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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
q-bio/0608002 | Leor Weinberger | Leor S. Weinberger, John C. Burnett, Jared E. Toettcher, Adam P.
Arkin, and David V. Schaffer | Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1
Tat Fluctuations Drive Phenotypic Diversity | Supplemental data available as q-bio.MN/0608003 | Cell. 2005 Jul 29;122(2):169-82 | null | null | q-bio.MN cond-mat.soft physics.bio-ph q-bio.CB | null | Stochastic gene expression has been implicated in a variety of cellular
processes, including cell differentiation and disease. In this issue of Cell,
Weinberger et al. (2005) take an integrated computational-experimental approach
to study the Tat transactivation feedback loop in HIV-1 and show that
fluctuations in a ... | [
{
"created": "Tue, 1 Aug 2006 19:37:32 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Weinberger",
"Leor S.",
""
],
[
"Burnett",
"John C.",
""
],
[
"Toettcher",
"Jared E.",
""
],
[
"Arkin",
"Adam P.",
""
],
[
"Schaffer",
"David V.",
""
]
] | Stochastic gene expression has been implicated in a variety of cellular processes, including cell differentiation and disease. In this issue of Cell, Weinberger et al. (2005) take an integrated computational-experimental approach to study the Tat transactivation feedback loop in HIV-1 and show that fluctuations in a ke... |
2011.12350 | Changchuan Yin Dr. | Changchuan Yin, Stephen S.-T. Yau | Inverted repeats in coronavirus SARS-CoV-2 genome and implications in
evolution | null | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The coronavirus disease (COVID-19) pandemic, caused by the coronavirus
SARS-CoV-2, has caused 60 millions of infections and 1.38 millions of
fatalities. Genomic analysis of SARS-CoV-2 can provide insights on drug design
and vaccine development for controlling the pandemic. Inverted repeats in a
genome greatly impact ... | [
{
"created": "Tue, 24 Nov 2020 20:11:40 GMT",
"version": "v1"
}
] | 2020-11-26 | [
[
"Yin",
"Changchuan",
""
],
[
"Yau",
"Stephen S. -T.",
""
]
] | The coronavirus disease (COVID-19) pandemic, caused by the coronavirus SARS-CoV-2, has caused 60 millions of infections and 1.38 millions of fatalities. Genomic analysis of SARS-CoV-2 can provide insights on drug design and vaccine development for controlling the pandemic. Inverted repeats in a genome greatly impact th... |
2003.13282 | Tarun Jain | Tarun Jain, Bijendra Nath Jain | Accelerated infection testing at scale: a proposal for inference with
single test on multiple patients | 8 pages | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In pandemics or epidemics, public health authorities need to rapidly test a
large number of individuals, both to determine the line of treatment as well as
to know the spread of infection to plan containment, mitigation and future
responses. However, the lack of adequate testing kits could be a bottleneck,
especially... | [
{
"created": "Mon, 30 Mar 2020 09:06:08 GMT",
"version": "v1"
}
] | 2020-03-31 | [
[
"Jain",
"Tarun",
""
],
[
"Jain",
"Bijendra Nath",
""
]
] | In pandemics or epidemics, public health authorities need to rapidly test a large number of individuals, both to determine the line of treatment as well as to know the spread of infection to plan containment, mitigation and future responses. However, the lack of adequate testing kits could be a bottleneck, especially i... |
2003.09564 | Nigel Goldenfeld | Sergei Maslov and Nigel Goldenfeld | Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity
in Chicago by COVID-19 | null | null | null | null | q-bio.PE physics.med-ph physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We estimate the growth in demand for ICU beds in Chicago during the emerging
COVID-19 epidemic, using state-of-the-art computer simulations calibrated for
the SARS-CoV-2 virus. The questions we address are these:
(1) Will the ICU capacity in Chicago be exceeded, and if so by how much?
(2) Can strong mitigation st... | [
{
"created": "Sat, 21 Mar 2020 02:47:39 GMT",
"version": "v1"
}
] | 2020-03-24 | [
[
"Maslov",
"Sergei",
""
],
[
"Goldenfeld",
"Nigel",
""
]
] | We estimate the growth in demand for ICU beds in Chicago during the emerging COVID-19 epidemic, using state-of-the-art computer simulations calibrated for the SARS-CoV-2 virus. The questions we address are these: (1) Will the ICU capacity in Chicago be exceeded, and if so by how much? (2) Can strong mitigation strategi... |
1404.0674 | Paulo Bandiera-Paiva | Paulo Bandiera-Paiva and Marcelo R.S. Briones | PGA: A Program for Genome Annotation by Comparative Analysis of Maximum
Likelihood Phylogenies of Genes and Species | arXiv admin note: substantial text overlap with arXiv:1404.0630 | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Phylogenetic Genome Annotator (PGA) is a computer program that enables
real-time comparison of 'gene trees' versus 'species trees' obtained from
predicted open reading frames of whole genome data. The gene phylogenies are
inferred for each individual genome predicted proteins whereas the species
phylogenies are i... | [
{
"created": "Wed, 2 Apr 2014 17:55:42 GMT",
"version": "v1"
}
] | 2014-04-04 | [
[
"Bandiera-Paiva",
"Paulo",
""
],
[
"Briones",
"Marcelo R. S.",
""
]
] | The Phylogenetic Genome Annotator (PGA) is a computer program that enables real-time comparison of 'gene trees' versus 'species trees' obtained from predicted open reading frames of whole genome data. The gene phylogenies are inferred for each individual genome predicted proteins whereas the species phylogenies are inf... |
1703.01999 | Quico Spaen | Quico Spaen, Dorit S. Hochbaum, Roberto As\'in-Ach\'a | HNCcorr: A Novel Combinatorial Approach for Cell Identification in
Calcium-Imaging Movies | null | null | 10.1523/ENEURO.0304-18.2019 | null | q-bio.QM math.OC q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calcium imaging has emerged as a workhorse method in neuroscience to
investigate patterns of neuronal activity. Instrumentation to acquire calcium
imaging movies has rapidly progressed and has become standard across labs.
Still, algorithms to automatically detect and extract activity signals from
calcium imaging movi... | [
{
"created": "Mon, 6 Mar 2017 17:42:25 GMT",
"version": "v1"
}
] | 2019-06-03 | [
[
"Spaen",
"Quico",
""
],
[
"Hochbaum",
"Dorit S.",
""
],
[
"Asín-Achá",
"Roberto",
""
]
] | Calcium imaging has emerged as a workhorse method in neuroscience to investigate patterns of neuronal activity. Instrumentation to acquire calcium imaging movies has rapidly progressed and has become standard across labs. Still, algorithms to automatically detect and extract activity signals from calcium imaging movies... |
1403.5376 | Suman Kumar Banik | Srijeeta Talukder, Shrabani Sen, Prantik Chakraborti, Ralf Metzler,
Suman K Banik, Pinaki Chaudhury | Breathing dynamics based parameter sensitivity analysis of
hetero-polymeric DNA | 10 pages, 3 figures, 4 tables | J. Chem. Phys. 140 (2014) 125101 | 10.1063/1.4869112 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the parameter sensitivity of hetero-polymeric DNA within the purview
of DNA breathing dynamics. The degree of correlation between the mean bubble
size and the model parameters are estimated for this purpose for three
different DNA sequences. The analysis leads us to a better understanding of the
sequence dep... | [
{
"created": "Fri, 21 Mar 2014 06:19:03 GMT",
"version": "v1"
}
] | 2014-03-27 | [
[
"Talukder",
"Srijeeta",
""
],
[
"Sen",
"Shrabani",
""
],
[
"Chakraborti",
"Prantik",
""
],
[
"Metzler",
"Ralf",
""
],
[
"Banik",
"Suman K",
""
],
[
"Chaudhury",
"Pinaki",
""
]
] | We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA sequences. The analysis leads us to a better understanding of the sequence depen... |
2111.00108 | Muhammad Ammar Malik | Muhammad Ammar Malik, Adriaan-Alexander Ludl, Tom Michoel | High-dimensional multi-trait GWAS by reverse prediction of genotypes | null | null | null | null | q-bio.GN cs.LG q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multi-trait genome-wide association studies (GWAS) use multi-variate
statistical methods to identify associations between genetic variants and
multiple correlated traits simultaneously, and have higher statistical power
than independent univariate analyses of traits. Reverse regression, where
genotypes of genetic var... | [
{
"created": "Fri, 29 Oct 2021 22:34:35 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Feb 2022 14:45:03 GMT",
"version": "v2"
}
] | 2022-02-10 | [
[
"Malik",
"Muhammad Ammar",
""
],
[
"Ludl",
"Adriaan-Alexander",
""
],
[
"Michoel",
"Tom",
""
]
] | Multi-trait genome-wide association studies (GWAS) use multi-variate statistical methods to identify associations between genetic variants and multiple correlated traits simultaneously, and have higher statistical power than independent univariate analyses of traits. Reverse regression, where genotypes of genetic varia... |
2210.16098 | Yiqiang Yi | Yiqiang Yi, Xu Wan, Kangfei Zhao, Le Ou-Yang, Peilin Zhao | Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph
Network | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Binding affinity prediction of three-dimensional (3D) protein ligand
complexes is critical for drug repositioning and virtual drug screening.
Existing approaches transform a 3D protein-ligand complex to a two-dimensional
(2D) graph, and then use graph neural networks (GNNs) to predict its binding
affinity. However, t... | [
{
"created": "Thu, 27 Oct 2022 02:15:52 GMT",
"version": "v1"
}
] | 2022-10-31 | [
[
"Yi",
"Yiqiang",
""
],
[
"Wan",
"Xu",
""
],
[
"Zhao",
"Kangfei",
""
],
[
"Ou-Yang",
"Le",
""
],
[
"Zhao",
"Peilin",
""
]
] | Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then use graph neural networks (GNNs) to predict its binding affinity. However, the... |
1305.6043 | Bjarki Eldon | Matthias Birkner, Jochen Blath, Bjarki Eldon | Statistical properties of the site-frequency spectrum associated with
Lambda-coalescents | 45 pages, 14 figures, 4 tables, Appendix, supporting information | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Statistical properties of the site frequency spectrum associated with
Lambda-coalescents are our objects of study. In particular, we derive
recursions for the expected value, variance, and covariance of the spectrum,
extending earlier results of Fu (1995) for the classical Kingman coalescent.
