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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0802.1056 | Miloje M. Rakocevic | Miloje M. Rakocevic | Genetic Code: Four-Codon and Non-Four-Codon Degeneracy | The 18 Pages, 16 Tables, 1 Figure and 5 Surveys. The paper represents
a step within further investigations of harmonic structure of the genetic
code (Rakocevic, 2004) | null | null | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work it is shown that 20 canonical amino acids (AAs) within genetic
code appear to be a whole system with strict distinction in Genetic Code Table
(GCT) into some different quantums: 20, 23, 61 amino acid molecules. These
molecules distinction is followed by specific balanced atom number and/or
nucleon number... | [
{
"created": "Thu, 7 Feb 2008 20:00:52 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2019 12:23:53 GMT",
"version": "v2"
}
] | 2019-09-23 | [
[
"Rakocevic",
"Miloje M.",
""
]
] | In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules distinction is followed by specific balanced atom number and/or nucleon number d... |
2203.14870 | Nelson Niemeyer | Nelson Niemeyer, Jan-Hendrik Schleimer, Susanne Schreiber | Biophysical models of intrinsic homeostasis: Firing rates and beyond | null | Current Opinion in Neurobiology, Volume 70, October 2021, Pages
81-88 | 10.1016/j.conb.2021.07.011 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In view of ever-changing conditions both in the external world and in
intrinsic brain states, maintaining the robustness of computations poses a
challenge, adequate solutions to which we are only beginning to understand. At
the level of cell-intrinsic properties, biophysical models of neurons permit
one to identify r... | [
{
"created": "Mon, 28 Mar 2022 16:25:20 GMT",
"version": "v1"
}
] | 2022-03-29 | [
[
"Niemeyer",
"Nelson",
""
],
[
"Schleimer",
"Jan-Hendrik",
""
],
[
"Schreiber",
"Susanne",
""
]
] | In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of cell-intrinsic properties, biophysical models of neurons permit one to identify rel... |
q-bio/0510007 | Michael Lachmann | Carl T. Bergstrom and Michael Lachmann | The fitness value of information | 18 pages, 3 figures (included in text). Submitted to PNAS | null | null | null | q-bio.PE cs.IT math.IT q-bio.NC | null | Biologists measure information in different ways. Neurobiologists and
researchers in bioinformatics often measure information using
information-theoretic measures such as Shannon's entropy or mutual information.
Behavioral biologists and evolutionary ecologists more commonly use
decision-theoretic measures, such the ... | [
{
"created": "Mon, 3 Oct 2005 22:24:48 GMT",
"version": "v1"
}
] | 2007-07-13 | [
[
"Bergstrom",
"Carl T.",
""
],
[
"Lachmann",
"Michael",
""
]
] | Biologists measure information in different ways. Neurobiologists and researchers in bioinformatics often measure information using information-theoretic measures such as Shannon's entropy or mutual information. Behavioral biologists and evolutionary ecologists more commonly use decision-theoretic measures, such the va... |
2203.02568 | Arnaud Delorme | Arnaud Delorme, Dung Truong, Choonhan Youn, Subha Sivagnanam, Kenneth
Yoshimoto, Russell A. Poldrack, Amit Majumdar, Scott Makeig | NEMAR: An open access data, tools, and compute resource operating on
NeuroElectroMagnetic data | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | To take advantage of recent and ongoing advances in large-scale computational
methods, and to preserve the scientific data created by publicly funded
research projects, data archives must be created as well as standards for
specifying, identifying, and annotating deposited data. The OpenNeuro.org
archive, begun as a ... | [
{
"created": "Fri, 4 Mar 2022 20:47:26 GMT",
"version": "v1"
}
] | 2022-03-08 | [
[
"Delorme",
"Arnaud",
""
],
[
"Truong",
"Dung",
""
],
[
"Youn",
"Choonhan",
""
],
[
"Sivagnanam",
"Subha",
""
],
[
"Yoshimoto",
"Kenneth",
""
],
[
"Poldrack",
"Russell A.",
""
],
[
"Majumdar",
"Amit",
""
]... | To take advantage of recent and ongoing advances in large-scale computational methods, and to preserve the scientific data created by publicly funded research projects, data archives must be created as well as standards for specifying, identifying, and annotating deposited data. The OpenNeuro.org archive, begun as a re... |
1507.00041 | Luca Ferretti | Luca Ferretti, Daniel Weinreich, Benjamin Schmiegelt, Atsushi
Yamauchi, Yutaka Kobayashi, Fumio Tajima and Guillaume Achaz | Epistasis and constraints in fitness landscapes | 37 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genotypic fitness landscapes are constructed by assessing the fitness of all
possible combinations of a given number of mutations. In the last years,
several experimental fitness landscapes have been completely resolved. As
fitness landscapes are high-dimensional, their characterization relies on
simple measures of t... | [
{
"created": "Tue, 30 Jun 2015 21:26:42 GMT",
"version": "v1"
}
] | 2015-07-02 | [
[
"Ferretti",
"Luca",
""
],
[
"Weinreich",
"Daniel",
""
],
[
"Schmiegelt",
"Benjamin",
""
],
[
"Yamauchi",
"Atsushi",
""
],
[
"Kobayashi",
"Yutaka",
""
],
[
"Tajima",
"Fumio",
""
],
[
"Achaz",
"Guillaume",
""... | Genotypic fitness landscapes are constructed by assessing the fitness of all possible combinations of a given number of mutations. In the last years, several experimental fitness landscapes have been completely resolved. As fitness landscapes are high-dimensional, their characterization relies on simple measures of the... |
1507.02940 | Fabio Chalub | Paulo Doutor, Paula Rodrigues, Maria do C\'eu Soares, Fabio A. C. C.
