""
]
] | Was the spread of agropastoralism from the Fertile Crescent throughout Europe influenced by extreme climate events, or was it independent of climate? We here generate idealized climate events using palaeoclimate records. In a mathematical model of regional sociocultural development, these events disturb the subsistence... |
q-bio/0412014 | Tobias Bollenbach | T. Bollenbach, K. Kruse, P. Pantazis, M. Gonz\'alez-Gait\'an, and F.
J\"ulicher | Robust formation of morphogen gradients | null | Physical Review Letters 94, 018103 (2005) | 10.1103/PhysRevLett.94.018103 | null | q-bio.OT physics.bio-ph | null | We discuss the formation of graded morphogen profiles in a cell layer by
nonlinear transport phenomena, important for patterning developing organisms.
We focus on a process termed transcytosis, where morphogen transport results
from binding of ligands to receptors on the cell surface, incorporation into
the cell and ... | [
{
"created": "Wed, 8 Dec 2004 14:53:16 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bollenbach",
"T.",
""
],
[
"Kruse",
"K.",
""
],
[
"Pantazis",
"P.",
""
],
[
"González-Gaitán",
"M.",
""
],
[
"Jülicher",
"F.",
""
]
] | We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from binding of ligands to receptors on the cell surface, incorporation into the cell and su... |
1606.01932 | Warren Lord | Warren M. Lord, Jie Sun, Nicholas T. Ouellette, and Erik M. Bollt | Inference of Causal Information Flow in Collective Animal Behavior | To appear in TMBMC special issue in honor of Claude Shannon's 100th
Birthday | null | 10.1109/TMBMC.2016.2632099 | null | q-bio.QM cs.IT math.DS math.IT q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding and even defining what constitutes animal interactions remains
a challenging problem. Correlational tools may be inappropriate for detecting
communication between a set of many agents exhibiting nonlinear behavior. A
different approach is to define coordinated motions in terms of an information
theoreti... | [
{
"created": "Fri, 3 Jun 2016 00:53:28 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Dec 2016 21:43:11 GMT",
"version": "v2"
}
] | 2017-01-02 | [
[
"Lord",
"Warren M.",
""
],
[
"Sun",
"Jie",
""
],
[
"Ouellette",
"Nicholas T.",
""
],
[
"Bollt",
"Erik M.",
""
]
] | Understanding and even defining what constitutes animal interactions remains a challenging problem. Correlational tools may be inappropriate for detecting communication between a set of many agents exhibiting nonlinear behavior. A different approach is to define coordinated motions in terms of an information theoretic ... |
q-bio/0611089 | Alain Destexhe | R. Brette, M. Rudolph, T. Carnevale, M. Hines, D. Beeman, J. M. Bower,
M. Diesmann, A. Morrison, P. H. Goodman, F. C. Harris Jr., M. Zirpe, T.
Natschlager, D. Pecevski, B. Ermentrout, M. Djurfeldt, A. Lansner, O. Rochel,
T. Vieville, E. Muller, A. P. Davison, S. El Boustani, A. Destexhe | Simulation of networks of spiking neurons: A review of tools and
strategies | 49 pages, 24 figures, 1 table; review article, Journal of
Computational Neuroscience, in press (2007) | Journal of Computational Neuroscience 2007 Dec;23(3):349-98. Epub
2007 Jul 12 | null | null | q-bio.NC | null | We review different aspects of the simulation of spiking neural networks. We
start by reviewing the different types of simulation strategies and algorithms
that are currently implemented. We next review the precision of those
simulation strategies, in particular in cases where plasticity depends on the
exact timing o... | [
{
"created": "Tue, 28 Nov 2006 14:35:19 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Apr 2007 21:41:07 GMT",
"version": "v2"
}
] | 2008-01-26 | [
[
"Brette",
"R.",
""
],
[
"Rudolph",
"M.",
""
],
[
"Carnevale",
"T.",
""
],
[
"Hines",
"M.",
""
],
[
"Beeman",
"D.",
""
],
[
"Bower",
"J. M.",
""
],
[
"Diesmann",
"M.",
""
],
[
"Morrison",
"A.",
... | We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of ... |
2101.04081 | Apostolos Gkatzionis | Apostolos Gkatzionis, Stephen Burgess and Paul J. Newcombe | Statistical Methods for cis-Mendelian Randomization with Two-sample
Summary-level Data | 39 pages (33 main text + 6 supplement), 4 figures, 7 tables | null | null | null | q-bio.QM q-bio.GN stat.AP | http://creativecommons.org/licenses/by/4.0/ | Mendelian randomization is the use of genetic variants to assess the
existence of a causal relationship between a risk factor and an outcome of
interest. Here, we focus on two-sample summary-data Mendelian randomization
analyses with many correlated variants from a single gene region, and
particularly on cis-Mendelia... | [
{
"created": "Mon, 11 Jan 2021 18:23:04 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Sep 2022 10:22:10 GMT",
"version": "v2"
}
] | 2022-09-16 | [
[
"Gkatzionis",
"Apostolos",
""
],
[
"Burgess",
"Stephen",
""
],
[
"Newcombe",
"Paul J.",
""
]
] | Mendelian randomization is the use of genetic variants to assess the existence of a causal relationship between a risk factor and an outcome of interest. Here, we focus on two-sample summary-data Mendelian randomization analyses with many correlated variants from a single gene region, and particularly on cis-Mendelian ... |
2403.02724 | Peng Li | Lingmin Zhan, Yuanyuan Zhang, Yingdong Wang, Aoyi Wang, Caiping Cheng,
Jinzhong Zhao, Wuxia Zhang, Peng Lia, Jianxin Chen | A genome-scale deep learning model to predict gene expression changes of
genetic perturbations from multiplex biological networks | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Systematic characterization of biological effects to genetic perturbation is
essential to the application of molecular biology and biomedicine. However, the
experimental exhaustion of genetic perturbations on the genome-wide scale is
challenging. Here, we show that TranscriptionNet, a deep learning model that
integra... | [
{
"created": "Tue, 5 Mar 2024 07:31:46 GMT",
"version": "v1"
}
] | 2024-03-06 | [
[
"Zhan",
"Lingmin",
""
],
[
"Zhang",
"Yuanyuan",
""
],
[
"Wang",
"Yingdong",
""
],
[
"Wang",
"Aoyi",
""
],
[
"Cheng",
"Caiping",
""
],
[
"Zhao",
"Jinzhong",
""
],
[
"Zhang",
"Wuxia",
""
],
[
"Lia",
... | Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is challenging. Here, we show that TranscriptionNet, a deep learning model that integrate... |
1804.01342 | Alexander Gorban | Alexander N. Gorban and Nurdan \c{C}abuko\v{g}lu | Mobility cost and degenerated diffusion in kinesis models | The final version submitted to the journal | Ecological Complexity 36 (2018), 16-21 | 10.1016/j.ecocom.2018.06.007 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | A new critical effect is predicted in population dispersal. It is based on
the fact that a trade-off between the advantages of mobility and the cost of
mobility breaks with a significant deterioration in living conditions. The
recently developed model of purposeful kinesis (Gorban \& \c{C}abuko\v{g}lu,
Ecological Com... | [
{
"created": "Wed, 4 Apr 2018 10:59:32 GMT",
"version": "v1"
},
{
"created": "Wed, 16 May 2018 08:52:53 GMT",
"version": "v2"
},
{
"created": "Thu, 28 Feb 2019 08:18:08 GMT",
"version": "v3"
}
] | 2019-03-01 | [
[
"Gorban",
"Alexander N.",
""
],
[
"Çabukoǧlu",
"Nurdan",
""
]
] | A new critical effect is predicted in population dispersal. It is based on the fact that a trade-off between the advantages of mobility and the cost of mobility breaks with a significant deterioration in living conditions. The recently developed model of purposeful kinesis (Gorban \& \c{C}abuko\v{g}lu, Ecological Compl... |
1210.4322 | Vladimir Chechetkin R. | V. R. Chechetkin and V.V. Lobzin | Stability of the genetic code and optimal parameters of amino acids | 9 pages, 3 figures | Journal of Theoretical Biology V. 269, Pp. 57-63, 2011 | 10.1016/j.jtbi.2010.10.015 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The standard genetic code is known to be much more efficient in minimizing
adverse effects of misreading errors and one-point mutations in comparison with
a random code having the same structure, i.e. the same number of codons coding
for each particular amino acid. We study the inverse problem, how the code
structure... | [
{
"created": "Tue, 16 Oct 2012 09:16:48 GMT",
"version": "v1"
}
] | 2012-10-17 | [
[
"Chechetkin",
"V. R.",
""
],
[
"Lobzin",
"V. V.",
""
]
] | The standard genetic code is known to be much more efficient in minimizing adverse effects of misreading errors and one-point mutations in comparison with a random code having the same structure, i.e. the same number of codons coding for each particular amino acid. We study the inverse problem, how the code structure a... |
0803.2085 | Conrad Burden | Sylvain Foret, Susan R. Wilson, Conrad J. Burden | Empirical distribution of k-word matches in biological sequences | 23 pages, 10 figures | Pattern Recognition 42 (2009) 539-548 | 10.1016/j.patcog.2008.06.026 | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This study focuses on an alignment-free sequence comparison method: the
number of words of length k shared between two sequences, also known as the D_2
statistic. The advantages of the use of this statistic over alignment-based
methods are firstly that it does not assume that homologous segments are
contiguous, and s... | [
{
"created": "Fri, 14 Mar 2008 05:14:55 GMT",
"version": "v1"
}
] | 2009-09-08 | [
[
"Foret",
"Sylvain",
""
],
[
"Wilson",
"Susan R.",
""
],
[
"Burden",
"Conrad J.",
""
]
] | This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are firstly that it does not assume that homologous segments are contiguous, and sec... |
1502.01061 | Robert Noble | Robert Noble, Oliver Kaltz, Michael E Hochberg | Statistical interpretations and new findings on Variation in Cancer Risk
Among Tissues | 17 pages | null | null | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Tomasetti and Vogelstein (2015a) find that the incidence of a set of cancer
types is correlated with the total number of normal stem cell divisions. Here,
we separate the effects of standing stem cell number (i.e., organ or tissue
size) and per stem cell lifetime replication rate. We show that each has a
statisticall... | [
{
"created": "Tue, 3 Feb 2015 22:58:02 GMT",
"version": "v1"
}
] | 2015-02-05 | [
[
"Noble",
"Robert",
""
],
[
"Kaltz",
"Oliver",
""
],
[
"Hochberg",
"Michael E",
""
]
] | Tomasetti and Vogelstein (2015a) find that the incidence of a set of cancer types is correlated with the total number of normal stem cell divisions. Here, we separate the effects of standing stem cell number (i.e., organ or tissue size) and per stem cell lifetime replication rate. We show that each has a statistically ... |
q-bio/0309023 | Bijan Pesaran | B. Pesaran and P. P. Mitra | Idl Signal Processing Library 1.0 | 13 IDL .pro files, 1 .html file, 1 .ps file, 1 license file. Download
the source for the IDL files (save as .tar.gz) Read idl_lib.ps for
instructions on use. Originally submitted to the neuro-sys archive which was
never publicly announced (was 9801001) | null | null | CMP-001 | q-bio.QM | null | We make available a library of documented IDL .pro files as well as a
shareable object library that allows IDL to call routines from LAPACK. The
routines are for use in the spectral analysis of time series data. The primary
focus of these routines are David Thomson's multitaper methods but a whole
range of functions ... | [
{
"created": "Tue, 20 Jan 1998 18:38:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pesaran",
"B.",
""
],
[
"Mitra",
"P. P.",
""
]
] | We make available a library of documented IDL .pro files as well as a shareable object library that allows IDL to call routines from LAPACK. The routines are for use in the spectral analysis of time series data. The primary focus of these routines are David Thomson's multitaper methods but a whole range of functions wi... |
1605.06925 | Lorenz K. Muller | Lorenz K. Muller and Giacomo Indiveri | Neural Sampling by Irregular Gating Inhibition of Spiking Neurons and
Attractor Networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A long tradition in theoretical neuroscience casts sensory processing in the
brain as the process of inferring the maximally consistent interpretations of
imperfect sensory input. Recently it has been shown that Gamma-band inhibition
can enable neural attractor networks to approximately carry out such a sampling
mech... | [
{
"created": "Mon, 23 May 2016 07:54:46 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Sep 2016 07:13:07 GMT",
"version": "v2"
},
{
"created": "Thu, 31 Aug 2017 08:43:49 GMT",
"version": "v3"
},
{
"created": "Fri, 1 Sep 2017 06:39:55 GMT",
"version": "v4"
}
] | 2017-09-04 | [
[
"Muller",
"Lorenz K.",
""
],
[
"Indiveri",
"Giacomo",
""
]
] | A long tradition in theoretical neuroscience casts sensory processing in the brain as the process of inferring the maximally consistent interpretations of imperfect sensory input. Recently it has been shown that Gamma-band inhibition can enable neural attractor networks to approximately carry out such a sampling mechan... |
1707.01974 | Dervis Vural | Aylin Acun, Dervis Can Vural, Pinar Zorlutuna | A Tissue Engineered Model of Aging: Interdependence and Cooperative
Effects in Failing Tissues | null | null | null | null | q-bio.TO q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Aging remains a fundamental open problem in modern biology. Although there
exist a number of theories on aging on the cellular scale, nearly nothing is
known about how microscopic failures cascade to macroscopic failures of
tissues, organs and ultimately the organism. The goal of this work is to bridge
microscopic ce... | [
{
"created": "Thu, 6 Jul 2017 21:38:39 GMT",
"version": "v1"
}
] | 2017-07-10 | [
[
"Acun",
"Aylin",
""
],
[
"Vural",
"Dervis Can",
""
],
[
"Zorlutuna",
"Pinar",
""
]
] | Aging remains a fundamental open problem in modern biology. Although there exist a number of theories on aging on the cellular scale, nearly nothing is known about how microscopic failures cascade to macroscopic failures of tissues, organs and ultimately the organism. The goal of this work is to bridge microscopic cell... |
1309.0267 | Wolfram Liebermeister | Wolfram Liebermeister | Structural thermokinetic modelling | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Translating metabolic networks into dynamic models is difficult if kinetic
constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction
elasticities by independent random numbers. Here I propose a variant that
accounts for reversible reactions and thermodynamics: in Structural
Thermokinetic Modelling (... | [
{
"created": "Sun, 1 Sep 2013 21:35:06 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Mar 2022 09:51:43 GMT",
"version": "v2"
}
] | 2022-03-08 | [
[
"Liebermeister",
"Wolfram",
""
]
] | Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant that accounts for reversible reactions and thermodynamics: in Structural Thermokinetic Modelling (ST... |
2401.17328 | Farnoush Shishehbori | Farnoush Shishehbori, Zainab Awan | Enhancing Cardiovascular Disease Risk Prediction with Machine Learning
Models | 46 pages (including references), 5 Figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Cardiovascular disease remains a leading global cause of mortality,
necessitating accurate risk prediction tools. Traditional methods, such as
QRISK and the Framingham heart score, exhibit limitations in their ability to
incorporate comprehensive patient data, potentially resulting in incomplete
risk factor considera... | [
{
"created": "Mon, 29 Jan 2024 19:08:33 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Feb 2024 10:42:53 GMT",
"version": "v2"
},
{
"created": "Fri, 9 Feb 2024 16:13:09 GMT",
"version": "v3"
}
] | 2024-02-12 | [
[
"Shishehbori",
"Farnoush",
""
],
[
"Awan",
"Zainab",
""
]
] | Cardiovascular disease remains a leading global cause of mortality, necessitating accurate risk prediction tools. Traditional methods, such as QRISK and the Framingham heart score, exhibit limitations in their ability to incorporate comprehensive patient data, potentially resulting in incomplete risk factor considerati... |
2105.01167 | Qi Su | Qi Su, Joshua. B Plotkin | Evolution of cooperation with asymmetric social interactions | 40 pages, 11 figures | null | 10.1073/pnas.2113468118 | null | q-bio.PE math.DS physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | How cooperation emerges in human societies is both an evolutionary enigma,
and a practical problem with tangible implications for societal health.