Estimating coalescent pa... | [
{
"created": "Sun, 26 May 2013 16:37:54 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Aug 2013 17:15:28 GMT",
"version": "v2"
}
] | 2013-08-27 | [
[
"Birkner",
"Matthias",
""
],
[
"Blath",
"Jochen",
""
],
[
"Eldon",
"Bjarki",
""
]
] | Statistical properties of the site frequency spectrum associated with Lambda-coalescents are our objects of study. In particular, we derive recursions for the expected value, variance, and covariance of the spectrum, extending earlier results of Fu (1995) for the classical Kingman coalescent. Estimating coalescent para... |
1707.00664 | Alessio Franci | Alessio Franci, Guillaume Drion, Rodolphe Sepulchre | Robust and tunable bursting requires slow positive feedback | null | null | null | null | q-bio.NC math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We highlight that the robustness and tunability of a bursting model
critically relies on currents that provide slow positive feedback to the
membrane potential. Such currents have the ability of making the total
conductance of the circuit negative in a time scale that is termed slow because
intermediate between the f... | [
{
"created": "Mon, 3 Jul 2017 17:29:04 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Jan 2018 15:56:43 GMT",
"version": "v2"
}
] | 2018-01-29 | [
[
"Franci",
"Alessio",
""
],
[
"Drion",
"Guillaume",
""
],
[
"Sepulchre",
"Rodolphe",
""
]
] | We highlight that the robustness and tunability of a bursting model critically relies on currents that provide slow positive feedback to the membrane potential. Such currents have the ability of making the total conductance of the circuit negative in a time scale that is termed slow because intermediate between the fas... |
1509.09192 | Mohammad Soltani | Thierry Platini, Mohammad Soltani, Abhyudai Singh | Stochastic Analysis Of An Incoherent Feedforward Genetic Motif | 8 pages | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene products (RNAs, proteins) often occur at low molecular counts inside
individual cells, and hence are subject to considerable random fluctuations
(noise) in copy number over time. Not surprisingly, cells encode diverse
regulatory mechanisms to buffer noise. One such mechanism is the incoherent
feedforward circuit... | [
{
"created": "Wed, 30 Sep 2015 14:30:08 GMT",
"version": "v1"
}
] | 2015-10-01 | [
[
"Platini",
"Thierry",
""
],
[
"Soltani",
"Mohammad",
""
],
[
"Singh",
"Abhyudai",
""
]
] | Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory mechanisms to buffer noise. One such mechanism is the incoherent feedforward circuit. ... |
1201.3170 | Pascal Buenzli | Peter Pivonka, Pascal R. Buenzli, Stefan Scheiner, Christian Hellmich,
Colin R. Dunstan | The influence of bone surface availability in bone remodelling - A
mathematical model including coupled geometrical and biomechanical
regulations of bone cells | 17 pages, 9 figures, 3 tables; Changes in v2: New title, C Hellmich
added as author for his contribution to biomechanical part of the model,
rewritten in this version. One figure (Fig 4) added. Some misprints and
errors of v1 corrected. Some sylistic rearrangements | Eng Struct (2013) 47:134-147 | 10.1016/j.engstruct.2012.09.006 | null | q-bio.TO physics.bio-ph physics.med-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bone is a biomaterial undergoing continuous renewal. The renewal process is
known as bone remodelling and is operated by bone-resorbing cells (osteoclasts)
and bone-forming cells (osteoblasts). Both biochemical and biomechanical
regulatory mechanisms have been identified in the interaction between
osteoclasts and ost... | [
{
"created": "Mon, 16 Jan 2012 07:45:23 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Feb 2012 07:16:49 GMT",
"version": "v2"
}
] | 2014-05-21 | [
[
"Pivonka",
"Peter",
""
],
[
"Buenzli",
"Pascal R.",
""
],
[
"Scheiner",
"Stefan",
""
],
[
"Hellmich",
"Christian",
""
],
[
"Dunstan",
"Colin R.",
""
]
] | Bone is a biomaterial undergoing continuous renewal. The renewal process is known as bone remodelling and is operated by bone-resorbing cells (osteoclasts) and bone-forming cells (osteoblasts). Both biochemical and biomechanical regulatory mechanisms have been identified in the interaction between osteoclasts and osteo... |
0709.2015 | Henrik Jeldtoft Jensen | Henrik Jeldtoft Jensen and Elsa Arcaute | Complexity, Collective Effects and Modelling of Ecosystems: formation,
function and stability | 11 pages and 1 figure | null | null | null | q-bio.PE q-bio.OT | null | We discuss the relevance of studying ecology within the framework of
Complexity Science from a statistical mechanics approach. Ecology is concerned
with understanding how systems level properties emerge out of the multitude of
interactions amongst large numbers of components, leading to ecosystems that
possess the pr... | [
{
"created": "Thu, 13 Sep 2007 08:13:14 GMT",
"version": "v1"
}
] | 2007-09-14 | [
[
"Jensen",
"Henrik Jeldtoft",
""
],
[
"Arcaute",
"Elsa",
""
]
] | We discuss the relevance of studying ecology within the framework of Complexity Science from a statistical mechanics approach. Ecology is concerned with understanding how systems level properties emerge out of the multitude of interactions amongst large numbers of components, leading to ecosystems that possess the prot... |
1606.05912 | Ricardo Martinez-Garcia | Ricardo Martinez-Garcia, Corina E. Tarnita | Seasonality can induce coexistence of multiple bet-hedging strategies in
Dictyostelium discoideum via storage effect | 33 pages, 7 figures | null | 10.1016/j.jtbi.2017.05.019 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | D. discoideum has been recently suggested as an example of bet-hedging. Upon
starvation a population of unicellular amoebae splits between aggregators,
which form a fruiting body made of a stalk and resistant spores, and
non-aggregators. Spores are favored by long starvation periods, but vegetative
cells can exploit ... | [
{
"created": "Sun, 19 Jun 2016 21:33:51 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Jun 2016 06:23:24 GMT",
"version": "v2"
},
{
"created": "Wed, 17 May 2017 16:37:10 GMT",
"version": "v3"
}
] | 2017-05-18 | [
[
"Martinez-Garcia",
"Ricardo",
""
],
[
"Tarnita",
"Corina E.",
""
]
] | D. discoideum has been recently suggested as an example of bet-hedging. Upon starvation a population of unicellular amoebae splits between aggregators, which form a fruiting body made of a stalk and resistant spores, and non-aggregators. Spores are favored by long starvation periods, but vegetative cells can exploit re... |
1306.4747 | Ricky Der | Ricky Der, Joshua B. Plotkin | The equilibrium allele frequency distribution for a population with
reproductive skew | Submitted to Genetics | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the population genetics of two neutral alleles under reversible
mutation in the \Lambda-processes, a population model that features a skewed
offspring distribution. We describe the shape of the equilibrium allele
frequency distribution as a function of the model parameters. We show that the
mutation rates ca... | [
{
"created": "Thu, 20 Jun 2013 03:29:40 GMT",
"version": "v1"
}
] | 2013-06-21 | [
[
"Der",
"Ricky",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | We study the population genetics of two neutral alleles under reversible mutation in the \Lambda-processes, a population model that features a skewed offspring distribution. We describe the shape of the equilibrium allele frequency distribution as a function of the model parameters. We show that the mutation rates can ... |
1302.0255 | Kieran Sharkey | Robert R. Wilkinson and Kieran J. Sharkey | An Exact Relationship Between Invasion Probability and Endemic
Prevalence for Markovian SIS Dynamics on Networks | 16 pages, 5 figures. Supplementary data available with published
version at http://dx.doi.org/10.1371/journal.pone.0069028 | WPLoS ONE 8(7): e69028 | 10.1371/journal.pone.0069028 | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding models which represent the invasion of network-based systems by
infectious agents can give important insights into many real-world situations,
including the prevention and control of infectious diseases and computer
viruses. Here we consider Markovian susceptible-infectious-susceptible (SIS)
dynamics on... | [
{
"created": "Fri, 1 Feb 2013 19:16:15 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Aug 2013 15:35:09 GMT",
"version": "v2"
}
] | 2013-08-02 | [
[
"Wilkinson",
"Robert R.",
""
],
[
"Sharkey",
"Kieran J.",
""
]
] | Understanding models which represent the invasion of network-based systems by infectious agents can give important insights into many real-world situations, including the prevention and control of infectious diseases and computer viruses. Here we consider Markovian susceptible-infectious-susceptible (SIS) dynamics on f... |
1605.09070 | Karel B\v{r}inda | Karel B\v{r}inda, Valentina Boeva, Gregory Kucherov | Dynamic read mapping and online consensus calling for better variant
detection | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Variant detection from high-throughput sequencing data is an essential step
in identification of alleles involved in complex diseases and cancer. To deal
with these massive data, elaborated sequence analysis pipelines are employed. A
core component of such pipelines is a read mapping module whose accuracy
strongly af... | [
{
"created": "Sun, 29 May 2016 22:25:55 GMT",
"version": "v1"
}
] | 2016-05-31 | [
[
"Břinda",
"Karel",
""
],
[
"Boeva",
"Valentina",
""
],
[
"Kucherov",
"Gregory",
""
]
] | Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core component of such pipelines is a read mapping module whose accuracy strongly affe... |
1311.5696 | Kieran Smallbone | Kieran Smallbone | Striking a balance with Recon 2.1 | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recon 2 is a highly curated reconstruction of the human metabolic network.
Whilst the network is state of the art, it has shortcomings, including the
presence of unbalanced reactions involving generic metabolites. By replacing
these generic molecules with each of their specific instances, we can ensure
full elemental... | [
{
"created": "Fri, 22 Nov 2013 10:19:06 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Nov 2014 00:38:24 GMT",
"version": "v2"
}
] | 2014-11-27 | [
[
"Smallbone",
"Kieran",
""
]
] | Recon 2 is a highly curated reconstruction of the human metabolic network. Whilst the network is state of the art, it has shortcomings, including the presence of unbalanced reactions involving generic metabolites. By replacing these generic molecules with each of their specific instances, we can ensure full elemental b... |
1609.04496 | Karina Mazzitello | K. I. Mazzitello, Q. Zhang, M. A. Chrenek, F. Family, H. E.
Grossniklaus, J. M. Nickerson, and Y. Jiang | Druse-Induced Morphology Evolution in Retinal Pigment Epithelium | 10 pages, 9 figures | null | null | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The retinal pigment epithelium (RPE) is a key site of pathogenesis for many
retina diseases. The formation of drusen in the retina is characteristic of
retinal degeneration. We investigate morphological changes in the RPE in the
presence of soft drusen using an integrated experimental and modeling approach.
We collec... | [
{
"created": "Thu, 15 Sep 2016 02:46:20 GMT",
"version": "v1"
},
{
"created": "Thu, 2 Mar 2017 17:43:01 GMT",
"version": "v2"
}
] | 2017-03-03 | [
[
"Mazzitello",
"K. I.",
""
],
[
"Zhang",
"Q.",
""
],
[
"Chrenek",
"M. A.",
""
],
[
"Family",
"F.",
""
],
[
"Grossniklaus",
"H. E.",
""
],
[
"Nickerson",
"J. M.",
""
],
[
"Jiang",
"Y.",
""
]
] | The retinal pigment epithelium (RPE) is a key site of pathogenesis for many retina diseases. The formation of drusen in the retina is characteristic of retinal degeneration. We investigate morphological changes in the RPE in the presence of soft drusen using an integrated experimental and modeling approach. We collect ... |
2011.04651 | Wengong Jin | Wengong Jin, Regina Barzilay, Tommi Jaakkola | Discovering Synergistic Drug Combinations for COVID with Biological
Bottleneck Models | Accepted to NeurIPS 2020 Machine Learning for Molecules Workshop | null | null | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Drug combinations play an important role in therapeutics due to its better
efficacy and reduced toxicity. Recent approaches have applied machine learning
to identify synergistic combinations for cancer, but they are not applicable to
new diseases with limited combination data. Given that drug synergy is closely
tied ... | [
{
"created": "Mon, 9 Nov 2020 03:30:44 GMT",
"version": "v1"
},
{
"created": "Sat, 28 Nov 2020 18:53:07 GMT",
"version": "v2"
}
] | 2020-12-01 | [
[
"Jin",
"Wengong",
""
],
[
"Barzilay",
"Regina",
""
],
[
"Jaakkola",
"Tommi",
""
]
] | Drug combinations play an important role in therapeutics due to its better efficacy and reduced toxicity. Recent approaches have applied machine learning to identify synergistic combinations for cancer, but they are not applicable to new diseases with limited combination data. Given that drug synergy is closely tied to... |
2404.17128 | Xiaoyu Zhang | Xiaoyu Zhang, Pengcheng Yang, Jiawei Feng, Qiang Luo, Wei Lin and Xin
Lu | Network Structure Trumps Neuron Dynamics: Insights from Drosophila
Connectome Simulations | null | null | null | null | q-bio.NC cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the success of artificial neural networks, the necessity of real
network structures in simulating intelligence remains unclear. Utilizing the
largest adult Drosophila connectome data set, we constructed a large-scale
network communication model framework based on simple neuronal activation
mechanisms to simul... | [
{
"created": "Fri, 26 Apr 2024 03:07:14 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Jun 2024 03:34:23 GMT",
"version": "v2"
},
{
"created": "Sun, 30 Jun 2024 13:25:32 GMT",
"version": "v3"
}
] | 2024-07-02 | [
[
"Zhang",
"Xiaoyu",
""
],
[
"Yang",
"Pengcheng",
""
],
[
"Feng",
"Jiawei",
""
],
[
"Luo",
"Qiang",
""
],
[
"Lin",
"Wei",
""
],
[
"Lu",
"Xin",
""
]
] | Despite the success of artificial neural networks, the necessity of real network structures in simulating intelligence remains unclear. Utilizing the largest adult Drosophila connectome data set, we constructed a large-scale network communication model framework based on simple neuronal activation mechanisms to simulat... |
2208.08896 | Shuqiang Wang | Heng Kong and Shuqiang Wang | Adversarial Learning Based Structural Brain-network Generative Model for
Analyzing Mild Cognitive Impairment | null | null | null | null | q-bio.NC cs.CV eess.IV eess.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mild cognitive impairment(MCI) is a precursor of Alzheimer's disease(AD), and
the detection of MCI is of great clinical significance. Analyzing the
structural brain networks of patients is vital for the recognition of MCI.
