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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2211.14373 | Fernando Bastos | Jaime Barros Silva Filho, Fernando de Souza Bastos, Diogo da Silva
Machado, Maria Luiza Ferreira Delfim | Application of Molecular Topology to the Prediction of Antioxidant
Activity in a Group of Phenolic Compounds | null | null | null | null | q-bio.BM stat.AP | http://creativecommons.org/licenses/by/4.0/ | The study of compounds with antioxidant capabilities is of great interest to
the scientific community, as it has implications in several areas, from
Agricultural Sciences to Biological Sciences, including Food Engineering,
Medicine and Pharmacy. In applications related to human health, it is known
that antioxidant ac... | [
{
"created": "Fri, 25 Nov 2022 21:06:08 GMT",
"version": "v1"
}
] | 2022-11-29 | [
[
"Filho",
"Jaime Barros Silva",
""
],
[
"Bastos",
"Fernando de Souza",
""
],
[
"Machado",
"Diogo da Silva",
""
],
[
"Delfim",
"Maria Luiza Ferreira",
""
]
] | The study of compounds with antioxidant capabilities is of great interest to the scientific community, as it has implications in several areas, from Agricultural Sciences to Biological Sciences, including Food Engineering, Medicine and Pharmacy. In applications related to human health, it is known that antioxidant acti... |
1910.14339 | Luis F Seoane PhD | Seoane LF, Sol\'e R | How Turing parasites expand the computational landscape of digital life | 16 pages, 10 figures in main paper, supporting material not included | Physical Review E. 2023 Oct 23;108(4):044407 | 10.1103/PhysRevE.108.044407 | null | q-bio.PE cond-mat.dis-nn nlin.AO nlin.CG q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Why are living systems complex? Why does the biosphere contain living beings
with complexity features beyond those of the simplest replicators? What kind of
evolutionary pressures result in more complex life forms? These are key
questions that pervade the problem of how complexity arises in evolution. One
particular ... | [
{
"created": "Thu, 31 Oct 2019 10:02:20 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Apr 2020 16:59:48 GMT",
"version": "v2"
},
{
"created": "Wed, 14 Oct 2020 14:24:03 GMT",
"version": "v3"
},
{
"created": "Fri, 10 Nov 2023 18:06:43 GMT",
"version": "v4"
}
] | 2023-11-13 | [
[
"LF",
"Seoane",
""
],
[
"R",
"Solé",
""
]
] | Why are living systems complex? Why does the biosphere contain living beings with complexity features beyond those of the simplest replicators? What kind of evolutionary pressures result in more complex life forms? These are key questions that pervade the problem of how complexity arises in evolution. One particular wa... |
2110.07069 | Bryan He | Bryan He, Matthew Thomson, Meena Subramaniam, Richard Perez, Chun
Jimmie Ye, James Zou | CloudPred: Predicting Patient Phenotypes From Single-cell RNA-seq | Preprint of an article published in Pacific Symposium on Biocomputing
\copyright\ 2021 World Scientific Publishing Co., Singapore,
http://psb.stanford.edu/ | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Single-cell RNA sequencing (scRNA-seq) has the potential to provide powerful,
high-resolution signatures to inform disease prognosis and precision medicine.
This paper takes an important first step towards this goal by developing an
interpretable machine learning algorithm, CloudPred, to predict individuals'
disease ... | [
{
"created": "Wed, 13 Oct 2021 22:41:30 GMT",
"version": "v1"
}
] | 2021-10-15 | [
[
"He",
"Bryan",
""
],
[
"Thomson",
"Matthew",
""
],
[
"Subramaniam",
"Meena",
""
],
[
"Perez",
"Richard",
""
],
[
"Ye",
"Chun Jimmie",
""
],
[
"Zou",
"James",
""
]
] | Single-cell RNA sequencing (scRNA-seq) has the potential to provide powerful, high-resolution signatures to inform disease prognosis and precision medicine. This paper takes an important first step towards this goal by developing an interpretable machine learning algorithm, CloudPred, to predict individuals' disease ph... |
2104.09182 | Elisabeth Rens | Elisabeth G. Rens and Leah Edelstein-Keshet | Cellular tango: How extracellular matrix adhesion choreographs Rac-Rho
signaling and cell movement | null | null | 10.1088/1478-3975/ac2888 | null | q-bio.CB math.DS | http://creativecommons.org/licenses/by/4.0/ | The small GTPases Rac and Rho are known to regulate eukaryotic cell shape,
promoting front protrusion (Rac) or rear retraction (Rho) of the cell edge.
Such cell deformation changes the contact and adhesion of cell to the
extracellular matrix (ECM), while ECM signaling through integrin receptors also
affects GTPase ac... | [
{
"created": "Mon, 19 Apr 2021 10:18:13 GMT",
"version": "v1"
}
] | 2021-12-15 | [
[
"Rens",
"Elisabeth G.",
""
],
[
"Edelstein-Keshet",
"Leah",
""
]
] | The small GTPases Rac and Rho are known to regulate eukaryotic cell shape, promoting front protrusion (Rac) or rear retraction (Rho) of the cell edge. Such cell deformation changes the contact and adhesion of cell to the extracellular matrix (ECM), while ECM signaling through integrin receptors also affects GTPase acti... |
2302.01019 | Serge Kernbach | Serge Kernbach, Olga Kernbach, Andreas Kernbach | Biophysical aspects of neurocognitive modeling with long-term sustained
temperature variations | null | null | null | null | q-bio.NC physics.bio-ph physics.med-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Long-term focused attention with visualization and breathing exercises is at
the core of various Eastern traditions. Neurocognitive and psychosomatic
phenomena demonstrated during such exercises were instrumentally explored with
EEG and other sensors. Neurocognitive modeling in the form of meditative
visualization pr... | [
{
"created": "Thu, 2 Feb 2023 11:14:43 GMT",
"version": "v1"
}
] | 2023-02-03 | [
[
"Kernbach",
"Serge",
""
],
[
"Kernbach",
"Olga",
""
],
[
"Kernbach",
"Andreas",
""
]
] | Long-term focused attention with visualization and breathing exercises is at the core of various Eastern traditions. Neurocognitive and psychosomatic phenomena demonstrated during such exercises were instrumentally explored with EEG and other sensors. Neurocognitive modeling in the form of meditative visualization prod... |
1407.4824 | Joseph Crawford | Joseph Crawford, Yihan Sun, Tijana Milenkovi\'c | Fair Evaluation of Global Network Aligners | 19 pages. 10 figures. Presented at the 2014 ISMB Conference, July
13-15, Boston, MA | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biological network alignment identifies topologically and functionally
conserved regions between networks of different species. It encompasses two
algorithmic steps: node cost function (NCF), which measures similarities
between nodes in different networks, and alignment strategy (AS), which uses
these similarities to... | [
{
"created": "Thu, 17 Jul 2014 20:23:00 GMT",
"version": "v1"
}
] | 2014-07-21 | [
[
"Crawford",
"Joseph",
""
],
[
"Sun",
"Yihan",
""
],
[
"Milenković",
"Tijana",
""
]
] | Biological network alignment identifies topologically and functionally conserved regions between networks of different species. It encompasses two algorithmic steps: node cost function (NCF), which measures similarities between nodes in different networks, and alignment strategy (AS), which uses these similarities to r... |
1406.3762 | Amir Toor | Max Jameson-Lee, Vishal Koparde, Phil Griffith, Allison F. Scalora,
Juliana K. Sampson, Haniya Khalid, Nihar U. Sheth, Michael Batalo, Myrna G.
Serrano, Catherine H. Roberts, Michael L. Hess, Gregory A. Buck, Michael C.
Neale, Masoud H. Manjili, Amir A. Toor | In Silico Derivation of HLA-Specific Alloreactivity Potential from Whole
Exome Sequencing of Stem Cell Transplant Donors and Recipients: Understanding
the Quantitative Immuno-biology of Allogeneic Transplantation | Abstract: 235, Words: 6422, Figures: 7, Tables: 3, Supplementary
figures: 2, Supplementary tables: 2 | Frontiers in Immunology 2014. 5:529 | 10.3389/fimmu.2014.00529 | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Donor T cell mediated graft vs. host effects may result from the aggregate
alloreactivity to minor histocompatibility antigens (mHA) presented by the HLA
in each donor-recipient pair (DRP) undergoing stem cell transplantation (SCT).
Whole exome sequencing has demonstrated extensive nucleotide sequence variation
in HL... | [
{
"created": "Sat, 14 Jun 2014 18:29:58 GMT",
"version": "v1"
}
] | 2014-12-16 | [
[
"Jameson-Lee",
"Max",
""
],
[
"Koparde",
"Vishal",
""
],
[
"Griffith",
"Phil",
""
],
[
"Scalora",
"Allison F.",
""
],
[
"Sampson",
"Juliana K.",
""
],
[
"Khalid",
"Haniya",
""
],
[
"Sheth",
"Nihar U.",
""
... | Donor T cell mediated graft vs. host effects may result from the aggregate alloreactivity to minor histocompatibility antigens (mHA) presented by the HLA in each donor-recipient pair (DRP) undergoing stem cell transplantation (SCT). Whole exome sequencing has demonstrated extensive nucleotide sequence variation in HLA-... |
q-bio/0608001 | Gyorgy Korniss | L. O'Malley, B. Kozma, G. Korniss, Z. Racz, T. Caraco | Fisher Waves and Front Roughening in a Two-Species Invasion Model with
Preemptive Competition | 8 pages, 5 figures; Papers on related work can be found at
http://www.rpi.edu/~korniss/Research | Phys. Rev. E 74, 041116 (2006) . | 10.1103/PhysRevE.74.041116 | null | q-bio.PE cond-mat.stat-mech | null | We study front propagation when an invading species competes with a resident;
we assume nearest-neighbor preemptive competition for resources in an
individual-based, two-dimensional lattice model. The asymptotic front velocity
exhibits power-law dependence on the difference between the two species' clonal
propagation... | [
{
"created": "Tue, 1 Aug 2006 14:41:42 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"O'Malley",
"L.",
""
],
[
"Kozma",
"B.",
""
],
[
"Korniss",
"G.",
""
],
[
"Racz",
"Z.",
""
],
[
"Caraco",
"T.",
""
]
] | We study front propagation when an invading species competes with a resident; we assume nearest-neighbor preemptive competition for resources in an individual-based, two-dimensional lattice model. The asymptotic front velocity exhibits power-law dependence on the difference between the two species' clonal propagation r... |
2011.06515 | Adriano de Albuquerque Batista | Adriano A. Batista and Severino Hor\'acio da Silva | An epidemiological compartmental model with automated parameter
estimation and forecasting of the spread of COVID-19 with analysis of data
from Germany and Brazil | 37 pages, 9 figures | Front. Appl. Math. Stat., 13 April 2022 | 10.3389/fams.2022.645614 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we adapt the epidemiological SIR model to study the evolution
of the dissemination of COVID-19 in Germany and Brazil (nationally, in the
State of Paraiba, and in the City of Campina Grande). We prove the well
posedness and the continuous dependence of the model dynamics on its
parameters. We also propos... | [
{
"created": "Wed, 11 Nov 2020 17:54:01 GMT",
"version": "v1"
}
] | 2022-04-20 | [
[
"Batista",
"Adriano A.",
""
],
[
"da Silva",
"Severino Horácio",
""
]
] | In this work, we adapt the epidemiological SIR model to study the evolution of the dissemination of COVID-19 in Germany and Brazil (nationally, in the State of Paraiba, and in the City of Campina Grande). We prove the well posedness and the continuous dependence of the model dynamics on its parameters. We also propose ... |
1308.6074 | Sohan Seth | Sohan Seth, Niko V\"alim\"aki, Samuel Kaski, Antti Honkela | Exploration and retrieval of whole-metagenome sequencing samples | 16 pages; additional results | null | null | null | q-bio.GN cs.CE cs.IR | http://creativecommons.org/licenses/by/3.0/ | Over the recent years, the field of whole metagenome shotgun sequencing has
witnessed significant growth due to the high-throughput sequencing technologies
that allow sequencing genomic samples cheaper, faster, and with better coverage
than before. This technical advancement has initiated the trend of sequencing
mult... | [
{
"created": "Wed, 28 Aug 2013 07:28:35 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Apr 2014 09:57:56 GMT",
"version": "v2"
}
] | 2014-04-04 | [
[
"Seth",
"Sohan",
""
],
[
"Välimäki",
"Niko",
""
],
[
"Kaski",
"Samuel",
""
],
[
"Honkela",
"Antti",
""
]
] | Over the recent years, the field of whole metagenome shotgun sequencing has witnessed significant growth due to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster, and with better coverage than before. This technical advancement has initiated the trend of sequencing multip... |
1312.2827 | Christian Althaus Ph.D. | Nicola Low, Janneke C.M. Heijne, Sereina A. Herzog, Christian L.