Chalub | Optimal Vaccination Strategies and Rational Behaviour in Seasonal
Epidemics | 27 pages, 4 figures | null | 10.1007/s00285-016-0997-1 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a SIR model with temporary immunity and time dependent
transmission rate. We assume time dependent vaccination which confers the same
immunity as natural infection. We study two types of vaccination strategies: i)
optimal vaccination, in the sense that it minimizes the effort of vaccination
in the set of ... | [
{
"created": "Fri, 10 Jul 2015 15:35:42 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Mar 2016 17:30:43 GMT",
"version": "v2"
}
] | 2016-04-06 | [
[
"Doutor",
"Paulo",
""
],
[
"Rodrigues",
"Paula",
""
],
[
"Soares",
"Maria do Céu",
""
],
[
"Chalub",
"Fabio A. C. C.",
""
]
] | We consider a SIR model with temporary immunity and time dependent transmission rate. We assume time dependent vaccination which confers the same immunity as natural infection. We study two types of vaccination strategies: i) optimal vaccination, in the sense that it minimizes the effort of vaccination in the set of va... |
2405.18768 | Divya Nori | Divya Nori, Wengong Jin | RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow
Matching | Accepted to ICML 2024 | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | The growing significance of RNA engineering in diverse biological
applications has spurred interest in developing AI methods for structure-based
RNA design. While diffusion models have excelled in protein design, adapting
them for RNA presents new challenges due to RNA's conformational flexibility
and the computation... | [
{
"created": "Wed, 29 May 2024 05:10:25 GMT",
"version": "v1"
},
{
"created": "Sun, 9 Jun 2024 16:13:02 GMT",
"version": "v2"
}
] | 2024-06-11 | [
[
"Nori",
"Divya",
""
],
[
"Jin",
"Wengong",
""
]
] | The growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA presents new challenges due to RNA's conformational flexibility and the computational... |
2008.09927 | Chang Sub Kim | Chang Sub Kim | Bayesian mechanics of perceptual inference and motor control in the
brain | 28 pages, 7 figures | null | 10.1007/s00422-021-00859-9 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The free energy principle (FEP) in the neurosciences stipulates that all
viable agents induce and minimize informational free energy in the brain to fit
their environmental niche. In this study, we continue our effort to make the
FEP a more physically principled formalism by implementing free energy
minimization base... | [
{
"created": "Sat, 22 Aug 2020 23:20:37 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Nov 2020 08:15:48 GMT",
"version": "v2"
},
{
"created": "Thu, 21 Jan 2021 23:52:45 GMT",
"version": "v3"
}
] | 2021-01-25 | [
[
"Kim",
"Chang Sub",
""
]
] | The free energy principle (FEP) in the neurosciences stipulates that all viable agents induce and minimize informational free energy in the brain to fit their environmental niche. In this study, we continue our effort to make the FEP a more physically principled formalism by implementing free energy minimization based ... |
2407.06295 | Ramya Deshpande | Ramya Deshpande, Francesco Mottes, Ariana-Dalia Vlad, Michael P.
Brenner, Alma dal Co | Engineering morphogenesis of cell clusters with differentiable
programming | 8 pages, 6 figures | null | null | null | q-bio.CB cs.LG | http://creativecommons.org/licenses/by/4.0/ | Understanding the rules underlying organismal development is a major unsolved
problem in biology. Each cell in a developing organism responds to signals in
its local environment by dividing, excreting, consuming, or reorganizing, yet
how these individual actions coordinate over a macroscopic number of cells to
grow c... | [
{
"created": "Mon, 8 Jul 2024 18:05:11 GMT",
"version": "v1"
}
] | 2024-07-10 | [
[
"Deshpande",
"Ramya",
""
],
[
"Mottes",
"Francesco",
""
],
[
"Vlad",
"Ariana-Dalia",
""
],
[
"Brenner",
"Michael P.",
""
],
[
"Co",
"Alma dal",
""
]
] | Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how these individual actions coordinate over a macroscopic number of cells to grow com... |
2206.08796 | Alexandre Triay Bagur | Alexandre Triay Bagur, Darryl McClymont, Chloe Hutton, Andrea
Borghetto, Michael L Gyngell, Paul Aljabar, Matthew D Robson, Michael Brady,
Daniel P Bulte | Estimation of Field Inhomogeneity Map Following Magnitude-Based
Ambiguity-Resolved Water-Fat Separation | 14 pages, 11 figures | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | PURPOSE: To extend magnitude-based PDFF (Proton Density Fat Fraction) and
$R_2^*$ mapping with resolved water-fat ambiguity to calculate field
inhomogeneity (field map) using the phase images.