However, the current studies on structural brain networks are totally dependent
on specific too... | [
{
"created": "Tue, 9 Aug 2022 02:45:53 GMT",
"version": "v1"
}
] | 2022-08-19 | [
[
"Kong",
"Heng",
""
],
[
"Wang",
"Shuqiang",
""
]
] | Mild cognitive impairment(MCI) is a precursor of Alzheimer's disease(AD), and the detection of MCI is of great clinical significance. Analyzing the structural brain networks of patients is vital for the recognition of MCI. However, the current studies on structural brain networks are totally dependent on specific toolb... |
1212.1117 | Alexander Stewart | Alexander J. Stewart, Robert M. Seymour, Andrew Pomiankowski, Max
Reuter | Under-dominance constrains the evolution of negative autoregulation in
diploids | null | PLoS Comput Biol, 2013, 9(3): e1002992 | 10.1371/journal.pcbi.1002992 | null | q-bio.PE q-bio.GN q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Regulatory networks have evolved to allow gene expression to rapidly track
changes in the environment as well as to buffer perturbations and maintain
cellular homeostasis in the absence of change. Theoretical work and empirical
investigation in Escherichia coli have shown that negative autoregulation
confers both rap... | [
{
"created": "Wed, 5 Dec 2012 18:04:15 GMT",
"version": "v1"
}
] | 2013-04-30 | [
[
"Stewart",
"Alexander J.",
""
],
[
"Seymour",
"Robert M.",
""
],
[
"Pomiankowski",
"Andrew",
""
],
[
"Reuter",
"Max",
""
]
] | Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical investigation in Escherichia coli have shown that negative autoregulation confers both rapid... |
1107.5192 | Ingo Lohmar | Ingo Lohmar and Baruch Meerson | Switching between phenotypes and population extinction | 11 pages, 5 figures. Additional discussion paragraph, minor language
improvements; content as published in Phys. Rev. E | Phys. Rev. E 84 (2011) 051901 | 10.1103/PhysRevE.84.051901 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many types of bacteria can survive under stress by switching stochastically
between two different phenotypes: the "normals" who multiply fast, but are
vulnerable to stress, and the "persisters" who hardly multiply, but are
resilient to stress. Previous theoretical studies of such bacterial populations
have focused on... | [
{
"created": "Tue, 26 Jul 2011 12:18:08 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Nov 2011 20:21:58 GMT",
"version": "v2"
}
] | 2011-11-10 | [
[
"Lohmar",
"Ingo",
""
],
[
"Meerson",
"Baruch",
""
]
] | Many types of bacteria can survive under stress by switching stochastically between two different phenotypes: the "normals" who multiply fast, but are vulnerable to stress, and the "persisters" who hardly multiply, but are resilient to stress. Previous theoretical studies of such bacterial populations have focused on t... |
q-bio/0703033 | Ioana Bena Dr. | Ioana Bena, Michel Droz, Janusz Szwabinski, Andrzej Pekalski | Complex population dynamics as a competition between multiple time-scale
phenomena | 15 pages, 12 figures. Accepted for publication in Phys. Rev. E | Physical Review E 76, 011908 (2007). | 10.1103/PhysRevE.76.011908 | null | q-bio.PE cond-mat.other cond-mat.stat-mech physics.bio-ph | null | The role of the selection pressure and mutation amplitude on the behavior of
a single-species population evolving on a two-dimensional lattice, in a
periodically changing environment, is studied both analytically and
numerically. The mean-field level of description allows to highlight the
delicate interplay between t... | [
{
"created": "Thu, 15 Mar 2007 00:16:27 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Jun 2007 14:29:38 GMT",
"version": "v2"
}
] | 2009-11-13 | [
[
"Bena",
"Ioana",
""
],
[
"Droz",
"Michel",
""
],
[
"Szwabinski",
"Janusz",
""
],
[
"Pekalski",
"Andrzej",
""
]
] | The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The mean-field level of description allows to highlight the delicate interplay between the... |
1711.00250 | Takashi Okada | Takashi Okada, Je-Chiang Tsai, and Atsushi Mochizuki | Structural Bifurcation Analysis in Chemical Reaction Networks | 29 pages, 12 figures. v2: FIG S4 corrected | Phys. Rev. E 98, 012417 (2018) | 10.1103/PhysRevE.98.012417 | RIKEN-iTHEMS-Report-18 | q-bio.MN math.DS physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In living cells, chemical reactions form a complex network. Complicated
dynamics arising from such networks are the origins of biological functions. We
propose a novel mathematical method to analyze bifurcation behaviors of a
reaction system from the network structure alone. The whole network is
decomposed into subne... | [
{
"created": "Wed, 1 Nov 2017 08:37:35 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Nov 2017 06:44:34 GMT",
"version": "v2"
}
] | 2018-08-08 | [
[
"Okada",
"Takashi",
""
],
[
"Tsai",
"Je-Chiang",
""
],
[
"Mochizuki",
"Atsushi",
""
]
] | In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction system from the network structure alone. The whole network is decomposed into subnetw... |
0705.4079 | Alpan Raval | Alpan Raval | Molecular Clock on a Neutral Network | 10 pages | null | 10.1103/PhysRevLett.99.138104 | null | q-bio.PE q-bio.MN | null | The number of fixed mutations accumulated in an evolving population often
displays a variance that is significantly larger than the mean (the
overdispersed molecular clock). By examining a generic evolutionary process on
a neutral network of high-fitness genotypes, we establish a formalism for
computing all cumulants... | [
{
"created": "Mon, 28 May 2007 19:01:45 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Raval",
"Alpan",
""
]
] | The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants o... |
1305.3902 | Sayak Mukherjee | Sayak Mukherjee, Sang-Cheol Seok, Veronica J. Vieland and Jayajit Das | Data-driven quantification of robustness and sensitivity of cell
signaling networks | 46 pages, 11 figures. Physical Biology, 2013 | null | 10.1088/1478-3975/10/6/066002 | null | q-bio.QM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Robustness and sensitivity of responses generated by cell signaling networks
has been associated with survival and evolvability of organisms. However,
existing methods analyzing robustness and sensitivity of signaling networks
ignore the experimentally observed cell-to-cell variations of protein
abundances and cell f... | [
{
"created": "Thu, 16 May 2013 19:46:09 GMT",
"version": "v1"
},
{
"created": "Tue, 29 Oct 2013 20:28:21 GMT",
"version": "v2"
}
] | 2013-10-31 | [
[
"Mukherjee",
"Sayak",
""
],
[
"Seok",
"Sang-Cheol",
""
],
[
"Vieland",
"Veronica J.",
""
],
[
"Das",
"Jayajit",
""
]
] | Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the experimentally observed cell-to-cell variations of protein abundances and cell fun... |
1203.3954 | Klaus Jaffe Dr | Klaus Jaffe, Guillermo Mascitti and Daniella Seguias | Gender differences in time perception and its relation with academic
performance: non-linear dynamics in the formation of cognitive systems | Politically incorrect paper practically impossible to publish in a
psychology journal | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-linear dynamics is probably much more common in the epigenetic dynamics
of living beings than hitherto recognized. Here we report a case of global
bifurcation triggered by gender that affects higher cognitive functions in
humans. We report a cross-cultural study showing deviations in time perception,
as assessed ... | [
{
"created": "Sun, 18 Mar 2012 14:29:30 GMT",
"version": "v1"
},
{
"created": "Sat, 24 Mar 2012 13:57:49 GMT",
"version": "v2"
}
] | 2012-03-27 | [
[
"Jaffe",
"Klaus",
""
],
[
"Mascitti",
"Guillermo",
""
],
[
"Seguias",
"Daniella",
""
]
] | Non-linear dynamics is probably much more common in the epigenetic dynamics of living beings than hitherto recognized. Here we report a case of global bifurcation triggered by gender that affects higher cognitive functions in humans. We report a cross-cultural study showing deviations in time perception, as assessed by... |
1607.00952 | Mahmoud Hassan | Aya Kabbara, Wassim El Falou, Mohamad Khalil, Fabrice Wendling and
Mahmoud Hassan | Graph analysis of spontaneous brain network using EEG source
connectivity | International Conference on Bio-engineering for Smart Technologies
(BioSMART 2016) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Exploring the human brain networks during rest is a topic of great interest.
Several structural and functional studies have previously been conducted to
study the intrinsic brain networks. In this paper, we focus on investigating
the human brain network topology using dense Electroencephalography (EEG)
source connect... | [
{
"created": "Mon, 4 Jul 2016 16:38:16 GMT",
"version": "v1"
}
] | 2016-07-05 | [
[
"Kabbara",
"Aya",
""
],
[
"Falou",
"Wassim El",
""
],
[
"Khalil",
"Mohamad",
""
],
[
"Wendling",
"Fabrice",
""
],
[
"Hassan",
"Mahmoud",
""
]
] | Exploring the human brain networks during rest is a topic of great interest. Several structural and functional studies have previously been conducted to study the intrinsic brain networks. In this paper, we focus on investigating the human brain network topology using dense Electroencephalography (EEG) source connectiv... |
2307.06495 | Benjamin Allen | Benjamin Allen | Symmetry in models of natural selection | 21 pages, 4 figures | null | null | null | q-bio.PE math.GR math.PR | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Symmetry arguments are frequently used -- often implicitly -- in mathematical
modeling of natural selection. Symmetry simplifies the analysis of models and
reduces the number of distinct population states to be considered. Here, I
introduce a formal definition of symmetry in mathematical models of natural
selection. ... | [
{
"created": "Thu, 13 Jul 2023 00:07:42 GMT",
"version": "v1"
}
] | 2023-07-14 | [
[
"Allen",
"Benjamin",
""
]
] | Symmetry arguments are frequently used -- often implicitly -- in mathematical modeling of natural selection. Symmetry simplifies the analysis of models and reduces the number of distinct population states to be considered. Here, I introduce a formal definition of symmetry in mathematical models of natural selection. Th... |
0706.1504 | George Bass Ph.D. | George E. Bass, Bernd Meibohm, James T. Dalton and Robert Sayre | Free Energy of Activation for the Comorosan Effect | 21 pages, 3 figures, 2 tables | null | null | null | q-bio.SC q-bio.BM | null | Initial reaction rate data for lactic dehydrogenase / pyruvate, lactic
dehydrogenase / lactate and malic dehydrogenase / malate enzyme reactions were
analyzed to obtain activation free energy changes of -329, -195 and -221
cal/mole, respectively, for rate increases associated with time-specific
irradiation of the cry... | [
{
"created": "Mon, 11 Jun 2007 16:03:22 GMT",
"version": "v1"
}
] | 2007-06-12 | [
[
"Bass",
"George E.",
""
],
[
"Meibohm",
"Bernd",
""
],
[
"Dalton",
"James T.",
""
],
[
"Sayre",
"Robert",
""
]
] | Initial reaction rate data for lactic dehydrogenase / pyruvate, lactic dehydrogenase / lactate and malic dehydrogenase / malate enzyme reactions were analyzed to obtain activation free energy changes of -329, -195 and -221 cal/mole, respectively, for rate increases associated with time-specific irradiation of the cryst... |
1104.2204 | Juergen Reingruber | Juergen Reingruber and David Holcman | Transcription factor search for a DNA promoter in a three-states model | 4 pages, 3 figures | null | 10.1103/PhysRevE.84.020901 | null | q-bio.SC q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To ensure fast gene activation, Transcription Factors (TF) use a mechanism
known as facilitated diffusion to find their DNA promoter site. Here we analyze
such a process where a TF alternates between 3D and 1D diffusion. In the latter
(TF bound to the DNA), the TF further switches between a fast translocation
state d... | [
{
"created": "Tue, 12 Apr 2011 13:16:09 GMT",
"version": "v1"
}
] | 2015-05-27 | [
[
"Reingruber",
"Juergen",
""
],
[
"Holcman",
"David",
""
]
] | To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF bound to the DNA), the TF further switches between a fast translocation state dom... |
2001.03019 | Burcu Gungor | Hilal Hacilar, O.Ufuk Nalbantoglu, Oya Aran, Burcu Bakir-Gungor | Inflammatory Bowel Disease Biomarkers of Human Gut Microbiota Selected
via Ensemble Feature Selection Methods | 9 pages, 10 figures | null | null | null | q-bio.QM cs.LG q-bio.GN stat.ML | http://creativecommons.org/licenses/by/4.0/ | The tremendous boost in the next generation sequencing and in the omics
technologies makes it possible to characterize human gut microbiome (the
collective genomes of the microbial community that reside in our
gastrointestinal tract). While some of these microorganisms are considered as
essential regulators of our im... | [
{
"created": "Wed, 8 Jan 2020 13:17:26 GMT",
"version": "v1"
}
] | 2020-01-10 | [
[
"Hacilar",
"Hilal",
""
],
[
"Nalbantoglu",
"O. Ufuk",
""
],
[
"Aran",
"Oya",
""
],
[
"Bakir-Gungor",
"Burcu",
""
]
] | The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While some of these microorganisms are considered as essential regulators of our immu... |
1312.7331 | Ziv Williams | Ziv M Williams | Trans-generational effect of trained aversive and appetitive experiences
in Drosophila | 11 pages, 3 figures | null | null | null | q-bio.NC q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | Associative learning allows animals to rapidly adapt to changes in the
environment. Whether and what aspects of such acquired traits may be
transmittable across generations remains unclear. Using prolonged olfactory
training and subsequent two-forced choice testing in Drosophila melanogaster,
it is observed that cert... | [
{
"created": "Fri, 27 Dec 2013 20:22:23 GMT",
"version": "v1"
}
] | 2013-12-30 | [
[
"Williams",
"Ziv M",
""
]
] | Associative learning allows animals to rapidly adapt to changes in the environment. Whether and what aspects of such acquired traits may be transmittable across generations remains unclear. Using prolonged olfactory training and subsequent two-forced choice testing in Drosophila melanogaster, it is observed that certai... |
1404.5441 | Sacha S. J. Laurent | Sacha Laurent and Marc Robinson-Rechavi and Nicolas Salamin | Detecting patterns of species diversification in the presence of both
rate shifts and mass extinctions | 34 pages, 11 figures | BMC Evolutionary Biology 2015 15:157 | 10.1186/s12862-015-0432-z | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Recent methodological advances are enabling better examination of speciation
and extinction processes and patterns. A major open question is the origin of
large discrepancies in species number between groups of the same age. Existing
frameworks to model this diversity either focus on changes between lineages,
neglect... | [
{
"created": "Tue, 22 Apr 2014 09:55:12 GMT",
"version": "v1"
},
{
"created": "Mon, 17 Nov 2014 17:13:46 GMT",
"version": "v2"
},
{
"created": "Mon, 31 Aug 2015 12:31:30 GMT",
"version": "v3"
}
] | 2015-09-01 | [
[
"Laurent",
"Sacha",
""
],
[
"Robinson-Rechavi",
"Marc",
""
],
[
"Salamin",
"Nicolas",
""
]
] | Recent methodological advances are enabling better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglectin... |
1804.00969 | Teodoro Dannemann | Teodoro Dannemann, Denis Boyer, Octavio Miramontes | L\'evy flight movements prevent extinctions and maximize population
abundances in fragile Lotka Volterra systems | null | PNAS. 201719889, 2018 | 10.1073/pnas.1719889115 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multiple-scale mobility is ubiquitous in nature and has become instrumental
for understanding and modeling animal foraging behavior. However, the impact of
individual movements on the long-term stability of populations remains largely
unexplored. We analyze deterministic and stochastic Lotka Volterra systems,
where m... | [
{
"created": "Fri, 30 Mar 2018 03:37:22 GMT",
"version": "v1"
}
] | 2018-04-04 | [
[
"Dannemann",
"Teodoro",
""
],
[
"Boyer",
"Denis",
""
],
[
"Miramontes",
"Octavio",
""
]
] | Multiple-scale mobility is ubiquitous in nature and has become instrumental for understanding and modeling animal foraging behavior. However, the impact of individual movements on the long-term stability of populations remains largely unexplored. We analyze deterministic and stochastic Lotka Volterra systems, where mob... |
2101.11656 | Sayan Ghosal | Sayan Ghosal, Qiang Chen, Giulio Pergola, Aaron L. Goldman, William
Ulrich, Karen F. Berman, Giuseppe Blasi, Leonardo Fazio, Antonio Rampino,
Alessandro Bertolino, Daniel R. Weinberger, Venkata S. Mattay, and Archana
Venkataraman | G-MIND: An End-to-End Multimodal Imaging-Genetics Framework for
Biomarker Identification and Disease Classification | null | null | null | null | q-bio.QM cs.LG eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We propose a novel deep neural network architecture to integrate imaging and
genetics data, as guided by diagnosis, that provides interpretable biomarkers.