Althaus | Re-infection by untreated partners of people treated for Chlamydia
trachomatis and Neisseria gonorrhoeae: mathematical modelling study | Short report, 1 figure | Sex Transm Infect. 2014 May;90(3):254-6 | 10.1136/sextrans-2013-051279 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objectives: Re-infection after treatment for Chlamydia trachomatis or
Neisseria gonorrhoeae reduces the effect of control interventions. We explored
the impact of delays in partner treatment on the expected probability of
re-infection of index cases using a mathematical model. Methods: We used
previously reported par... | [
{
"created": "Tue, 10 Dec 2013 15:10:13 GMT",
"version": "v1"
}
] | 2014-08-20 | [
[
"Low",
"Nicola",
""
],
[
"Heijne",
"Janneke C. M.",
""
],
[
"Herzog",
"Sereina A.",
""
],
[
"Althaus",
"Christian L.",
""
]
] | Objectives: Re-infection after treatment for Chlamydia trachomatis or Neisseria gonorrhoeae reduces the effect of control interventions. We explored the impact of delays in partner treatment on the expected probability of re-infection of index cases using a mathematical model. Methods: We used previously reported param... |
q-bio/0501021 | Michael Stiber | Michael Stiber | Spike timing precision and neural error correction: local behavior | 23 pages, 27 figures, to be published in Neural Computation | Neural Computation, v. 17, n. 7, 1577-1601, 2005 | null | null | q-bio.NC cs.NE math.DS | null | The effects of spike timing precision and dynamical behavior on error
correction in spiking neurons were investigated. Stationary discharges -- phase
locked, quasiperiodic, or chaotic -- were induced in a simulated neuron by
presenting pacemaker presynaptic spike trains across a model of a prototypical
inhibitory syn... | [
{
"created": "Fri, 14 Jan 2005 13:25:42 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Stiber",
"Michael",
""
]
] | The effects of spike timing precision and dynamical behavior on error correction in spiking neurons were investigated. Stationary discharges -- phase locked, quasiperiodic, or chaotic -- were induced in a simulated neuron by presenting pacemaker presynaptic spike trains across a model of a prototypical inhibitory synap... |
1707.08284 | Johannes M\"uller | Lukas Heinrich, Johannes M\"uller, Aur\'elien Tellier, Daniel
Zivkovi\'c | Effects of population- and seed bank noise on neutral evolution and
efficacy of natural selection | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population genetics models typically consider a fixed population size and a
unique selection coefficient. However, population dynamics inherently generate
noise in numbers of individuals and selection acts on various components of the
individuals' fitness. In plant species with seed banks, the size of both the
above-... | [
{
"created": "Wed, 26 Jul 2017 04:16:12 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Dec 2017 12:46:26 GMT",
"version": "v2"
}
] | 2017-12-12 | [
[
"Heinrich",
"Lukas",
""
],
[
"Müller",
"Johannes",
""
],
[
"Tellier",
"Aurélien",
""
],
[
"Zivković",
"Daniel",
""
]
] | Population genetics models typically consider a fixed population size and a unique selection coefficient. However, population dynamics inherently generate noise in numbers of individuals and selection acts on various components of the individuals' fitness. In plant species with seed banks, the size of both the above- a... |
1911.06107 | Joe Kileel | Nathan Zelesko, Amit Moscovich, Joe Kileel, Amit Singer | Earthmover-based manifold learning for analyzing molecular conformation
spaces | 5 pages, 4 figures, 1 table | IEEE 17th International Symposium on Biomedical Imaging (ISBI)
2020 | 10.1109/ISBI45749.2020.9098723 | null | q-bio.BM cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we propose a novel approach for manifold learning that
combines the Earthmover's distance (EMD) with the diffusion maps method for
dimensionality reduction. We demonstrate the potential benefits of this
approach for learning shape spaces of proteins and other flexible
macromolecules using a simulated d... | [
{
"created": "Wed, 16 Oct 2019 01:38:52 GMT",
"version": "v1"
}
] | 2022-05-24 | [
[
"Zelesko",
"Nathan",
""
],
[
"Moscovich",
"Amit",
""
],
[
"Kileel",
"Joe",
""
],
[
"Singer",
"Amit",
""
]
] | In this paper, we propose a novel approach for manifold learning that combines the Earthmover's distance (EMD) with the diffusion maps method for dimensionality reduction. We demonstrate the potential benefits of this approach for learning shape spaces of proteins and other flexible macromolecules using a simulated dat... |
1908.10166 | Casimiro Adays Curbelo Monta\~nez | Casimiro Aday Curbelo Monta\~nez, Paul Fergus, Carl Chalmers, Nurul
Ahamed Hassain Malim, Basma Abdulaimma, Denis Reilly, and Francesco Falciani | SAERMA: Stacked Autoencoder Rule Mining Algorithm for the Interpretation
of Epistatic Interactions in GWAS for Extreme Obesity | 12 pages, 6 figures, 12 tables, 9 equations, journal | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the most important challenges in the analysis of high-throughput
genetic data is the development of efficient computational methods to identify
statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide
association studies (GWAS) use single-locus analysis where each SNP is
independently test... | [
{
"created": "Tue, 27 Aug 2019 12:49:05 GMT",
"version": "v1"
}
] | 2019-08-28 | [
[
"Montañez",
"Casimiro Aday Curbelo",
""
],
[
"Fergus",
"Paul",
""
],
[
"Chalmers",
"Carl",
""
],
[
"Malim",
"Nurul Ahamed Hassain",
""
],
[
"Abdulaimma",
"Basma",
""
],
[
"Reilly",
"Denis",
""
],
[
"Falciani",
... | One of the most important challenges in the analysis of high-throughput genetic data is the development of efficient computational methods to identify statistically significant Single Nucleotide Polymorphisms (SNPs). Genome-wide association studies (GWAS) use single-locus analysis where each SNP is independently tested... |
1802.01211 | Casper Beentjes | Casper H. L. Beentjes and Ruth E. Baker | Quasi-Monte Carlo methods applied to tau-leaping in stochastic
biological systems | null | Bull. Math. Biol. (2019) 81: 2931 | 10.1007/s11538-018-0442-2 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quasi-Monte Carlo methods have proven to be effective extensions of
traditional Monte Carlo methods in, amongst others, problems of quadrature and
the sample path simulation of stochastic differential equations. By replacing
the random number input stream in a simulation procedure by a low-discrepancy
number input st... | [
{
"created": "Sun, 4 Feb 2018 22:32:21 GMT",
"version": "v1"
},
{
"created": "Tue, 1 May 2018 10:41:02 GMT",
"version": "v2"
}
] | 2019-12-12 | [
[
"Beentjes",
"Casper H. L.",
""
],
[
"Baker",
"Ruth E.",
""
]
] | Quasi-Monte Carlo methods have proven to be effective extensions of traditional Monte Carlo methods in, amongst others, problems of quadrature and the sample path simulation of stochastic differential equations. By replacing the random number input stream in a simulation procedure by a low-discrepancy number input stre... |
1610.01898 | Christian Geier | Christian Geier, Alexander Rothkegel, Christian E. Elger, Klaus
Lehnertz | Bursting and Synchrony in Networks of Model Neurons | null | R. Tetzlaff and C. E. Elger and K. Lehnertz (2013), Recent
Advances in Predicting and Preventing Epileptic Seizures, page 108-116,
Singapore, World Scientific | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bursting neurons are considered to be a potential cause of over-excitability
and seizure susceptibility. The functional influence of these neurons in
extended epileptic networks is still poorly understood. There is mounting
evidence that the dynamics of neuronal networks is influenced not only by
neuronal and synapti... | [
{
"created": "Thu, 6 Oct 2016 14:52:22 GMT",
"version": "v1"
}
] | 2016-10-07 | [
[
"Geier",
"Christian",
""
],
[
"Rothkegel",
"Alexander",
""
],
[
"Elger",
"Christian E.",
""
],
[
"Lehnertz",
"Klaus",
""
]
] | Bursting neurons are considered to be a potential cause of over-excitability and seizure susceptibility. The functional influence of these neurons in extended epileptic networks is still poorly understood. There is mounting evidence that the dynamics of neuronal networks is influenced not only by neuronal and synaptic ... |
1810.04412 | Ankit Kumar Shukla | Ashutosh Gupta, Somya Mani, and Ankit Shukla | Synthesis for Vesicle Traffic Systems | 18 pages, 2 figures, 1 table | null | 10.1007/978-3-319-99429-1_6 | null | q-bio.SC cs.CE cs.LO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vesicle Traffic Systems (VTSs) are the material transport mechanisms among
the compartments inside the biological cells. The compartments are viewed as
nodes that are labeled with the containing chemicals and the transport channels
are similarly viewed as labeled edges between the nodes. Understanding VTSs is
an ongo... | [
{
"created": "Wed, 10 Oct 2018 08:34:50 GMT",
"version": "v1"
}
] | 2018-10-12 | [
[
"Gupta",
"Ashutosh",
""
],
[
"Mani",
"Somya",
""
],
[
"Shukla",
"Ankit",
""
]
] | Vesicle Traffic Systems (VTSs) are the material transport mechanisms among the compartments inside the biological cells. The compartments are viewed as nodes that are labeled with the containing chemicals and the transport channels are similarly viewed as labeled edges between the nodes. Understanding VTSs is an ongoin... |
2012.10295 | Andrew Whitwham | Petr Danecek, James K. Bonfield, Jennifer Liddle, John Marshall,
Valeriu Ohan, Martin O Pollard, Andrew Whitwham, Thomas Keane, Shane A.
McCarthy, Robert M. Davies, Heng Li | Twelve years of SAMtools and BCFtools | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Background
SAMtools and BCFtools are widely used programs for processing and analysing
high-throughput sequencing data.
Findings
The first version appeared online twelve years ago and has been maintained
and further developed ever since, with many new features and improvements added
over the years. The SAMtools... | [
{
"created": "Fri, 18 Dec 2020 15:19:36 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Feb 2021 11:19:20 GMT",
"version": "v2"
}
] | 2021-02-03 | [
[
"Danecek",
"Petr",
""
],
[
"Bonfield",
"James K.",
""
],
[
"Liddle",
"Jennifer",
""
],
[
"Marshall",
"John",
""
],
[
"Ohan",
"Valeriu",
""
],
[
"Pollard",
"Martin O",
""
],
[
"Whitwham",
"Andrew",
""
],
... | Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCF... |
2001.10535 | Jinsong Meng | Jinsong Meng | Bridging the Gap Between Consciousness and Matter: Recurrent Out-of-Body
Projection of Visual Awareness Revealed by the Law of Non-Identity | 20 pages, 9 figures, and 1 table. Comments: 21 pages, 9 figures, and
1 table: typos corrected, references added, a figure moved from the
supplementary part to the main text, typesetting changed from double columns
to one column. Comments: 28 pages, 10 figures, and 1 table: style changed to
APA, title changed, t... | Integrative Psychological and Behavioral Science,Volume 57 Issue
2, June 2023 | 10.1007/s12124-023-09775-y | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Consciousness is an explicit outcome of brain activity. However, the link
between consciousness and the material world remains to be explored. We applied
a new logic tool, the non-identity law, to the analysis of the visual dynamics
related to the naturalistic observation of a night-shot still life. We show
that visu... | [
{
"created": "Wed, 29 Jan 2020 18:20:37 GMT",
"version": "v1"
},
{
"created": "Wed, 18 Nov 2020 18:55:10 GMT",
"version": "v2"
},
{
"created": "Thu, 15 Jul 2021 14:35:15 GMT",
"version": "v3"
}
] | 2023-05-25 | [
[
"Meng",
"Jinsong",
""
]
] | Consciousness is an explicit outcome of brain activity. However, the link between consciousness and the material world remains to be explored. We applied a new logic tool, the non-identity law, to the analysis of the visual dynamics related to the naturalistic observation of a night-shot still life. We show that visual... |
q-bio/0409010 | Bernd Burghardt | Bernd Burghardt and Alexander K. Hartmann | Dependence of RNA secondary structure on the energy model | 8 pages, 9 figures | null | 10.1103/PhysRevE.71.021913 | null | q-bio.QM | null | We analyze a microscopic RNA model, which includes two widely used models as
limiting cases, namely it contains terms for bond as well as for stacking
energies. We numerically investigate possible changes in the qualitative and
quantitative behaviour while going from one model to the other; in particular
we test, whe... | [
{
"created": "Tue, 7 Sep 2004 09:04:35 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Burghardt",
"Bernd",
""
],
[
"Hartmann",
"Alexander K.",
""
]
] | We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative behaviour while going from one model to the other; in particular we test, wheth... |
1410.1836 | Stuart Kauffman | Stuart Kauffman | A Holistic, Non-algorithmic View of Cultural Evolution: Commentary on
Review Article by Prof. Liane Gabora | 3 pages | Physics of Life Reviews, 10(2), 154-155 | 10.1016/j.plrev.2013.05.005 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is surely some truth to the notion that culture evolves, but the
Darwinian view of culture is trivial. Gabora does two things in this paper.
First, she levels a reasoned and devastating attack on the adequacy of a
Darwinian theory of cultural evolution, showing that cultural evolution
violates virtually all pre... | [
{
"created": "Tue, 7 Oct 2014 18:25:05 GMT",
"version": "v1"
}
] | 2015-06-23 | [
[
"Kauffman",
"Stuart",
""
]
] | There is surely some truth to the notion that culture evolves, but the Darwinian view of culture is trivial. Gabora does two things in this paper. First, she levels a reasoned and devastating attack on the adequacy of a Darwinian theory of cultural evolution, showing that cultural evolution violates virtually all prere... |
2405.02524 | Danilo Bernardo | Danilo Bernardo, Xihe Xie, Parul Verma, Jonathan Kim, Virginia Liu,
Adam L. Numis, Ye Wu, Hannah C. Glass, Pew-Thian Yap, Srikantan S. Nagarajan,
Ashish Raj | Simulation-based Inference of Developmental EEG Maturation with the
Spectral Graph Model | 40 pages, 6 figures, 19 supplementary figures | Commun Phys 7, 255 (2024) | 10.1038/s42005-024-01748-w | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The spectral content of macroscopic neural activity evolves throughout
development, yet how this maturation relates to underlying brain network
formation and dynamics remains unknown. Here, we assess the developmental
maturation of electroencephalogram spectra via Bayesian model inversion of the
spectral graph model,... | [
{
"created": "Fri, 3 May 2024 23:44:30 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Jul 2024 21:48:14 GMT",
"version": "v2"
},
{
"created": "Fri, 26 Jul 2024 08:34:40 GMT",
"version": "v3"
}
] | 2024-08-05 | [
[
"Bernardo",
"Danilo",
""
],
[
"Xie",
"Xihe",
""
],
[
"Verma",
"Parul",
""
],
[
"Kim",
"Jonathan",
""
],
[
"Liu",
"Virginia",
""
],
[
"Numis",
"Adam L.",
""
],
[
"Wu",
"Ye",
""
],
[
"Glass",
"Han... | The spectral content of macroscopic neural activity evolves throughout development, yet how this maturation relates to underlying brain network formation and dynamics remains unknown. Here, we assess the developmental maturation of electroencephalogram spectra via Bayesian model inversion of the spectral graph model, a... |
1808.07785 | Karen Petrosyan | K.G. Petrosyan | Inter-state switching in stochastic gene expression: Exact solution, an
adiabatic limit and oscillations in molecular distributions | 6 pages, 6 figures | null | null | null | q-bio.MN cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the stochastic gene expression process with inter-state
flip-flops. An exact steady-state solution to the master equation is
calculated. One of the main goals in this paper is to investigate whether the
probability distribution of gene copies contains even-odd number oscillations.