Population structure has long been recognized as a catalyst for cooperation
because local interactions enable reciprocity. Analysis of this phenomenon
typically assumes bi... | [
{
"created": "Mon, 3 May 2021 20:57:10 GMT",
"version": "v1"
},
{
"created": "Thu, 20 May 2021 19:50:15 GMT",
"version": "v2"
}
] | 2022-01-06 | [
[
"Su",
"Qi",
""
],
[
"Plotkin",
"Joshua. B",
""
]
] | How cooperation emerges in human societies is both an evolutionary enigma, and a practical problem with tangible implications for societal health. Population structure has long been recognized as a catalyst for cooperation because local interactions enable reciprocity. Analysis of this phenomenon typically assumes bi-d... |
1702.06405 | David Caldwell | David J. Caldwell, Jing Wu, Kaitlyn Casimo, Jeffrey G. Ojemann, Rajesh
P.N. Rao | Interactive Web Application for Exploring Matrices of Neural
Connectivity | 4 pages, IEEE NER 2017 | null | 10.1109/NER.2017.8008287 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present here a browser-based application for visualizing patterns of
connectivity in 3D stacked data matrices with large numbers of pairwise
relations. Visualizing a connectivity matrix, looking for trends and patterns,
and dynamically manipulating these values is a challenge for scientists from
diverse fields, in... | [
{
"created": "Tue, 21 Feb 2017 14:36:17 GMT",
"version": "v1"
}
] | 2018-01-04 | [
[
"Caldwell",
"David J.",
""
],
[
"Wu",
"Jing",
""
],
[
"Casimo",
"Kaitlyn",
""
],
[
"Ojemann",
"Jeffrey G.",
""
],
[
"Rao",
"Rajesh P. N.",
""
]
] | We present here a browser-based application for visualizing patterns of connectivity in 3D stacked data matrices with large numbers of pairwise relations. Visualizing a connectivity matrix, looking for trends and patterns, and dynamically manipulating these values is a challenge for scientists from diverse fields, incl... |
q-bio/0509007 | Isaac Hubner | Isaac A. Hubner, Eric J. Deeds, and Eugene I. Shakhnovich | High resolution protein folding with a transferable potential | submitted to PNAS 2005-03-16 | null | 10.1073/pnas.0502181102 | null | q-bio.BM | null | A generalized computational method for folding proteins with a fully
transferable potential and geometrically realistic all-atom model is presented
and tested on seven different helix bundle proteins. The protocol, which
includes graph-theoretical analysis of the ensemble of resulting folded
conformations, was system... | [
{
"created": "Wed, 7 Sep 2005 14:24:27 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Hubner",
"Isaac A.",
""
],
[
"Deeds",
"Eric J.",
""
],
[
"Shakhnovich",
"Eugene I.",
""
]
] | A generalized computational method for folding proteins with a fully transferable potential and geometrically realistic all-atom model is presented and tested on seven different helix bundle proteins. The protocol, which includes graph-theoretical analysis of the ensemble of resulting folded conformations, was systemat... |
1007.0327 | Michael Assaf | Michael Assaf and Mauro Mobilia | Large Fluctuations and Fixation in Evolutionary Games | 17 pages, 10 figures, to appear in JSTAT | J. Stat. Mech., (2010) P09009 | 10.1088/1742-5468/2010/09/P09009 | null | q-bio.PE cond-mat.stat-mech nlin.AO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study large fluctuations in evolutionary games belonging to the
coordination and anti-coordination classes. The dynamics of these games,
modeling cooperation dilemmas, is characterized by a coexistence fixed point
separating two absorbing states. We are particularly interested in the problem
of fixation that refer... | [
{
"created": "Fri, 2 Jul 2010 10:03:34 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Aug 2010 12:42:45 GMT",
"version": "v2"
},
{
"created": "Thu, 26 Aug 2010 10:36:31 GMT",
"version": "v3"
}
] | 2015-05-19 | [
[
"Assaf",
"Michael",
""
],
[
"Mobilia",
"Mauro",
""
]
] | We study large fluctuations in evolutionary games belonging to the coordination and anti-coordination classes. The dynamics of these games, modeling cooperation dilemmas, is characterized by a coexistence fixed point separating two absorbing states. We are particularly interested in the problem of fixation that refers ... |
1907.00230 | Alessandro Torcini Dr | Hongjie Bi, Marco Segneri, Matteo di Volo, Alessandro Torcini | Coexistence of fast and slow gamma oscillations in one population of
inhibitory spiking neurons | 20 pages, 14 figures | Phys. Rev. Research 2, 013042 (2020) | 10.1103/PhysRevResearch.2.013042 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Oscillations are a hallmark of neural population activity in various brain
regions with a spectrum covering a wide range of frequencies. Within this
spectrum gamma oscillations have received particular attention due to their
ubiquitous nature and to their correlation with higher brain functions.
Recently, it has been... | [
{
"created": "Sat, 29 Jun 2019 16:09:48 GMT",
"version": "v1"
}
] | 2020-01-22 | [
[
"Bi",
"Hongjie",
""
],
[
"Segneri",
"Marco",
""
],
[
"di Volo",
"Matteo",
""
],
[
"Torcini",
"Alessandro",
""
]
] | Oscillations are a hallmark of neural population activity in various brain regions with a spectrum covering a wide range of frequencies. Within this spectrum gamma oscillations have received particular attention due to their ubiquitous nature and to their correlation with higher brain functions. Recently, it has been r... |
1301.7734 | Pablo Cordero | Pablo Cordero, Wipapat Kladwang, Christopher C. VanLang and Rhiju Das | A mutate-and-map protocol for inferring base pairs in structured RNA | 22 pages, 5 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chemical mapping is a widespread technique for structural analysis of nucleic
acids in which a molecule's reactivity to different probes is quantified at
single-nucleotide resolution and used to constrain structural modeling. This
experimental framework has been extensively revisited in the past decade with
new strat... | [
{
"created": "Thu, 31 Jan 2013 19:58:16 GMT",
"version": "v1"
}
] | 2013-02-01 | [
[
"Cordero",
"Pablo",
""
],
[
"Kladwang",
"Wipapat",
""
],
[
"VanLang",
"Christopher C.",
""
],
[
"Das",
"Rhiju",
""
]
] | Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strateg... |
2204.07186 | Naoki Hiratani | Naoki Hiratani, Haim Sompolinsky | Optimal quadratic binding for relational reasoning in vector symbolic
neural architectures | 32 pages, 9 figures | null | null | null | q-bio.NC cs.AI | http://creativecommons.org/licenses/by/4.0/ | Binding operation is fundamental to many cognitive processes, such as
cognitive map formation, relational reasoning, and language comprehension. In
these processes, two different modalities, such as location and objects, events
and their contextual cues, and words and their roles, need to be bound
together, but littl... | [
{
"created": "Thu, 14 Apr 2022 18:41:27 GMT",
"version": "v1"
}
] | 2022-04-18 | [
[
"Hiratani",
"Naoki",
""
],
[
"Sompolinsky",
"Haim",
""
]
] | Binding operation is fundamental to many cognitive processes, such as cognitive map formation, relational reasoning, and language comprehension. In these processes, two different modalities, such as location and objects, events and their contextual cues, and words and their roles, need to be bound together, but little ... |
1409.1933 | Alessandro Torcini Dr | Stefano Luccioli, Eshel Ben-Jacob, Ari Barzilai, Paolo Bonifazi,
Alessandro Torcini | Clique of functional hubs orchestrates population bursts in
developmentally regulated neural networks | 39 pages, 15 figures, to appear in PLOS Computational Biology | PLoS Comput Biol 10(9) (2014) e1003823 | 10.1371/journal.pcbi.1003823 | null | q-bio.NC cond-mat.dis-nn physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It has recently been discovered that single neuron stimulation can impact
network dynamics in immature and adult neuronal circuits. Here we report a
novel mechanism which can explain in neuronal circuits, at an early stage of
development, the peculiar role played by a few specific neurons in
promoting/arresting the p... | [
{
"created": "Fri, 5 Sep 2014 20:11:32 GMT",
"version": "v1"
}
] | 2015-04-14 | [
[
"Luccioli",
"Stefano",
""
],
[
"Ben-Jacob",
"Eshel",
""
],
[
"Barzilai",
"Ari",
""
],
[
"Bonifazi",
"Paolo",
""
],
[
"Torcini",
"Alessandro",
""
]
] | It has recently been discovered that single neuron stimulation can impact network dynamics in immature and adult neuronal circuits. Here we report a novel mechanism which can explain in neuronal circuits, at an early stage of development, the peculiar role played by a few specific neurons in promoting/arresting the pop... |
2003.14284 | Alfonso M. Ganan-Calvo | Alfonso M. Ganan-Calvo and Juan A. Hernandez Ramos | The fractal time growth of COVID-19 pandemic: an accurate self-similar
model, and urgent conclusions | null | null | null | null | q-bio.PE nlin.AO physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Current available data of the worldwide impact of the COVID-19 pandemic has
been analyzed using dimensional analysis and self-similarity hypotheses. We
show that the time series of infected population and deaths of the most
impacted and unprepared countries exhibits an asymptotic power law behavior,
compatible with t... | [
{
"created": "Tue, 31 Mar 2020 15:17:54 GMT",
"version": "v1"
}
] | 2020-04-01 | [
[
"Ganan-Calvo",
"Alfonso M.",
""
],
[
"Ramos",
"Juan A. Hernandez",
""
]
] | Current available data of the worldwide impact of the COVID-19 pandemic has been analyzed using dimensional analysis and self-similarity hypotheses. We show that the time series of infected population and deaths of the most impacted and unprepared countries exhibits an asymptotic power law behavior, compatible with the... |
2407.03441 | Simon Coetzee | Simon G. Coetzee and Dennis J. Hazelett | MotifbreakR v2: extended capability and database integration | 4 pages of text, 1 figure with 2 panels, 12 total pages. Source code,
documentation, and tutorials are available on Bioconductor at
https://bioconductor.org/packages/release/bioc/html/motifbreakR.html and
GitHub at https://github.com/Simon-Coetzee/motifBreakR | null | null | null | q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by-sa/4.0/ | MotifbreakR is a software tool that scans genetic variants against position
weight matrices of transcription factors (TF) to determine the potential for
the disruption of TF binding at the site of the variant. It leverages the
Bioconductor suite of software packages and annotations to operate across a
diverse array o... | [
{
"created": "Wed, 3 Jul 2024 18:34:03 GMT",
"version": "v1"
}
] | 2024-07-08 | [
[
"Coetzee",
"Simon G.",
""
],
[
"Hazelett",
"Dennis J.",
""
]
] | MotifbreakR is a software tool that scans genetic variants against position weight matrices of transcription factors (TF) to determine the potential for the disruption of TF binding at the site of the variant. It leverages the Bioconductor suite of software packages and annotations to operate across a diverse array of ... |
2008.11491 | Sam Blakeman | Sam Blakeman, Denis Mareschal | Selective Particle Attention: Visual Feature-Based Attention in Deep
Reinforcement Learning | null | null | null | null | q-bio.NC cs.CV cs.LG cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human brain uses selective attention to filter perceptual input so that