Our model consists of an encoder, a decoder and a classifier. The encoder
learns a non-linear subspace shared between the input data modalities. The
classifier an... | [
{
"created": "Wed, 27 Jan 2021 19:28:04 GMT",
"version": "v1"
}
] | 2021-01-29 | [
[
"Ghosal",
"Sayan",
""
],
[
"Chen",
"Qiang",
""
],
[
"Pergola",
"Giulio",
""
],
[
"Goldman",
"Aaron L.",
""
],
[
"Ulrich",
"William",
""
],
[
"Berman",
"Karen F.",
""
],
[
"Blasi",
"Giuseppe",
""
],
[
... | We propose a novel deep neural network architecture to integrate imaging and genetics data, as guided by diagnosis, that provides interpretable biomarkers. Our model consists of an encoder, a decoder and a classifier. The encoder learns a non-linear subspace shared between the input data modalities. The classifier and ... |
2312.11700 | Seongwon Kim | Seongwon Kim, Parisa Mollaei, Amir Barati Farimani and Anne Skaja
Robinson | Characterization of Phosphorylated Tau-Microtubule complex with
Molecular Dynamics (MD) simulation | 27pages, 12 figure | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Alzheimer's Disease (AD), a neurodegenerative disorder, is reported as one of
the most severe health and socioeconomic problems in current public health. Tau
proteins are assumed to be a crucial driving factor of AD that detach from
microtubules (MT) and accumulate as neurotoxic aggregates in the brains of AD
patient... | [
{
"created": "Mon, 18 Dec 2023 20:56:13 GMT",
"version": "v1"
}
] | 2023-12-20 | [
[
"Kim",
"Seongwon",
""
],
[
"Mollaei",
"Parisa",
""
],
[
"Farimani",
"Amir Barati",
""
],
[
"Robinson",
"Anne Skaja",
""
]
] | Alzheimer's Disease (AD), a neurodegenerative disorder, is reported as one of the most severe health and socioeconomic problems in current public health. Tau proteins are assumed to be a crucial driving factor of AD that detach from microtubules (MT) and accumulate as neurotoxic aggregates in the brains of AD patients.... |
2311.10403 | Junbo Jia | Junbo Jia and Luonan Chen | Velde: constructing cell potential landscapes by RNA velocity vector
field decomposition | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Waddington landscape serves as a metaphor illustrating the developmental
process of cells, likening it to a small ball rolling down various trajectories
into valleys. Constructing an epigenetic landscape of this nature aids in
visualizing and gaining insights into cell differentiation. Development
encompasses int... | [
{
"created": "Fri, 17 Nov 2023 09:08:54 GMT",
"version": "v1"
}
] | 2023-11-20 | [
[
"Jia",
"Junbo",
""
],
[
"Chen",
"Luonan",
""
]
] | The Waddington landscape serves as a metaphor illustrating the developmental process of cells, likening it to a small ball rolling down various trajectories into valleys. Constructing an epigenetic landscape of this nature aids in visualizing and gaining insights into cell differentiation. Development encompasses intri... |
2308.07465 | Nikolai Slavov | Andrew Leduc, Hannah Harens, and Nikolai Slavov | Modeling and interpretation of single-cell proteogenomic data | null | null | null | null | q-bio.GN q-bio.BM q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Biological functions stem from coordinated interactions among proteins,
nucleic acids and small molecules. Mass spectrometry technologies for reliable,
high throughput single-cell proteomics will add a new modality to genomics and
enable data-driven modeling of the molecular mechanisms coordinating proteins
and nucle... | [
{
"created": "Mon, 14 Aug 2023 21:25:56 GMT",
"version": "v1"
},
{
"created": "Sat, 4 Nov 2023 20:55:46 GMT",
"version": "v2"
}
] | 2023-11-07 | [
[
"Leduc",
"Andrew",
""
],
[
"Harens",
"Hannah",
""
],
[
"Slavov",
"Nikolai",
""
]
] | Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable data-driven modeling of the molecular mechanisms coordinating proteins and nucleic... |
2004.12836 | Christina Bohk-Ewald | Christina Bohk-Ewald and Christian Dudel and Mikko Myrskyl\"a | A demographic scaling model for estimating the total number of COVID-19
infections | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding how widely COVID-19 has spread is critical for examining the
pandemic's progression. Despite efforts to carefully monitor the pandemic, the
number of confirmed cases may underestimate the total number of infections. We
introduce a demographic scaling model to estimate COVID-19 infections using an
broadl... | [
{
"created": "Fri, 24 Apr 2020 17:26:50 GMT",
"version": "v1"
},
{
"created": "Tue, 26 May 2020 08:46:18 GMT",
"version": "v2"
}
] | 2020-05-27 | [
[
"Bohk-Ewald",
"Christina",
""
],
[
"Dudel",
"Christian",
""
],
[
"Myrskylä",
"Mikko",
""
]
] | Understanding how widely COVID-19 has spread is critical for examining the pandemic's progression. Despite efforts to carefully monitor the pandemic, the number of confirmed cases may underestimate the total number of infections. We introduce a demographic scaling model to estimate COVID-19 infections using an broadly ... |
1910.06113 | Thomas Bolton | Thomas A. W. Bolton, Constantin Tuleasca, Gwladys Rey, Diana Wotruba,
Julian Gaviria, Herberto Dhanis, Eva Blondiaux, Baptise Gauthier, Lukasz
Smigielski, Dimitri Van De Ville | TbCAPs: A ToolBox for Co-Activation Pattern Analysis | 15 pages, 4 figures, 1 table | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Functional magnetic resonance imaging provides rich spatio-temporal data of
human brain activity during task and rest. Many recent efforts have focussed on
characterising dynamics of brain activity. One notable instance is
co-activation pattern (CAP) analysis, a frame-wise analytical approach that
disentangles the di... | [
{
"created": "Mon, 14 Oct 2019 12:53:52 GMT",
"version": "v1"
}
] | 2019-10-15 | [
[
"Bolton",
"Thomas A. W.",
""
],
[
"Tuleasca",
"Constantin",
""
],
[
"Rey",
"Gwladys",
""
],
[
"Wotruba",
"Diana",
""
],
[
"Gaviria",
"Julian",
""
],
[
"Dhanis",
"Herberto",
""
],
[
"Blondiaux",
"Eva",
""
... | Functional magnetic resonance imaging provides rich spatio-temporal data of human brain activity during task and rest. Many recent efforts have focussed on characterising dynamics of brain activity. One notable instance is co-activation pattern (CAP) analysis, a frame-wise analytical approach that disentangles the diff... |
2004.05895 | Audrey B\"urki | A. B\"urki, S. Elbuy, S. Madec, S. Vasishth | What did we learn from forty years of research on semantic interference?
A Bayesian metaanalysis | null | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When participants in an experiment have to name pictures while ignoring
distractor words superimposed on the picture or presented auditorily (i.e.,
picture-word interference paradigm), they take more time when the word to be
named (or target) and distractor words are from the same semantic category
(e.g., cat-dog). T... | [
{
"created": "Thu, 2 Apr 2020 15:07:26 GMT",
"version": "v1"
},
{
"created": "Sun, 26 Apr 2020 09:41:47 GMT",
"version": "v2"
}
] | 2020-04-28 | [
[
"Bürki",
"A.",
""
],
[
"Elbuy",
"S.",
""
],
[
"Madec",
"S.",
""
],
[
"Vasishth",
"S.",
""
]
] | When participants in an experiment have to name pictures while ignoring distractor words superimposed on the picture or presented auditorily (i.e., picture-word interference paradigm), they take more time when the word to be named (or target) and distractor words are from the same semantic category (e.g., cat-dog). Thi... |
1209.5760 | Suzanne Bowen Dr | Suzanne Bowen | Protein function influences frequency of encoded regions containing
VNTRs and number of unique interactions | 21 pages, 4 figures | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins encoded by genes containing regions of variable number tandem
repeats (VNTRs) are known to be polymorphic within species but the influence of
their instability in molecular interactions remains unclear. VNTRs are
overrepresented in encoding sequence of particular functional groups where
their presence could ... | [
{
"created": "Tue, 25 Sep 2012 20:32:43 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Sep 2012 14:05:17 GMT",
"version": "v2"
}
] | 2012-09-28 | [
[
"Bowen",
"Suzanne",
""
]
] | Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRs are overrepresented in encoding sequence of particular functional groups where their presence could in... |
2306.01935 | Vivek N. Prakash | Setareh Gooshvar, Gopika Madhu, Melissa Ruszczyk, and Vivek N. Prakash | Non-bilaterians as Model Systems for Tissue Mechanics | Review paper, Comments/suggestions are welcome | Integrative and Comparative Biology, 2023 | 10.1093/icb/icad074 | null | q-bio.TO physics.bio-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In animals, epithelial tissues are barriers against the external environment,
providing protection against biological, chemical, and physical damage.
Depending on the animal's physiology and behavior, these tissues encounter
different types of mechanical forces and need to provide a suitable adaptive
response to ensu... | [
{
"created": "Fri, 2 Jun 2023 22:28:16 GMT",
"version": "v1"
}
] | 2023-12-29 | [
[
"Gooshvar",
"Setareh",
""
],
[
"Madhu",
"Gopika",
""
],
[
"Ruszczyk",
"Melissa",
""
],
[
"Prakash",
"Vivek N.",
""
]
] | In animals, epithelial tissues are barriers against the external environment, providing protection against biological, chemical, and physical damage. Depending on the animal's physiology and behavior, these tissues encounter different types of mechanical forces and need to provide a suitable adaptive response to ensure... |
2407.08224 | Wenwen Min | Shuailin Xue, Fangfang Zhu, Changmiao Wang and Wenwen Min | stEnTrans: Transformer-based deep learning for spatial transcriptomics
enhancement | ISBRA2024, Code: https://github.com/shuailinxue/stEnTrans | null | null | null | q-bio.QM cs.AI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The spatial location of cells within tissues and organs is crucial for the
manifestation of their specific functions.Spatial transcriptomics technology
enables comprehensive measurement of the gene expression patterns in tissues
while retaining spatial information. However, current popular spatial
transcriptomics tec... | [
{
"created": "Thu, 11 Jul 2024 06:50:34 GMT",
"version": "v1"
}
] | 2024-07-12 | [
[
"Xue",
"Shuailin",
""
],
[
"Zhu",
"Fangfang",
""
],
[
"Wang",
"Changmiao",
""
],
[
"Min",
"Wenwen",
""
]
] | The spatial location of cells within tissues and organs is crucial for the manifestation of their specific functions.Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while retaining spatial information. However, current popular spatial transcriptomics techn... |
1611.08259 | Antti Niemi | Alexandr Nasedkin, Jan Davidsson, Antti J. Niemi, Xubiao Peng | Solution X-ray scattering (S/WAXS) and structure formation in protein
dynamics | 10 figures | Phys. Rev. E 96, 062405 (2017) | 10.1103/PhysRevE.96.062405 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose to develop mean field theory in combination with Glauber
algorithm, to model and interpret protein dynamics and structure formation in
small to wide angle x-ray scattering (S/WAXS) experiments. We develop the
methodology by analysing the Engrailed homeodomain protein as an example. We
demonstrate how to in... | [
{
"created": "Thu, 24 Nov 2016 17:09:22 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Jun 2017 11:22:17 GMT",
"version": "v2"
}
] | 2017-12-20 | [
[
"Nasedkin",
"Alexandr",
""
],
[
"Davidsson",
"Jan",
""
],
[
"Niemi",
"Antti J.",
""
],
[
"Peng",
"Xubiao",
""
]
] | We propose to develop mean field theory in combination with Glauber algorithm, to model and interpret protein dynamics and structure formation in small to wide angle x-ray scattering (S/WAXS) experiments. We develop the methodology by analysing the Engrailed homeodomain protein as an example. We demonstrate how to inte... |
1206.0889 | Gilles Guillot | Gilles Guillot | Detection of correlation between genotypes and environmental variables.
A fast computational approach for genomewide studies | To appear in Spatial Statistics | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genomic regions (or loci) displaying outstanding correlation with some
environmental variables are likely to be under selection and this is the
rationale of recent methods of identifying selected loci and retrieving
functional information about them. To be efficient, such methods need to be
able to disentangle the po... | [
{
"created": "Tue, 5 Jun 2012 11:55:13 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Aug 2013 08:11:53 GMT",
"version": "v2"
}
] | 2013-08-13 | [
[
"Guillot",
"Gilles",
""
]
] | Genomic regions (or loci) displaying outstanding correlation with some environmental variables are likely to be under selection and this is the rationale of recent methods of identifying selected loci and retrieving functional information about them. To be efficient, such methods need to be able to disentangle the pote... |
2103.16606 | Jia Li | Jia Li, Ilias Rentzeperis, Cees van Leeuwen | Functional and spatial rewiring jointly generate convergent-divergent
units in self-organizing networks | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Self-organization through adaptive rewiring of random neural networks
generates brain-like topologies comprising modular small-world structures with
rich club effects, merely as the product of optimizing the network topology. In
the nervous system, spatial organization is optimized no less by rewiring,
through minimi... | [
{
"created": "Tue, 30 Mar 2021 18:26:34 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Nov 2022 13:37:25 GMT",
"version": "v2"
}
] | 2022-11-04 | [
[
"Li",
"Jia",
""
],
[
"Rentzeperis",
"Ilias",
""
],
[
"van Leeuwen",
"Cees",
""
]
] | Self-organization through adaptive rewiring of random neural networks generates brain-like topologies comprising modular small-world structures with rich club effects, merely as the product of optimizing the network topology. In the nervous system, spatial organization is optimized no less by rewiring, through minimizi... |
0805.3675 | Michael Yampolsky | Carolyn M. Salafia, Dawn P. Misra, Michael Yampolsky, Adrian K.