A master equation previo... | [
{
"created": "Thu, 23 Aug 2018 14:53:13 GMT",
"version": "v1"
},
{
"created": "Thu, 28 Mar 2019 08:44:58 GMT",
"version": "v2"
},
{
"created": "Thu, 24 Sep 2020 07:57:20 GMT",
"version": "v3"
}
] | 2020-09-25 | [
[
"Petrosyan",
"K. G.",
""
]
] | We consider the stochastic gene expression process with inter-state flip-flops. An exact steady-state solution to the master equation is calculated. One of the main goals in this paper is to investigate whether the probability distribution of gene copies contains even-odd number oscillations. A master equation previous... |
1805.10892 | Eero Satuvuori | Eero Satuvuori, Mario Mulansky, Andreas Daffertshofer, Thomas Kreuz | Using spike train distances to identify the most discriminative neuronal
subpopulation | 14 pages, 9 Figures | null | 10.1016/j.jneumeth.2018.09.008 | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Spike trains of multiple neurons can be analyzed following the
summed population (SP) or the labeled line (LL) hypothesis. Responses to
external stimuli are generated by a neuronal population as a whole or the
individual neurons have encoding capacities of their own. The SPIKE-distance
estimated either fo... | [
{
"created": "Mon, 28 May 2018 12:40:10 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Sep 2018 09:10:05 GMT",
"version": "v2"
}
] | 2018-09-17 | [
[
"Satuvuori",
"Eero",
""
],
[
"Mulansky",
"Mario",
""
],
[
"Daffertshofer",
"Andreas",
""
],
[
"Kreuz",
"Thomas",
""
]
] | Background: Spike trains of multiple neurons can be analyzed following the summed population (SP) or the labeled line (LL) hypothesis. Responses to external stimuli are generated by a neuronal population as a whole or the individual neurons have encoding capacities of their own. The SPIKE-distance estimated either for ... |
1108.0673 | Mois\'es Santill\'an Dr. | Eder Zavala-L\'opez, Mois\'es Santill\'an | Oscillation arrest in the mouse somitogenesis clock presumably takes
place via an infinite period bifurcation | 13 pages, 2 figures | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we address the question of how oscillations are arrested in the
mouse somitogenesis clock when the determination front reaches presomitic
cells. Based upon available experimental evidence we hypothesize that the
mechanism underlying such a phenomenon involves the interaction between a limit
cycle (origin... | [
{
"created": "Tue, 2 Aug 2011 20:05:23 GMT",
"version": "v1"
}
] | 2015-03-13 | [
[
"Zavala-López",
"Eder",
""
],
[
"Santillán",
"Moisés",
""
]
] | In this work we address the question of how oscillations are arrested in the mouse somitogenesis clock when the determination front reaches presomitic cells. Based upon available experimental evidence we hypothesize that the mechanism underlying such a phenomenon involves the interaction between a limit cycle (originat... |
0707.0804 | Brigitte Gaillard | M. Boos (DEPE-Iphc), C. Zimmer (DEPE-Iphc), A. Carriere (DEPE-Iphc),
J.P. Robin (DEPE-Iphc), O. Petit (DEPE-Iphc) | Post-hatching parental care behaviour and hormonal status in a precocial
bird | null | Behavioural Processes (18/05/2007) sous presse | 10.1016/j.beproc.2007.05.003 | null | q-bio.PE | null | In birds, the link between parental care behaviour and prolactin release
during incubation persists after hatching in altricial birds, but has never
been precisely studied during the whole rearing period in precocial species,
such as ducks. The present study aims to understand how changes in parental
care after hatch... | [
{
"created": "Thu, 5 Jul 2007 15:12:49 GMT",
"version": "v1"
}
] | 2007-07-06 | [
[
"Boos",
"M.",
"",
"DEPE-Iphc"
],
[
"Zimmer",
"C.",
"",
"DEPE-Iphc"
],
[
"Carriere",
"A.",
"",
"DEPE-Iphc"
],
[
"Robin",
"J. P.",
"",
"DEPE-Iphc"
],
[
"Petit",
"O.",
"",
"DEPE-Iphc"
]
] | In birds, the link between parental care behaviour and prolactin release during incubation persists after hatching in altricial birds, but has never been precisely studied during the whole rearing period in precocial species, such as ducks. The present study aims to understand how changes in parental care after hatchin... |
1603.05343 | Roberto D. Pascual-Marqui | RD Pascual-Marqui, P Faber, T Kinoshita, Y Kitaura, K Kochi, P Milz, K
Nishida, M Yoshimura | The dual frequency RV-coupling coefficient: a novel measure for
quantifying cross-frequency information transactions in the brain | technical report, pre-print, 2016-03-16 | null | null | null | q-bio.NC stat.ME | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Identifying dynamic transactions between brain regions has become
increasingly important. Measurements within and across brain structures,
demonstrating the occurrence of bursts of beta/gamma oscillations only during
one specific phase of each theta/alpha cycle, have motivated the need to
advance beyond linear and st... | [
{
"created": "Thu, 17 Mar 2016 03:02:50 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Mar 2016 00:52:48 GMT",
"version": "v2"
}
] | 2016-03-21 | [
[
"Pascual-Marqui",
"RD",
""
],
[
"Faber",
"P",
""
],
[
"Kinoshita",
"T",
""
],
[
"Kitaura",
"Y",
""
],
[
"Kochi",
"K",
""
],
[
"Milz",
"P",
""
],
[
"Nishida",
"K",
""
],
[
"Yoshimura",
"M",
"... | Identifying dynamic transactions between brain regions has become increasingly important. Measurements within and across brain structures, demonstrating the occurrence of bursts of beta/gamma oscillations only during one specific phase of each theta/alpha cycle, have motivated the need to advance beyond linear and stat... |
1107.2223 | Marc de Lussanet H.E. | Marc H. E. de Lussanet | A hexamer origin of the echinoderms' five rays | 10 pages, 6 figures | Evolution and Development 2011, 13(2):228-238 | 10.1111/j.1525-142x.2011.00472.x | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Of the major deuterostome groups, the echinoderms with their multiple forms
and complex development are arguably the most mysterious. Although larval
echinoderms are bilaterally symmetric, the adult body seems to abandon the
larval body plan and to develop independently a new structure with different
symmetries. The ... | [
{
"created": "Tue, 12 Jul 2011 09:32:28 GMT",
"version": "v1"
},
{
"created": "Mon, 1 Apr 2013 19:45:10 GMT",
"version": "v2"
}
] | 2013-04-02 | [
[
"de Lussanet",
"Marc H. E.",
""
]
] | Of the major deuterostome groups, the echinoderms with their multiple forms and complex development are arguably the most mysterious. Although larval echinoderms are bilaterally symmetric, the adult body seems to abandon the larval body plan and to develop independently a new structure with different symmetries. The pr... |
2005.05595 | Yves Dumont | Maria Soledad Aronna (FGV), Yves Dumont (UMR AMAP) | On nonlinear pest/vector control via the Sterile Insect Technique:
impact of residual fertility | null | null | null | null | q-bio.PE math.DS math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a minimalist model for the Sterile Insect Technique (SIT),
assuming that residual fertility can occur in the sterile male
population.Taking into account that we are able to get regular measurements
from the biological system along the control duration, such as the size of the
wild insect population, we st... | [
{
"created": "Tue, 12 May 2020 08:04:01 GMT",
"version": "v1"
}
] | 2020-05-13 | [
[
"Aronna",
"Maria Soledad",
"",
"FGV"
],
[
"Dumont",
"Yves",
"",
"UMR AMAP"
]
] | We consider a minimalist model for the Sterile Insect Technique (SIT), assuming that residual fertility can occur in the sterile male population.Taking into account that we are able to get regular measurements from the biological system along the control duration, such as the size of the wild insect population, we stud... |
2107.08010 | Rebekah Rogers | Rebekah L. Rogers, Stephanie L. Grizzard, and Jeffrey T. Garner | Strong, recent selective sweeps reshape genetic diversity in freshwater
bivalve Megalonaias nervosa | 7 figures, 6 supplementary tables, 21 supplementary figures. 60 pages
total | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Freshwater Unionid bivalves have recently faced ecological upheaval through
pollution, barriers to dispersal, human harvesting, and changes in fish-host
prevalence. Currently, over 70% of species are threatened, endangered or
extinct. To characterize the genetic response to these recent selective
pressures, we collec... | [
{
"created": "Fri, 16 Jul 2021 16:56:48 GMT",
"version": "v1"
},
{
"created": "Fri, 27 May 2022 21:17:31 GMT",
"version": "v2"
},
{
"created": "Thu, 17 Nov 2022 16:35:08 GMT",
"version": "v3"
}
] | 2022-11-18 | [
[
"Rogers",
"Rebekah L.",
""
],
[
"Grizzard",
"Stephanie L.",
""
],
[
"Garner",
"Jeffrey T.",
""
]
] | Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, human harvesting, and changes in fish-host prevalence. Currently, over 70% of species are threatened, endangered or extinct. To characterize the genetic response to these recent selective pressures, we collecte... |
1410.0566 | Nadya Morozova | Nadya Morozova and Robert Penner | Geometry of Morphogenesis | null | null | null | null | q-bio.OT math.MG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce a formalism for the geometry of eukaryotic cells and
organisms.Cells are taken to be star-convex with good biological reason. This
allows for a convenient description of their extent in space as well as all
manner of cell surface gradients. We assume that a spectrum of such cell
surface markers determine... | [
{
"created": "Wed, 1 Oct 2014 10:23:46 GMT",
"version": "v1"
}
] | 2014-10-03 | [
[
"Morozova",
"Nadya",
""
],
[
"Penner",
"Robert",
""
]
] | We introduce a formalism for the geometry of eukaryotic cells and organisms.Cells are taken to be star-convex with good biological reason. This allows for a convenient description of their extent in space as well as all manner of cell surface gradients. We assume that a spectrum of such cell surface markers determines ... |
1303.3963 | Ovidiu Radulescu | Vincent Noel, Dima Grigoriev, Sergei Vakulenko and Ovidiu Radulescu | Tropicalization and tropical equilibration of chemical reactions | 13 pages, 1 figure, workshop Tropical-12, Moskow, August 26-31, 2012;
in press Contemporary Mathematics | null | null | null | q-bio.MN math.AG | http://creativecommons.org/licenses/publicdomain/ | Systems biology uses large networks of biochemical reactions to model the
functioning of biological cells from the molecular to the cellular scale. The
dynamics of dissipative reaction networks with many well separated time scales
can be described as a sequence of successive equilibrations of different
subsets of var... | [
{
"created": "Sat, 16 Mar 2013 10:17:45 GMT",
"version": "v1"
},
{
"created": "Mon, 27 May 2013 10:07:03 GMT",
"version": "v2"
}
] | 2013-05-28 | [
[
"Noel",
"Vincent",
""
],
[
"Grigoriev",
"Dima",
""
],
[
"Vakulenko",
"Sergei",
""
],
[
"Radulescu",
"Ovidiu",
""
]
] | Systems biology uses large networks of biochemical reactions to model the functioning of biological cells from the molecular to the cellular scale. The dynamics of dissipative reaction networks with many well separated time scales can be described as a sequence of successive equilibrations of different subsets of varia... |
1711.08548 | Mohd Almie Alias | Mohd Almie Alias and Pascal R Buenzli | Osteoblasts infill irregular pores under curvature and porosity
controls: A hypothesis-testing analysis of cell behaviours | 14 pages, 11 figures, Appendix | Biomech Model Mechanobiol (2018) 17:1357-1371 | 10.1007/s10237-018-1031-x | null | q-bio.CB physics.bio-ph q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The geometric control of bone tissue growth plays a significant role in bone
remodelling, age-related bone loss, and tissue engineering. However, how
exactly geometry influences the behaviour of bone-forming cells remains
elusive. Geometry modulates cell populations collectively through the evolving
space available t... | [
{
"created": "Thu, 23 Nov 2017 01:15:35 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Apr 2018 14:40:53 GMT",
"version": "v2"
}
] | 2020-05-28 | [
[
"Alias",
"Mohd Almie",
""
],
[
"Buenzli",
"Pascal R",
""
]
] | The geometric control of bone tissue growth plays a significant role in bone remodelling, age-related bone loss, and tissue engineering. However, how exactly geometry influences the behaviour of bone-forming cells remains elusive. Geometry modulates cell populations collectively through the evolving space available to ... |
1503.07396 | Delfim F. M. Torres | Amira Rachah, Delfim F. M. Torres | Mathematical Modelling, Simulation, and Optimal Control of the 2014
Ebola Outbreak in West Africa | This is a preprint of a paper whose final and definite form is
Discrete Dynamics in Nature and Society (Print ISSN: 1026-0226; Online ISSN:
1607-887X) 2015, Article ID 842792, 9 pp. See
http://dx.doi.org/10.1155/2015/842792 Submitted 26-Dec-2014; revised
27-Feb-2015; accepted 28-Feb-2015 | Discrete Dyn. Nat. Soc. 2015 (2015), Art. ID 842792, 9 pp | 10.1155/2015/842792 | null | q-bio.PE math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Ebola virus is currently one of the most virulent pathogens for humans.