only the components that are useful for behaviour are processed using its
limited computational resources. We focus on one particular form of visual
attention known as feature-based attention, which is concerned with identifying
features of t... | [
{
"created": "Wed, 26 Aug 2020 11:07:50 GMT",
"version": "v1"
}
] | 2020-08-31 | [
[
"Blakeman",
"Sam",
""
],
[
"Mareschal",
"Denis",
""
]
] | The human brain uses selective attention to filter perceptual input so that only the components that are useful for behaviour are processed using its limited computational resources. We focus on one particular form of visual attention known as feature-based attention, which is concerned with identifying features of the... |
1902.08511 | David Papo | David Papo | Gauging functional brain activity: from distinguishability to
accessibility | 7 pages, 0 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Standard neuroimaging techniques provide non-invasive access not only to
human brain anatomy but also to its physiology. The activity recorded with
these techniques is generally called functional imaging, but what is observed
per se is an instance of dynamics, from which functional brain activity should
be extracted.... | [
{
"created": "Fri, 22 Feb 2019 14:39:40 GMT",
"version": "v1"
}
] | 2019-02-25 | [
[
"Papo",
"David",
""
]
] | Standard neuroimaging techniques provide non-invasive access not only to human brain anatomy but also to its physiology. The activity recorded with these techniques is generally called functional imaging, but what is observed per se is an instance of dynamics, from which functional brain activity should be extracted. D... |
2004.11841 | Felix Sattler | Felix Sattler, Jackie Ma, Patrick Wagner, David Neumann, Markus
Wenzel, Ralf Sch\"afer, Wojciech Samek, Klaus-Robert M\"uller, Thomas Wiegand | Risk Estimation of SARS-CoV-2 Transmission from Bluetooth Low Energy
Measurements | null | null | null | null | q-bio.QM cs.LG q-bio.PE stat.AP stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Digital contact tracing approaches based on Bluetooth low energy (BLE) have
the potential to efficiently contain and delay outbreaks of infectious diseases
such as the ongoing SARS-CoV-2 pandemic. In this work we propose a novel
machine learning based approach to reliably detect subjects that have spent
enough time i... | [
{
"created": "Wed, 22 Apr 2020 20:10:35 GMT",
"version": "v1"
}
] | 2020-04-27 | [
[
"Sattler",
"Felix",
""
],
[
"Ma",
"Jackie",
""
],
[
"Wagner",
"Patrick",
""
],
[
"Neumann",
"David",
""
],
[
"Wenzel",
"Markus",
""
],
[
"Schäfer",
"Ralf",
""
],
[
"Samek",
"Wojciech",
""
],
[
"Müll... | Digital contact tracing approaches based on Bluetooth low energy (BLE) have the potential to efficiently contain and delay outbreaks of infectious diseases such as the ongoing SARS-CoV-2 pandemic. In this work we propose a novel machine learning based approach to reliably detect subjects that have spent enough time in ... |
1406.6424 | Corey Bradshaw | Richard Frankham, Corey J. A. Bradshaw, Barry W. Brook | 50/500 or 100/1000 debate is not about the time frame - Reply to
Rosenfeld | 5 pages, 0 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Letter from Rosenfeld (2014, Biological Conservation) in response to
Jamieson and Allendorf (2012, Trends in Ecology and Evolution) and Frankham et
al. (2014, Biological Conservation) and related papers is misleading in places
and requires clarification and correction. We provide those here.
| [
{
"created": "Wed, 25 Jun 2014 00:41:47 GMT",
"version": "v1"
},
{
"created": "Tue, 1 Jul 2014 01:10:01 GMT",
"version": "v2"
}
] | 2014-07-02 | [
[
"Frankham",
"Richard",
""
],
[
"Bradshaw",
"Corey J. A.",
""
],
[
"Brook",
"Barry W.",
""
]
] | The Letter from Rosenfeld (2014, Biological Conservation) in response to Jamieson and Allendorf (2012, Trends in Ecology and Evolution) and Frankham et al. (2014, Biological Conservation) and related papers is misleading in places and requires clarification and correction. We provide those here. |
1511.00255 | Carina Curto | Carina Curto and Nora Youngs | Neural ring homomorphisms and maps between neural codes | 15 pages, 2 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural codes are binary codes that are used for information processing and
representation in the brain. In previous work, we have shown how an algebraic
structure, called the {\it neural ring}, can be used to efficiently encode
geometric and combinatorial properties of a neural code [1]. In this work, we
consider map... | [
{
"created": "Sun, 1 Nov 2015 14:29:03 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Nov 2018 16:40:08 GMT",
"version": "v2"
},
{
"created": "Wed, 13 Feb 2019 18:33:31 GMT",
"version": "v3"
}
] | 2019-02-14 | [
[
"Curto",
"Carina",
""
],
[
"Youngs",
"Nora",
""
]
] | Neural codes are binary codes that are used for information processing and representation in the brain. In previous work, we have shown how an algebraic structure, called the {\it neural ring}, can be used to efficiently encode geometric and combinatorial properties of a neural code [1]. In this work, we consider maps ... |
1412.3893 | Ian Ochs | Ian E. Ochs and Michael M. Desai | The competition between simple and complex evolutionary trajectories in
asexual populations | 8 pages, 3 figures | BMC Evolutionary Biology 2015, 15:55 | 10.1186/s12862-015-0334-0 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | On rugged fitness landscapes where sign epistasis is common, adaptation can
often involve either individually beneficial "uphill" mutations or more complex
mutational trajectories involving fitness valleys or plateaus. The dynamics of
the evolutionary process determine the probability that evolution will take any
spe... | [
{
"created": "Fri, 12 Dec 2014 05:35:40 GMT",
"version": "v1"
}
] | 2015-10-06 | [
[
"Ochs",
"Ian E.",
""
],
[
"Desai",
"Michael M.",
""
]
] | On rugged fitness landscapes where sign epistasis is common, adaptation can often involve either individually beneficial "uphill" mutations or more complex mutational trajectories involving fitness valleys or plateaus. The dynamics of the evolutionary process determine the probability that evolution will take any speci... |
1404.5252 | Wolfram Liebermeister | Wolfram Liebermeister | Enzyme economy and metabolic control | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The metabolic state of a cell, comprising fluxes, metabolite concentrations
and enzyme levels, is shaped by a compromise between metabolic benefit and
enzyme cost. This hypothesis and its consequences can be studied by
computational models and using a theory of metabolic value. In optimal
metabolic states, any increa... | [
{
"created": "Mon, 21 Apr 2014 17:45:13 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Oct 2022 08:00:18 GMT",
"version": "v2"
}
] | 2022-10-05 | [
[
"Liebermeister",
"Wolfram",
""
]
] | The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models and using a theory of metabolic value. In optimal metabolic states, any increase... |
2211.09705 | Divyanshu Aggarwal | Divyanshu Aggarwal and Yasha Hasija | A Review of Deep Learning Techniques for Protein Function Prediction | null | 2021 2nd International Conference for Emerging Technology (INCET)
Belgaum, India. May 21-23, 2021 | null | null | q-bio.BM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Deep Learning and big data have shown tremendous success in bioinformatics
and computational biology in recent years; artificial intelligence methods have
also significantly contributed in the task of protein function classification.
This review paper analyzes the recent developments in approaches for the task
of pre... | [
{
"created": "Thu, 27 Oct 2022 20:30:25 GMT",
"version": "v1"
}
] | 2022-11-18 | [
[
"Aggarwal",
"Divyanshu",
""
],
[
"Hasija",
"Yasha",
""
]
] | Deep Learning and big data have shown tremendous success in bioinformatics and computational biology in recent years; artificial intelligence methods have also significantly contributed in the task of protein function classification. This review paper analyzes the recent developments in approaches for the task of predi... |
0907.4386 | Leonard M. Sander | David A. Kessler and Leonard M. Sander | Fluctuations and Dispersal Rates in Population Dyanmics | 4 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dispersal of species to find a more favorable habitat is important in
population dynamics. Dispersal rates evolve in response to the relative success
of different dispersal strategies. In a simplified deterministic treatment (J.
Dockery, V. Hutson, K. Mischaikow, et al., J. Math. Bio. 37, 61 (1998)) of two
species wh... | [
{
"created": "Fri, 24 Jul 2009 21:50:33 GMT",
"version": "v1"
}
] | 2009-07-28 | [
[
"Kessler",
"David A.",
""
],
[
"Sander",
"Leonard M.",
""
]
] | Dispersal of species to find a more favorable habitat is important in population dynamics. Dispersal rates evolve in response to the relative success of different dispersal strategies. In a simplified deterministic treatment (J. Dockery, V. Hutson, K. Mischaikow, et al., J. Math. Bio. 37, 61 (1998)) of two species whic... |
1910.08784 | James McIntosh | J. R. McIntosh, P. Sajda | Estimation of phase in EEG rhythms for real-time applications | null | null | 10.1088/1741-2552/ab8683 | null | q-bio.QM eess.SP q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective. We identify two linked problems related to estimating the phase of
the alpha rhythm when the signal after a specific event is unknown (real-time
case), or corrupted (offline analysis). We propose methods to estimate the
phase prior to such events. Approach. Machine learning is used to mimic a
non-causal si... | [
{
"created": "Sat, 19 Oct 2019 14:56:26 GMT",
"version": "v1"
}
] | 2020-04-07 | [
[
"McIntosh",
"J. R.",
""
],
[
"Sajda",
"P.",
""
]
] | Objective. We identify two linked problems related to estimating the phase of the alpha rhythm when the signal after a specific event is unknown (real-time case), or corrupted (offline analysis). We propose methods to estimate the phase prior to such events. Approach. Machine learning is used to mimic a non-causal sign... |
1903.05590 | Jennifer Creaser | Jennifer Creaser, Peter Ashwin, Claire Postlethwaite, and Juliane
Britz | Noisy network attractor models for transitions between EEG microstates | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain is intrinsically organized into large-scale networks that
constantly re-organize on multiple timescales, even when the brain is at rest.
The timing of these dynamics is crucial for sensation, perception, cognition
and ultimately consciousness, but the underlying dynamics governing the
constant reorganizatio... | [
{
"created": "Wed, 13 Mar 2019 16:40:59 GMT",
"version": "v1"
}
] | 2019-03-14 | [
[
"Creaser",
"Jennifer",
""
],
[
"Ashwin",
"Peter",
""
],
[
"Postlethwaite",
"Claire",
""
],
[
"Britz",
"Juliane",
""
]
] | The brain is intrinsically organized into large-scale networks that constantly re-organize on multiple timescales, even when the brain is at rest. The timing of these dynamics is crucial for sensation, perception, cognition and ultimately consciousness, but the underlying dynamics governing the constant reorganization ... |
1404.6684 | Domenico Gatti | Greg W. Clark, Sharon H. Ackerman, Elisabeth R. Tillier, Domenico L.