Charles, Richard K. Miller | Allometric metabolic scaling and fetal and placental weight | null | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We tested the hypothesis that the fetal-placental relationship scales
allometrically and identified modifying factors.
Among women delivering after 34 weeks but prior to 43 weeks gestation, 24,601
participants in the Collaborative Perinatal Project (CPP) had complete data for
placental gross proportion measures, sp... | [
{
"created": "Fri, 23 May 2008 18:03:08 GMT",
"version": "v1"
},
{
"created": "Fri, 25 Jul 2008 16:31:57 GMT",
"version": "v2"
},
{
"created": "Sun, 22 Mar 2009 22:02:32 GMT",
"version": "v3"
}
] | 2009-03-23 | [
[
"Salafia",
"Carolyn M.",
""
],
[
"Misra",
"Dawn P.",
""
],
[
"Yampolsky",
"Michael",
""
],
[
"Charles",
"Adrian K.",
""
],
[
"Miller",
"Richard K.",
""
]
] | We tested the hypothesis that the fetal-placental relationship scales allometrically and identified modifying factors. Among women delivering after 34 weeks but prior to 43 weeks gestation, 24,601 participants in the Collaborative Perinatal Project (CPP) had complete data for placental gross proportion measures, specif... |
0709.3237 | Matthias Keil | Matthias S. Keil | Gradient Representations and the Perception of Luminosity | This is the longer version of an article which is under review for
publication in Vision Research | null | null | null | q-bio.NC | null | The neuronal mechanisms that serve to distinguish between light-emitting and
light reflecting objects are largely unknown. It has been suggested that
luminosity perception implements a separate pathway in the visual system, such
that luminosity constitutes an independent perceptual feature. Recently, a
psychophysical... | [
{
"created": "Thu, 20 Sep 2007 14:06:43 GMT",
"version": "v1"
}
] | 2007-09-21 | [
[
"Keil",
"Matthias S.",
""
]
] | The neuronal mechanisms that serve to distinguish between light-emitting and light reflecting objects are largely unknown. It has been suggested that luminosity perception implements a separate pathway in the visual system, such that luminosity constitutes an independent perceptual feature. Recently, a psychophysical s... |
2005.01200 | Gurdip Uppal | Gurdip Uppal, Weiyi Hu, Dervis Can Vural | Evolution of chemotactic hitchhiking | 10 pages, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bacteria typically reside in heterogeneous environments with various
chemogradients where motile cells can gain an advantage over non-motile cells.
Since motility is energetically costly, cells must optimize their swimming
speed and behavior to maximize their fitness. Here we investigate how cheating
strategies might... | [
{
"created": "Sun, 3 May 2020 22:34:18 GMT",
"version": "v1"
}
] | 2020-05-05 | [
[
"Uppal",
"Gurdip",
""
],
[
"Hu",
"Weiyi",
""
],
[
"Vural",
"Dervis Can",
""
]
] | Bacteria typically reside in heterogeneous environments with various chemogradients where motile cells can gain an advantage over non-motile cells. Since motility is energetically costly, cells must optimize their swimming speed and behavior to maximize their fitness. Here we investigate how cheating strategies might e... |
1503.04059 | Frederic Bartumeus | Joan Garriga, John R. Palmer, Aitana Oltra, Frederic Bartumeus | Expectation-Maximization Binary Clustering for Behavioural Annotation | 34 pages main text including 11 (full page) figures | null | 10.1371/journal.pone.0151984 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a variant of the well sounded Expectation-Maximization Clustering
algorithm that is constrained to generate partitions of the input space into
high and low values. The motivation of splitting input variables into high and
low values is to favour the semantic interpretation of the final clustering.
The Expe... | [
{
"created": "Fri, 13 Mar 2015 13:30:36 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Dec 2015 16:51:01 GMT",
"version": "v2"
}
] | 2016-04-27 | [
[
"Garriga",
"Joan",
""
],
[
"Palmer",
"John R.",
""
],
[
"Oltra",
"Aitana",
""
],
[
"Bartumeus",
"Frederic",
""
]
] | We present a variant of the well sounded Expectation-Maximization Clustering algorithm that is constrained to generate partitions of the input space into high and low values. The motivation of splitting input variables into high and low values is to favour the semantic interpretation of the final clustering. The Expect... |
2401.01811 | Andrij Rovenchak | Andrij Rovenchak and Maksym Druchok | Machine learning-assisted search for novel coagulants: when machine
learning can be efficient even if data availability is low | null | J. Comput. Chem. 45, No. 13, 937-952 (2024) | 10.1002/jcc.27292 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Design of new drugs is a challenging process: a candidate molecule should
satisfy multiple conditions to act properly and make the least side-effect --
perfect candidates selectively attach to and influence only targets, leaving
off-targets intact. The amount of experimental data about various properties of
molecules... | [
{
"created": "Wed, 3 Jan 2024 16:14:37 GMT",
"version": "v1"
}
] | 2024-05-07 | [
[
"Rovenchak",
"Andrij",
""
],
[
"Druchok",
"Maksym",
""
]
] | Design of new drugs is a challenging process: a candidate molecule should satisfy multiple conditions to act properly and make the least side-effect -- perfect candidates selectively attach to and influence only targets, leaving off-targets intact. The amount of experimental data about various properties of molecules c... |
2403.11516 | Ya Li | Yue Ding, Hongqiao Shi, Shuang Song, Yonghui Wang and Ya Li | Perceptual learning in contour detection transfer across changes in
contour path and orientation | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The integration of local elements into shape contours is critical for target
detection and identification in cluttered scenes. Previous studies have shown
that observers can learn to use image regularities for contour integration and
target identification. However, we still know little about the generalization
of per... | [
{
"created": "Mon, 18 Mar 2024 07:06:03 GMT",
"version": "v1"
}
] | 2024-03-19 | [
[
"Ding",
"Yue",
""
],
[
"Shi",
"Hongqiao",
""
],
[
"Song",
"Shuang",
""
],
[
"Wang",
"Yonghui",
""
],
[
"Li",
"Ya",
""
]
] | The integration of local elements into shape contours is critical for target detection and identification in cluttered scenes. Previous studies have shown that observers can learn to use image regularities for contour integration and target identification. However, we still know little about the generalization of perce... |
0801.3382 | Jose Luis Toca-Herrera | Veronica Saravia | Hepatocyte Aggregates: Methods of Preparation in the Microgravity
Simulating Bioreactor Use in Tissue Engineering | MSc Thesis (Chemical Engineering Department, Rovira i Virgili
University, Spain) Supervisors: Dr. Petros Lenas and Dr. Jose L. Toca-Herrera
Pages:32, Figures:15 | null | null | null | q-bio.TO | null | Tissue Engineering concerns the three-dimensional cell growth so that
bio-artificial tissues could be created and used for transplantation. The
recently expressed concerns from the Tissue Engineering research community for
a re-direction of the research activities necessitate the proposition of new
methodologies. We ... | [
{
"created": "Tue, 22 Jan 2008 14:40:33 GMT",
"version": "v1"
}
] | 2008-01-23 | [
[
"Saravia",
"Veronica",
""
]
] | Tissue Engineering concerns the three-dimensional cell growth so that bio-artificial tissues could be created and used for transplantation. The recently expressed concerns from the Tissue Engineering research community for a re-direction of the research activities necessitate the proposition of new methodologies. We pr... |
1011.5108 | Fabien Campillo | Fabien Campillo (INRIA Sophia Antipolis - INRA/SupAgro UMR 0729 MISTEA
- Montpellier), Marc Joannides (INRIA Sophia Antipolis - INRA/SupAgro UMR
0729 MISTEA - Montpellier, I3M), Ir\`ene Larramendy (I3M) | Stochastic models of the chemostat | null | N° RR-7458 (2010) | null | RR-7458 | q-bio.QM math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the modeling of the dynamics of the chemostat at its very source.
The chemostat is classically represented as a system of ordinary differential
equations. Our goal is to establish a stochastic model that is valid at the
scale immediately preceding the one corresponding to the deterministic model.
At a mic... | [
{
"created": "Mon, 22 Nov 2010 10:30:20 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Jul 2011 05:47:22 GMT",
"version": "v2"
}
] | 2011-07-07 | [
[
"Campillo",
"Fabien",
"",
"INRIA Sophia Antipolis - INRA/SupAgro UMR 0729 MISTEA\n - Montpellier"
],
[
"Joannides",
"Marc",
"",
"INRIA Sophia Antipolis - INRA/SupAgro UMR\n 0729 MISTEA - Montpellier, I3M"
],
[
"Larramendy",
"Irène",
"",
"I3M"
]
] | We consider the modeling of the dynamics of the chemostat at its very source. The chemostat is classically represented as a system of ordinary differential equations. Our goal is to establish a stochastic model that is valid at the scale immediately preceding the one corresponding to the deterministic model. At a micro... |
2408.05224 | Liu Hong | Mengshou Wang, Liangrong Pengb, Baoguo Jia, Liu Hong | Optimal Strategy for Stabilizing Protein Folding Intermediates | 19 pages, 5 figures, 2 tables | null | null | null | q-bio.BM math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To manipulate the protein population at certain functional state through
chemical stabilizers is crucial for protein-related studies. It not only plays
a key role in protein structure analysis and protein folding kinetics, but also
affects protein functionality to a large extent and thus has wide applications
in medi... | [
{
"created": "Sun, 28 Jul 2024 11:36:29 GMT",
"version": "v1"
}
] | 2024-08-13 | [
[
"Wang",
"Mengshou",
""
],
[
"Pengb",
"Liangrong",
""
],
[
"Jia",
"Baoguo",
""
],
[
"Hong",
"Liu",
""
]
] | To manipulate the protein population at certain functional state through chemical stabilizers is crucial for protein-related studies. It not only plays a key role in protein structure analysis and protein folding kinetics, but also affects protein functionality to a large extent and thus has wide applications in medici... |
1210.0120 | Brant Faircloth | Michael E. Alfaro and Brant C. Faircloth and Laurie Sorenson and
Francesco Santini | A phylogenomic perspective on the radiation of ray-finned fishes based
upon targeted sequencing of ultraconserved elements | null | (2013) PLoS ONE 8(6): e65923 | 10.1371/journal.pone.0065923 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Ray-finned fishes constitute the dominant radiation of vertebrates with over
30,000 species. Although molecular phylogenetics has begun to disentangle major
evolutionary relationships within this vast section of the Tree of Life, there
is no widely available approach for efficiently collecting phylogenomic data
withi... | [
{
"created": "Sat, 29 Sep 2012 16:00:44 GMT",
"version": "v1"
}
] | 2013-06-20 | [
[
"Alfaro",
"Michael E.",
""
],
[
"Faircloth",
"Brant C.",
""
],
[
"Sorenson",
"Laurie",
""
],
[
"Santini",
"Francesco",
""
]
] | Ray-finned fishes constitute the dominant radiation of vertebrates with over 30,000 species. Although molecular phylogenetics has begun to disentangle major evolutionary relationships within this vast section of the Tree of Life, there is no widely available approach for efficiently collecting phylogenomic data within ... |
1410.3972 | Eran Elhaik | Eran Elhaik, Tatiana V. Tatarinova, Anatole A. Klyosov, and Dan Graur | An extended reply to Mendez et al.: The 'extremely ancient' chromosome
that still isn't | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Earlier this year, we published a scathing critique of a paper by Mendez et
al. (2013) in which the claim was made that a Y chromosome was 237,000-581,000
years old. Elhaik et al. (2014) also attacked a popular article in Scientific
American by the senior author of Mendez et al. (2013), whose title was "Sex