The latest major outbreak occurred in Guinea, Sierra Leonne and Liberia in
2014. With the aim of understanding the spread of infection in the affected
countries, it is crucial to modelize the virus and simulate it. In this paper,
we begin by ... | [
{
"created": "Fri, 13 Mar 2015 01:02:33 GMT",
"version": "v1"
}
] | 2015-03-26 | [
[
"Rachah",
"Amira",
""
],
[
"Torres",
"Delfim F. M.",
""
]
] | The Ebola virus is currently one of the most virulent pathogens for humans. The latest major outbreak occurred in Guinea, Sierra Leonne and Liberia in 2014. With the aim of understanding the spread of infection in the affected countries, it is crucial to modelize the virus and simulate it. In this paper, we begin by st... |
1612.08550 | Giovanni Bussi | Richard A. Cunha and Giovanni Bussi | Unravelling Mg$^{2+}$-RNA binding with atomistic molecular dynamics | null | RNA 2017, 23, 628-638 | 10.1261/rna.060079.116 | null | q-bio.BM physics.bio-ph physics.chem-ph physics.comp-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interaction with divalent cations is of paramount importance for RNA
structural stability and function. We here report a detailed molecular dynamics
study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex,
including both direct (inner sphere) and indirect (outer sphere) binding. In
order to tackle sampl... | [
{
"created": "Tue, 27 Dec 2016 09:28:58 GMT",
"version": "v1"
}
] | 2017-04-19 | [
[
"Cunha",
"Richard A.",
""
],
[
"Bussi",
"Giovanni",
""
]
] | Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both direct (inner sphere) and indirect (outer sphere) binding. In order to tackle samplin... |
1509.07918 | Daniele Ramazzotti | Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Rebeca
Sanz-Pamplona, Luca De Sano, Giancarlo Mauri, Victor Moreno, Marco
Antoniotti, Bud Mishra | Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer
Progression | null | null | 10.1073/pnas.1520213113 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The genomic evolution inherent to cancer relates directly to a renewed focus
on the voluminous next generation sequencing (NGS) data, and machine learning
for the inference of explanatory models of how the (epi)genomic events are
choreographed in cancer initiation and development. However, despite the
increasing avai... | [
{
"created": "Fri, 25 Sep 2015 23:01:37 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Oct 2015 15:13:30 GMT",
"version": "v2"
},
{
"created": "Thu, 19 May 2016 17:49:26 GMT",
"version": "v3"
},
{
"created": "Wed, 8 Mar 2017 21:08:33 GMT",
"version": "v4"
}
] | 2017-03-10 | [
[
"Caravagna",
"Giulio",
""
],
[
"Graudenzi",
"Alex",
""
],
[
"Ramazzotti",
"Daniele",
""
],
[
"Sanz-Pamplona",
"Rebeca",
""
],
[
"De Sano",
"Luca",
""
],
[
"Mauri",
"Giancarlo",
""
],
[
"Moreno",
"Victor",
"... | The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next generation sequencing (NGS) data, and machine learning for the inference of explanatory models of how the (epi)genomic events are choreographed in cancer initiation and development. However, despite the increasing availa... |
1805.01349 | Mansoor Sheikh | A Santaolalla, M Sheikh, M Van Hemelrijck, A Portieri, ACC Coolen | Improved resection margins in breast-conserving surgery using Terahertz
Pulsed imaging data | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | New statistical methods were employed to improve the ability to distinguish
benign from malignant breast tissue ex vivo in a recent study. The ultimately
aim was to improve the intraoperative assessment of positive tumour margins in
breast-conserving surgery (BCS), potentially reducing patient re-operation
rates. A m... | [
{
"created": "Thu, 3 May 2018 15:02:40 GMT",
"version": "v1"
}
] | 2018-05-04 | [
[
"Santaolalla",
"A",
""
],
[
"Sheikh",
"M",
""
],
[
"Van Hemelrijck",
"M",
""
],
[
"Portieri",
"A",
""
],
[
"Coolen",
"ACC",
""
]
] | New statistical methods were employed to improve the ability to distinguish benign from malignant breast tissue ex vivo in a recent study. The ultimately aim was to improve the intraoperative assessment of positive tumour margins in breast-conserving surgery (BCS), potentially reducing patient re-operation rates. A mul... |
1404.7842 | Howard Deutsch | Howard M. Deutsch, Xiaocong Michael Ye and Margaret M. Schweri | Synthesis and Pharmacology of Ester Modified (+/-)-threo-Methylphenidate
Analogs | 15 pages, 1 figure | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As part of a program to develop compounds with potential to treat cocaine
abuse, eleven (+/-)-threo-methylphenidate (TMP; Ritalin) derivatives were
synthesized and tested in rat striatal tissue preparations for inhibitory
potency against [3H]WIN 35,428 binding (WIN) to the dopamine (DA) transporter,
[3H]citalopram bi... | [
{
"created": "Wed, 30 Apr 2014 19:24:18 GMT",
"version": "v1"
}
] | 2014-05-01 | [
[
"Deutsch",
"Howard M.",
""
],
[
"Ye",
"Xiaocong Michael",
""
],
[
"Schweri",
"Margaret M.",
""
]
] | As part of a program to develop compounds with potential to treat cocaine abuse, eleven (+/-)-threo-methylphenidate (TMP; Ritalin) derivatives were synthesized and tested in rat striatal tissue preparations for inhibitory potency against [3H]WIN 35,428 binding (WIN) to the dopamine (DA) transporter, [3H]citalopram bind... |
0801.2982 | John Rhodes | Elizabeth S. Allman, John A. Rhodes | The Identifiability of Covarion Models in Phylogenetics | 12 pages, 2 figures; Final version | null | null | null | q-bio.PE | null | Covarion models of character evolution describe inhomogeneities in
substitution processes through time. In phylogenetics, such models are used to
describe changing functional constraints or selection regimes during the
evolution of biological sequences. In this work the identifiability of such
models for generic para... | [
{
"created": "Fri, 18 Jan 2008 21:37:45 GMT",
"version": "v1"
},
{
"created": "Mon, 26 May 2008 22:43:41 GMT",
"version": "v2"
}
] | 2008-05-27 | [
[
"Allman",
"Elizabeth S.",
""
],
[
"Rhodes",
"John A.",
""
]
] | Covarion models of character evolution describe inhomogeneities in substitution processes through time. In phylogenetics, such models are used to describe changing functional constraints or selection regimes during the evolution of biological sequences. In this work the identifiability of such models for generic parame... |
1707.03922 | Peter Clote | Peter Clote and Amir H. Bayegan | RNA folding kinetics using Monte Carlo and Gillespie algorithms? | 30 pages, 10 figures, with appendix | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA secondary structure folding kinetics is known to be important for the
biological function of certain processes, such as the hok/sok system in E.
coli. Although linear algebra provides an exact computational solution of
secondary structure folding kinetics with respect to the Turner energy model
for tiny (~ 20 nt)... | [
{
"created": "Wed, 12 Jul 2017 22:08:16 GMT",
"version": "v1"
}
] | 2017-07-14 | [
[
"Clote",
"Peter",
""
],
[
"Bayegan",
"Amir H.",
""
]
] | RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary structure folding kinetics with respect to the Turner energy model for tiny (~ 20 nt) R... |
1805.02124 | Hiroshi Isshiki | Hiroshi Isshiki | Genetic Drift and Mutation | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In genetic drift of small population, it is well known that even when the
ratio of alleles is 0.5, specific genes are fixed in or disappear from the
population. It seems the reason why inbreeding is avoided. On the other hand,
this phenomenon suggests an interesting possibility. The mutant gene does not
increase the ... | [
{
"created": "Sat, 5 May 2018 23:21:49 GMT",
"version": "v1"
}
] | 2018-05-08 | [
[
"Isshiki",
"Hiroshi",
""
]
] | In genetic drift of small population, it is well known that even when the ratio of alleles is 0.5, specific genes are fixed in or disappear from the population. It seems the reason why inbreeding is avoided. On the other hand, this phenomenon suggests an interesting possibility. The mutant gene does not increase the nu... |
2111.06115 | Katharina Huber | Katharina T. Huber and Vincent Moulton and Megan Owen and Andreas
Spillner and Katherine St. John | The space of equidistant phylogenetic cactuses | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We introduce and investigate the space of \emph{equidistant}
$X$-\emph{cactuses}. These are rooted, arc weighted, phylogenetic networks with
leaf set $X$, where $X$ is a finite set of species, and all leaves have the
same distance from the root. The space contains as a subset the space of
ultrametric trees on $X$ tha... | [
{
"created": "Thu, 11 Nov 2021 09:27:12 GMT",
"version": "v1"
}
] | 2021-11-12 | [
[
"Huber",
"Katharina T.",
""
],
[
"Moulton",
"Vincent",
""
],
[
"Owen",
"Megan",
""
],
[
"Spillner",
"Andreas",
""
],
[
"John",
"Katherine St.",
""
]
] | We introduce and investigate the space of \emph{equidistant} $X$-\emph{cactuses}. These are rooted, arc weighted, phylogenetic networks with leaf set $X$, where $X$ is a finite set of species, and all leaves have the same distance from the root. The space contains as a subset the space of ultrametric trees on $X$ that ... |
q-bio/0412032 | Marek Cieplak | Marek Cieplak | Mechanical Stretching of Proteins: Calmodulin and Titin | To be published in a special bio-issue of Physica A; 14 figures | null | 10.1016/j.physa.2004.12.032 | null | q-bio.BM cond-mat.stat-mech | null | Mechanical unfolding of several domains of calmodulin and titin is studied
using a Go-like model with a realistic contact map and Lennard-Jones contact
interactions. It is shown that this simple model captures the experimentally
observed difference between the two proteins: titin is a spring that is tough
and strong ... | [
{
"created": "Thu, 16 Dec 2004 16:32:37 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Cieplak",
"Marek",
""
]
] | Mechanical unfolding of several domains of calmodulin and titin is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. It is shown that this simple model captures the experimentally observed difference between the two proteins: titin is a spring that is tough and strong wh... |
2203.06665 | Moo K. Chung | Moo K. Chung, Jamie L. Hanson, Seth D. Pollak | Statistical Analysis on Brain Surfaces | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In this paper, we review widely used statistical analysis frameworks for data
defined along cortical and subcortical surfaces that have been developed in
last two decades. The cerebral cortex has the topology of a 2D highly
convoluted sheet. For data obtained along curved non-Euclidean surfaces,
traditional statistic... | [
{
"created": "Sun, 13 Mar 2022 14:35:21 GMT",
"version": "v1"
}
] | 2022-03-15 | [
[
"Chung",
"Moo K.",
""
],
[
"Hanson",
"Jamie L.",
""
],
[
"Pollak",
"Seth D.",
""
]
] | In this paper, we review widely used statistical analysis frameworks for data defined along cortical and subcortical surfaces that have been developed in last two decades. The cerebral cortex has the topology of a 2D highly convoluted sheet. For data obtained along curved non-Euclidean surfaces, traditional statistical... |
2009.01060 | Andrew Eckford | Hadeel Elayan, Andrew W. Eckford, and Raviraj Adve | Information Rates of Controlled Protein Interactions Using Terahertz
Communication | Accepted for publication in IEEE Transactions on Nanobioscience | null | null | null | q-bio.MN cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we present a paradigm bridging electromagnetic (EM) and
molecular communication through a stimuli-responsive intra-body model. It has
been established that protein molecules, which play a key role in governing
cell behavior, can be selectively stimulated using Terahertz (THz) band
frequencies. By trigge... | [
{
"created": "Wed, 2 Sep 2020 13:34:10 GMT",
"version": "v1"
}
] | 2020-09-03 | [
[
"Elayan",
"Hadeel",
""
],
[
"Eckford",
"Andrew W.",
""
],
[
"Adve",
"Raviraj",
""
]
] | In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior, can be selectively stimulated using Terahertz (THz) band frequencies. By triggeri... |
1304.2468 | Takumi Tsutaya | Takumi Tsutaya and Minoru Yoneda | WARN: an R package for quantitative reconstruction of weaning ages in
archaeological populations using bone collagen nitrogen isotope ratios | 18 pages, 1 table, and 3 figures | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nitrogen isotope analysis of bone collagen has been used to reconstruct the
breastfeeding practices of archaeological human populations. However, weaning
ages have been estimated subjectively because of a lack of both information on