Gatti | Multidimensional mutual information methods for the analysis of
covariation in multiple sequence alignments | 21 pages, 4 figures, 1 table, supporting information containing 2
additional figures is included at the end of the manuscript | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several methods are available for the detection of covarying positions from a
multiple sequence alignment (MSA). If the MSA contains a large number of
sequences, information about the proximities between residues derived from
covariation maps can be sufficient to predict a protein fold. If the structure
is already kn... | [
{
"created": "Sat, 26 Apr 2014 21:10:57 GMT",
"version": "v1"
}
] | 2014-04-29 | [
[
"Clark",
"Greg W.",
""
],
[
"Ackerman",
"Sharon H.",
""
],
[
"Tillier",
"Elisabeth R.",
""
],
[
"Gatti",
"Domenico L.",
""
]
] | Several methods are available for the detection of covarying positions from a multiple sequence alignment (MSA). If the MSA contains a large number of sequences, information about the proximities between residues derived from covariation maps can be sufficient to predict a protein fold. If the structure is already know... |
1407.5328 | Dean Wyatte | Dean Wyatte | What happens next and when "next" happens: Mechanisms of spatial and
temporal prediction | Doctoral thesis (May 2014) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The physics of the environment provide a rich spatiotemporal structure for
our experience. Objects move in predictable ways and their features and
identity remain stable across time and space. How does the brain leverage this
structure to make predictions about and learn from the environment? This thesis
describes re... | [
{
"created": "Sun, 20 Jul 2014 19:11:51 GMT",
"version": "v1"
}
] | 2014-07-22 | [
[
"Wyatte",
"Dean",
""
]
] | The physics of the environment provide a rich spatiotemporal structure for our experience. Objects move in predictable ways and their features and identity remain stable across time and space. How does the brain leverage this structure to make predictions about and learn from the environment? This thesis describes rese... |
2009.07479 | Anisleidy Gonz\'alez-Mitjans | A. Gonz\'alez-Mitjans, D. Paz-Linares, A. Areces-Gonzalez, M. Li, Y.
Wang, ML. Bringas-Vega, and P.A Vald\'es-Sosa | Accurate and efficient Simulation of very high-dimensional Neural Mass
Models with distributed-delay Connectome Tensors | 12 pages, 6 figures, 2 tables | null | null | null | q-bio.NC cs.CE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper introduces methods and a novel toolbox that efficiently integrates
any high-dimensional Neural Mass Models (NMMs) specified by two essential
components. The first is the set of nonlinear Random Differential Equations of
the dynamics of each neural mass. The second is the highly sparse
three-dimensional Con... | [
{
"created": "Wed, 16 Sep 2020 05:55:17 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Sep 2020 02:17:54 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Feb 2021 07:02:09 GMT",
"version": "v3"
},
{
"created": "Fri, 14 May 2021 05:54:11 GMT",
"version": "v4"
},
{
"c... | 2022-06-13 | [
[
"González-Mitjans",
"A.",
""
],
[
"Paz-Linares",
"D.",
""
],
[
"Areces-Gonzalez",
"A.",
""
],
[
"Li",
"M.",
""
],
[
"Wang",
"Y.",
""
],
[
"Bringas-Vega",
"ML.",
""
],
[
"Valdés-Sosa",
"P. A",
""
]
] | This paper introduces methods and a novel toolbox that efficiently integrates any high-dimensional Neural Mass Models (NMMs) specified by two essential components. The first is the set of nonlinear Random Differential Equations of the dynamics of each neural mass. The second is the highly sparse three-dimensional Conne... |
1812.03783 | Noemi Kurt | Jochen Blath, Adri\'an Gonz\'alez Casanova, Noemi Kurt, Maite
Wilke-Berenguer | The seed bank coalescent with simultaneous switching | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a new Wright-Fisher type model for seed banks incorporating
"simultaneous switching", which is motivated by recent work on microbial
dormancy. We show that the simultaneous switching mechanism leads to a new
jump-diffusion limit for the scaled frequency processes, extending the
classical Wright-Fisher an... | [
{
"created": "Mon, 10 Dec 2018 13:36:30 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Dec 2018 10:24:57 GMT",
"version": "v2"
}
] | 2018-12-24 | [
[
"Blath",
"Jochen",
""
],
[
"Casanova",
"Adrián González",
""
],
[
"Kurt",
"Noemi",
""
],
[
"Wilke-Berenguer",
"Maite",
""
]
] | We introduce a new Wright-Fisher type model for seed banks incorporating "simultaneous switching", which is motivated by recent work on microbial dormancy. We show that the simultaneous switching mechanism leads to a new jump-diffusion limit for the scaled frequency processes, extending the classical Wright-Fisher and ... |
2204.11747 | Chottiwatt Jittprasong | Chottiwatt Jittprasong (Biomedical Robotics Laboratory, Department of
Biomedical Engineering, City University of Hong Kong) | A feasibility study proposal of the predictive model to enable the
prediction of population susceptibility to COVID-19 by analysis of vaccine
utilization for advising deployment of a booster dose | 4 pages with 7 figures, pdfLaTeX | null | null | null | q-bio.PE cs.LG | http://creativecommons.org/licenses/by-nc-sa/4.0/ | With the present highly infectious dominant SARS-CoV-2 strain of B1.1.529 or
Omicron spreading around the globe, there is concern that the COVID-19 pandemic
will not end soon and that it will be a race against time until a more
contagious and virulent variant emerges. One of the most promising approaches
for preventi... | [
{
"created": "Mon, 25 Apr 2022 16:05:59 GMT",
"version": "v1"
}
] | 2022-04-26 | [
[
"Jittprasong",
"Chottiwatt",
"",
"Biomedical Robotics Laboratory, Department of\n Biomedical Engineering, City University of Hong Kong"
]
] | With the present highly infectious dominant SARS-CoV-2 strain of B1.1.529 or Omicron spreading around the globe, there is concern that the COVID-19 pandemic will not end soon and that it will be a race against time until a more contagious and virulent variant emerges. One of the most promising approaches for preventing... |
2004.07937 | Syed Muhammad Usman | Syed Muhammad Usman, Shahzad Latif, Arshad Beg | Principle components analysis for seizures prediction using wavelet
transform | null | null | null | null | q-bio.NC cs.LG eess.SP stat.ML | http://creativecommons.org/licenses/by/4.0/ | Epilepsy is a disease in which frequent seizures occur due to abnormal
activity of neurons. Patients affected by this disease can be treated with the
help of medicines or surgical procedures. However, both of these methods are
not quite useful. The only method to treat epilepsy patients effectively is to
predict the ... | [
{
"created": "Mon, 9 Mar 2020 04:32:57 GMT",
"version": "v1"
}
] | 2020-04-20 | [
[
"Usman",
"Syed Muhammad",
""
],
[
"Latif",
"Shahzad",
""
],
[
"Beg",
"Arshad",
""
]
] | Epilepsy is a disease in which frequent seizures occur due to abnormal activity of neurons. Patients affected by this disease can be treated with the help of medicines or surgical procedures. However, both of these methods are not quite useful. The only method to treat epilepsy patients effectively is to predict the se... |
1907.10790 | Katsuyoshi Matsushita | Katsuyoshi Matsushita and Kazuya Horibe and Naoya Kamamoto and Koichi
Fujimoto | Cell Motion Alignment as Polarity Memory Effect | 6 pages, 3 figures | null | 10.7566/JPSJ.88.103801 | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The clarification of the motion alignment mechanism in collective cell
migration is an important issue commonly in physics and biology. In analogy
with the self-propelled disk, the polarity memory effect of eukaryotic cell is
a fundamental candidate for this alignment mechanism. In the present paper, we
theoretically... | [
{
"created": "Thu, 25 Jul 2019 01:44:15 GMT",
"version": "v1"
}
] | 2019-10-02 | [
[
"Matsushita",
"Katsuyoshi",
""
],
[
"Horibe",
"Kazuya",
""
],
[
"Kamamoto",
"Naoya",
""
],
[
"Fujimoto",
"Koichi",
""
]
] | The clarification of the motion alignment mechanism in collective cell migration is an important issue commonly in physics and biology. In analogy with the self-propelled disk, the polarity memory effect of eukaryotic cell is a fundamental candidate for this alignment mechanism. In the present paper, we theoretically e... |
q-bio/0611044 | Nils Becker | Nils B. Becker and Ralf Everaers | DNA: From rigid base-pairs to semiflexible polymers | 13 pages, 6 figures, 6 tables | null | 10.1103/PhysRevE.76.021923 | null | q-bio.BM | null | The sequence-dependent elasticity of double-helical DNA on a nm length scale
can be captured by the rigid base-pair model, whose strains are the relative
position and orientation of adjacent base-pairs. Corresponding elastic
potentials have been obtained from all-atom MD simulation and from
high-resolution structural... | [
{
"created": "Wed, 15 Nov 2006 09:13:40 GMT",
"version": "v1"
}
] | 2013-05-29 | [
[
"Becker",
"Nils B.",
""
],
[
"Everaers",
"Ralf",
""
]
] | The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have been obtained from all-atom MD simulation and from high-resolution structural d... |
1704.08994 | Jian-Jun Shu | Jian-Jun Shu, Kian-Yan Yong | Fourier-based classification of protein secondary structures | null | Biochemical and Biophysical Research Communications, Vol. 485, No.
4, pp. 731-735, 2017 | 10.1016/j.bbrc.2017.02.117 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The correct prediction of protein secondary structures is one of the key
issues in predicting the correct protein folded shape, which is used for
determining gene function. Existing methods make use of amino acids properties
as indices to classify protein secondary structures, but are faced with a
significant number ... | [
{
"created": "Fri, 28 Apr 2017 16:20:50 GMT",
"version": "v1"
}
] | 2017-05-01 | [
[
"Shu",
"Jian-Jun",
""
],
[
"Yong",
"Kian-Yan",
""
]
] | The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of... |
1611.04193 | Stuart Hagler | Stuart Hagler | Patterns of Selection of Human Movements III: Energy Efficiency,
Mechanical Advantage, and Walking Gait | 21 pages, 5 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human movements are physical processes combining the classical mechanics of
the human body moving in space and the biomechanics of the muscles generating
the forces acting on the body under sophisticated sensory-motor control. One
way to characterize movement performance is through measures of energy
efficiency that ... | [
{
"created": "Sun, 13 Nov 2016 21:16:15 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Nov 2016 22:50:17 GMT",
"version": "v2"
},
{
"created": "Sun, 9 Dec 2018 19:52:31 GMT",
"version": "v3"
}
] | 2018-12-11 | [
[
"Hagler",
"Stuart",
""
]
] | Human movements are physical processes combining the classical mechanics of the human body moving in space and the biomechanics of the muscles generating the forces acting on the body under sophisticated sensory-motor control. One way to characterize movement performance is through measures of energy efficiency that re... |
2303.16209 | Kyoungmin Min | Myeonghun Lee and Kyoungmin Min | AmorProt: Amino Acid Molecular Fingerprints Repurposing based Protein
Fingerprint | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | As protein therapeutics play an important role in almost all medical fields,
numerous studies have been conducted on proteins using artificial intelligence.
Artificial intelligence has enabled data driven predictions without the need
for expensive experiments. Nevertheless, unlike the various molecular
fingerprint al... | [
{
"created": "Mon, 27 Mar 2023 23:57:47 GMT",
"version": "v1"
}
] | 2023-03-30 | [
[
"Lee",
"Myeonghun",
""
],
[
"Min",
"Kyoungmin",
""
]
] | As protein therapeutics play an important role in almost all medical fields, numerous studies have been conducted on proteins using artificial intelligence. Artificial intelligence has enabled data driven predictions without the need for expensive experiments. Nevertheless, unlike the various molecular fingerprint algo... |
q-bio/0312040 | Peng-Ye Wang | Ping Xie, Shuo-Xing Dou, Peng-Ye Wang | A model for processivity of molecular motors | 10 pages, 7 figures | Chinese Physics, 13, 1569 (2004) | 10.1088/1009-1963/13/9/036 | null | q-bio.BM | null | We propose a two-dimensional model for a complete description of the dynamics
of molecular motors, including both the processive movement along track
filaments and the dissociation from the filaments. The theoretical results on
the distributions of the run length and dwell time at a given ATP
concentration, the depen... | [
{
"created": "Thu, 25 Dec 2003 09:58:52 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Xie",
"Ping",
""
],
[
"Dou",
"Shuo-Xing",
""
],
[
"Wang",
"Peng-Ye",
""
]
] | We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the distributions of the run length and dwell time at a given ATP concentration, the depende... |
1402.0511 | Charles Fisher | Charles K. Fisher, Pankaj Mehta | Identifying Keystone Species in the Human Gut Microbiome from
Metagenomic Timeseries using Sparse Linear Regression | null | null | 10.1371/journal.pone.0102451 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human associated microbial communities exert tremendous influence over human
health and disease. With modern metagenomic sequencing methods it is possible
to follow the relative abundance of microbes in a community over time. These
microbial communities exhibit rich ecological dynamics and an important goal of
microb... | [
{
"created": "Mon, 3 Feb 2014 21:00:29 GMT",
"version": "v1"
}
] | 2015-06-18 | [
[
"Fisher",
"Charles K.",
""
],
[
"Mehta",
"Pankaj",
""
]
] | Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbia... |
1810.01452 | Arni S.R. Srinivasa Rao | Arni S.R. Srinivasa Rao | A Partition Theorem for a Randomly Selected Large Population | 12 pages, 4 figures. A new result in population dynamics | Acta Biotheoretica (Springer) 2021 | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We state and prove a theorem on the partitioning of a randomly selected large
population into stationary and non-stationary components by using a property of
stationary population identity. Applications of this theorem for practical
purposes is summarized at the end.