with othe... | [
{
"created": "Wed, 15 Oct 2014 08:45:15 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Oct 2014 21:22:26 GMT",
"version": "v2"
}
] | 2014-10-22 | [
[
"Elhaik",
"Eran",
""
],
[
"Tatarinova",
"Tatiana V.",
""
],
[
"Klyosov",
"Anatole A.",
""
],
[
"Graur",
"Dan",
""
]
] | Earlier this year, we published a scathing critique of a paper by Mendez et al. (2013) in which the claim was made that a Y chromosome was 237,000-581,000 years old. Elhaik et al. (2014) also attacked a popular article in Scientific American by the senior author of Mendez et al. (2013), whose title was "Sex with other ... |
1707.04192 | Marco Lehmann | Marco Lehmann, He Xu, Vasiliki Liakoni, Michael Herzog, Wulfram
Gerstner, Kerstin Preuschoff | One-shot learning and behavioral eligibility traces in sequential
decision making | null | eLife 2019; 8:e47463 | 10.7554/eLife.47463 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In many daily tasks we make multiple decisions before reaching a goal. In
order to learn such sequences of decisions, a mechanism to link earlier actions
to later reward is necessary. Reinforcement learning theory suggests two
classes of algorithms solving this credit assignment problem: In classic
temporal-differenc... | [
{
"created": "Thu, 13 Jul 2017 16:04:34 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Feb 2019 15:22:49 GMT",
"version": "v2"
},
{
"created": "Tue, 12 Nov 2019 10:00:22 GMT",
"version": "v3"
}
] | 2019-11-13 | [
[
"Lehmann",
"Marco",
""
],
[
"Xu",
"He",
""
],
[
"Liakoni",
"Vasiliki",
""
],
[
"Herzog",
"Michael",
""
],
[
"Gerstner",
"Wulfram",
""
],
[
"Preuschoff",
"Kerstin",
""
]
] | In many daily tasks we make multiple decisions before reaching a goal. In order to learn such sequences of decisions, a mechanism to link earlier actions to later reward is necessary. Reinforcement learning theory suggests two classes of algorithms solving this credit assignment problem: In classic temporal-difference ... |
1805.05433 | Joshua M. Deutsch | J. M. Deutsch | Computational mechanisms in genetic regulation by RNA | 18 pages, 10 figures | null | null | null | q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of the genome has led to very sophisticated and complex
regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell,
different species will promiscuously associate with each other, suggesting
collective dynamics similar to artificial neural networks. Here we present a
simple mechanism all... | [
{
"created": "Mon, 14 May 2018 20:39:02 GMT",
"version": "v1"
}
] | 2018-05-16 | [
[
"Deutsch",
"J. M.",
""
]
] | The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics similar to artificial neural networks. Here we present a simple mechanism allow... |
0711.2531 | Hendrik Blok | Michael Doebeli, Hendrik J. Blok, Olof Leimar, Ulf Dieckmann | Multimodal pattern formation in phenotype distributions of sexual
populations | null | Proc. R. Soc. B (2007) 274, 347-357 | 10.1098/rspb.2006.3725 | null | q-bio.PE | null | During bouts of evolutionary diversification, such as adaptive radiations,
the emerging species cluster around different locations in phenotype space, How
such multimodal patterns in phenotype space can emerge from a single ancestral
species is a fundamental question in biology. Frequency-dependent competition
is one... | [
{
"created": "Thu, 15 Nov 2007 23:25:00 GMT",
"version": "v1"
}
] | 2007-11-19 | [
[
"Doebeli",
"Michael",
""
],
[
"Blok",
"Hendrik J.",
""
],
[
"Leimar",
"Olof",
""
],
[
"Dieckmann",
"Ulf",
""
]
] | During bouts of evolutionary diversification, such as adaptive radiations, the emerging species cluster around different locations in phenotype space, How such multimodal patterns in phenotype space can emerge from a single ancestral species is a fundamental question in biology. Frequency-dependent competition is one p... |
2306.07812 | Xu Wang | Xu Wang and Huan Zhao and Weiwei Tu and Quanming Yao | Automated 3D Pre-Training for Molecular Property Prediction | null | null | 10.1145/3580305.3599252 | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular property prediction is an important problem in drug discovery and
materials science. As geometric structures have been demonstrated necessary for
molecular property prediction, 3D information has been combined with various
graph learning methods to boost prediction performance. However, obtaining the
geomet... | [
{
"created": "Tue, 13 Jun 2023 14:43:13 GMT",
"version": "v1"
},
{
"created": "Sun, 2 Jul 2023 13:03:27 GMT",
"version": "v2"
}
] | 2023-07-04 | [
[
"Wang",
"Xu",
""
],
[
"Zhao",
"Huan",
""
],
[
"Tu",
"Weiwei",
""
],
[
"Yao",
"Quanming",
""
]
] | Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph learning methods to boost prediction performance. However, obtaining the geometri... |
1806.07477 | Heyrim Cho | Heyrim Cho and Doron Levy | The Impact of Competition Between Cancer Cells and Healthy Cells on
Optimal Drug Delivery | 18 pages | null | 10.1051/mmnp/2019043 | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cell competition is recognized to be instrumental to the dynamics and
structure of the tumor-host interface in invasive cancers. In mild competition
scenarios, the healthy tissue and cancer cells can coexist. When the
competition is aggressive, competitive cells, the so called super-competitors,
expand by killing oth... | [
{
"created": "Tue, 19 Jun 2018 21:26:02 GMT",
"version": "v1"
}
] | 2022-04-19 | [
[
"Cho",
"Heyrim",
""
],
[
"Levy",
"Doron",
""
]
] | Cell competition is recognized to be instrumental to the dynamics and structure of the tumor-host interface in invasive cancers. In mild competition scenarios, the healthy tissue and cancer cells can coexist. When the competition is aggressive, competitive cells, the so called super-competitors, expand by killing other... |
2308.09725 | Ziwei Yang | Ziwei Yang, Zheng Chen, Yasuko Matsubara, Yasushi Sakurai | MoCLIM: Towards Accurate Cancer Subtyping via Multi-Omics Contrastive
Learning with Omics-Inference Modeling | CIKM'23 Long/Full Papers | null | 10.1145/3583780.3614970 | null | q-bio.GN cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Precision medicine fundamentally aims to establish causality between
dysregulated biochemical mechanisms and cancer subtypes. Omics-based cancer
subtyping has emerged as a revolutionary approach, as different level of omics
records the biochemical products of multistep processes in cancers. This paper
focuses on full... | [
{
"created": "Thu, 17 Aug 2023 10:49:48 GMT",
"version": "v1"
},
{
"created": "Thu, 24 Aug 2023 04:38:45 GMT",
"version": "v2"
}
] | 2023-08-25 | [
[
"Yang",
"Ziwei",
""
],
[
"Chen",
"Zheng",
""
],
[
"Matsubara",
"Yasuko",
""
],
[
"Sakurai",
"Yasushi",
""
]
] | Precision medicine fundamentally aims to establish causality between dysregulated biochemical mechanisms and cancer subtypes. Omics-based cancer subtyping has emerged as a revolutionary approach, as different level of omics records the biochemical products of multistep processes in cancers. This paper focuses on fully ... |
2003.03580 | Pengli Lu | Pengli Lu and JingJuan Yu | Two new methods for identifying proteins based on the domain protein
complexes and topological properties | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The recognition of essential proteins not only can help to understand the
mechanism of cell operation, but also help to study the mechanism of biological
evolution. At present, many scholars have been discovering essential proteins
according to the topological structure of protein network and complexes. While
some pr... | [
{
"created": "Sat, 7 Mar 2020 13:56:35 GMT",
"version": "v1"
}
] | 2020-03-10 | [
[
"Lu",
"Pengli",
""
],
[
"Yu",
"JingJuan",
""
]
] | The recognition of essential proteins not only can help to understand the mechanism of cell operation, but also help to study the mechanism of biological evolution. At present, many scholars have been discovering essential proteins according to the topological structure of protein network and complexes. While some prot... |
2305.05086 | Brian Sun | Braden Barnett, Yiqi Lyu, Kyle Pichney, Brian Sun, Jixiao Wu | Mechanical Evidence for the Phylogenetic Origin of the Red Panda's False
Thumb as an Adaptation to Arboreal Locomotion | 14 pages, 10 figures | null | null | null | q-bio.PE cs.RO | http://creativecommons.org/licenses/by/4.0/ | We constructed a modular, biomimetic red panda paw with which to
experimentally investigate the evolutionary reason for the existence of the
false thumbs of red pandas. These thumbs were once believed to have shared a
common origin with the similar false thumbs of giant pandas; however, the
discovery of a carnivorous... | [
{
"created": "Mon, 8 May 2023 23:05:39 GMT",
"version": "v1"
}
] | 2023-05-10 | [
[
"Barnett",
"Braden",
""
],
[
"Lyu",
"Yiqi",
""
],
[
"Pichney",
"Kyle",
""
],
[
"Sun",
"Brian",
""
],
[
"Wu",
"Jixiao",
""
]
] | We constructed a modular, biomimetic red panda paw with which to experimentally investigate the evolutionary reason for the existence of the false thumbs of red pandas. These thumbs were once believed to have shared a common origin with the similar false thumbs of giant pandas; however, the discovery of a carnivorous f... |
q-bio/0507018 | Toby Johnson | Toby Johnson | Bayesian Method for Disease QTL Detection and Mapping, using a Case and
Control Design and DNA Pooling | null | Biostatistics (2007) 8:546--565 | 10.1093/biostatistics/kxl028 | null | q-bio.GN q-bio.PE q-bio.QM | null | This paper describes a Bayesian statistical method for determining the
genetic basis of a complex genetic trait. The method uses a sample of unrelated
individuals classified into two groups, for example cases and controls. Each
group is assumed to have been genotyped at a battery of marker loci using a
laboratory eff... | [
{
"created": "Wed, 13 Jul 2005 11:59:52 GMT",
"version": "v1"
}
] | 2008-02-21 | [
[
"Johnson",
"Toby",
""
]
] | This paper describes a Bayesian statistical method for determining the genetic basis of a complex genetic trait. The method uses a sample of unrelated individuals classified into two groups, for example cases and controls. Each group is assumed to have been genotyped at a battery of marker loci using a laboratory effor... |
2405.03707 | Lixin Lin | Lixin Lin, Homayoun Hamedmoghadam, Robert Shorten, Lewi Stone | Quantifying indirect and direct vaccination effects arising in the SIR
model | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Vaccination campaigns have both direct and indirect effects that act to
control an infectious disease as it spreads through a population. Indirect
effects arise when vaccinated individuals block disease transmission in any
infection chains they are part of, and this in turn can benefit both vaccinated
and unvaccinate... | [
{
"created": "Fri, 3 May 2024 20:57:57 GMT",
"version": "v1"
}
] | 2024-05-08 | [
[
"Lin",
"Lixin",
""
],
[
"Hamedmoghadam",
"Homayoun",
""
],
[
"Shorten",
"Robert",
""
],
[
"Stone",
"Lewi",
""
]
] | Vaccination campaigns have both direct and indirect effects that act to control an infectious disease as it spreads through a population. Indirect effects arise when vaccinated individuals block disease transmission in any infection chains they are part of, and this in turn can benefit both vaccinated and unvaccinated ... |
1612.02035 | Donald Forsdyke Dr. | Donald R. Forsdyke | Elusive preferred hosts or nucleic acid level selection? A commentary
on: Evolutionary interpretations of mycobacteriophage biodiversity and
host-range through the analysis of codon usage bias (Esposito et al. 2016) | Submitted (less the reference to Meyer et al. 2016) to Microbial
Genomics on 8th November 2016 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While confirming the long held view that viruses do not closely imitate the
use of their host's codon catalogue, Esposito and coworkers nevertheless
consider it surprising that, despite having the ability to infect the same
host, many mycobacteriophages share little or no genetic similarity (i.e.