THEORY: The estimation is formulated in matrix form, resolving the field map
in a least-squares sense. PDFF and $R_2^*$ fro... | [
{
"created": "Fri, 17 Jun 2022 14:18:40 GMT",
"version": "v1"
},
{
"created": "Fri, 26 Aug 2022 16:10:34 GMT",
"version": "v2"
},
{
"created": "Thu, 1 Sep 2022 12:03:27 GMT",
"version": "v3"
},
{
"created": "Wed, 14 Sep 2022 18:50:06 GMT",
"version": "v4"
}
] | 2022-09-16 | [
[
"Bagur",
"Alexandre Triay",
""
],
[
"McClymont",
"Darryl",
""
],
[
"Hutton",
"Chloe",
""
],
[
"Borghetto",
"Andrea",
""
],
[
"Gyngell",
"Michael L",
""
],
[
"Aljabar",
"Paul",
""
],
[
"Robson",
"Matthew D",
... | PURPOSE: To extend magnitude-based PDFF (Proton Density Fat Fraction) and $R_2^*$ mapping with resolved water-fat ambiguity to calculate field inhomogeneity (field map) using the phase images. THEORY: The estimation is formulated in matrix form, resolving the field map in a least-squares sense. PDFF and $R_2^*$ from ma... |
2010.02555 | Jacob Moss | Jacob Moss, Pietro Li\'o | Gene Regulatory Network Inference with Latent Force Models | null | null | null | null | q-bio.MN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Delays in protein synthesis cause a confounding effect when constructing Gene
Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs
can be very insightful when modelling development, disease pathways, and drug
side-effects. We present a model which incorporates translation delays by
combining... | [
{
"created": "Tue, 6 Oct 2020 09:03:34 GMT",
"version": "v1"
}
] | 2020-10-07 | [
[
"Moss",
"Jacob",
""
],
[
"Lió",
"Pietro",
""
]
] | Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug side-effects. We present a model which incorporates translation delays by combining m... |
1507.06303 | Eugene Rosenfeld | Eugene V. Rosenfeld | Bond rupture mechanism enables to explain in block asymmetry of
elaxation, force-velocity curve and the path of energy dissipation in muscle | in Russian, 11 pages | null | null | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bond rupture mechanism enables to explain in block asymmetry of elaxation,
force-velocity curve and the path of energy dissipation in muscle
| [
{
"created": "Wed, 22 Jul 2015 10:40:18 GMT",
"version": "v1"
}
] | 2015-07-24 | [
[
"Rosenfeld",
"Eugene V.",
""
]
] | Bond rupture mechanism enables to explain in block asymmetry of elaxation, force-velocity curve and the path of energy dissipation in muscle |
2003.11859 | Chiara De Luca | Bruno Golosio, Chiara De Luca, Cristiano Capone, Elena Pastorelli,
Giovanni Stegel, Gianmarco Tiddia, Giulia De Bonis and Pier Stanislao
Paolucci | Thalamo-cortical spiking model of incremental learning combining
perception, context and NREM-sleep-mediated noise-resilience | null | PLOS Computational Biology 17(6): e1009045 (2021) | 10.1371/journal.pcbi.1009045 | null | q-bio.NC cs.DC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain exhibits capabilities of fast incremental learning from few noisy
examples, as well as the ability to associate similar memories in
autonomously-created categories and to combine contextual hints with sensory
perceptions. Together with sleep, these mechanisms are thought to be key
components of many high-le... | [
{
"created": "Thu, 26 Mar 2020 12:18:35 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jan 2021 07:42:16 GMT",
"version": "v2"
},
{
"created": "Fri, 19 Mar 2021 10:30:45 GMT",
"version": "v3"
},
{
"created": "Thu, 5 Aug 2021 07:15:18 GMT",
"version": "v4"
}
] | 2021-08-31 | [
[
"Golosio",
"Bruno",
""
],
[
"De Luca",
"Chiara",
""
],
[
"Capone",
"Cristiano",
""
],
[
"Pastorelli",
"Elena",
""
],
[
"Stegel",
"Giovanni",
""
],
[
"Tiddia",
"Gianmarco",
""
],
[
"De Bonis",
"Giulia",
""
... | The brain exhibits capabilities of fast incremental learning from few noisy examples, as well as the ability to associate similar memories in autonomously-created categories and to combine contextual hints with sensory perceptions. Together with sleep, these mechanisms are thought to be key components of many high-leve... |
1512.09233 | Yougan Cheng | Yougan Cheng and Hans Othmer | A Model for Direction Sensing in Dictyostelium Discoideum: Ras Activity
and Symmetry Breaking Driven by a Gbetagamma- Mediated, Galpha2-Ric8 --