| [
{
"created": "Tue, 2 Oct 2018 18:47:37 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Oct 2018 02:07:38 GMT",
"version": "v2"
},
{
"created": "Thu, 1 Jul 2021 17:16:42 GMT",
"version": "v3"
}
] | 2021-10-20 | [
[
"Rao",
"Arni S. R. Srinivasa",
""
]
] | We state and prove a theorem on the partitioning of a randomly selected large population into stationary and non-stationary components by using a property of stationary population identity. Applications of this theorem for practical purposes is summarized at the end. |
1201.2900 | Mikhail Peslyak | Mikhail Peslyak | Model of pathogenesis of psoriasis. Part 2. Local processes | English edition e1.3, Russia, Moscow, MYPE, 2012, 110 pages, 30
figures, ISBN 9785905504044 | null | null | null | q-bio.CB q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Analytical research of results of experimental and theoretical studies on
pathogenesis of psoriatic disease is carried out. The new model of pathogenesis
- skin reaction to systemic psoriatic process SPP is formulated. ... Psoriatic
inflammation is regarded as a reaction of the skin immune system to activity of
Mo-R ... | [
{
"created": "Fri, 13 Jan 2012 17:31:10 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Apr 2012 16:47:02 GMT",
"version": "v2"
}
] | 2012-04-20 | [
[
"Peslyak",
"Mikhail",
""
]
] | Analytical research of results of experimental and theoretical studies on pathogenesis of psoriatic disease is carried out. The new model of pathogenesis - skin reaction to systemic psoriatic process SPP is formulated. ... Psoriatic inflammation is regarded as a reaction of the skin immune system to activity of Mo-R an... |
0911.1844 | Anne Feltz | Norbert Weiss, Christophe Arnoult, Anne Feltz (NEURO), Michel De Waard | Contribution of the kinetics of G protein dissociation to the
characteristic modifications of N-type calcium channel activity | null | Neuroscience Research 56, 3 (2006) 332-43 | 10.1016/j.neures.2006.08.002 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Direct G protein inhibition of N-type calcium channels is recognized by
characteristic biophysical modifications. In this study, we quantify and
simulate the importance of G protein dissociation on the phenotype of G
protein-regulated whole-cell currents. Based on the observation that the
voltage-dependence of the ti... | [
{
"created": "Tue, 10 Nov 2009 07:28:18 GMT",
"version": "v1"
}
] | 2009-11-11 | [
[
"Weiss",
"Norbert",
"",
"NEURO"
],
[
"Arnoult",
"Christophe",
"",
"NEURO"
],
[
"Feltz",
"Anne",
"",
"NEURO"
],
[
"De Waard",
"Michel",
""
]
] | Direct G protein inhibition of N-type calcium channels is recognized by characteristic biophysical modifications. In this study, we quantify and simulate the importance of G protein dissociation on the phenotype of G protein-regulated whole-cell currents. Based on the observation that the voltage-dependence of the time... |
2407.19328 | Nicholas Dimonaco | Nicholas J. Dimonaco | PyamilySeq: A Python Tool for Interpretable Gene (Re)Clustering and
Pangenomic Inference Across Species and Genera | See here for installation and use:
https://pypi.org/project/PyamilySeq/ | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | PyamilySeq is a Python-based tool designed for interpretable gene clustering
and pangenomic inference, supporting analyses at both species and genus levels.
It facilitates the clustering of gene sequences into families based on sequence
similarity using CD-HIT, and can take the output of tried-and-tested sequence
clu... | [
{
"created": "Sat, 27 Jul 2024 19:32:35 GMT",
"version": "v1"
}
] | 2024-07-30 | [
[
"Dimonaco",
"Nicholas J.",
""
]
] | PyamilySeq is a Python-based tool designed for interpretable gene clustering and pangenomic inference, supporting analyses at both species and genus levels. It facilitates the clustering of gene sequences into families based on sequence similarity using CD-HIT, and can take the output of tried-and-tested sequence clust... |
1810.03282 | Suman Kumar Banik | Mintu Nandi, Ayan Biswas, Suman K Banik and Pinaki Chaudhury | Information processing in a simple one-step cascade | 26 pages, 5 figures | null | 10.1103/PhysRevE.98.042310 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Using the formalism of information theory, we analyze the mechanism of
information transduction in a simple one-step signaling cascade S$\rightarrow$X
representing the gene regulatory network. Approximating the signaling channel
to be Gaussian, we describe the dynamics using Langevin equations. Upon
discretization, w... | [
{
"created": "Mon, 8 Oct 2018 06:44:40 GMT",
"version": "v1"
}
] | 2018-11-14 | [
[
"Nandi",
"Mintu",
""
],
[
"Biswas",
"Ayan",
""
],
[
"Banik",
"Suman K",
""
],
[
"Chaudhury",
"Pinaki",
""
]
] | Using the formalism of information theory, we analyze the mechanism of information transduction in a simple one-step signaling cascade S$\rightarrow$X representing the gene regulatory network. Approximating the signaling channel to be Gaussian, we describe the dynamics using Langevin equations. Upon discretization, we ... |
2107.13709 | Tom Chou | Mingtao Xia, Lucas B\"ottcher, Tom Chou | Controlling epidemics through optimal allocation of test kits and
vaccine doses across networks | 13 pages, 8 figures, Submitted to IEEE Transactions on Network
Science and Engineering | IEEE Trans. Netw. Sci. Eng. 9, 1422-1436 (2022) | 10.1109/TNSE.2022.3144624 | null | q-bio.PE cs.SI math.OC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Efficient testing and vaccination protocols are critical aspects of epidemic
management. To study the optimal allocation of limited testing and vaccination
resources in a heterogeneous contact network of interacting susceptible,
recovered, and infected individuals, we present a degree-based testing and
vaccination mo... | [
{
"created": "Thu, 29 Jul 2021 02:23:45 GMT",
"version": "v1"
},
{
"created": "Sat, 31 Jul 2021 01:57:19 GMT",
"version": "v2"
}
] | 2022-06-22 | [
[
"Xia",
"Mingtao",
""
],
[
"Böttcher",
"Lucas",
""
],
[
"Chou",
"Tom",
""
]
] | Efficient testing and vaccination protocols are critical aspects of epidemic management. To study the optimal allocation of limited testing and vaccination resources in a heterogeneous contact network of interacting susceptible, recovered, and infected individuals, we present a degree-based testing and vaccination mode... |
1712.04223 | Andrew Francis | Andrew Francis and Vincent Moulton | Identifiability of tree-child phylogenetic networks under a
probabilistic recombination-mutation model of evolution | 18 pages, 4 figures | Journal of Theoretical Biology, Volume 446, 7 June 2018, Pages
160-167 | 10.1016/j.jtbi.2018.03.011 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks are an extension of phylogenetic trees which are used
to represent evolutionary histories in which reticulation events (such as
recombination and hybridization) have occurred. A central question for such
networks is that of identifiability, which essentially asks under what
circumstances can we ... | [
{
"created": "Tue, 12 Dec 2017 10:51:45 GMT",
"version": "v1"
}
] | 2018-03-28 | [
[
"Francis",
"Andrew",
""
],
[
"Moulton",
"Vincent",
""
]
] | Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is that of identifiability, which essentially asks under what circumstances can we re... |
1801.08366 | Stephen Coombes | S Coombes, Y-M Lai, M Sayli and R Thul | Networks of piecewise linear neural mass models | null | null | null | null | q-bio.NC math.DS nlin.AO | http://creativecommons.org/licenses/by/4.0/ | Neural mass models are ubiquitous in large scale brain modelling. At the node
level they are written in terms of a set of ODEs with a nonlinearity that is
typically a sigmoidal shape. Using structural data from brain atlases they may
be connected into a network to investigate the emergence of functional dynamic
state... | [
{
"created": "Thu, 25 Jan 2018 11:55:24 GMT",
"version": "v1"
}
] | 2018-01-26 | [
[
"Coombes",
"S",
""
],
[
"Lai",
"Y-M",
""
],
[
"Sayli",
"M",
""
],
[
"Thul",
"R",
""
]
] | Neural mass models are ubiquitous in large scale brain modelling. At the node level they are written in terms of a set of ODEs with a nonlinearity that is typically a sigmoidal shape. Using structural data from brain atlases they may be connected into a network to investigate the emergence of functional dynamic states,... |
1112.1733 | Petter Holme | Sungmin Lee, Petter Holme, Zhi-Xi Wu | Cooperation, structure and hierarchy in multiadaptive games | null | Phys. Rev. E. 84, 061148 (2011) | 10.1103/PhysRevE.84.061148 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Game-theoretical models where the rules of the game and the interaction
structure both coevolves with the game dynamics -- multiadaptive games --
capture very flexible situations where cooperation among selfish agents can
emerge. In this work, we will discuss a multiadaptive model presented in a
recent Letter [Phys. ... | [
{
"created": "Wed, 7 Dec 2011 23:30:13 GMT",
"version": "v1"
}
] | 2012-10-10 | [
[
"Lee",
"Sungmin",
""
],
[
"Holme",
"Petter",
""
],
[
"Wu",
"Zhi-Xi",
""
]
] | Game-theoretical models where the rules of the game and the interaction structure both coevolves with the game dynamics -- multiadaptive games -- capture very flexible situations where cooperation among selfish agents can emerge. In this work, we will discuss a multiadaptive model presented in a recent Letter [Phys. Re... |
2112.13273 | Seyedeh Sajedeh Mousavi Dr | S. Sajedeh Mousavi, Mohammad Jalil Zorriehzahra | High Expression of CDK1 and NDC80 Predicts Poor Prognosis of Bladder
Cancer | Talk in 4th International biotechnology congress of Islamic Republic
of Iran (2021) | null | null | null | q-bio.GN q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Background: Bladder cancer is the 10th most common cancer worldwide, and its
prevalence is increasing, especially in developing countries. Objective: In the
present study, we employed gene expression profiles from the GSE163209 data set
in the GEO database to identify potential molecular and genetic markers in BC
pat... | [
{
"created": "Sat, 25 Dec 2021 19:25:47 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Mousavi",
"S. Sajedeh",
""
],
[
"Zorriehzahra",
"Mohammad Jalil",
""
]
] | Background: Bladder cancer is the 10th most common cancer worldwide, and its prevalence is increasing, especially in developing countries. Objective: In the present study, we employed gene expression profiles from the GSE163209 data set in the GEO database to identify potential molecular and genetic markers in BC patie... |
1310.5202 | Omur Arslan | Omur Arslan, Dan P. Guralnik and Daniel E. Koditschek | Discriminative Measures for Comparison of Phylogenetic Trees | 24 pages, 7 figures, 1 table, a new graph-theoretic formulation of
the NNI navigation dissimilarity | null | null | null | q-bio.PE cs.CE cs.CG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we introduce and study three new measures for efficient
discriminative comparison of phylogenetic trees. The NNI navigation
dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest
Neighbor Interchange (NNI) graph of binary hierarchies, providing an efficient
approximation to the (NP-ha... | [
{
"created": "Sat, 19 Oct 2013 05:03:23 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Oct 2015 14:10:43 GMT",