similarity in their ... | [
{
"created": "Tue, 6 Dec 2016 21:29:26 GMT",
"version": "v1"
}
] | 2016-12-08 | [
[
"Forsdyke",
"Donald R.",
""
]
] | While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many mycobacteriophages share little or no genetic similarity (i.e. similarity in their GC... |
2303.06423 | Herv\'e Isambert | Marcel da C\^amara Ribeiro-Dantas, Honghao Li, Vincent Cabeli, Louise
Dupuis, Franck Simon, Liza Hettal, Anne-Sophie Hamy, and Herv\'e Isambert | Learning interpretable causal networks from very large datasets,
application to 400,000 medical records of breast cancer patients | 19 pages, 6 figures, 8 supplementary figures and 5 pages supporting
information | null | null | null | q-bio.QM cs.LG physics.data-an q-bio.MN stat.ME | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Discovering causal effects is at the core of scientific investigation but
remains challenging when only observational data is available. In practice,
causal networks are difficult to learn and interpret, and limited to relatively
small datasets. We report a more reliable and scalable causal discovery method
(iMIIC), ... | [
{
"created": "Sat, 11 Mar 2023 15:18:19 GMT",
"version": "v1"
}
] | 2023-03-14 | [
[
"Ribeiro-Dantas",
"Marcel da Câmara",
""
],
[
"Li",
"Honghao",
""
],
[
"Cabeli",
"Vincent",
""
],
[
"Dupuis",
"Louise",
""
],
[
"Simon",
"Franck",
""
],
[
"Hettal",
"Liza",
""
],
[
"Hamy",
"Anne-Sophie",
""... | Discovering causal effects is at the core of scientific investigation but remains challenging when only observational data is available. In practice, causal networks are difficult to learn and interpret, and limited to relatively small datasets. We report a more reliable and scalable causal discovery method (iMIIC), ba... |
1905.08129 | Carsten Conradi | Carsten Conradi and Elisenda Feliu and Maya Mincheva | On the existence of Hopf bifurcations in the sequential and distributive
double phosphorylation cycle | null | null | 10.3934/mbe.2020027 | null | q-bio.MN math.AG math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein phosphorylation cycles are important mechanisms of the post
translational modification of a protein and as such an integral part of
intracellular signaling and control. We consider the sequential phosphorylation
and dephosphorylation of a protein at two binding sites. While it is known that
proteins where pho... | [
{
"created": "Mon, 20 May 2019 14:11:54 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Sep 2019 10:37:29 GMT",
"version": "v2"
}
] | 2019-11-06 | [
[
"Conradi",
"Carsten",
""
],
[
"Feliu",
"Elisenda",
""
],
[
"Mincheva",
"Maya",
""
]
] | Protein phosphorylation cycles are important mechanisms of the post translational modification of a protein and as such an integral part of intracellular signaling and control. We consider the sequential phosphorylation and dephosphorylation of a protein at two binding sites. While it is known that proteins where phosp... |
2310.10978 | Ka My Dang Dr | Ka My Dang, Yi Jia Zhang, Tianchen Zhang, Chao Wang, Anton Sinner,
Piero Coronica, and Joyce K. S. Poon | NeuroQuantify -- An Image Analysis Software for Detection and
Quantification of Neurons and Neurites using Deep Learning | null | null | null | null | q-bio.QM eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The segmentation of cells and neurites in microscopy images of neuronal
networks provides valuable quantitative information about neuron growth and
neuronal differentiation, including the number of cells, neurites, neurite
length and neurite orientation. This information is essential for assessing the
development of ... | [
{
"created": "Mon, 16 Oct 2023 13:11:59 GMT",
"version": "v1"
},
{
"created": "Thu, 19 Oct 2023 08:33:52 GMT",
"version": "v2"
}
] | 2023-10-20 | [
[
"Dang",
"Ka My",
""
],
[
"Zhang",
"Yi Jia",
""
],
[
"Zhang",
"Tianchen",
""
],
[
"Wang",
"Chao",
""
],
[
"Sinner",
"Anton",
""
],
[
"Coronica",
"Piero",
""
],
[
"Poon",
"Joyce K. S.",
""
]
] | The segmentation of cells and neurites in microscopy images of neuronal networks provides valuable quantitative information about neuron growth and neuronal differentiation, including the number of cells, neurites, neurite length and neurite orientation. This information is essential for assessing the development of ne... |
2011.04354 | Fedor Garbuzov | F. E. Garbuzov, V. V. Gursky | Nonequilibrium model of short-range repression in gene transcription
regulation | null | Phys. Rev. E 104, 014407 (2021) | 10.1103/PhysRevE.104.014407 | null | q-bio.MN q-bio.GN | http://creativecommons.org/licenses/by-sa/4.0/ | Transcription factors are proteins that regulate gene activity by activating
or repressing gene transcription. A special class of transcriptional repressors
operates via a short-range mechanism, making local DNA regions inaccessible to
binding by activators, and thus providing an indirect repressive action on the
tar... | [
{
"created": "Mon, 9 Nov 2020 11:38:13 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Apr 2022 20:01:05 GMT",
"version": "v2"
}
] | 2022-04-13 | [
[
"Garbuzov",
"F. E.",
""
],
[
"Gursky",
"V. V.",
""
]
] | Transcription factors are proteins that regulate gene activity by activating or repressing gene transcription. A special class of transcriptional repressors operates via a short-range mechanism, making local DNA regions inaccessible to binding by activators, and thus providing an indirect repressive action on the targe... |
2001.03207 | Sally Ellingson | Brian Davis, Kevin Mcloughlin, Jonathan Allen, and Sally Ellingson | Split Optimization for Protein/Ligand Binding Models | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we investigate potential biases in datasets used to make drug
binding predictions using machine learning. We investigate a recently published
metric called the Asymmetric Validation Embedding (AVE) bias which is used to
quantify this bias and detect overfitting. We compare it to a slightly revised
vers... | [
{
"created": "Thu, 9 Jan 2020 20:07:57 GMT",
"version": "v1"
}
] | 2020-01-13 | [
[
"Davis",
"Brian",
""
],
[
"Mcloughlin",
"Kevin",
""
],
[
"Allen",
"Jonathan",
""
],
[
"Ellingson",
"Sally",
""
]
] | In this paper, we investigate potential biases in datasets used to make drug binding predictions using machine learning. We investigate a recently published metric called the Asymmetric Validation Embedding (AVE) bias which is used to quantify this bias and detect overfitting. We compare it to a slightly revised versio... |
q-bio/0604020 | Jesus M. Cortes | J. Marro, J.J. Torres, J.M. Cortes | Chaotic hopping between attractors in neural networks | 12 pages, 5 figures | null | null | null | q-bio.NC | null | We present a neurobiologically--inspired stochastic cellular automaton whose
state jumps with time between the attractors corresponding to a series of
stored patterns. The jumping varies from regular to chaotic as the model
parameters are modified. The resulting irregular behavior, which mimics the
state of attention... | [
{
"created": "Sun, 16 Apr 2006 21:26:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Marro",
"J.",
""
],
[
"Torres",
"J. J.",
""
],
[
"Cortes",
"J. M.",
""
]
] | We present a neurobiologically--inspired stochastic cellular automaton whose state jumps with time between the attractors corresponding to a series of stored patterns. The jumping varies from regular to chaotic as the model parameters are modified. The resulting irregular behavior, which mimics the state of attention i... |
2006.09454 | Wenxing Hu | Wenxing Hu, Xianghe Meng, Yuntong Bai, Aiying Zhang, Biao Cai, Gemeng
Zhang, Tony W. Wilson, Julia M. Stephen, Vince D. Calhoun, Yu-Ping Wang | Interpretable multimodal fusion networks reveal mechanisms of brain
cognition | null | null | null | null | q-bio.NC cs.CV cs.LG eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multimodal fusion benefits disease diagnosis by providing a more
comprehensive perspective. Developing algorithms is challenging due to data
heterogeneity and the complex within- and between-modality associations.
Deep-network-based data-fusion models have been developed to capture the
complex associations and the pe... | [
{
"created": "Tue, 16 Jun 2020 18:52:50 GMT",
"version": "v1"
}
] | 2020-06-18 | [
[
"Hu",
"Wenxing",
""
],
[
"Meng",
"Xianghe",
""
],
[
"Bai",
"Yuntong",
""
],
[
"Zhang",
"Aiying",
""
],
[
"Cai",
"Biao",
""
],
[
"Zhang",
"Gemeng",
""
],
[
"Wilson",
"Tony W.",
""
],
[
"Stephen",
... | Multimodal fusion benefits disease diagnosis by providing a more comprehensive perspective. Developing algorithms is challenging due to data heterogeneity and the complex within- and between-modality associations. Deep-network-based data-fusion models have been developed to capture the complex associations and the perf... |
0905.2875 | Guido Tiana | C. Camilloni, G. Tiana and R. A. Broglia | Atomic-detailed milestones along the folding trajectory of protein G | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The high computational cost of carrying out molecular dynamics simulations of
even small-size proteins is a major obstacle in the study, at atomic detail and
in explicit solvent, of the physical mechanism which is at the basis of the
folding of proteins. Making use of a biasing algorithm, based on the principle
of th... | [
{
"created": "Mon, 18 May 2009 12:35:51 GMT",
"version": "v1"
}
] | 2009-05-19 | [
[
"Camilloni",
"C.",
""
],
[
"Tiana",
"G.",
""
],
[
"Broglia",
"R. A.",
""
]
] | The high computational cost of carrying out molecular dynamics simulations of even small-size proteins is a major obstacle in the study, at atomic detail and in explicit solvent, of the physical mechanism which is at the basis of the folding of proteins. Making use of a biasing algorithm, based on the principle of the ... |
1902.07942 | Janusz Szwabi\'nski | Patrycja Kowalek and Hanna Loch-Olszewska and Janusz Szwabi\'nski | Classification of diffusion modes in single-particle tracking data:
Feature-based versus deep-learning approach | null | Phys. Rev. E 100, 032410 (2019) | 10.1103/PhysRevE.100.032410 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Single-particle trajectories measured in microscopy experiments contain
important information about dynamic processes undergoing in a range of
materials including living cells and tissues. However, extracting that
information is not a trivial task due to the stochastic nature of particles'
movement and the sampling n... | [
{
"created": "Thu, 21 Feb 2019 10:05:48 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Feb 2019 08:59:01 GMT",
"version": "v2"
},
{
"created": "Thu, 4 Jul 2019 07:56:37 GMT",
"version": "v3"
},
{
"created": "Mon, 2 Sep 2019 08:25:19 GMT",
"version": "v4"
}
] | 2019-09-25 | [
[
"Kowalek",
"Patrycja",
""
],
[
"Loch-Olszewska",
"Hanna",
""
],
[
"Szwabiński",
"Janusz",
""
]
] | Single-particle trajectories measured in microscopy experiments contain important information about dynamic processes undergoing in a range of materials including living cells and tissues. However, extracting that information is not a trivial task due to the stochastic nature of particles' movement and the sampling noi... |
1910.08724 | Zhongqi Tian | Zhong-Qi Kyle Tian and Douglas Zhou | Design Efficient Exponential Time Differencing method For Hodgkin-Huxley
Neural Networks | null | null | 10.3389/fncom.2020.00040 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The exponential time differencing (ETD) method allows using a large time step
to efficiently evolve the stiff system such as Hodgkin-Huxley (HH) neural
networks.
For pulse-coupled HH networks, the synaptic spike times cannot be
predetermined and are convoluted with neuron's trajectory itself.
This presents a chal... | [
{
"created": "Sat, 19 Oct 2019 08:41:15 GMT",
"version": "v1"
},
{
"created": "Sun, 17 Nov 2019 05:33:00 GMT",
"version": "v2"
},
{
"created": "Thu, 21 Nov 2019 13:25:31 GMT",
"version": "v3"
},
{
"created": "Wed, 27 Nov 2019 14:49:11 GMT",
"version": "v4"
}
] | 2020-06-29 | [
[
"Tian",
"Zhong-Qi Kyle",
""
],
[
"Zhou",
"Douglas",
""
]
] | The exponential time differencing (ETD) method allows using a large time step to efficiently evolve the stiff system such as Hodgkin-Huxley (HH) neural networks. For pulse-coupled HH networks, the synaptic spike times cannot be predetermined and are convoluted with neuron's trajectory itself. This presents a challengin... |
1403.5519 | Manuel Jim\'enez-Mart\'in | Manuel Jim\'enez-Mart\'in and Juan Manuel Pastor and Juan Carlos
Losada and Javier Galeano | Link aggregation process for modelling weighted mutualistic networks | 6 Figures, 2 Tables | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutualism is a biological interaction mutually beneficial for both species
involved, such as the interaction between plants and their pollinators. Real
mutualistic communities can be understood as weighted bipartite networks and
they present a nested structure and truncated power law degree and strength
distributions... | [
{
"created": "Fri, 21 Mar 2014 16:58:13 GMT",
"version": "v1"
}
] | 2014-03-24 | [
[
"Jiménez-Martín",
"Manuel",
""
],
[
"Pastor",
"Juan Manuel",
""
],
[
"Losada",
"Juan Carlos",
""
],
[
"Galeano",
"Javier",
""
]
] | Mutualism is a biological interaction mutually beneficial for both species involved, such as the interaction between plants and their pollinators. Real mutualistic communities can be understood as weighted bipartite networks and they present a nested structure and truncated power law degree and strength distributions. ... |
2212.08211 | Carina Curto | Caitlyn Parmelee, Juliana Londono Alvarez, Carina Curto, Katherine
Morrison | Sequence generation in inhibition-dominated neural networks | 6 pages, 4 figures, appeared in SIAM DSWeb, 2022 | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This is a brief overview of results from [arXiv:2107.10244, ref 11], on
network architectures that produce sequential dynamics in a special family of
inhibition-dominated neural networks. It was written for SIAM DSWeb.
| [
{
"created": "Fri, 16 Dec 2022 00:51:05 GMT",
"version": "v1"
}
] | 2022-12-19 | [
[
"Parmelee",
"Caitlyn",
""
],
[
"Alvarez",
"Juliana Londono",
""
],
[
"Curto",
"Carina",
""
],
[
"Morrison",
"Katherine",
""
]
] | This is a brief overview of results from [arXiv:2107.10244, ref 11], on network architectures that produce sequential dynamics in a special family of inhibition-dominated neural networks. It was written for SIAM DSWeb. |
1805.09107 | Viktor Stojkoski MSc | Viktor Stojkoski, Zoran Utkovski, Elisabeth Andre, Ljupco Kocarev | Multiplex Network Structure Enhances the Role of Generalized Reciprocity
in Promoting Cooperation | Extended abstract of "The Role of Multiplex Network Structure in
Cooperation through Generalized Reciprocity" | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In multi-agent systems, cooperative behavior is largely determined by the
network structure which dictates the interactions among neighboring agents.