subadult bone collagen turnover rates and appropriate analytical models. Here,
we pre... | [
{
"created": "Tue, 9 Apr 2013 06:44:37 GMT",
"version": "v1"
}
] | 2013-04-10 | [
[
"Tsutaya",
"Takumi",
""
],
[
"Yoneda",
"Minoru",
""
]
] | Nitrogen isotope analysis of bone collagen has been used to reconstruct the breastfeeding practices of archaeological human populations. However, weaning ages have been estimated subjectively because of a lack of both information on subadult bone collagen turnover rates and appropriate analytical models. Here, we prese... |
1505.06956 | Nadav M. Shnerb | Matan Danino and Nadav M. Shnerb | Age-abundance relationships for neutral communities | null | null | 10.1103/PhysRevE.92.042706 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neutral models for the dynamics of a system of competing species are used,
nowadays, to describe a wide variety of empirical communities. These models are
used in many situations, ranging from population genetics and ecological
biodiversity to macroevolution and cancer tumors. One of the main issues
discussed within ... | [
{
"created": "Tue, 26 May 2015 14:00:16 GMT",
"version": "v1"
}
] | 2015-10-28 | [
[
"Danino",
"Matan",
""
],
[
"Shnerb",
"Nadav M.",
""
]
] | Neutral models for the dynamics of a system of competing species are used, nowadays, to describe a wide variety of empirical communities. These models are used in many situations, ranging from population genetics and ecological biodiversity to macroevolution and cancer tumors. One of the main issues discussed within th... |
1606.00897 | Stefan Bauer | Stefan Bauer and Nicolas Carion and Peter Sch\"uffler and Thomas Fuchs
and Peter Wild and Joachim M. Buhmann | Multi-Organ Cancer Classification and Survival Analysis | null | null | null | null | q-bio.QM cs.LG q-bio.TO stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate and robust cell nuclei classification is the cornerstone for a wider
range of tasks in digital and Computational Pathology. However, most machine
learning systems require extensive labeling from expert pathologists for each
individual problem at hand, with no or limited abilities for knowledge transfer
betwe... | [
{
"created": "Thu, 2 Jun 2016 21:09:00 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Dec 2016 20:06:14 GMT",
"version": "v2"
}
] | 2016-12-05 | [
[
"Bauer",
"Stefan",
""
],
[
"Carion",
"Nicolas",
""
],
[
"Schüffler",
"Peter",
""
],
[
"Fuchs",
"Thomas",
""
],
[
"Wild",
"Peter",
""
],
[
"Buhmann",
"Joachim M.",
""
]
] | Accurate and robust cell nuclei classification is the cornerstone for a wider range of tasks in digital and Computational Pathology. However, most machine learning systems require extensive labeling from expert pathologists for each individual problem at hand, with no or limited abilities for knowledge transfer between... |
1011.4134 | John Rhodes | John A. Rhodes and Seth Sullivant | Identifiability of Large Phylogenetic Mixture Models | 15 pages | null | null | null | q-bio.PE math.AG math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic mixture models are statistical models of character evolution
allowing for heterogeneity. Each of the classes in some unknown partition of
the characters may evolve by different processes, or even along different
trees. The fundamental question of whether parameters of such a model are
identifiable is dif... | [
{
"created": "Thu, 18 Nov 2010 04:47:20 GMT",
"version": "v1"
}
] | 2010-11-19 | [
[
"Rhodes",
"John A.",
""
],
[
"Sullivant",
"Seth",
""
]
] | Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The fundamental question of whether parameters of such a model are identifiable is diffi... |
2107.05386 | Herbert Sauro Dr | Herbert M. Sauro | The Practice of Ensuring Repeatable and Reproducible Computational
Models | # figures | null | null | null | q-bio.OT q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent studies have shown that the majority of published computational models
in systems biology and physiology are not repeatable or reproducible. There are
a variety of reasons for this. One of the most likely reasons is that given how
busy modern researchers are and the fact that no credit is given to authors for
... | [
{
"created": "Wed, 7 Jul 2021 19:59:04 GMT",
"version": "v1"
}
] | 2021-07-13 | [
[
"Sauro",
"Herbert M.",
""
]
] | Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how busy modern researchers are and the fact that no credit is given to authors for pu... |
1905.01540 | Justin Yeakel | Uttam Bhat and Christopher P. Kempes and Justin D. Yeakel | Scaling of the risk landscape drives optimal life history strategies and
the evolution of grazing | 9 pages, 5 figures, 3 Supplementary Appendices, 2 Supplementary
Figures | null | 10.1073/pnas.1907998117 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Consumers face numerous risks that can be minimized by incorporating
different life-history strategies. How much and when a consumer adds to its
energetic reserves or invests in reproduction are key behavioral and
physiological adaptations that structure much of how organisms interact. Here
we develop a theoretical f... | [
{
"created": "Sat, 4 May 2019 18:53:29 GMT",
"version": "v1"
}
] | 2022-10-12 | [
[
"Bhat",
"Uttam",
""
],
[
"Kempes",
"Christopher P.",
""
],
[
"Yeakel",
"Justin D.",
""
]
] | Consumers face numerous risks that can be minimized by incorporating different life-history strategies. How much and when a consumer adds to its energetic reserves or invests in reproduction are key behavioral and physiological adaptations that structure much of how organisms interact. Here we develop a theoretical fra... |
2212.00741 | Benjamin Hayden | Nisarg Desai, Praneet Bala, Rebecca Richardson, Jessica Raper, Jan
Zimmermann, Benjamin Hayden | OpenApePose: a database of annotated ape photographs for pose estimation | null | null | null | null | q-bio.QM cs.CV | http://creativecommons.org/licenses/by/4.0/ | Because of their close relationship with humans, non-human apes (chimpanzees,
bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great
scientific interest. The goal of understanding their complex behavior would be
greatly advanced by the ability to perform video-based pose tracking. Tracking,
howe... | [
{
"created": "Wed, 30 Nov 2022 16:53:18 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Sep 2023 14:53:04 GMT",
"version": "v2"
}
] | 2023-09-25 | [
[
"Desai",
"Nisarg",
""
],
[
"Bala",
"Praneet",
""
],
[
"Richardson",
"Rebecca",
""
],
[
"Raper",
"Jessica",
""
],
[
"Zimmermann",
"Jan",
""
],
[
"Hayden",
"Benjamin",
""
]
] | Because of their close relationship with humans, non-human apes (chimpanzees, bonobos, gorillas, orangutans, and gibbons, including siamangs) are of great scientific interest. The goal of understanding their complex behavior would be greatly advanced by the ability to perform video-based pose tracking. Tracking, howeve... |
2201.01855 | Xu Wang | XU Wang and Huan Zhao and Weiwei TU and Hao Li and Yu Sun and Xiaochen
Bo | Graph Neural Networks for Double-Strand DNA Breaks Prediction | null | null | null | null | q-bio.QM cs.AI cs.LG | http://creativecommons.org/licenses/by/4.0/ | Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause
abnormal chromosomal rearrangements. Recent technologies based on
high-throughput experiments have obvious high costs and technical
challenges.Therefore, we design a graph neural network based method to predict
DSBs (GraphDSB), using DNA sequence... | [
{
"created": "Tue, 4 Jan 2022 08:40:08 GMT",
"version": "v1"
}
] | 2022-01-07 | [
[
"Wang",
"XU",
""
],
[
"Zhao",
"Huan",
""
],
[
"TU",
"Weiwei",
""
],
[
"Li",
"Hao",
""
],
[
"Sun",
"Yu",
""
],
[
"Bo",
"Xiaochen",
""
]
] | Double-strand DNA breaks (DSBs) are a form of DNA damage that can cause abnormal chromosomal rearrangements. Recent technologies based on high-throughput experiments have obvious high costs and technical challenges.Therefore, we design a graph neural network based method to predict DSBs (GraphDSB), using DNA sequence f... |
1204.3683 | Balaji Sriram | Balaji Sriram and Pamela Reinagel | Strong surround antagonism in the dLGN of the awake rat | 29 pages, 6 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Classical center-surround antagonism in the early visual system is thought to
serve important functions such as enhancing edge detection and increasing
sparseness. The relative strength of the center and surround determine the
specific computation achieved. For example, weak surrounds achieve low-pass
spatial frequen... | [
{
"created": "Tue, 17 Apr 2012 01:46:27 GMT",
"version": "v1"
}
] | 2012-04-18 | [
[
"Sriram",
"Balaji",
""
],
[
"Reinagel",
"Pamela",
""
]
] | Classical center-surround antagonism in the early visual system is thought to serve important functions such as enhancing edge detection and increasing sparseness. The relative strength of the center and surround determine the specific computation achieved. For example, weak surrounds achieve low-pass spatial frequency... |
2207.03523 | Mikail Khona | Mikail Khona, Sarthak Chandra, Joy J. Ma, Ila Fiete | Winning the lottery with neural connectivity constraints: faster
learning across cognitive tasks with spatially constrained sparse RNNs | 12 pages, 5 main text figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Recurrent neural networks (RNNs) are often used to model circuits in the
brain, and can solve a variety of difficult computational problems requiring
memory, error-correction, or selection [Hopfield, 1982, Maass et al., 2002,
Maass, 2011]. However, fully-connected RNNs contrast structurally with their
biological coun... | [
{
"created": "Thu, 7 Jul 2022 18:37:29 GMT",
"version": "v1"
},
{
"created": "Mon, 29 May 2023 19:49:38 GMT",
"version": "v2"
}
] | 2023-05-31 | [
[
"Khona",
"Mikail",
""
],
[
"Chandra",
"Sarthak",
""
],
[
"Ma",
"Joy J.",
""
],
[
"Fiete",
"Ila",
""
]
] | Recurrent neural networks (RNNs) are often used to model circuits in the brain, and can solve a variety of difficult computational problems requiring memory, error-correction, or selection [Hopfield, 1982, Maass et al., 2002, Maass, 2011]. However, fully-connected RNNs contrast structurally with their biological counte... |
2306.16819 | Kai Yi | Kai Yi, Bingxin Zhou, Yiqing Shen, Pietro Li\`o, Yu Guang Wang | Graph Denoising Diffusion for Inverse Protein Folding | NeurIPS 2023 | null | null | null | q-bio.QM cs.AI | http://creativecommons.org/licenses/by/4.0/ | Inverse protein folding is challenging due to its inherent one-to-many
mapping characteristic, where numerous possible amino acid sequences can fold
into a single, identical protein backbone. This task involves not only
identifying viable sequences but also representing the sheer diversity of
potential solutions. How... | [
{
"created": "Thu, 29 Jun 2023 09:55:30 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Nov 2023 08:28:11 GMT",
"version": "v2"
}
] | 2023-11-08 | [
[
"Yi",
"Kai",
""
],
[
"Zhou",
"Bingxin",
""
],
[
"Shen",
"Yiqing",
""
],
[
"Liò",
"Pietro",
""
],
[
"Wang",
"Yu Guang",
""
]
] | Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable sequences but also representing the sheer diversity of potential solutions. Howev... |
1603.03238 | Pierre Casadebaig | Victor Picheny and Pierre Casadebaig and Ronan Tr\'epos and Robert
Faivre and David Da Silva and Patrick Vincourt and Evelyne Costes | Using numerical plant models and phenotypic correlation space to design
achievable ideotypes | 25 pages, 5 figures, 2017, Plant, Cell and Environment | null | 10.1111/pce.13001 | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Numerical plant models can predict the outcome of plant traits modifications
resulting from genetic variations, on plant performance, by simulating
physiological processes and their interaction with the environment.
Optimization methods complement those models to design ideotypes, i.e. ideal
values of a set of plant ... | [
{
"created": "Thu, 10 Mar 2016 12:43:04 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Sep 2016 12:33:11 GMT",
"version": "v2"
},
{
"created": "Mon, 19 Jun 2017 07:42:58 GMT",
"version": "v3"
}
] | 2017-06-20 | [
[
"Picheny",
"Victor",
""
],
[
"Casadebaig",
"Pierre",
""
],
[
"Trépos",
"Ronan",
""
],
[
"Faivre",
"Robert",
""
],
[
"Da Silva",
"David",
""
],
[
"Vincourt",
"Patrick",
""
],
[
"Costes",
"Evelyne",
""
]
] | Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant tr... |
2206.11233 | Navid Ghassemi | Parisa Moridian, Navid Ghassemi, Mahboobeh Jafari, Salam
Salloum-Asfar, Delaram Sadeghi, Marjane Khodatars, Afshin Shoeibi, Abbas
Khosravi, Sai Ho Ling, Abdulhamit Subasi, Roohallah Alizadehsani, Juan M.