Dependent Signal Transduction Network | null | null | 10.1371/journal.pcbi.1004900 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many eukaryotic cells, including Dictyostelium discoideum (Dicty),
neutrophils and other cells of the immune system, can detect and reliably
orient themselves in chemoattractant gradients. In Dicty, signal detection and
transduction involves a G-protein-coupled receptor (GPCR) through which
extracellular cAMP signals... | [
{
"created": "Thu, 31 Dec 2015 07:26:07 GMT",
"version": "v1"
}
] | 2016-09-28 | [
[
"Cheng",
"Yougan",
""
],
[
"Othmer",
"Hans",
""
]
] | Many eukaryotic cells, including Dictyostelium discoideum (Dicty), neutrophils and other cells of the immune system, can detect and reliably orient themselves in chemoattractant gradients. In Dicty, signal detection and transduction involves a G-protein-coupled receptor (GPCR) through which extracellular cAMP signals a... |
2110.01554 | Sebastian Contreras | Sebastian Contreras, Philipp D\"onges, Joel Wagner, Simon Bauer,
Sebastian B. Mohr, Emil N. Iftekhar, Mirjam Kretzschmar, Michael Maes, Kai
Nagel, Andr\'e Calero Valdez, Viola Priesemann | The winter dilemma | Estimation of COVID-19 case numbers for the coming winter | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With winter coming in the northern hemisphere, disadvantageous seasonality of
SARS-CoV-2 requires high immunity levels in the population or increasing
non-pharmaceutical interventions (NPIs), compared to summer. Otherwise
intensive care units (ICUs) might fill up. However, compliance with mandatory
NPIs, vaccine upta... | [
{
"created": "Mon, 4 Oct 2021 16:47:06 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Oct 2021 17:50:43 GMT",
"version": "v2"
}
] | 2021-10-18 | [
[
"Contreras",
"Sebastian",
""
],
[
"Dönges",
"Philipp",
""
],
[
"Wagner",
"Joel",
""
],
[
"Bauer",
"Simon",
""
],
[
"Mohr",
"Sebastian B.",
""
],
[
"Iftekhar",
"Emil N.",
""
],
[
"Kretzschmar",
"Mirjam",
""
... | With winter coming in the northern hemisphere, disadvantageous seasonality of SARS-CoV-2 requires high immunity levels in the population or increasing non-pharmaceutical interventions (NPIs), compared to summer. Otherwise intensive care units (ICUs) might fill up. However, compliance with mandatory NPIs, vaccine uptake... |
2205.03920 | Wei Xie | Wei Xie, Giulia Pedrielli | From Discovery to Production: Challenges and Novel Methodologies for
Next Generation Biomanufacturing | 15 pages, 5 figures | null | null | null | q-bio.QM cs.SY eess.SY | http://creativecommons.org/licenses/by/4.0/ | The increasingly pressing demand of novel drugs (e.g., gene therapies for
personalized cancer care, ever evolving vaccines) with unprecedented levels of
personalization, has put a remarkable pressure on the traditionally long time
required by the pharma R&D and manufacturing to go from design to production of
new pro... | [
{
"created": "Sun, 8 May 2022 17:32:17 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Jun 2022 05:50:08 GMT",
"version": "v2"
}
] | 2022-06-29 | [
[
"Xie",
"Wei",
""
],
[
"Pedrielli",
"Giulia",
""
]
] | The increasingly pressing demand of novel drugs (e.g., gene therapies for personalized cancer care, ever evolving vaccines) with unprecedented levels of personalization, has put a remarkable pressure on the traditionally long time required by the pharma R&D and manufacturing to go from design to production of new produ... |
2004.02944 | Bo Zhang | Bo Zhang, Ting Ye, Siyu Heng, Michael Z. Levy, Dylan S. Small | Protocol for an Observational Study on the Effects of Social Distancing
on Influenza-Like Illness and COVID-19 | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The novel coronavirus disease (COVID-19) is a highly contagious respiratory
disease that was first detected in Wuhan, China in December 2019, and has since
spread around the globe, claiming more than 69,000 lives by the time this
protocol is written. It has been widely acknowledged that the most effective
public poli... | [
{
"created": "Mon, 6 Apr 2020 19:11:58 GMT",
"version": "v1"
}
] | 2020-04-08 | [
[
"Zhang",
"Bo",
""
],
[
"Ye",
"Ting",
""
],
[
"Heng",
"Siyu",
""
],
[
"Levy",
"Michael Z.",
""
],
[
"Small",
"Dylan S.",
""
]