"version": "v2"
}
] | 2015-10-21 | [
[
"Arslan",
"Omur",
""
],
[
"Guralnik",
"Dan P.",
""
],
[
"Koditschek",
"Daniel E.",
""
]
] | In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI) graph of binary hierarchies, providing an efficient approximation to the (NP-hard... |
2307.03415 | Oliver Eales | Oliver Eales, Steven Riley | Differences between the true reproduction number and the apparent
reproduction number of an epidemic time series | null | null | null | null | q-bio.PE q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The time-varying reproduction number $R(t)$ measures the number of new
infections per infectious individual and is closely correlated with the time
series of infection incidence by definition. The timings of actual infections
are rarely known, and analysis of epidemics usually relies on time series data
for other out... | [
{
"created": "Fri, 7 Jul 2023 06:53:25 GMT",
"version": "v1"
}
] | 2023-07-10 | [
[
"Eales",
"Oliver",
""
],
[
"Riley",
"Steven",
""
]
] | The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outco... |
0806.3823 | Francois Bonneton | Fran\c{c}ois Bonneton (IGFL), Arnaud Chaumot (UR BELY), Vincent Laudet
(IGFL) | Annotation of Tribolium nuclear receptors reveals an evolutionary
overacceleration of a network controlling the ecdysone cascade | null | Insect Biochemistry and Molecular Biology 4, 38 (2008) 416-429 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Tribolium genome contains 21 nuclear receptors, representing all of the
six known subfamilies. When compared to other species, this first complete set
for a Coleoptera reveals a strong conservation of the number and identity of
nuclear receptors in holometabolous insects. Two novelties are observed: the
atypical ... | [
{
"created": "Tue, 24 Jun 2008 06:20:29 GMT",
"version": "v1"
}
] | 2008-12-18 | [
[
"Bonneton",
"François",
"",
"IGFL"
],
[
"Chaumot",
"Arnaud",
"",
"UR BELY"
],
[
"Laudet",
"Vincent",
"",
"IGFL"
]
] | The Tribolium genome contains 21 nuclear receptors, representing all of the six known subfamilies. When compared to other species, this first complete set for a Coleoptera reveals a strong conservation of the number and identity of nuclear receptors in holometabolous insects. Two novelties are observed: the atypical NR... |
1907.01681 | Fabio Chalub | Fabio A. C. C. Chalub and L\'eonard Monsaingeon and Ana Margarida
Ribeiro and Max O. Souza | Gradient flow formulations of discrete and continuous evolutionary
models: a unifying perspective | null | null | null | null | q-bio.PE math.AP math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider three classical models of biological evolution: (i) the Moran
process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a
particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator
Equation, a paradigm in Evolutionary Game Theory. While these approaches are
not complet... | [
{
"created": "Tue, 2 Jul 2019 23:37:47 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Oct 2020 15:53:44 GMT",
"version": "v2"
}
] | 2020-10-09 | [
[
"Chalub",
"Fabio A. C. C.",
""
],
[
"Monsaingeon",
"Léonard",
""
],
[
"Ribeiro",
"Ana Margarida",
""
],
[
"Souza",
"Max O.",
""
]
] | We consider three classical models of biological evolution: (i) the Moran process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator Equation, a paradigm in Evolutionary Game Theory. While these approaches are not completel... |
1809.03866 | Divine Wanduku (Dr. ) | Divine Wanduku | The stochastic permanence of malaria, and the existence of a stationary
distribution for a class of malaria models | International Journal of Biomathematics, 2020. arXiv admin note: text
overlap with arXiv:1808.09842 | null | 10.1142/S1793524520500242 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | This paper investigates the stochastic permanence of malaria and the
existence of a stationary distribution for the stochastic process describing
the disease dynamics over sufficiently longtime. The malaria system is highly
random with fluctuations from the disease transmission and natural deathrates,
which are expre... | [
{
"created": "Sat, 8 Sep 2018 18:15:41 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Wanduku",
"Divine",
""
]
] | This paper investigates the stochastic permanence of malaria and the existence of a stationary distribution for the stochastic process describing the disease dynamics over sufficiently longtime. The malaria system is highly random with fluctuations from the disease transmission and natural deathrates, which are express... |
0710.5625 | Daniel Rockmore | Gregory Leibon, Daniel Rockmore, Martin Pollak | A simple computational method for the identification of
disease-associated loci in complex, incomplete pedigrees | 20 pages, 9 figures | null | null | null | q-bio.GN q-bio.QM | null | We present an approach, called the "Shadow Method," for the identification of
disease loci from dense genetic marker maps in complex, potentially incomplete
pedigrees. "Shadow" is a simple method based on an analysis of the patterns of
obligate meiotic recombination events in genotypic data. This method can be
applie... | [
{
"created": "Tue, 30 Oct 2007 02:27:11 GMT",
"version": "v1"
}
] | 2007-10-31 | [
[
"Leibon",
"Gregory",
""
],
[
"Rockmore",
"Daniel",
""
],
[
"Pollak",
"Martin",
""
]
] | We present an approach, called the "Shadow Method," for the identification of disease loci from dense genetic marker maps in complex, potentially incomplete pedigrees. "Shadow" is a simple method based on an analysis of the patterns of obligate meiotic recombination events in genotypic data. This method can be applied ... |
2211.03051 | Christopher Fusco | Christopher Fusco, Angel Allen | Multilayer Perceptron Network Discriminates Larval Zebrafish Genotype
using Behaviour | Preprint | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | Zebrafish are a common model organism used to identify new disease
therapeutics. High-throughput drug screens can be performed on larval zebrafish
in multi-well plates by observing changes in behaviour following a treatment.
Analysis of this behaviour can be difficult, however, due to the high
dimensionality of the d... | [
{
"created": "Sun, 6 Nov 2022 07:36:31 GMT",
"version": "v1"
},
{
"created": "Tue, 8 Nov 2022 01:48:45 GMT",
"version": "v2"
}
] | 2022-11-09 | [
[
"Fusco",
"Christopher",
""
],
[
"Allen",
"Angel",
""
]
] | Zebrafish are a common model organism used to identify new disease therapeutics. High-throughput drug screens can be performed on larval zebrafish in multi-well plates by observing changes in behaviour following a treatment. Analysis of this behaviour can be difficult, however, due to the high dimensionality of the dat... |
2005.12513 | Fernanda Ribeiro | Fernanda L. Ribeiro, Steffen Bollmann, Alexander M. Puckett | DeepRetinotopy: Predicting the Functional Organization of Human Visual
Cortex from Structural MRI Data using Geometric Deep Learning | null | null | 10.1101/2020.02.11.934471 | MIDL/2020/ExtendedAbstract/Nw_trRFjPE | q-bio.NC cs.CV cs.LG q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Whether it be in a man-made machine or a biological system, form and function
are often directly related. In the latter, however, this particular
relationship is often unclear due to the intricate nature of biology. Here we
developed a geometric deep learning model capable of exploiting the actual
structure of the co... | [
{
"created": "Tue, 26 May 2020 04:54:31 GMT",
"version": "v1"
}
] | 2020-05-27 | [
[
"Ribeiro",
"Fernanda L.",
""
],
[
"Bollmann",
"Steffen",
""
],
[
"Puckett",
"Alexander M.",
""
]
] | Whether it be in a man-made machine or a biological system, form and function are often directly related. In the latter, however, this particular relationship is often unclear due to the intricate nature of biology. Here we developed a geometric deep learning model capable of exploiting the actual structure of the cort... |
2307.09169 | Zihan Liu | Zihan Liu, Jiaqi Wang, Yun Luo, Shuang Zhao, Wenbin Li, Stan Z. Li | Efficient Prediction of Peptide Self-assembly through Sequential and
Graphical Encoding | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, there has been an explosion of research on the application
of deep learning to the prediction of various peptide properties, due to the
significant development and market potential of peptides. Molecular dynamics
has enabled the efficient collection of large peptide datasets, providing
reliable train... | [
{
"created": "Mon, 17 Jul 2023 00:43:33 GMT",
"version": "v1"
}
] | 2023-07-19 | [
[
"Liu",
"Zihan",
""
],
[
"Wang",
"Jiaqi",
""
],
[
"Luo",
"Yun",
""
],
[
"Zhao",
"Shuang",
""
],
[
"Li",
"Wenbin",
""
],
[
"Li",
"Stan Z.",
""
]
] | In recent years, there has been an explosion of research on the application of deep learning to the prediction of various peptide properties, due to the significant development and market potential of peptides. Molecular dynamics has enabled the efficient collection of large peptide datasets, providing reliable trainin... |
2010.12857 | William McCorkindale Mr. | William McCorkindale, Carl Poelking, Alpha A. Lee | Investigating 3D Atomic Environments for Enhanced QSAR | null | null | null | null | q-bio.QM cs.LG physics.comp-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Predicting bioactivity and physical properties of molecules is a longstanding
challenge in drug design. Most approaches use molecular descriptors based on a
2D representation of molecules as a graph of atoms and bonds, abstracting away
the molecular shape. A difficulty in accounting for 3D shape is in designing
molec... | [
{
"created": "Sat, 24 Oct 2020 10:04:48 GMT",
"version": "v1"
}
] | 2020-10-27 | [
[
"McCorkindale",
"William",
""
],
[
"Poelking",
"Carl",
""
],
[
"Lee",
"Alpha A.",
""
]
] | Predicting bioactivity and physical properties of molecules is a longstanding challenge in drug design. Most approaches use molecular descriptors based on a 2D representation of molecules as a graph of atoms and bonds, abstracting away the molecular shape. A difficulty in accounting for 3D shape is in designing molecul... |
1412.0291 | Viola Priesemann | Michael Wibral, Joseph T. Lizier, Viola Priesemann | Bits from Biology for Computational Intelligence | null | Frontiers in Robotics and AI, 2:5 (2015) | 10.3389/frobt.2015.00005 | null | q-bio.NC cs.IT math.IT physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Computational intelligence is broadly defined as biologically-inspired
computing. Usually, inspiration is drawn from neural systems. This article
shows how to analyze neural systems using information theory to obtain
constraints that help identify the algorithms run by such systems and the
information they represent.... | [
{
"created": "Sun, 30 Nov 2014 21:47:15 GMT",
"version": "v1"
}
] | 2018-05-11 | [
[
"Wibral",
"Michael",
""
],
[
"Lizier",
"Joseph T.",
""
],
[
"Priesemann",
"Viola",
""
]
] | Computational intelligence is broadly defined as biologically-inspired computing. Usually, inspiration is drawn from neural systems. This article shows how to analyze neural systems using information theory to obtain constraints that help identify the algorithms run by such systems and the information they represent. A... |
1408.0463 | Peter O. Fedichev | Valeria Kogan, Ivan Molodtcov, Leonid I. Menshikov, Robert J.