Gorriz, Sara A Abdulla, U. Rajendra Acharya | Automatic autism spectrum disorder detection using artificial
intelligence methods with MRI neuroimaging: A review | null | Moridian, et. al., Automatic autism spectrum disorder detection
using artificial intelligence methods with MRI neuroimaging: A review,
Frontiers in Molecular Neuroscience, Volume 15, 2022 | 10.3389/fnmol.2022.999605 | null | q-bio.NC cs.LG eess.IV | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Autism spectrum disorder (ASD) is a brain condition characterized by diverse
signs and symptoms that appear in early childhood. ASD is also associated with
communication deficits and repetitive behavior in affected individuals. Various
ASD detection methods have been developed, including neuroimaging modalities
and p... | [
{
"created": "Mon, 20 Jun 2022 16:14:21 GMT",
"version": "v1"
},
{
"created": "Sun, 17 Jul 2022 09:39:33 GMT",
"version": "v2"
},
{
"created": "Thu, 6 Oct 2022 15:58:56 GMT",
"version": "v3"
}
] | 2022-10-07 | [
[
"Moridian",
"Parisa",
""
],
[
"Ghassemi",
"Navid",
""
],
[
"Jafari",
"Mahboobeh",
""
],
[
"Salloum-Asfar",
"Salam",
""
],
[
"Sadeghi",
"Delaram",
""
],
[
"Khodatars",
"Marjane",
""
],
[
"Shoeibi",
"Afshin",
... | Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psy... |
2106.02785 | Kenji Doya | Kenji Doya | Canonical Cortical Circuits and the Duality of Bayesian Inference and
Optimal Control | 13 pages, 3 figure | Current Opinion in Behavioral Sciences, 41, 160-166 (2021) | 10.1016/j.cobeha.2021.07.003 | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | The duality of sensory inference and motor control has been known since the
1960s and has recently been recognized as the commonality in computations
required for the posterior distributions in Bayesian inference and the value
functions in optimal control. Meanwhile, an intriguing question about the brain
is why the ... | [
{
"created": "Sat, 5 Jun 2021 03:23:13 GMT",
"version": "v1"
},
{
"created": "Sat, 3 Jul 2021 22:13:31 GMT",
"version": "v2"
}
] | 2021-10-12 | [
[
"Doya",
"Kenji",
""
]
] | The duality of sensory inference and motor control has been known since the 1960s and has recently been recognized as the commonality in computations required for the posterior distributions in Bayesian inference and the value functions in optimal control. Meanwhile, an intriguing question about the brain is why the en... |
1810.04726 | Sergei Maslov | Veronika Dubinkina, Yulia Fridman, Parth Pandey, and Sergei Maslov | Alternative stable states in a model of microbial community limited by
multiple essential nutrients | null | null | null | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Microbial communities routinely have several alternative stable states
observed for the same environmental parameters. Sudden and irreversible
transitions between these states make external manipulation of these systems
more complicated. To better understand the mechanisms and origins of
multistability in microbial c... | [
{
"created": "Wed, 10 Oct 2018 19:44:47 GMT",
"version": "v1"
}
] | 2018-10-12 | [
[
"Dubinkina",
"Veronika",
""
],
[
"Fridman",
"Yulia",
""
],
[
"Pandey",
"Parth",
""
],
[
"Maslov",
"Sergei",
""
]
] | Microbial communities routinely have several alternative stable states observed for the same environmental parameters. Sudden and irreversible transitions between these states make external manipulation of these systems more complicated. To better understand the mechanisms and origins of multistability in microbial com... |
0803.0635 | Luca Sbano | Markus Kirkilionis and Luca Sbano | An Averaging Principle for Combined Interaction Graphs. Part I:
Connectivity and Applications to Genetic Switches | To appear in Advances in Complex Systems | null | null | null | q-bio.MN math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Time-continuous dynamical systems defined on graphs are often used to model
complex systems with many interacting components in a non-spatial context. In
the reverse sense attaching meaningful dynamics to given 'interaction diagrams'
is a central bottleneck problem in many application areas, especially in cell
biolog... | [
{
"created": "Wed, 5 Mar 2008 11:14:55 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Mar 2008 13:57:55 GMT",
"version": "v2"
},
{
"created": "Thu, 1 Jul 2010 10:04:29 GMT",
"version": "v3"
}
] | 2010-07-02 | [
[
"Kirkilionis",
"Markus",
""
],
[
"Sbano",
"Luca",
""
]
] | Time-continuous dynamical systems defined on graphs are often used to model complex systems with many interacting components in a non-spatial context. In the reverse sense attaching meaningful dynamics to given 'interaction diagrams' is a central bottleneck problem in many application areas, especially in cell biology ... |
2303.15552 | Christine Heitsch | Forrest Hurley and Christine Heitsch | RNAprofiling 2.0: Enhanced cluster analysis of structural ensembles | 9 pages, 2 figures; supplement 6 pages, 3 figures, 1 table | null | 10.1016/j.jmb.2023.168047 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Understanding the base pairing of an RNA sequence provides insight into its
molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0
identifies the dominant helices in low-energy secondary structures as features,
organizes them into profiles which partition the Boltzmann sample, and
highlights key sim... | [
{
"created": "Mon, 27 Mar 2023 19:10:37 GMT",
"version": "v1"
}
] | 2023-03-29 | [
[
"Hurley",
"Forrest",
""
],
[
"Heitsch",
"Christine",
""
]
] | Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes them into profiles which partition the Boltzmann sample, and highlights key simil... |
1406.3828 | Conor Smyth | Conor Smyth, Iva \v{S}pakulova, Owen Cotton-Barratt, Sajjad Rafiq,
William Tapper, Rosanna Upstill-Goddard, John L. Hopper, Enes Makalic, Daniel
F. Schmidt, Miroslav Kapuscinski, J\"org Fliege, Andrew Collins, Jacek
Brodzki, Diana M. Eccles, Ben D. MacArthur | Genome disorder and breast cancer susceptibility | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many common diseases have a complex genetic basis in which large numbers of
genetic variations combine with environmental and lifestyle factors to
determine risk. However, quantifying such polygenic effects and their
relationship to disease risk has been challenging. In order to address these
difficulties we develope... | [
{
"created": "Sun, 15 Jun 2014 15:47:35 GMT",
"version": "v1"
}
] | 2014-06-17 | [
[
"Smyth",
"Conor",
""
],
[
"Špakulova",
"Iva",
""
],
[
"Cotton-Barratt",
"Owen",
""
],
[
"Rafiq",
"Sajjad",
""
],
[
"Tapper",
"William",
""
],
[
"Upstill-Goddard",
"Rosanna",
""
],
[
"Hopper",
"John L.",
""
... | Many common diseases have a complex genetic basis in which large numbers of genetic variations combine with environmental and lifestyle factors to determine risk. However, quantifying such polygenic effects and their relationship to disease risk has been challenging. In order to address these difficulties we developed ... |
2211.01313 | Michael Levin | Joel Grodstein, Michael Levin | Closing the Loop on Morphogenesis: A Mathematical Model of Morphogenesis
by Closed-Loop Reaction-Diffusion | 20 pages, 3 tables, 5 figures | null | null | null | q-bio.MN q-bio.CB q-bio.QM q-bio.SC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Morphogenesis, the establishment and repair of emergent complex anatomy by
groups of cells, is a fascinating and biomedically-relevant problem. One of its
most fascinating aspects is that a developing embryo can reliably recover from
disturbances, such as splitting into twins. While this reliability implies some
type... | [
{
"created": "Wed, 2 Nov 2022 17:35:53 GMT",
"version": "v1"
}
] | 2022-11-03 | [
[
"Grodstein",
"Joel",
""
],
[
"Levin",
"Michael",
""
]
] | Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from disturbances, such as splitting into twins. While this reliability implies some type o... |
1805.09774 | Dorian Florescu Dr | Dorian Florescu, Daniel Coca | Learning with precise spike times: A new decoding algorithm for liquid
state machines | 34 pages, 7 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is extensive evidence that biological neural networks encode
information in the precise timing of the spikes generated and transmitted by
neurons, which offers several advantages over rate-based codes. Here we adopt a
vector space formulation of spike train sequences and introduce a new liquid
state machine (LS... | [
{
"created": "Thu, 24 May 2018 16:52:59 GMT",
"version": "v1"
},
{
"created": "Sat, 13 Jul 2019 22:50:09 GMT",
"version": "v2"
}
] | 2019-07-16 | [
[
"Florescu",
"Dorian",
""
],
[
"Coca",
"Daniel",
""
]
] | There is extensive evidence that biological neural networks encode information in the precise timing of the spikes generated and transmitted by neurons, which offers several advantages over rate-based codes. Here we adopt a vector space formulation of spike train sequences and introduce a new liquid state machine (LSM)... |
2108.04820 | Thi Ngan Dong | Thi Ngan Dong and Megha Khosla | MuCoMiD: A Multitask Convolutional Learning Framework for miRNA-Disease
Association Prediction | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Growing evidence from recent studies implies that microRNA or miRNA could
serve as biomarkers in various complex human diseases. Since wet-lab
experiments are expensive and time-consuming, computational techniques for
miRNA-disease association prediction have attracted a lot of attention in
recent years. Data scarcit... | [
{
"created": "Sun, 8 Aug 2021 10:01:46 GMT",
"version": "v1"
},
{
"created": "Sun, 21 Nov 2021 13:57:22 GMT",
"version": "v2"
},
{
"created": "Mon, 29 Nov 2021 09:37:28 GMT",
"version": "v3"
}
] | 2021-11-30 | [
[
"Dong",
"Thi Ngan",
""
],
[
"Khosla",
"Megha",
""
]
] | Growing evidence from recent studies implies that microRNA or miRNA could serve as biomarkers in various complex human diseases. Since wet-lab experiments are expensive and time-consuming, computational techniques for miRNA-disease association prediction have attracted a lot of attention in recent years. Data scarcity ... |
1401.3587 | Mahashweta Basu | Mahashweta Basu | Communities of dense weighted networks: MicroRNA co-target network as an
example | 14 pages, 6 eps figures | null | null | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complex networks are intrinsically modular. Resolving small modules is
particularly difficult when the network is densely connected; wide variation of
link weights invites additional complexities. In this article we present an
algorithm to detect community structure in densely connected weighted networks.
First, modu... | [
{
"created": "Wed, 15 Jan 2014 13:52:47 GMT",
"version": "v1"
}
] | 2014-01-16 | [
[
"Basu",
"Mahashweta",
""
]
] | Complex networks are intrinsically modular. Resolving small modules is particularly difficult when the network is densely connected; wide variation of link weights invites additional complexities. In this article we present an algorithm to detect community structure in densely connected weighted networks. First, modula... |
2302.05338 | Cameron Smith | Ximo Pechuan-Jorge, Raymond S. Puzio, Cameron Smith | Algebraic structure of hierarchic first-order reaction networks
applicable to models of clone size distribution and stochastic gene
expression | 9 pages | null | null | null | q-bio.MN math-ph math.MP math.PR q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In biology, stochastic branching processes with a two-stage, hierarchical
structure arise in the study of population dynamics, gene expression, and
phylogenetic inference. These models have been commonly analyzed using
generating functions, the method of characteristics and various perturbative
approximations. Here w... | [
{
"created": "Thu, 2 Feb 2023 21:19:12 GMT",
"version": "v1"
}
] | 2023-02-13 | [
[
"Pechuan-Jorge",
"Ximo",
""
],
[
"Puzio",
"Raymond S.",
""
],
[
"Smith",
"Cameron",
""
]
] | In biology, stochastic branching processes with a two-stage, hierarchical structure arise in the study of population dynamics, gene expression, and phylogenetic inference. These models have been commonly analyzed using generating functions, the method of characteristics and various perturbative approximations. Here we ... |
1409.1838 | Christopher Lester | Christopher Lester, Christian A. Yates, Michael B. Giles, Ruth E.
Baker | An adaptive multi-level simulation algorithm for stochastic biological
systems | 23 pages | J. Chem. Phys. 142, 024113 (2015) | 10.1063/1.4904980 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Discrete-state, continuous-time Markov models are widely used in the modeling
of biochemical reaction networks. Their complexity often precludes analytic
solution, and we rely on stochastic simulation algorithms to estimate system
statistics. The Gillespie algorithm is exact, but computationally costly as it
simulate... | [
{
"created": "Fri, 5 Sep 2014 15:31:17 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Dec 2014 15:18:47 GMT",
"version": "v2"
}
] | 2016-05-20 | [
[
"Lester",
"Christopher",
""
],
[
"Yates",
"Christian A.",
""
],
[
"Giles",
"Michael B.",
""
],
[
"Baker",
"Ruth E.",
""
]
] | Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates ... |
1403.6171 | Timothy Phan | Timothy S. Phan, John K-J. Li | Propagation of Uncertainty and Analysis of Signal-to-Noise in Nonlinear
Compliance Estimations of an Arterial System Model | Conference on Information Sciences and Systems (CISS) 2014 | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The arterial system dynamically loads the heart through changes in arterial
compliance. The pressure-volume relation of arteries is known to be nonlinear,
but arterial compliance is often modeled as a constant value, due to ease of
estimation and interpretation. Incorporating nonlinear arterial compliance
affords ins... | [
{
"created": "Mon, 24 Mar 2014 22:24:57 GMT",
"version": "v1"
}
] | 2014-03-26 | [
[
"Phan",
"Timothy S.",
""
],
[
"Li",
"John K-J.",
""
]
] | The arterial system dynamically loads the heart through changes in arterial compliance. The pressure-volume relation of arteries is known to be nonlinear, but arterial compliance is often modeled as a constant value, due to ease of estimation and interpretation. Incorporating nonlinear arterial compliance affords insig... |
1405.1611 | Karsten Kruse | L. Wettmann, M. Bonny, K. Kruse | Bistable protein distributions in rod-shaped bacteria | 13 pages, 6 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The distributions of many proteins in rod-shaped bacteria are far from
homogenous. Often they accumulate at the cell poles or in the cell center. At
the same time, the copy number of proteins in a single cell is relatively small
making the patterns noisy. To explore limits to protein patterns due to
molecular noise, ... | [
{
"created": "Wed, 7 May 2014 14:16:24 GMT",
"version": "v1"
}
] | 2014-05-08 | [
[
"Wettmann",
"L.",
""
],
[
"Bonny",
"M.",
""
],
[
"Kruse",
"K.",
""
]
] | The distributions of many proteins in rod-shaped bacteria are far from homogenous. Often they accumulate at the cell poles or in the cell center. At the same time, the copy number of proteins in a single cell is relatively small making the patterns noisy. To explore limits to protein patterns due to molecular noise, we... |
2206.14706 | Diego Ferreiro | Ignacio E. S\'anchez, Ezequiel A. Galpern, Mart\'in M. Garibaldi,
Diego U. Ferreiro | Molecular information theory meets protein folding | 33pages, 2 figures, plus supporting information | null | null | null | q-bio.BM cs.IT math.IT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We propose an application of molecular information theory to analyze the
folding of single domain proteins. We analyze results from various areas of
protein science, such as sequence-based potentials, reduced amino acid
alphabets, backbone configurational entropy, secondary structure content,
residue burial layers, a... | [
{
"created": "Wed, 29 Jun 2022 15:16:10 GMT",
"version": "v1"
}
] | 2022-06-30 | [
[
"Sánchez",
"Ignacio E.",
""
],
[
"Galpern",
"Ezequiel A.",
""
],
[
"Garibaldi",
"Martín M.",
""
],
[
"Ferreiro",
"Diego U.",
""
]
] | We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and... |
2004.06916 | Edilson Arruda | L. Tarrataca, C.M. Dias, D. B. Haddad, and E. F. Arruda | Flattening the curves: on-off lock-down strategies for COVID-19 with an
application to Brazi | null | null | 10.1186/s13362-020-00098-w | null | q-bio.PE cs.LG cs.SY eess.SY q-bio.QM stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The current COVID-19 pandemic is affecting different countries in different
ways. The assortment of reporting techniques alongside other issues, such as
underreporting and budgetary constraints, makes predicting the spread and
lethality of the virus a challenging task. This work attempts to gain a better
understandin... | [
{
"created": "Wed, 15 Apr 2020 07:37:08 GMT",
"version": "v1"
}
] | 2021-01-08 | [
[
"Tarrataca",
"L.",
""
],
[
"Dias",
"C. M.",
""
],
[
"Haddad",
"D. B.",
""
],
[
"Arruda",
"E. F.",
""
]
] | The current COVID-19 pandemic is affecting different countries in different ways. The assortment of reporting techniques alongside other issues, such as underreporting and budgetary constraints, makes predicting the spread and lethality of the virus a challenging task. This work attempts to gain a better understanding ... |
1806.08634 | Juan Eugenio Iglesias | Juan Eugenio Iglesias, Ricardo Insausti, Garikoitz Lerma-Usabiaga,
Martina Bocchetta, Koen Van Leemput, Douglas N Greve, Andre van der Kouwe,
Bruce Fischl, Cesar Caballero-Gaudes, Pedro M Paz-Alonso | A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI
and histology | null | null | null | null | q-bio.NC cs.CV physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human thalamus is a brain structure that comprises numerous, highly
specific nuclei. Since these nuclei are known to have different functions and
to be connected to different areas of the cerebral cortex, it is of great
interest for the neuroimaging community to study their volume, shape and
connectivity in vivo ... | [
{
"created": "Fri, 22 Jun 2018 12:42:37 GMT",
"version": "v1"
}
] | 2018-06-25 | [
[
"Iglesias",
"Juan Eugenio",
""
],
[
"Insausti",
"Ricardo",
""
],
[
"Lerma-Usabiaga",
"Garikoitz",
""
],
[
"Bocchetta",
"Martina",
""
],
[
"Van Leemput",
"Koen",
""
],
[
"Greve",
"Douglas N",
""
],
[
"van der Kouwe"... | The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo wi... |
1804.01203 | Min Xu | Yixiu Zhao, Xiangrui Zeng, Qiang Guo, Min Xu | An integration of fast alignment and maximum-likelihood methods for
electron subtomogram averaging and classification | 17 pages | Intelligent Systems for Molecular Biology (ISMB) 2018,
Bioinformatics | 10.1093/bioinformatics/bty267 | null | q-bio.QM cs.CV stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Cellular Electron CryoTomography (CECT) is an emerging 3D imaging
technique that visualizes subcellular organization of single cells at
submolecular resolution and in near-native state. CECT captures large numbers
of macromolecular complexes of highly diverse structures and abundances.