] | The novel coronavirus disease (COVID-19) is a highly contagious respiratory disease that was first detected in Wuhan, China in December 2019, and has since spread around the globe, claiming more than 69,000 lives by the time this protocol is written. It has been widely acknowledged that the most effective public policy... |
1606.02151 | Carsten Baldauf | Matti Ropo and Volker Blum and Carsten Baldauf | Trends for isolated amino acids and dipeptides: Conformation, divalent
ion binding, and remarkable similarity of binding to calcium and lead | submitted, underlying data can be found here:
http://aminoaciddb.rz-berlin.mpg.de/ | null | null | null | q-bio.BM physics.atm-clus physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We derive structural and binding energy trends for twenty amino acids, their
dipeptides, and their interactions with the divalent cations Ca$^{2+}$,
Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data
set consists of 45,892 first-principles predicted conformers with relative
energies up to ... | [
{
"created": "Tue, 7 Jun 2016 14:24:21 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Sep 2016 09:20:23 GMT",
"version": "v2"
}
] | 2016-09-15 | [
[
"Ropo",
"Matti",
""
],
[
"Blum",
"Volker",
""
],
[
"Baldauf",
"Carsten",
""
]
] | We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists of 45,892 first-principles predicted conformers with relative energies up to ab... |
1004.2020 | Chris Adami | Dimitris Iliopoulos, Arend Hintze, and Christoph Adami | Critical dynamics in the evolution of stochastic strategies for the
iterated Prisoner's Dilemma | 27 pages, including supplementary information. 5 figures, 4 suppl.
figures. Version accepted for publication in PLoS Comp. Biol | PLos Computational Biology 6 (2010) e1000948 | 10.1371/journal.pcbi.1000948 | null | q-bio.PE q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The observed cooperation on the level of genes, cells, tissues, and
individuals has been the object of intense study by evolutionary biologists,
mainly because cooperation often flourishes in biological systems in apparent
contradiction to the selfish goal of survival inherent in Darwinian evolution.
In order to reso... | [
{
"created": "Mon, 12 Apr 2010 18:21:04 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Sep 2010 16:38:58 GMT",
"version": "v2"
}
] | 2010-10-21 | [
[
"Iliopoulos",
"Dimitris",
""
],
[
"Hintze",
"Arend",
""
],
[
"Adami",
"Christoph",
""
]
] | The observed cooperation on the level of genes, cells, tissues, and individuals has been the object of intense study by evolutionary biologists, mainly because cooperation often flourishes in biological systems in apparent contradiction to the selfish goal of survival inherent in Darwinian evolution. In order to resolv... |
2003.13997 | Min Lu | Min Lu and Hemant Ishwaran | Dynamic Competing Risk Modeling COVID-19 in a Pandemic Scenario | https://minlu.shinyapps.io/killCOVID19/ | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emergence of coronavirus disease 2019 (COVID-19) in the United States has
forced federal and local governments to implement containment measures.
Moreover, the severity of the situation has sparked engagement by both the
research and clinical community with the goal of developing effective
treatments for the dise... | [
{
"created": "Tue, 31 Mar 2020 07:30:40 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Apr 2020 02:12:07 GMT",
"version": "v2"
},
{
"created": "Thu, 9 Apr 2020 21:35:22 GMT",
"version": "v3"
},
{
"created": "Wed, 1 Jul 2020 22:48:58 GMT",
"version": "v4"
}
] | 2020-07-03 | [
[
"Lu",
"Min",
""
],
[
"Ishwaran",
"Hemant",
""
]
] | The emergence of coronavirus disease 2019 (COVID-19) in the United States has forced federal and local governments to implement containment measures. Moreover, the severity of the situation has sparked engagement by both the research and clinical community with the goal of developing effective treatments for the diseas... |
1705.07614 | Robert Legenstein | Zeno Jonke, Robert Legenstein, Stefan Habenschuss, Wolfgang Maass | Feedback inhibition shapes emergent computational properties of cortical
microcircuit motifs | 25 pages, 6 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cortical microcircuits are very complex networks, but they are composed of a