These interactions often exhibit multidimensional features, either as
relationships of different types or temporal dynamics, both of which may be
modeled as a "multiple... | [
{
"created": "Wed, 23 May 2018 13:02:34 GMT",
"version": "v1"
}
] | 2018-05-24 | [
[
"Stojkoski",
"Viktor",
""
],
[
"Utkovski",
"Zoran",
""
],
[
"Andre",
"Elisabeth",
""
],
[
"Kocarev",
"Ljupco",
""
]
] | In multi-agent systems, cooperative behavior is largely determined by the network structure which dictates the interactions among neighboring agents. These interactions often exhibit multidimensional features, either as relationships of different types or temporal dynamics, both of which may be modeled as a "multiplex"... |
1907.02730 | Koh Onimaru | Koh Onimaru, Luciano Marcon | Systems biology approach to the origin of the tetrapod limb | 22 pages, 5 figures | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | It is still not understood how similar genomic sequences have generated
diverse and spectacular forms during evolution. The difficulty to bridge
phenotypes and genotypes stems from the complexity of multicellular systems,
where thousands of genes and cells interact with each other providing
developmental non-linearit... | [
{
"created": "Fri, 5 Jul 2019 09:03:15 GMT",
"version": "v1"
}
] | 2019-07-08 | [
[
"Onimaru",
"Koh",
""
],
[
"Marcon",
"Luciano",
""
]
] | It is still not understood how similar genomic sequences have generated diverse and spectacular forms during evolution. The difficulty to bridge phenotypes and genotypes stems from the complexity of multicellular systems, where thousands of genes and cells interact with each other providing developmental non-linearity.... |
2305.00338 | Jorge Arroyo-Esquivel | Jorge Arroyo-Esquivel and Christopher A Klausmeier and Elena Litchman | Using neural ordinary differential equations to predict complex
ecological dynamics from population density data | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Simple models have been used to describe ecological processes for over a
century. However, the complexity of ecological systems makes simple models
subject to modeling bias due to simplifying assumptions or unaccounted factors,
limiting their predictive power. Neural Ordinary Differential Equations (NODEs)
have surge... | [
{
"created": "Sat, 29 Apr 2023 20:26:42 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Aug 2023 14:25:56 GMT",
"version": "v2"
},
{
"created": "Tue, 23 Jan 2024 18:35:46 GMT",
"version": "v3"
}
] | 2024-01-24 | [
[
"Arroyo-Esquivel",
"Jorge",
""
],
[
"Klausmeier",
"Christopher A",
""
],
[
"Litchman",
"Elena",
""
]
] | Simple models have been used to describe ecological processes for over a century. However, the complexity of ecological systems makes simple models subject to modeling bias due to simplifying assumptions or unaccounted factors, limiting their predictive power. Neural Ordinary Differential Equations (NODEs) have surged ... |
2312.07899 | Yanjun Li | Qiaosi Tang, Ranjala Ratnayake, Gustavo Seabra, Zhe Jiang, Ruogu Fang,
Lina Cui, Yousong Ding, Tamer Kahveci, Jiang Bian, Chenglong Li, Hendrik
Luesch, Yanjun Li | Morphological Profiling for Drug Discovery in the Era of Deep Learning | 44 pages, 5 figure, 5 tables | null | null | null | q-bio.QM cs.AI cs.CV cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Morphological profiling is a valuable tool in phenotypic drug discovery. The
advent of high-throughput automated imaging has enabled the capturing of a wide
range of morphological features of cells or organisms in response to
perturbations at the single-cell resolution. Concurrently, significant advances
in machine l... | [
{
"created": "Wed, 13 Dec 2023 05:08:32 GMT",
"version": "v1"
},
{
"created": "Mon, 15 Jan 2024 21:22:46 GMT",
"version": "v2"
}
] | 2024-01-17 | [
[
"Tang",
"Qiaosi",
""
],
[
"Ratnayake",
"Ranjala",
""
],
[
"Seabra",
"Gustavo",
""
],
[
"Jiang",
"Zhe",
""
],
[
"Fang",
"Ruogu",
""
],
[
"Cui",
"Lina",
""
],
[
"Ding",
"Yousong",
""
],
[
"Kahveci",
... | Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations at the single-cell resolution. Concurrently, significant advances in machine lea... |
2405.13182 | Zachary Kilpatrick PhD | Heather L Cihak and Zachary P Kilpatrick | Robustly encoding certainty in a metastable neural circuit model | 15 pages, 10 figures | null | null | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Localized persistent neural activity can encode delayed estimates of
continuous variables. Common experiments require that subjects store and report
the feature value (e.g., orientation) of a particular cue (e.g., oriented bar
on a screen) after a delay. Visualizing recorded activity of neurons along
their feature tu... | [
{
"created": "Tue, 21 May 2024 20:13:35 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Jul 2024 19:15:50 GMT",
"version": "v2"
}
] | 2024-08-01 | [
[
"Cihak",
"Heather L",
""
],
[
"Kilpatrick",
"Zachary P",
""
]
] | Localized persistent neural activity can encode delayed estimates of continuous variables. Common experiments require that subjects store and report the feature value (e.g., orientation) of a particular cue (e.g., oriented bar on a screen) after a delay. Visualizing recorded activity of neurons along their feature tuni... |
q-bio/0608029 | Michael Deem | D. B. Saakian, E. Munoz, Chin-Kun Hu, and M. W. Deem | Quasispecies Theory for Multiple-Peak Fitness Landscapes | 10 pages, 3 figures, 2 tables | Phys. Rev. E 73 (2006) 041913 | 10.1103/PhysRevE.73.041913 | null | q-bio.PE cond-mat.stat-mech | null | We use a path integral representation to solve the Eigen and Crow-Kimura
molecular evolution models for the case of multiple fitness peaks with
arbitrary fitness and degradation functions. In the general case, we find that
the solution to these molecular evolution models can be written as the optimum
of a fitness fun... | [
{
"created": "Tue, 15 Aug 2006 19:39:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Saakian",
"D. B.",
""
],
[
"Munoz",
"E.",
""
],
[
"Hu",
"Chin-Kun",
""
],
[
"Deem",
"M. W.",
""
]
] | We use a path integral representation to solve the Eigen and Crow-Kimura molecular evolution models for the case of multiple fitness peaks with arbitrary fitness and degradation functions. In the general case, we find that the solution to these molecular evolution models can be written as the optimum of a fitness funct... |
1707.08984 | Amit Chattopadhyay | Jason Laurie, Amit K Chattopadhyay and Darren R Flower | Protein Lipograms | 8 pages, 2 columns, 5 figures | Journal of Theoretical Biology, vol 430, pg 109, 2017 | 10.1016/j.jtbi.2017.07.009 | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Linguistic analysis of protein sequences is an underexploited technique.
Here, we capitalize on the concept of the lipogram to characterize sequences at
the proteome levels. A lipogram is a literary composition which omits one or
more letters. A protein lipogram likewise omits one or more types of amino
acid. In this... | [
{
"created": "Tue, 25 Jul 2017 11:44:23 GMT",
"version": "v1"
}
] | 2017-07-31 | [
[
"Laurie",
"Jason",
""
],
[
"Chattopadhyay",
"Amit K",
""
],
[
"Flower",
"Darren R",
""
]
] | Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this a... |
1009.0118 | Amaury Lambert | Amaury Lambert | Species abundance distributions in neutral models with immigration or
mutation and general lifetimes | 16 pages, 4 figures. To appear in Journal of Mathematical Biology.
The final publication is available at http://www.springerlink.com | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a general, neutral, dynamical model of biodiversity. Individuals
have i.i.d. lifetime durations, which are not necessarily exponentially
distributed, and each individual gives birth independently at constant rate
\lambda. We assume that types are clonally inherited. We consider two classes
of speciation m... | [
{
"created": "Wed, 1 Sep 2010 08:32:05 GMT",
"version": "v1"
}
] | 2010-09-02 | [
[
"Lambert",
"Amaury",
""
]
] | We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate \lambda. We assume that types are clonally inherited. We consider two classes of speciation mod... |
2101.10056 | Vitor Manuel Dinis Pereira | Vitor Manuel Dinis Pereira | Occipital and left temporal instantaneous amplitude and frequency
oscillations correlated with access and phenomenal consciousness | 31 pages, 23 figures, according to the Philpapers.org, my manuscript
"Occipital and left temporal instantaneous amplitude and frequency
oscillations correlated with access and phenomenal consciousness" has been
downloaded 161 times until today (since 2017-11-30) without any substantial
critic, at least any subs... | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Given the hard problem of consciousness (Chalmers, 1995) there are no brain
electrophysiological correlates of the subjective experience (the felt quality
of redness or the redness of red, the experience of dark and light, the quality
of depth in a visual field, the sound of a clarinet, the smell of mothball,
bodily ... | [
{
"created": "Sat, 26 Dec 2020 16:30:40 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Feb 2021 18:23:30 GMT",
"version": "v2"
},
{
"created": "Fri, 5 Mar 2021 18:36:30 GMT",
"version": "v3"
}
] | 2021-03-08 | [
[
"Pereira",
"Vitor Manuel Dinis",
""
]
] | Given the hard problem of consciousness (Chalmers, 1995) there are no brain electrophysiological correlates of the subjective experience (the felt quality of redness or the redness of red, the experience of dark and light, the quality of depth in a visual field, the sound of a clarinet, the smell of mothball, bodily se... |
1208.3570 | Darya Novopashina S | D. S. Novopashina, E. K. Apartsin, A. G. Venyaminova | Fluorecently labeled bionanotransporters of nucleic acid based on carbon
nanotubes | http://www.ujp.bitp.kiev.ua | Ukrainian Journal of Physics, 2009, Vol. 54, no. 1-2, pp. 207-215 | null | null | q-bio.BM cond-mat.mtrl-sci physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Here we propose the approach to design of the new type of hybrids of
oligonucleotides with fluorescein-functionalized single-walled carbon
nanotubes. The approach is based on stacking interactions of functionalized
nanotubes with pyrene residues in conjugates of oligonucleotides. The amino-
and fluorescein-modified s... | [
{
"created": "Fri, 17 Aug 2012 10:32:53 GMT",
"version": "v1"
}
] | 2015-03-13 | [
[
"Novopashina",
"D. S.",
""
],
[
"Apartsin",
"E. K.",
""
],
[
"Venyaminova",
"A. G.",
""
]
] | Here we propose the approach to design of the new type of hybrids of oligonucleotides with fluorescein-functionalized single-walled carbon nanotubes. The approach is based on stacking interactions of functionalized nanotubes with pyrene residues in conjugates of oligonucleotides. The amino- and fluorescein-modified sin... |
1604.02193 | Yana Safonova | Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Yana Safonova | New algorithmic challenges of adaptive immune repertoire construction | Paper accepted at the RECOMB-Seq 2016 | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: The analysis of antibodies and T-cell receptors (TCRs)
concentrations in serum is a fundamental problem in immunoinformatics.
Repertoire construction is a preliminary step of analysis of clonal lineages,
understanding of immune response dynamics, population analysis of
immunoglobulin and TCR loci. Emergen... | [
{
"created": "Thu, 7 Apr 2016 23:04:37 GMT",
"version": "v1"
}
] | 2016-04-11 | [
[
"Shlemov",
"Alexander",
""
],
[
"Bankevich",
"Sergey",
""
],
[
"Bzikadze",
"Andrey",
""
],
[
"Safonova",
"Yana",
""
]
] | Motivation: The analysis of antibodies and T-cell receptors (TCRs) concentrations in serum is a fundamental problem in immunoinformatics. Repertoire construction is a preliminary step of analysis of clonal lineages, understanding of immune response dynamics, population analysis of immunoglobulin and TCR loci. Emergence... |
0912.4472 | John Rhodes | Elizabeth S. Allman, James H. Degnan, John A. Rhodes | Identifying the Rooted Species Tree from the Distribution of Unrooted
Gene Trees under the Coalescent | Additional material extends results to polytomous species trees | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene trees are evolutionary trees representing the ancestry of genes sampled
from multiple populations. Species trees represent populations of individuals
-- each with many genes -- splitting into new populations or species. The
coalescent process, which models ancestry of gene copies within populations, is
often use... | [
{
"created": "Tue, 22 Dec 2009 18:00:39 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Jul 2010 18:07:14 GMT",
"version": "v2"
}
] | 2010-07-30 | [
[
"Allman",
"Elizabeth S.",
""
],
[
"Degnan",
"James H.",
""
],
[
"Rhodes",
"John A.",
""
]
] | Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used ... |
1006.0020 | Teruhiko Yoneyama | Teruhiko Yoneyama and Mukkai S. Krishnamoorthy | Influence of the Cold War upon Influenza Pandemic of 1957-1958 | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/3.0/ | Influenza Pandemic of 1957-1958, also called Asian Flu Pandemic, was one of
the most widespread pandemics in history. In this paper, we model the pandemic,
considering the effect of the Cold War. There were some restrictions between
Western and Eastern nations due to the Cold War during the pandemic. We expect
that s... | [
{
"created": "Tue, 11 May 2010 22:07:38 GMT",
"version": "v1"
}
] | 2010-06-02 | [
[
"Yoneyama",
"Teruhiko",
""
],
[
"Krishnamoorthy",
"Mukkai S.",
""
]
] | Influenza Pandemic of 1957-1958, also called Asian Flu Pandemic, was one of the most widespread pandemics in history. In this paper, we model the pandemic, considering the effect of the Cold War. There were some restrictions between Western and Eastern nations due to the Cold War during the pandemic. We expect that suc... |
2311.04567 | Robert Petryszak | Kevin Troul\'e, Robert Petryszak, Martin Prete, James Cranley, Alicia
Harasty, Zewen Kelvin Tuong, Sarah A Teichmann, Luz Garcia-Alonso, Roser
Vento-Tormo | CellPhoneDB v5: inferring cell-cell communication from single-cell
multiomics data | 30 pages, 3 figures and 2 tables. Added previously missing figures
and tables; Updated the reference for 'An integrated single-cell reference
atlas of the human endometrium' paper | null | null | null | q-bio.CB q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Cell-cell communication is essential for tissue development, regeneration and
function, and its disruption can lead to diseases and developmental
abnormalities. The revolution of single-cell genomics technologies offers
unprecedented insights into cellular identities, opening new avenues to resolve
the intricate cell... | [
{
"created": "Wed, 8 Nov 2023 09:59:03 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Nov 2023 13:41:51 GMT",
"version": "v2"
}
] | 2023-11-14 | [
[
"Troulé",
"Kevin",
""
],
[
"Petryszak",
"Robert",
""
],
[
"Prete",
"Martin",
""
],
[
"Cranley",
"James",
""
],
[
"Harasty",
"Alicia",
""
],
[
"Tuong",
"Zewen Kelvin",
""
],
[
"Teichmann",
"Sarah A",
""
],... | Cell-cell communication is essential for tissue development, regeneration and function, and its disruption can lead to diseases and developmental abnormalities. The revolution of single-cell genomics technologies offers unprecedented insights into cellular identities, opening new avenues to resolve the intricate cellul... |
q-bio/0402003 | Hiro-Sato Niwa | Hiro-Sato Niwa | Space-irrelevant scaling law for fish school sizes | 23 pages, 12 figures, to appear in J. Theor. Biol | J. Theor. Biol. 228 (2004) 347-357 | 10.1016/j.jtbi.2004.01.011 | null | q-bio.PE cond-mat.stat-mech | null | Universal scaling in the power-law size distribution of pelagic fish schools
is established. The power-law exponent of size distributions is extracted
through the data collapse. The distribution depends on the school size only
through the ratio of the size to the expected size of the schools an arbitrary
individual e... | [
{
"created": "Sun, 1 Feb 2004 21:11:39 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Niwa",
"Hiro-Sato",
""
]
] | Universal scaling in the power-law size distribution of pelagic fish schools is established. The power-law exponent of size distributions is extracted through the data collapse. The distribution depends on the school size only through the ratio of the size to the expected size of the schools an arbitrary individual eng... |
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