However, the struct... | [
{
"created": "Wed, 4 Apr 2018 01:16:20 GMT",
"version": "v1"
}
] | 2018-05-16 | [
[
"Zhao",
"Yixiu",
""
],
[
"Zeng",
"Xiangrui",
""
],
[
"Guo",
"Qiang",
""
],
[
"Xu",
"Min",
""
]
] | Motivation: Cellular Electron CryoTomography (CECT) is an emerging 3D imaging technique that visualizes subcellular organization of single cells at submolecular resolution and in near-native state. CECT captures large numbers of macromolecular complexes of highly diverse structures and abundances. However, the structur... |
1411.2136 | Alexander Mathis | Alexander Mathis and Martin B. Stemmler and Andreas V.M. Herz | Probable nature of higher-dimensional symmetries underlying mammalian
grid-cell activity patterns | 12 pages, 6 figures | null | 10.7554/eLife.05979 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lattices abound in nature - from the crystal structure of minerals to the
honey-comb organization of ommatidia in the compound eye of insects. Such
regular arrangements provide solutions for optimally dense packings, efficient
resource distribution and cryptographic schemes, highlighting the importance of
lattice the... | [
{
"created": "Sat, 8 Nov 2014 16:37:00 GMT",
"version": "v1"
}
] | 2015-05-12 | [
[
"Mathis",
"Alexander",
""
],
[
"Stemmler",
"Martin B.",
""
],
[
"Herz",
"Andreas V. M.",
""
]
] | Lattices abound in nature - from the crystal structure of minerals to the honey-comb organization of ommatidia in the compound eye of insects. Such regular arrangements provide solutions for optimally dense packings, efficient resource distribution and cryptographic schemes, highlighting the importance of lattice theor... |
0911.1066 | Mireille Regnier | Anatoly Ivashchenko, Galina Boldina, Aizhan Turmagambetova, Mireille
R\'egnier | Using profiles based on hydropathy properties to define essential
regions for splicing | null | International Journal of Biological Sciences (2009) 10 p | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We define new profiles based on hydropathy properties and point out specific
profiles for regions surrounding splice sites. We built a set T of flanking
regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes
contained 313 introns and 385 exons and were extracted from GenBank. They were
used in ... | [
{
"created": "Thu, 5 Nov 2009 16:04:23 GMT",
"version": "v1"
}
] | 2009-11-06 | [
[
"Ivashchenko",
"Anatoly",
""
],
[
"Boldina",
"Galina",
""
],
[
"Turmagambetova",
"Aizhan",
""
],
[
"Régnier",
"Mireille",
""
]
] | We define new profiles based on hydropathy properties and point out specific profiles for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes. These genes contained 313 introns and 385 exons and were extracted from GenBank. They were used in or... |
1911.08188 | Matteo De Rosa | Michela Bollati, Emanuele Scalone, Francesco Bon\`i, Eloise
Mastrangelo, Toni Giorgino, Mario Milani, Matteo de Rosa | High-resolution crystal structure of gelsolin domain 2 in complex with
the physiological calcium ion | null | Biochem Biophys Res Commun. 2019 Oct 8;518(1):94-99 | 10.1016/j.bbrc.2019.08.013 | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The second domain of gelsolin (G2) hosts mutations responsible for a
hereditary form of amyloidosis. The active form of gelsolin is Ca2+-bound; it
is also a dynamic protein, hence structural biologists often rely on the study
of the isolated G2. However, the wild type G2 structure that have been used so
far in compar... | [
{
"created": "Tue, 19 Nov 2019 10:08:27 GMT",
"version": "v1"
}
] | 2019-11-20 | [
[
"Bollati",
"Michela",
""
],
[
"Scalone",
"Emanuele",
""
],
[
"Bonì",
"Francesco",
""
],
[
"Mastrangelo",
"Eloise",
""
],
[
"Giorgino",
"Toni",
""
],
[
"Milani",
"Mario",
""
],
[
"de Rosa",
"Matteo",
""
]
... | The second domain of gelsolin (G2) hosts mutations responsible for a hereditary form of amyloidosis. The active form of gelsolin is Ca2+-bound; it is also a dynamic protein, hence structural biologists often rely on the study of the isolated G2. However, the wild type G2 structure that have been used so far in comparat... |
0810.4099 | Vahid Rezania | Vahid Rezania and Jack Tuszynski | A first principle (3+1) dimensional model for microtubule polymerization | 12 pages, 2 figures. Accepted in Physics Letters A | Physics Letters A 372 (2008) 7051--7056 | 10.1016/j.physleta.2008.10.038 | null | q-bio.QM cond-mat.stat-mech q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we propose a microscopic model to study the polymerization of
microtubules (MTs). Starting from fundamental reactions during MT's assembly
and disassembly processes, we systematically derive a nonlinear system of
equations that determines the dynamics of microtubules in 3D. %coexistence with
tubulin dim... | [
{
"created": "Wed, 22 Oct 2008 15:57:35 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Rezania",
"Vahid",
""
],
[
"Tuszynski",
"Jack",
""
]
] | In this paper we propose a microscopic model to study the polymerization of microtubules (MTs). Starting from fundamental reactions during MT's assembly and disassembly processes, we systematically derive a nonlinear system of equations that determines the dynamics of microtubules in 3D. %coexistence with tubulin dimer... |
1312.1673 | David McCandlish | David M. McCandlish, Charles L. Epstein, and Joshua B. Plotkin | Formal properties of the probability of fixation: identities,
inequalities and approximations | Minor edits; added appendix | Theoretical Population Biology, 99: 98-113 (2015) | 10.1016/j.tpb.2014.11.004 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The formula for the probability of fixation of a new mutation is widely used
in theoretical population genetics and molecular evolution. Here we derive a
series of identities, inequalities and approximations for the exact probability
of fixation of a new mutation under the Moran process (equivalent results hold
for t... | [
{
"created": "Thu, 5 Dec 2013 20:27:01 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Jan 2014 20:13:47 GMT",
"version": "v2"
},
{
"created": "Wed, 26 Feb 2014 19:48:58 GMT",
"version": "v3"
},
{
"created": "Thu, 10 Apr 2014 22:00:44 GMT",
"version": "v4"
}
] | 2015-03-10 | [
[
"McCandlish",
"David M.",
""
],
[
"Epstein",
"Charles L.",
""
],
[
"Plotkin",
"Joshua B.",
""
]
] | The formula for the probability of fixation of a new mutation is widely used in theoretical population genetics and molecular evolution. Here we derive a series of identities, inequalities and approximations for the exact probability of fixation of a new mutation under the Moran process (equivalent results hold for the... |
1412.2786 | Guowei Wei | Kristopher Opron and Kelin Xia and Guo-Wei Wei | Fast and Anisotropic Flexibility-Rigidity Index | 10 figures and 50 references | Journal of Chemical Physics, 140(23), 234105, (2014) | 10.1063/1.4882258 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The flexibility-rigidity index (FRI) is a newly proposed method for the
construction of atomic rigidity functions. The FRI method analyzes protein
rigidity and flexibility and is capable of predicting protein B-factors without
resorting to matrix diagonalization. A fundamental assumption used in the FRI
is that prote... | [
{
"created": "Mon, 8 Dec 2014 21:46:23 GMT",
"version": "v1"
}
] | 2014-12-10 | [
[
"Opron",
"Kristopher",
""
],
[
"Xia",
"Kelin",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | The flexibility-rigidity index (FRI) is a newly proposed method for the construction of atomic rigidity functions. The FRI method analyzes protein rigidity and flexibility and is capable of predicting protein B-factors without resorting to matrix diagonalization. A fundamental assumption used in the FRI is that protein... |
1609.07068 | Yujiang Wang | Yujiang Wang, Andrew J Trevelyan, Antonio Valentin, Gonzalo Alarcon,
Peter N Taylor, Marcus Kaiser | Mechanisms underlying different onset patterns of focal seizures | null | PLOS Computational Biology 2017 13(5): e1005475 | 10.1371/journal.pcbi.1005475 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Focal seizures are episodes of pathological brain activity that appear to
arise from a localised area of the brain. The onset patterns of focal seizure
activity have been studied intensively, and they have largely been
distinguished into two types - low amplitude fast oscillations (LAF), or high
amplitude spikes (HAS... | [
{
"created": "Thu, 22 Sep 2016 17:03:08 GMT",
"version": "v1"
},
{
"created": "Fri, 5 May 2017 13:20:15 GMT",
"version": "v2"
}
] | 2017-05-08 | [
[
"Wang",
"Yujiang",
""
],
[
"Trevelyan",
"Andrew J",
""
],
[
"Valentin",
"Antonio",
""
],
[
"Alarcon",
"Gonzalo",
""
],
[
"Taylor",
"Peter N",
""
],
[
"Kaiser",
"Marcus",
""
]
] | Focal seizures are episodes of pathological brain activity that appear to arise from a localised area of the brain. The onset patterns of focal seizure activity have been studied intensively, and they have largely been distinguished into two types - low amplitude fast oscillations (LAF), or high amplitude spikes (HAS).... |
2104.08989 | Sara Clifton | Kylie J Landa, Lauren M Mossman, Rachel J Whitaker, Zoi Rapti, Sara M
Clifton | Phage-antibiotic synergy inhibited by temperate and chronic virus
competition | 23 pages, 5 figures, 3 tables. arXiv admin note: text overlap with
arXiv:1911.07233 | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | As antibiotic resistance grows more frequent for common bacterial infections,
alternative treatment strategies such as phage therapy have become more widely
studied in the medical field. While many studies have explored the efficacy of
antibiotics, phage therapy, or synergistic combinations of phages and
antibiotics,... | [
{
"created": "Mon, 19 Apr 2021 00:43:21 GMT",
"version": "v1"
}
] | 2021-04-20 | [
[
"Landa",
"Kylie J",
""
],
[
"Mossman",
"Lauren M",
""
],
[
"Whitaker",
"Rachel J",
""
],
[
"Rapti",
"Zoi",
""
],
[
"Clifton",
"Sara M",
""
]
] | As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, t... |
1411.6341 | Brandon Barker | Brandon Barker, Lin Xu, Zhenglong Gu | Dynamic Epistasis under Varying Environmental Perturbations | 22 pages, 9 figures | PLoS ONE 10(1): e0114911 | 10.1371/journal.pone.0114911 | null | q-bio.MN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epistasis describes the phenomenon that mutations at different loci do not
have independent effects with regard to certain phenotypes. Understanding the
global epistatic landscape is vital for many genetic and evolutionary theories.