relatively small number of stereotypical motifs. Hence one strategy for
throwing light on the computational function of cortical microcircuits is to
analyze emergent computational properties of these stereotypical microcircuit
motifs. We are... | [
{
"created": "Mon, 22 May 2017 08:52:31 GMT",
"version": "v1"
}
] | 2017-05-23 | [
[
"Jonke",
"Zeno",
""
],
[
"Legenstein",
"Robert",
""
],
[
"Habenschuss",
"Stefan",
""
],
[
"Maass",
"Wolfgang",
""
]
] | Cortical microcircuits are very complex networks, but they are composed of a relatively small number of stereotypical motifs. Hence one strategy for throwing light on the computational function of cortical microcircuits is to analyze emergent computational properties of these stereotypical microcircuit motifs. We are a... |
1211.6179 | Chao Yang Mr. | Chao Yang, Zengyou He, and Weichuan Yu | A Combinatorial Perspective of the Protein Inference Problem | null | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In a shotgun proteomics experiment, proteins are the most biologically
meaningful output. The success of proteomics studies depends on the ability to
accurately and efficiently identify proteins. Many methods have been proposed
to facilitate the identification of proteins from the results of peptide
identification. H... | [
{
"created": "Tue, 27 Nov 2012 02:14:18 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Nov 2012 02:19:55 GMT",
"version": "v2"
}
] | 2012-11-30 | [
[
"Yang",
"Chao",
""
],
[
"He",
"Zengyou",
""
],
[
"Yu",
"Weichuan",
""
]
] | In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to facilitate the identification of proteins from the results of peptide identification. How... |
2103.08247 | Pawel Kulakowski | Jakub Kmiecik, Pawel Kulakowski, Krzysztof Wojcik, Andrzej Jajszczyk | Transmitting FRET signals to nerve cells | null | 5th ACM/IEEE International Conference on Nanoscale Computing and
Communication, September 2018 | 10.1145/3233188.3233223 | null | q-bio.MN cs.NI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper is concerned with a novel method allowing communication between
FRET nanonetworks and nerve cells. It is focused on two system components:
fluorophores and channelrhodopsins which serve as transmitters and receivers,
respectively. Channelrhodopsins are used here also as a FRET signal-to-voltage
converter. ... | [
{
"created": "Mon, 15 Mar 2021 09:57:33 GMT",
"version": "v1"
}
] | 2021-03-16 | [
[
"Kmiecik",
"Jakub",
""
],
[
"Kulakowski",
"Pawel",
""
],
[
"Wojcik",
"Krzysztof",
""
],
[
"Jajszczyk",
"Andrzej",
""
]
] | This paper is concerned with a novel method allowing communication between FRET nanonetworks and nerve cells. It is focused on two system components: fluorophores and channelrhodopsins which serve as transmitters and receivers, respectively. Channelrhodopsins are used here also as a FRET signal-to-voltage converter. Th... |
2001.08346 | Charles Fieseler | Charles Fieseler, Manuel Zimmer, J. Nathan Kutz | Unsupervised learning of control signals and their encodings in
$\textit{C. elegans}$ whole-brain recordings | 10 pages, 5 figures | null | null | null | q-bio.QM q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Recent whole brain imaging experiments on $\textit{C. elegans}$ has revealed
that the neural population dynamics encode motor commands and stereotyped
transitions between behaviors on low dimensional manifolds. Efforts to
characterize the dynamics on this manifold have used piecewise linear models to
describe the ent... | [
{
"created": "Thu, 23 Jan 2020 02:37:34 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Feb 2020 19:50:02 GMT",
"version": "v2"
},
{
"created": "Mon, 13 Apr 2020 21:33:46 GMT",
"version": "v3"
}
] | 2020-04-15 | [
[
"Fieseler",
"Charles",
""
],
[
"Zimmer",
"Manuel",
""
],
[
"Kutz",
"J. Nathan",
""
]
] | Recent whole brain imaging experiments on $\textit{C. elegans}$ has revealed that the neural population dynamics encode motor commands and stereotyped transitions between behaviors on low dimensional manifolds. Efforts to characterize the dynamics on this manifold have used piecewise linear models to describe the entir... |
0805.2298 | Luciano da Fontoura Costa | Matheus P. Viana, Bruno A. N. Travencolo, E. Tanck and Luciano da F.