Shmookler Reis and Peter Fedichev | Stability analysis of a model gene network links aging, stress
resistance, and negligible senescence | 8 pages, 2 figures | Scientific Reports 5, Article number: 13589 (2015) | 10.1038/srep13589 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several animal species are considered to exhibit what is called negligible
senescence, i.e. they do not show signs of functional decline or any increase
of mortality with age, and do not have measurable reductions in reproductive
capacity with age. Recent studies in Naked Mole Rat (NMR) and long- lived sea
urchin sho... | [
{
"created": "Sun, 3 Aug 2014 07:14:09 GMT",
"version": "v1"
}
] | 2015-10-15 | [
[
"Kogan",
"Valeria",
""
],
[
"Molodtcov",
"Ivan",
""
],
[
"Menshikov",
"Leonid I.",
""
],
[
"Reis",
"Robert J. Shmookler",
""
],
[
"Fedichev",
"Peter",
""
]
] | Several animal species are considered to exhibit what is called negligible senescence, i.e. they do not show signs of functional decline or any increase of mortality with age, and do not have measurable reductions in reproductive capacity with age. Recent studies in Naked Mole Rat (NMR) and long- lived sea urchin showe... |
1611.03952 | Christoph Adami | A. Gupta and C. Adami | Shared information between residues is sufficient to detect pair-wise
epistasis in a protein | 4 pages, 1 figure. To appear in PLoS Genetics | PLoS Genetics 12 (2016) e1006471 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a comment on our manuscript "Strong selection significantly increases
epistatic interactions in the long-term evolution of a protein", Dr. Crona
challenges our assertion that shared entropy (that is, information) between two
residues implies epistasis between those residues, by constructing an explicit
example of ... | [
{
"created": "Sat, 12 Nov 2016 04:18:18 GMT",
"version": "v1"
}
] | 2016-12-07 | [
[
"Gupta",
"A.",
""
],
[
"Adami",
"C.",
""
]
] | In a comment on our manuscript "Strong selection significantly increases epistatic interactions in the long-term evolution of a protein", Dr. Crona challenges our assertion that shared entropy (that is, information) between two residues implies epistasis between those residues, by constructing an explicit example of th... |
1406.0399 | Nikolai Slavov | Nikolai Slavov, Sefan Semrau, Edoardo Airoldi, Bogdan Budnik,
Alexander van Oudenaarden | Differential stoichiometry among core ribosomal proteins | 31 pages, 8 figures | Cell Reports 13: 865 - 873, 2015 | 10.1016/j.celrep.2015.09.056 | null | q-bio.GN q-bio.BM q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the regulation and structure of ribosomes is essential to
understanding protein synthesis and its deregulation in disease. While
ribosomes are believed to have a fixed stoichiometry among their core ribosomal
proteins (RPs), some experiments suggest a more variable composition. Testing
such variability ... | [
{
"created": "Mon, 2 Jun 2014 14:57:33 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Apr 2015 12:17:10 GMT",
"version": "v2"
}
] | 2015-11-24 | [
[
"Slavov",
"Nikolai",
""
],
[
"Semrau",
"Sefan",
""
],
[
"Airoldi",
"Edoardo",
""
],
[
"Budnik",
"Bogdan",
""
],
[
"van Oudenaarden",
"Alexander",
""
]
] | Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs), some experiments suggest a more variable composition. Testing such variability re... |
1702.06977 | Carsten Lemmen | Carsten Lemmen and Detlef Gronenborn | The Diffusion of Humans and Cultures in the Course of the Spread of
Farming | 20 pages, 5 figures, submitted to Diffusive Spreading in Nature,
Technology and Society, edited by Armin Bunde, J\"urgen Caro, J\"org
K\"arger, Gero Vogl, Chapter 17 | In: Bunde A., Caro J., K\"arger J., Vogl G. (eds) Diffusive
Spreading in Nature, Technology and Society. Springer, Cham | 10.1007/978-3-319-67798-9_17 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The most profound change in the relationship between humans and their
environment was the introduction of agriculture and pastoralism. [....] For an
understanding of the expansion process, it appears appropriate to apply a
diffusive model. Broadly, these numerical modeling approaches can be catego-
rized in correlati... | [
{
"created": "Wed, 22 Feb 2017 19:28:18 GMT",
"version": "v1"
}
] | 2018-05-10 | [
[
"Lemmen",
"Carsten",
""
],
[
"Gronenborn",
"Detlef",
""
]
] | The most profound change in the relationship between humans and their environment was the introduction of agriculture and pastoralism. [....] For an understanding of the expansion process, it appears appropriate to apply a diffusive model. Broadly, these numerical modeling approaches can be catego- rized in correlative... |
2109.11616 | K.S. Joseph | D.W. Rurak, M.Y. Shen and K.S. Joseph | Fetal oxygen delivery and consumption and blood gases in relation to
gestational age | 88 pages, 26 Figures 233 references and | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Fetal oxygen delivery and consumption and blood gases in relation to
gestational age. Oxygen crosses the placenta by diffusion and placental
permeability to O$_2$ is high. Thus, the fetus receives adequate amounts, but
vascular Po$_2$ is much lower than after birth. Studies of sustained fetal
hypoxemia and acute 40-4... | [
{
"created": "Thu, 23 Sep 2021 19:41:14 GMT",
"version": "v1"
}
] | 2021-09-27 | [
[
"Rurak",
"D. W.",
""
],
[
"Shen",
"M. Y.",
""
],
[
"Joseph",
"K. S.",
""
]
] | Fetal oxygen delivery and consumption and blood gases in relation to gestational age. Oxygen crosses the placenta by diffusion and placental permeability to O$_2$ is high. Thus, the fetus receives adequate amounts, but vascular Po$_2$ is much lower than after birth. Studies of sustained fetal hypoxemia and acute 40-45%... |
1110.1739 | Graciano Dieck Kattas | Graciano Dieck Kattas, Xiao-Ke Xu and Michael Small | Dynamical modeling of collective behavior from pigeon flight data: flock
cohesion and dispersion | null | null | 10.1371/journal.pcbi.1002449 | null | q-bio.OT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Several models of flocking have been promoted based on simulations with
qualitatively naturalistic behavior. In this paper we provide the first direct
application of computational modeling methods to infer flocking behavior from
experimental field data. We show that this approach is able to infer general
rules for in... | [
{
"created": "Sat, 8 Oct 2011 14:08:23 GMT",
"version": "v1"
}
] | 2015-05-30 | [
[
"Kattas",
"Graciano Dieck",
""
],
[
"Xu",
"Xiao-Ke",
""
],
[
"Small",
"Michael",
""
]
] | Several models of flocking have been promoted based on simulations with qualitatively naturalistic behavior. In this paper we provide the first direct application of computational modeling methods to infer flocking behavior from experimental field data. We show that this approach is able to infer general rules for inte... |
2110.11339 | Li Liu | Hengyang Wang, Xianghao Zhan, Li Liu, Asif Ullah, Huiyan Li, Han Gao,
You Wang, Guang Li | Unsupervised cross-user adaptation in taste sensation recognition based
on surface electromyography with conformal prediction and domain regularized
component analysis | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human taste sensation can be qualitatively described with surface
electromyography. However, the pattern recognition models trained on one
subject (the source domain) do not generalize well on other subjects (the
target domain). To improve the generalizability and transferability of taste
sensation models developed w... | [
{
"created": "Wed, 20 Oct 2021 09:11:14 GMT",
"version": "v1"
},
{
"created": "Sat, 11 Dec 2021 12:40:39 GMT",
"version": "v2"
}
] | 2021-12-14 | [
[
"Wang",
"Hengyang",
""
],
[
"Zhan",
"Xianghao",
""
],
[
"Liu",
"Li",
""
],
[
"Ullah",
"Asif",
""
],
[
"Li",
"Huiyan",
""
],
[
"Gao",
"Han",
""
],
[
"Wang",
"You",
""
],
[
"Li",
"Guang",
""
... | Human taste sensation can be qualitatively described with surface electromyography. However, the pattern recognition models trained on one subject (the source domain) do not generalize well on other subjects (the target domain). To improve the generalizability and transferability of taste sensation models developed wit... |
2404.10854 | Matthew Andres Moreno | Matthew Andres Moreno | Methods to Estimate Cryptic Sequence Complexity | null | null | null | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complexity is a signature quality of interest in artificial life systems.
Alongside other dimensions of assessment, it is common to quantify genome sites
that contribute to fitness as a complexity measure. However, limitations to the
sensitivity of fitness assays in models with implicit replication criteria
involving... | [
{
"created": "Tue, 16 Apr 2024 19:04:03 GMT",
"version": "v1"
},
{
"created": "Fri, 31 May 2024 13:59:27 GMT",
"version": "v2"
}
] | 2024-06-03 | [
[
"Moreno",
"Matthew Andres",
""
]
] | Complexity is a signature quality of interest in artificial life systems. Alongside other dimensions of assessment, it is common to quantify genome sites that contribute to fitness as a complexity measure. However, limitations to the sensitivity of fitness assays in models with implicit replication criteria involving r... |
1307.2461 | Martin Kapun PhD | Martin Kapun, Hester van Schalkwyk, Bryant McAllister, Thomas Flatt
and Christian Schl\"otterer | Inference of chromosomal inversion dynamics from Pool-Seq data in
natural and laboratory populations of Drosophila melanogaster | 31 pages, 4 main figures, 1 main table, 7 supporting figures, 11
supporting tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-
effective approach for estimating genome-wide SNP and transposable element
insertion frequencies. However, Pool-Seq does not provide direct information on
haplotypes so that for example obtaining inversion frequencies has not been
possible ... | [
{
"created": "Tue, 9 Jul 2013 14:04:06 GMT",
"version": "v1"
}
] | 2013-07-10 | [
[
"Kapun",
"Martin",
""
],
[
"van Schalkwyk",
"Hester",
""
],
[
"McAllister",
"Bryant",
""
],
[
"Flatt",
"Thomas",
""
],
[
"Schlötterer",
"Christian",
""
]
] | Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost- effective approach for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq does not provide direct information on haplotypes so that for example obtaining inversion frequencies has not been possible un... |
1707.03360 | Haozhe Shan | Haozhe Shan, Peggy Mason | Unsupervised identification of rat behavioral motifs across timescales | 9 pages, 6 figures | NeurIPS 2020 Learning Meaningful Representations of Life (LMRL)
workshop | null | null | q-bio.QM stat.ML | http://creativecommons.org/licenses/by/4.0/ | Behaviors of several laboratory animals can be modeled as sequences of
stereotyped behaviors, or behavioral motifs. However, identifying such motifs
is a challenging problem. Behaviors have a multi-scale structure: the animal
can be simultaneously performing a small-scale motif and a large-scale one
(e.g. \textit{che... | [
{
"created": "Tue, 11 Jul 2017 16:55:48 GMT",
"version": "v1"
},
{
"created": "Wed, 23 Aug 2017 16:13:48 GMT",
"version": "v2"
},
{
"created": "Wed, 1 Jul 2020 14:51:26 GMT",
"version": "v3"
}
] | 2021-05-12 | [
[
"Shan",
"Haozhe",
""
],
[
"Mason",
"Peggy",
""
]
] | Behaviors of several laboratory animals can be modeled as sequences of stereotyped behaviors, or behavioral motifs. However, identifying such motifs is a challenging problem. Behaviors have a multi-scale structure: the animal can be simultaneously performing a small-scale motif and a large-scale one (e.g. \textit{chewi... |
2004.02069 | Nikolai Slavov | Nikolai Slavov | Single-cell protein analysis by mass-spectrometry | keywords: single-cell analysis; single-cell proteomics;
mass-spectrometry; isobaric carrier; sample preparation; systems biology | Current Opinion in Chemical Biology (2020) | 10.1016/j.cbpa.2020.04.018 | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Human physiology and pathology arise from the coordinated interactions of
diverse single cells. However, analyzing single cells has been limited by the
low sensitivity and throughput of analytical methods. DNA sequencing has
recently made such analysis feasible for nucleic acids, but single-cell protein
analysis rema... | [
{
"created": "Sun, 5 Apr 2020 02:05:20 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Apr 2020 17:18:09 GMT",
"version": "v2"
},
{
"created": "Sat, 20 Jun 2020 19:51:36 GMT",
"version": "v3"
}
] | 2020-06-23 | [
[
"Slavov",
"Nikolai",
""
]
] | Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids, but single-cell protein analysis remain... |
1502.05667 | Giovanni Bussi | Sandro Bottaro, Francesco Di Palma and Giovanni Bussi | Towards de novo RNA 3D structure prediction | Accepted for publication on RNA & Disease | RNA & Disease 2, e544 (2015) | 10.14800/rd.544 | null | q-bio.BM physics.bio-ph physics.chem-ph physics.comp-ph | http://creativecommons.org/licenses/by/3.0/ | RNA is a fundamental class of biomolecules that mediate a large variety of
molecular processes within the cell. Computational algorithms can be of great
help in the understanding of RNA structure-function relationship. One of the
main challenges in this field is the development of structure-prediction
algorithms, whi... | [
{
"created": "Thu, 19 Feb 2015 18:42:46 GMT",
"version": "v1"
}
] | 2015-02-20 | [
[
"Bottaro",
"Sandro",
""
],
[
"Di Palma",
"Francesco",
""
],
[
"Bussi",
"Giovanni",
""
]
] | RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which... |
1409.1542 | Norman Poh | Norman Poh, Andrew McGovern and Simon de Lusignan | Towards automated identification of changes in laboratory measurement of
renal function: implications for longitudinal research and observing trends
in glomerular filtration rate (GFR) | null | null | null | TR-14-03 | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Introduction: Kidney function is reported using estimates of glomerular
filtration rate (eGFR). However, eGFR values are recorded without reference to
the creatinine (SCr) assays used to derive them, and newer assays were
introduced at different time points across laboratories in UK. These changes
may cause systemati... | [
{
"created": "Wed, 3 Sep 2014 09:53:20 GMT",
"version": "v1"
}
] | 2014-09-05 | [
[
"Poh",
"Norman",
""
],
[
"McGovern",
"Andrew",
""
],
[
"de Lusignan",
"Simon",
""
]