Current knowledge for epistatic dynamics under multiple conditions is limited
by the ... | [
{
"created": "Mon, 24 Nov 2014 03:36:11 GMT",
"version": "v1"
}
] | 2015-02-11 | [
[
"Barker",
"Brandon",
""
],
[
"Xu",
"Lin",
""
],
[
"Gu",
"Zhenglong",
""
]
] | Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current knowledge for epistatic dynamics under multiple conditions is limited by the te... |
2109.08898 | Deeptajyoti Sen Dr. | Deeptajyoti Sen, Andrew Morozov, S. Ghorai and Malay Banerjee | Bifurcation analysis of the predator-prey model with the Allee effect in
the predator | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The use of predator-prey models in theoretical ecology has a long history,
and the model equations have largely evolved since the original Lotka-Volterra
system towards more realistic descriptions of the processes of predation,
reproduction and mortality. One important aspect is the recognition of the fact
that the g... | [
{
"created": "Sat, 18 Sep 2021 10:44:35 GMT",
"version": "v1"
}
] | 2021-09-21 | [
[
"Sen",
"Deeptajyoti",
""
],
[
"Morozov",
"Andrew",
""
],
[
"Ghorai",
"S.",
""
],
[
"Banerjee",
"Malay",
""
]
] | The use of predator-prey models in theoretical ecology has a long history, and the model equations have largely evolved since the original Lotka-Volterra system towards more realistic descriptions of the processes of predation, reproduction and mortality. One important aspect is the recognition of the fact that the gro... |
1410.0930 | Octavio Miramontes | Octavio Miramontes, Og DeSouza, Leticia Ribeiro Paiva, Alessandra
Marins and Sirio Orozco | L\'evy flights and self-similar exploratory behaviour of termite
workers: beyond model fitting | 13 pages, 11 figures. Unrevised version. Final version to appear in
Plos ONE | null | 10.1371/journal.pone.0111183 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Animal movements have been related to optimal foraging strategies where
self-similar trajectories are central. Most of the experimental studies done so
far have focused mainly on fitting statistical models to data in order to test
for movement patterns described by power-laws. Here we show by analyzing over
half a mi... | [
{
"created": "Fri, 3 Oct 2014 18:06:02 GMT",
"version": "v1"
}
] | 2015-06-23 | [
[
"Miramontes",
"Octavio",
""
],
[
"DeSouza",
"Og",
""
],
[
"Paiva",
"Leticia Ribeiro",
""
],
[
"Marins",
"Alessandra",
""
],
[
"Orozco",
"Sirio",
""
]
] | Animal movements have been related to optimal foraging strategies where self-similar trajectories are central. Most of the experimental studies done so far have focused mainly on fitting statistical models to data in order to test for movement patterns described by power-laws. Here we show by analyzing over half a mill... |
1411.6684 | Feng Fu | Feng Fu, Martin A. Nowak, and Sebastian Bonhoeffer | Spatial heterogeneity in drug concentrations can facilitate the
emergence of resistance to cancer therapy | Collaborations on further followup work are extremely welcome. Please
see contact details at
http://www.tb.ethz.ch/people/person-detail.html?persid=189998 | null | 10.1371/journal.pcbi.1004142 | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Acquired resistance is one of the major barriers to successful cancer
therapy. The development of resistance is commonly attributed to genetic
heterogeneity. However, heterogeneity of drug penetration of the tumor
microenvironment both on the microscopic level within solid tumors as well as
on the macroscopic level a... | [
{
"created": "Mon, 24 Nov 2014 23:19:50 GMT",
"version": "v1"
}
] | 2015-08-19 | [
[
"Fu",
"Feng",
""
],
[
"Nowak",
"Martin A.",
""
],
[
"Bonhoeffer",
"Sebastian",
""
]
] | Acquired resistance is one of the major barriers to successful cancer therapy. The development of resistance is commonly attributed to genetic heterogeneity. However, heterogeneity of drug penetration of the tumor microenvironment both on the microscopic level within solid tumors as well as on the macroscopic level acr... |
2008.12473 | Xianggen Liu | Xianggen Liu, Yunan Luo, Sen Song and Jian Peng | Pre-training of Graph Neural Network for Modeling Effects of Mutations
on Protein-Protein Binding Affinity | null | null | 10.1371/journal.pcbi.1009284 | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modeling the effects of mutations on the binding affinity plays a crucial
role in protein engineering and drug design. In this study, we develop a novel
deep learning based framework, named GraphPPI, to predict the binding affinity
changes upon mutations based on the features provided by a graph neural network
(GNN).... | [
{
"created": "Fri, 28 Aug 2020 04:07:39 GMT",
"version": "v1"
}
] | 2021-09-15 | [
[
"Liu",
"Xianggen",
""
],
[
"Luo",
"Yunan",
""
],
[
"Song",
"Sen",
""
],
[
"Peng",
"Jian",
""
]
] | Modeling the effects of mutations on the binding affinity plays a crucial role in protein engineering and drug design. In this study, we develop a novel deep learning based framework, named GraphPPI, to predict the binding affinity changes upon mutations based on the features provided by a graph neural network (GNN). I... |
1603.01794 | Pu Tian | Kai Wang, Lanru Liu and Pu Tian | Utility of potential energy span as an approximate free energy proxy | 18 pages, 8 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Free energy calculation is critical in predictive tasks such as protein
folding, docking and design. However, rigorous calculation of free energy
change is prohibitively expensive in these practical applications. The minimum
potential energy is therefore widely utilized to approximate free energy. In
this study, base... | [
{
"created": "Sun, 6 Mar 2016 06:26:28 GMT",
"version": "v1"
}
] | 2016-03-08 | [
[
"Wang",
"Kai",
""
],
[
"Liu",
"Lanru",
""
],
[
"Tian",
"Pu",
""
]
] | Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential energy is therefore widely utilized to approximate free energy. In this study, based ... |
2304.14799 | Agustina Fragueiro | Agustina Fragueiro (EMPENN), Giorgia Committeri (Ud'A), Claire Cury
(EMPENN) | Incomplete hippocampal inversion and hippocampal subfield volumes:
Implementation and inter-reliability of automatic segmentation | null | null | null | null | q-bio.NC eess.IV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The incomplete hippocampal inversion (IHI) is an atypical anatomical pattern
of the hippocampus. However, the hippocampus is not a homogeneous structure, as
it consists of segregated subfields with specific characteristics. While IHI is
not related to whole hippocampal volume, higher IHI scores have been associated
t... | [
{
"created": "Fri, 28 Apr 2023 12:16:56 GMT",
"version": "v1"
}
] | 2023-05-01 | [
[
"Fragueiro",
"Agustina",
"",
"EMPENN"
],
[
"Committeri",
"Giorgia",
"",
"Ud'A"
],
[
"Cury",
"Claire",
"",
"EMPENN"
]
] | The incomplete hippocampal inversion (IHI) is an atypical anatomical pattern of the hippocampus. However, the hippocampus is not a homogeneous structure, as it consists of segregated subfields with specific characteristics. While IHI is not related to whole hippocampal volume, higher IHI scores have been associated to ... |
0807.4765 | Corey S. O'Hern | Aitziber L. Cortajarena, Gregg Lois, Eilon Sherman, Corey S. O'Hern,
Lynne Regan, and Gilad Haran | Non-random coil behavior as a consequence of extensive PPII structure in
the denatured state | 32 pages, 4 figures, 1 table | J. Mol. Biol. 382, 203 (2008) | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unfolded proteins may contain native or non-native residual structure, which
has important implications for the thermodynamics and kinetics of folding as
well as for misfolding and aggregation diseases. However, it has been
universally accepted that residual structure should not affect the global size
scaling of the ... | [
{
"created": "Wed, 30 Jul 2008 01:26:19 GMT",
"version": "v1"
}
] | 2008-09-12 | [
[
"Cortajarena",
"Aitziber L.",
""
],
[
"Lois",
"Gregg",
""
],
[
"Sherman",
"Eilon",
""
],
[
"O'Hern",
"Corey S.",
""
],
[
"Regan",
"Lynne",
""
],
[
"Haran",
"Gilad",
""
]
] | Unfolded proteins may contain native or non-native residual structure, which has important implications for the thermodynamics and kinetics of folding as well as for misfolding and aggregation diseases. However, it has been universally accepted that residual structure should not affect the global size scaling of the de... |
2206.15158 | Gerald Cooray PhD | Gerald Cooray, Richard Rosch, Karl Friston | Global dynamics of neural mass models | 40 pages, 8 figures | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Neural mass models are used to simulate cortical dynamics and to explain the
electrical and magnetic fields measured using electro- and
magnetoencephalography. Simulations evince a complex phase-space structure for
these kinds of models; including stationary points and limit cycles and the
possibility for bifurcation... | [
{
"created": "Thu, 30 Jun 2022 09:44:15 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Aug 2022 19:16:54 GMT",
"version": "v2"
}
] | 2022-08-25 | [
[
"Cooray",
"Gerald",
""
],
[
"Rosch",
"Richard",
""
],
[
"Friston",
"Karl",
""
]
] | Neural mass models are used to simulate cortical dynamics and to explain the electrical and magnetic fields measured using electro- and magnetoencephalography. Simulations evince a complex phase-space structure for these kinds of models; including stationary points and limit cycles and the possibility for bifurcations ... |
2405.07858 | Prajwal Ghimire | Prajwal Ghimire, Ben Kinnersley, Golestan Karami, Prabhu Arumugam,
Richard Houlston, Keyoumars Ashkan, Marc Modat, Thomas C Booth | Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic
review of magnetic resonance imaging studies | Published in Neuro-Oncology Advances 2024 | null | 10.1093/noajnl/vdae055 | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Immunotherapy is an effective precision medicine treatment for several
cancers. Imaging signatures of the underlying genome (radiogenomics) in
glioblastoma patients may serve as preoperative biomarkers of the tumor-host
immune apparatus. Validated biomarkers would have the potential to stratify
patients during immuno... | [
{
"created": "Mon, 13 May 2024 15:44:40 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Ghimire",
"Prajwal",
""
],
[
"Kinnersley",
"Ben",
""
],
[
"Karami",
"Golestan",
""
],
[
"Arumugam",
"Prabhu",
""
],
[
"Houlston",
"Richard",
""
],
[
"Ashkan",
"Keyoumars",
""
],
[
"Modat",
"Marc",
""
],
... | Immunotherapy is an effective precision medicine treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunoth... |
0710.5195 | Herbert Sauro Dr | Herbert M Sauro and Brian Ingalls | MAPK Cascades as Feedback Amplifiers | 21 pages and 8 figures | null | null | null | q-bio.MN q-bio.SC | null | Interconvertible enzyme cascades, exemplified by the mitogen activated
protein kinase (MAPK) cascade, are a frequent mechanism in signal transduction
pathways. There has been much speculation as to the role of these pathways, and
how their structure is related to their function. A common conclusion is that
the cascad... | [
{
"created": "Fri, 26 Oct 2007 23:38:14 GMT",
"version": "v1"
}
] | 2007-10-30 | [
[
"Sauro",
"Herbert M",
""
],
[
"Ingalls",
"Brian",
""
]
] | Interconvertible enzyme cascades, exemplified by the mitogen activated protein kinase (MAPK) cascade, are a frequent mechanism in signal transduction pathways. There has been much speculation as to the role of these pathways, and how their structure is related to their function. A common conclusion is that the cascades... |
1906.07917 | Vikas Desai | Sai Vikas Desai, Vineeth N Balasubramanian, Tokihiro Fukatsu, Seishi
Ninomiya and Wei Guo | Automatic estimation of heading date of paddy rice using deep learning | null | null | 10.1186/s13007-019-0457-1 | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate estimation of heading date of paddy rice greatly helps the breeders
to understand the adaptability of different crop varieties in a given location.
The heading date also plays a vital role in determining grain yield for
research experiments. Visual examination of the crop is laborious and time
consuming. The... | [
{
"created": "Wed, 19 Jun 2019 05:02:43 GMT",
"version": "v1"
}
] | 2019-08-08 | [
[
"Desai",
"Sai Vikas",
""
],
[
"Balasubramanian",
"Vineeth N",
""
],
[
"Fukatsu",
"Tokihiro",
""
],
[
"Ninomiya",
"Seishi",
""
],
[
"Guo",
"Wei",
""
]
] | Accurate estimation of heading date of paddy rice greatly helps the breeders to understand the adaptability of different crop varieties in a given location. The heading date also plays a vital role in determining grain yield for research experiments. Visual examination of the crop is laborious and time consuming. There... |
1012.1808 | Joachim Krug | Alexander Altland, Andrej Fischer, Joachim Krug, and Ivan G. Szendro | Rare events in population genetics: Stochastic tunneling in a two-locus
model with recombination | 4 pages, 3 figures | Physical Review Letters 106 (2011) 088101 | 10.1103/PhysRevLett.106.088101 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the evolution of a population in a two-locus genotype space, in
which the negative effects of two single mutations are overcompensated in a
high fitness double mutant. We discuss how the interplay of finite population
size, $N$, and sexual recombination at rate $r$ affects the escape times
$t_\mathrm{esc}$ t... | [
{
"created": "Wed, 8 Dec 2010 17:05:13 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Feb 2011 16:41:38 GMT",
"version": "v2"
}
] | 2011-02-23 | [
[
"Altland",
"Alexander",
""
],
[
"Fischer",
"Andrej",
""
],
[
"Krug",
"Joachim",
""
],
[
"Szendro",
"Ivan G.",
""
]
] | We study the evolution of a population in a two-locus genotype space, in which the negative effects of two single mutations are overcompensated in a high fitness double mutant. We discuss how the interplay of finite population size, $N$, and sexual recombination at rate $r$ affects the escape times $t_\mathrm{esc}$ to ... |
1609.01015 | Arian Ashourvan | Arian Ashourvan, Shi Gu, Marcelo G. Mattar, Jean M. Vettel, Danielle
S. Bassett | The Energy Landscape Underpinning Module Dynamics in the Human Brain
Connectome | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human brain dynamics can be profitably viewed through the lens of statistical
mechanics, where neurophysiological activity evolves around and between local
attractors representing preferred mental states. Many physically-inspired
models of these dynamics define the state of the brain based on instantaneous
measuremen... | [
{
"created": "Mon, 5 Sep 2016 01:51:59 GMT",
"version": "v1"
}
] | 2016-09-06 | [
[
"Ashourvan",
"Arian",
""
],
[
"Gu",
"Shi",
""
],
[
"Mattar",
"Marcelo G.",
""
],
[
"Vettel",
"Jean M.",
""
],
[
"Bassett",
"Danielle S.",
""
]
] | Human brain dynamics can be profitably viewed through the lens of statistical mechanics, where neurophysiological activity evolves around and between local attractors representing preferred mental states. Many physically-inspired models of these dynamics define the state of the brain based on instantaneous measurements... |
2208.02564 | Tongyue Shi | Tongyue Shi and Haining Wang | Mathematical Modeling Analysis and Optimization of Fungal Diversity
Growth | 19 pages | null | null | null | q-bio.PE math.OC | http://creativecommons.org/licenses/by/4.0/ | This paper studied the relationship between the decomposition rate of fungi
and temperature, humidity, fungus elongation, moisture tolerance and fungus
density in a given volume in the presence of a variety of fungi, and
established a series of models to describe the decomposition of fungi in
different states. Since ... | [
{
"created": "Thu, 4 Aug 2022 10:13:52 GMT",
"version": "v1"
}
] | 2022-08-05 | [
[
"Shi",
"Tongyue",
""
],
[
"Wang",
"Haining",
""
]
] | This paper studied the relationship between the decomposition rate of fungi and temperature, humidity, fungus elongation, moisture tolerance and fungus density in a given volume in the presence of a variety of fungi, and established a series of models to describe the decomposition of fungi in different states. Since th... |
1507.04416 | Iaroslav Ispolatov | Iaroslav Ispolatov, Vaibhav Madhok, and Michael Doebeli | Individual-Based models for adaptive diversification in high-dimensional
phenotype spaces | 23 pages, 7 figures, please open pdf with Acrobat to see movies | J. Theor. Biol, 390 (2016) 97-105 | 10.1016/j.jtbi.2015.10.009 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most theories of evolutionary diversification are based on equilibrium
assumptions: they are either based on optimality arguments involving static
fitness landscapes, or they assume that populations first evolve to an
equilibrium state before diversification occurs, as exemplified by the concept
of evolutionary branc... | [
{
"created": "Thu, 16 Jul 2015 00:07:19 GMT",
"version": "v1"
}
] | 2017-02-07 | [
[
"Ispolatov",
"Iaroslav",
""
],
[
"Madhok",
"Vaibhav",
""
],
[
"Doebeli",
"Michael",
""
]
] | Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branchi... |
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