Costa | Characterizing the Diversity of Dynamics in Complex Networks Without
Border Effects | 15 pages, 7 figures. A working manuscript | null | null | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The importance of structured, complex connectivity patterns found in several
real-world systems is to a great extent related to their respective effects in
constraining and even defining the respective dynamics. Yet, while complex
networks have been comprehensively investigated along the last decade in terms
of their... | [
{
"created": "Thu, 15 May 2008 13:14:46 GMT",
"version": "v1"
}
] | 2008-05-16 | [
[
"Viana",
"Matheus P.",
""
],
[
"Travencolo",
"Bruno A. N.",
""
],
[
"Tanck",
"E.",
""
],
[
"Costa",
"Luciano da F.",
""
]
] | The importance of structured, complex connectivity patterns found in several real-world systems is to a great extent related to their respective effects in constraining and even defining the respective dynamics. Yet, while complex networks have been comprehensively investigated along the last decade in terms of their t... |
1809.07275 | Elisenda Feliu | Elisenda Feliu | On the reaction rate constants that enable multistationarity in the
two-site phosphorylation cycle | null | null | null | null | q-bio.MN math.AG math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Parametrized polynomial ordinary differential equation systems are broadly
used for modeling, specially in the study of biochemical reaction networks
under the assumption of mass-action kinetics. Understanding the qualitative
behavior of the solutions with respect to the parameter values gives rise to
complex problem... | [
{
"created": "Tue, 18 Sep 2018 08:13:39 GMT",
"version": "v1"
}
] | 2018-10-15 | [
[
"Feliu",
"Elisenda",
""
]
] | Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of the solutions with respect to the parameter values gives rise to complex problems ... |
0710.2301 | Ruben Moreno Bote | Ruben Moreno-Bote, Nestor Parga | Auto and crosscorrelograms for the spike response of LIF neurons with
slow synapses | 5 pages, 3 figures | PRL 96, 028101 (2006) | 10.1103/PhysRevLett.96.028101 | null | q-bio.NC physics.bio-ph | null | An analytical description of the response properties of simple but realistic
neuron models in the presence of noise is still lacking. We determine
completely up to the second order the firing statistics of a single and a pair
of leaky integrate-and-fire neurons (LIFs) receiving some common slowly
filtered white noise... | [
{
"created": "Thu, 11 Oct 2007 17:33:25 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Moreno-Bote",
"Ruben",
""
],
[
"Parga",
"Nestor",
""
]
] | An analytical description of the response properties of simple but realistic neuron models in the presence of noise is still lacking. We determine completely up to the second order the firing statistics of a single and a pair of leaky integrate-and-fire neurons (LIFs) receiving some common slowly filtered white noise. ... |
1112.3082 | Alexander Peyser | Alexander Peyser | Theoretical Studies of Structure-Function Relationships in Kv Channels:
Electrostatics of the Voltage Sensor | null | null | null | null | q-bio.BM physics.bio-ph q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Voltage-gated ion channels mediate electrical excitability of cellular
membranes. Reduced models of the voltage sensor (VS) of Kv channels produce
insight into the electrostatic physics underlying the response of the highly
positively charged S4 transmembrane domain to changes in membrane potential and
other electros... | [
{
"created": "Wed, 14 Dec 2011 00:38:39 GMT",
"version": "v1"
}
] | 2015-03-13 | [
[
"Peyser",
"Alexander",
""
]
] | Voltage-gated ion channels mediate electrical excitability of cellular membranes. Reduced models of the voltage sensor (VS) of Kv channels produce insight into the electrostatic physics underlying the response of the highly positively charged S4 transmembrane domain to changes in membrane potential and other electrosta... |
1810.13302 | Nicole Voges | Jeyathevy Sukiban, Nicole Voges, Till A. Dembek, Robin Pauli, Michael
Denker, Immo Weber, Lars Timmermann, Sonja Gr\"un | Evaluation of spike sorting algorithms: Simulations and application to
human Subthalamic Nucleus recordings | 9 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An important prerequisite for the analysis of spike synchrony in
extracellular recordings is the extraction of single unit activity from the
recorded multi unit signal. To identify single units (SUs), potential spikes
are detected and separated with respect to their potential neuronal origins
('spike sorting'). Howev... | [
{
"created": "Wed, 31 Oct 2018 14:32:45 GMT",
"version": "v1"
}
] | 2018-11-01 | [
[
"Sukiban",
"Jeyathevy",
""
],
[
"Voges",
"Nicole",
""
],
[
"Dembek",
"Till A.",
""
],
[
"Pauli",
"Robin",
""
],
[
"Denker",
"Michael",
""
],
[
"Weber",
"Immo",
""
],
[
"Timmermann",
"Lars",
""
],
[
... | An important prerequisite for the analysis of spike synchrony in extracellular recordings is the extraction of single unit activity from the recorded multi unit signal. To identify single units (SUs), potential spikes are detected and separated with respect to their potential neuronal origins ('spike sorting'). However... |
2302.07134 | Shuqi Lu | Yuejiang Yu, Shuqi Lu, Zhifeng Gao, Hang Zheng and Guolin Ke | Do Deep Learning Models Really Outperform Traditional Approaches in