] | Introduction: Kidney function is reported using estimates of glomerular filtration rate (eGFR). However, eGFR values are recorded without reference to the creatinine (SCr) assays used to derive them, and newer assays were introduced at different time points across laboratories in UK. These changes may cause systematic ... |
1911.05663 | Rohan Gala | Rohan Gala, Nathan Gouwens, Zizhen Yao, Agata Budzillo, Osnat Penn,
Bosiljka Tasic, Gabe Murphy, Hongkui Zeng, Uygar S\"umb\"ul | A coupled autoencoder approach for multi-modal analysis of cell types | Main text : 10 pages, 5 figures. Supp text : 6 pages, 3 figures | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent developments in high throughput profiling of individual neurons have
spurred data driven exploration of the idea that there exist natural groupings
of neurons referred to as cell types. The promise of this idea is that the
immense complexity of brain circuits can be reduced, and effectively studied by
means of... | [
{
"created": "Wed, 6 Nov 2019 00:58:02 GMT",
"version": "v1"
}
] | 2019-11-14 | [
[
"Gala",
"Rohan",
""
],
[
"Gouwens",
"Nathan",
""
],
[
"Yao",
"Zizhen",
""
],
[
"Budzillo",
"Agata",
""
],
[
"Penn",
"Osnat",
""
],
[
"Tasic",
"Bosiljka",
""
],
[
"Murphy",
"Gabe",
""
],
[
"Zeng",
... | Recent developments in high throughput profiling of individual neurons have spurred data driven exploration of the idea that there exist natural groupings of neurons referred to as cell types. The promise of this idea is that the immense complexity of brain circuits can be reduced, and effectively studied by means of i... |
2208.09871 | Mattia Miotto | Greta Grassmann, Lorenzo Di Rienzo, Giorgio Gosti, Marco Leonetti,
Giancarlo Ruocco, Mattia Miotto, Edoardo Milanetti | Electrostatic complementarity at the interface drives transient
protein-protein interactions | 16 pages, 5 figures, 3 tables | Sci Rep 13, 10207 (2023) | 10.1038/s41598-023-37130-z | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Understanding the molecular mechanisms driving the binding between
bio-molecules is a crucial challenge in molecular biology. In this respect,
characteristics like the preferentially hydrophobic composition of the binding
interfaces, the role of van der Waals interactions (short range forces), and
the consequent shap... | [
{
"created": "Sun, 21 Aug 2022 11:55:07 GMT",
"version": "v1"
}
] | 2023-10-23 | [
[
"Grassmann",
"Greta",
""
],
[
"Di Rienzo",
"Lorenzo",
""
],
[
"Gosti",
"Giorgio",
""
],
[
"Leonetti",
"Marco",
""
],
[
"Ruocco",
"Giancarlo",
""
],
[
"Miotto",
"Mattia",
""
],
[
"Milanetti",
"Edoardo",
""
... | Understanding the molecular mechanisms driving the binding between bio-molecules is a crucial challenge in molecular biology. In this respect, characteristics like the preferentially hydrophobic composition of the binding interfaces, the role of van der Waals interactions (short range forces), and the consequent shape ... |
2207.07215 | Mohsen Annabestani | Ali Olyanasab, Zahra Meskar, Mohsen Annabestani, Ali Mousavi Shaegh,
and Mehdi Fardmanesh | Warp and Weft Wiring method for rapid, modifiable, self-aligned, and
bonding-free fabrication of multi electrodes microfluidic sensors | null | null | null | null | q-bio.QM physics.app-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The need for rapid fabrication of microfluidic devices has become
increasingly critical as microfluidics become part of biomedical sensors. Using
Warp and Weft Wiring (WWW) of copper wires, this paper presents a novel
low-cost method for rapid, self-aligned, bonding-free, and modifiable
fabrication of multi-electrode... | [
{
"created": "Thu, 14 Jul 2022 21:42:49 GMT",
"version": "v1"
}
] | 2022-07-18 | [
[
"Olyanasab",
"Ali",
""
],
[
"Meskar",
"Zahra",
""
],
[
"Annabestani",
"Mohsen",
""
],
[
"Shaegh",
"Ali Mousavi",
""
],
[
"Fardmanesh",
"Mehdi",
""
]
] | The need for rapid fabrication of microfluidic devices has become increasingly critical as microfluidics become part of biomedical sensors. Using Warp and Weft Wiring (WWW) of copper wires, this paper presents a novel low-cost method for rapid, self-aligned, bonding-free, and modifiable fabrication of multi-electrodes ... |
2101.11929 | Shiva Rudraraju | Debabrata Auddya, Xiaoxuan Zhang, Rahul Gulati, Ritvik Vasan, Krishna
Garikipati, Padmini Rangamani, Shiva Rudraraju | Biomembranes undergo complex, non-axisymmetric deformations governed by
Kirchhoff-Love kinematics and revealed by a three dimensional computational
framework | null | null | 10.1098/rspa.2021.0246 | null | q-bio.QM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biomembranes play a central role in various phenomena like locomotion of
cells, cell-cell interactions, packaging of nutrients, and in maintaining
organelle morphology and functionality. During these processes, the membranes
undergo significant morphological changes through deformation, scission, and
fusion. Modeling... | [
{
"created": "Thu, 28 Jan 2021 11:04:49 GMT",
"version": "v1"
}
] | 2021-12-01 | [
[
"Auddya",
"Debabrata",
""
],
[
"Zhang",
"Xiaoxuan",
""
],
[
"Gulati",
"Rahul",
""
],
[
"Vasan",
"Ritvik",
""
],
[
"Garikipati",
"Krishna",
""
],
[
"Rangamani",
"Padmini",
""
],
[
"Rudraraju",
"Shiva",
""
... | Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging of nutrients, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modeling t... |
2311.12040 | Xiaoqiong Xia | Xiaoqiong Xia, Chaoyu Zhu, Yuqi Shan, Fan Zhong, and Lei Liu | TransCDR: a deep learning model for enhancing the generalizability of
cancer drug response prediction through transfer learning and multimodal data
fusion for drug representation | 8 figures | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate and robust drug response prediction is of utmost importance in
precision medicine. Although many models have been developed to utilize the
representations of drugs and cancer cell lines for predicting cancer drug
responses (CDR), their performances can be improved by addressing issues such
as insufficient da... | [
{
"created": "Fri, 17 Nov 2023 14:55:12 GMT",
"version": "v1"
}
] | 2023-11-22 | [
[
"Xia",
"Xiaoqiong",
""
],
[
"Zhu",
"Chaoyu",
""
],
[
"Shan",
"Yuqi",
""
],
[
"Zhong",
"Fan",
""
],
[
"Liu",
"Lei",
""
]
] | Accurate and robust drug response prediction is of utmost importance in precision medicine. Although many models have been developed to utilize the representations of drugs and cancer cell lines for predicting cancer drug responses (CDR), their performances can be improved by addressing issues such as insufficient data... |
1702.05288 | Roland Kr\"amer | Ulrich Warttinger, Roland Kr\"amer | Instant determination of the potential biomarker heparan sulfate in
human plasma by a mix-and-read fluorescence assay | 18 pages, 5 figures, 2 schemes, 5 tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Heparan sulfate (HS) is a linear, polydisperse sulfated polysaccharide
belonging to the glycosaminoglycan family. HS proteoglycans are ubiquitously
found at the cell surface and extracellular matrix in animal species. HS is
involved in the interaction with a wide variety of proteins and the regulation
of many biologi... | [
{
"created": "Fri, 17 Feb 2017 10:19:36 GMT",
"version": "v1"
}
] | 2017-02-20 | [
[
"Warttinger",
"Ulrich",
""
],
[
"Krämer",
"Roland",
""
]
] | Heparan sulfate (HS) is a linear, polydisperse sulfated polysaccharide belonging to the glycosaminoglycan family. HS proteoglycans are ubiquitously found at the cell surface and extracellular matrix in animal species. HS is involved in the interaction with a wide variety of proteins and the regulation of many biologica... |
1810.12663 | Michael Adamer | Michael F Adamer, Heather A Harrington, Eamonn A Gaffney, Thomas E
Woolley | Coloured Noise from Stochastic Inflows in Reaction-Diffusion Systems | 31 pages, 8 figures | null | null | null | q-bio.QM physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we present a framework for investigating coloured noise in
reaction-diffusion systems. We start by considering a deterministic
reaction-diffusion equation and show how external forcing can cause temporally
correlated or coloured noise. Here, the main source of external noise is
considered to be fluctuat... | [
{
"created": "Tue, 30 Oct 2018 11:19:58 GMT",
"version": "v1"
},
{
"created": "Fri, 30 Nov 2018 13:14:15 GMT",
"version": "v2"
}
] | 2018-12-03 | [
[
"Adamer",
"Michael F",
""
],
[
"Harrington",
"Heather A",
""
],
[
"Gaffney",
"Eamonn A",
""
],
[
"Woolley",
"Thomas E",
""
]
] | In this paper we present a framework for investigating coloured noise in reaction-diffusion systems. We start by considering a deterministic reaction-diffusion equation and show how external forcing can cause temporally correlated or coloured noise. Here, the main source of external noise is considered to be fluctuatio... |
1704.00940 | Antonino Sciarrino | A. Sciarrino and P.Sorba | Symmetry and Minimum Principle at the Basis of the Genetic Code | To appear in BIOMAT 2016, 326 - 362, 2017 | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The importance of the notion of symmetry in physics is well established:
could it also be the case for the genetic code? In this spirit, a model for the
Genetic Code based on continuous symmetries and entitled the "Crystal Basis
Model" has been proposed a few years ago. The present paper is a review of the
model, of ... | [
{
"created": "Tue, 4 Apr 2017 10:17:00 GMT",
"version": "v1"
}
] | 2017-04-05 | [
[
"Sciarrino",
"A.",
""
],
[
"Sorba",
"P.",
""
]
] | The importance of the notion of symmetry in physics is well established: could it also be the case for the genetic code? In this spirit, a model for the Genetic Code based on continuous symmetries and entitled the "Crystal Basis Model" has been proposed a few years ago. The present paper is a review of the model, of so... |
1504.00698 | Richard McMurtrey | Richard J. McMurtrey | Novel Advancements in Three-Dimensional Neural Tissue Engineering and
Regenerative Medicine | null | Neural Regen. Res. 2015;10(3):352-4 | 10.4103/1673-5374.153674 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurological diseases and injuries present some of the greatest challenges in
modern medicine, often causing irreversible and lifelong burdens in the people
whom they afflict. These diagnoses have devastating consequences on millions of
people each year, and yet there are currently no therapies or interventions
that ... | [
{
"created": "Thu, 2 Apr 2015 21:59:26 GMT",
"version": "v1"
}
] | 2015-04-06 | [
[
"McMurtrey",
"Richard J.",
""
]
] | Neurological diseases and injuries present some of the greatest challenges in modern medicine, often causing irreversible and lifelong burdens in the people whom they afflict. These diagnoses have devastating consequences on millions of people each year, and yet there are currently no therapies or interventions that ca... |
1412.6325 | Robert Leech | Peter J. Hellyer, Barbara Jachs, Robert Leech, Claudia Clopath | Local inhibitory plasticity tunes global brain dynamics and allows the
emergence of functional brain networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Rich, spontaneous brain activity has been observed across a range of
different temporal and spatial scales. These dynamics are thought to be
important t for efficient neural functioning. Experimental evidence suggests
that these neural dynamics are maintained across a variety of different
cognitive states, in respons... | [
{
"created": "Fri, 19 Dec 2014 13:08:04 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Jan 2015 00:02:22 GMT",
"version": "v2"
}
] | 2015-01-21 | [
[
"Hellyer",
"Peter J.",
""
],
[
"Jachs",
"Barbara",
""
],
[
"Leech",
"Robert",
""
],
[
"Clopath",
"Claudia",
""
]
] | Rich, spontaneous brain activity has been observed across a range of different temporal and spatial scales. These dynamics are thought to be important t for efficient neural functioning. Experimental evidence suggests that these neural dynamics are maintained across a variety of different cognitive states, in response ... |
1907.05064 | Francesc Rossell\'o | Tom\'as M. Coronado, Mareike Fischer, Lina Herbst, Francesc
Rossell\'o, Kristina Wicke | On the minimum value of the Colless index and the bifurcating trees that
achieve it | 61 pages. This paper is the result of merging our previous preprints
arXiv:1903.11670 [q-bio.PE] and arXiv:1904.09771 [math.CO] into a single
joint manuscript. Several proofs are new | null | null | null | q-bio.PE cs.DM math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Measures of tree balance play an important role in the analysis of
phylogenetic trees. One of the oldest and most popular indices in this regard
is the Colless index for rooted bifurcating trees, introduced by Colless
(1982). While many of its statistical properties under different probabilistic
models for phylogenet... | [
{
"created": "Thu, 11 Jul 2019 09:07:29 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Feb 2020 17:31:14 GMT",
"version": "v2"
}
] | 2020-02-18 | [
[
"Coronado",
"Tomás M.",
""
],
[
"Fischer",
"Mareike",
""
],
[
"Herbst",
"Lina",
""
],
[
"Rosselló",
"Francesc",
""
],
[
"Wicke",
"Kristina",
""
]
] | Measures of tree balance play an important role in the analysis of phylogenetic trees. One of the oldest and most popular indices in this regard is the Colless index for rooted bifurcating trees, introduced by Colless (1982). While many of its statistical properties under different probabilistic models for phylogenetic... |
1603.04023 | Greg Stephens | Onno D Broekmans, Jarlath B Rodgers, William S Ryu and Greg J Stephens | Resolving coiled shapes reveals new reorientation behaviors in C.
elegans | 14 pages and 8 figures, including supplementary information | eLife 2016;5:e17227 | 10.7554/eLife.17227 | null | q-bio.QM physics.bio-ph q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We exploit the reduced space of C. elegans postures to develop a novel
tracking algorithm which captures both simple shapes and also self-occluding
coils, an important, yet unexplored, component of worm behavior. We apply our
algorithm to show that visually complex, coiled sequences are a superposition
of two simpler... | [
{
"created": "Sun, 13 Mar 2016 12:38:01 GMT",
"version": "v1"
}
] | 2016-11-01 | [
[
"Broekmans",
"Onno D",
""
],
[
"Rodgers",
"Jarlath B",
""
],
[
"Ryu",
"William S",
""
],
[
"Stephens",
"Greg J",
""
]
] | We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of worm behavior. We apply our algorithm to show that visually complex, coiled sequences are a superposition of two simpler p... |
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