Molecular Docking? | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Molecular docking, given a ligand molecule and a ligand binding site (called
``pocket'') on a protein, predicting the binding mode of the protein-ligand
complex, is a widely used technique in drug design. Many deep learning models
have been developed for molecular docking, while most existing deep learning
models per... | [
{
"created": "Tue, 14 Feb 2023 15:45:45 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Feb 2023 05:47:01 GMT",
"version": "v2"
},
{
"created": "Thu, 23 Feb 2023 09:09:30 GMT",
"version": "v3"
}
] | 2023-02-24 | [
[
"Yu",
"Yuejiang",
""
],
[
"Lu",
"Shuqi",
""
],
[
"Gao",
"Zhifeng",
""
],
[
"Zheng",
"Hang",
""
],
[
"Ke",
"Guolin",
""
]
] | Molecular docking, given a ligand molecule and a ligand binding site (called ``pocket'') on a protein, predicting the binding mode of the protein-ligand complex, is a widely used technique in drug design. Many deep learning models have been developed for molecular docking, while most existing deep learning models perfo... |
1405.6466 | Dante Chialvo | Enzo Tagliazucchi, Robin Carhart-Harris, Robert Leech, David Nutt,
Dante R. Chialvo | Enhanced repertoire of brain dynamical states during the psychedelic
experience | null | Hum. Brain Mapp., 35: 5442-5456, 2014 | 10.1002/hbm.22562 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The study of rapid changes in brain dynamics and functional connectivity (FC)
is of increasing interest in neuroimaging. Brain states departing from normal
waking consciousness are expected to be accompanied by alterations in the
aforementioned dynamics. In particular, the psychedelic experience produced by
psilocybi... | [
{
"created": "Mon, 26 May 2014 05:50:15 GMT",
"version": "v1"
}
] | 2014-11-03 | [
[
"Tagliazucchi",
"Enzo",
""
],
[
"Carhart-Harris",
"Robin",
""
],
[
"Leech",
"Robert",
""
],
[
"Nutt",
"David",
""
],
[
"Chialvo",
"Dante R.",
""
]
] | The study of rapid changes in brain dynamics and functional connectivity (FC) is of increasing interest in neuroimaging. Brain states departing from normal waking consciousness are expected to be accompanied by alterations in the aforementioned dynamics. In particular, the psychedelic experience produced by psilocybin ... |
1912.03395 | Jakub Otwinowski | Jakub Otwinowski, Colin LaMont | Information-geometric optimization with natural selection | changed title | null | 10.3390/e22090967 | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary algorithms, inspired by natural evolution, aim to optimize
difficult objective functions without computing derivatives. Here we detail the
relationship between population genetics and evolutionary optimization and
formulate a new evolutionary algorithm. Optimization of a continuous objective
function is ... | [
{
"created": "Fri, 6 Dec 2019 23:57:16 GMT",
"version": "v1"
},
{
"created": "Wed, 19 Feb 2020 23:52:24 GMT",
"version": "v2"
}
] | 2023-07-19 | [
[
"Otwinowski",
"Jakub",
""
],
[
"LaMont",
"Colin",
""
]
] | Evolutionary algorithms, inspired by natural evolution, aim to optimize difficult objective functions without computing derivatives. Here we detail the relationship between population genetics and evolutionary optimization and formulate a new evolutionary algorithm. Optimization of a continuous objective function is an... |
2212.04535 | Yizi Zhang | Yizi Zhang, Meimei Liu, Zhengwu Zhang, and David Dunson | Motion-Invariant Variational Auto-Encoding of Brain Structural
Connectomes | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Mapping of human brain structural connectomes via diffusion MRI offers a
unique opportunity to understand brain structural connectivity and relate it to
various human traits, such as cognition. However, the presence of motion
artifacts during image acquisition can compromise the accuracy of connectome
reconstructions... | [
{
"created": "Thu, 8 Dec 2022 19:54:25 GMT",
"version": "v1"
},
{
"created": "Mon, 10 Jul 2023 19:48:29 GMT",
"version": "v2"
}
] | 2023-07-12 | [
[
"Zhang",
"Yizi",
""
],
[
"Liu",
"Meimei",
""
],
[
"Zhang",
"Zhengwu",
""
],
[
"Dunson",
"David",
""
]
] | Mapping of human brain structural connectomes via diffusion MRI offers a unique opportunity to understand brain structural connectivity and relate it to various human traits, such as cognition. However, the presence of motion artifacts during image acquisition can compromise the accuracy of connectome reconstructions a... |
2208.05019 | Stephen Turner | VP Nagraj, Chris Hulme-Lowe, Shakeel Jessa, Stephen D. Turner | Automated Infectious Disease Forecasting: Use-cases and Practical
Considerations for Pipeline Implementation | Submitted to epiDAMIK 5.0: The 5th International workshop on
Epidemiology meets Data Mining and Knowledge discovery | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by-sa/4.0/ | Real-time forecasting of disease outbreaks requires standardized outputs
generated in a timely manner. Development of pipelines to automate infectious
disease forecasts can ensure that parameterization and software dependencies
are common to any execution of the forecasting code. Here we present our
implementation of... | [
{
"created": "Tue, 9 Aug 2022 19:50:13 GMT",
"version": "v1"
}
] | 2022-08-11 | [
[
"Nagraj",
"VP",
""
],
[
"Hulme-Lowe",
"Chris",
""
],
[
"Jessa",
"Shakeel",
""
],
[
"Turner",
"Stephen D.",
""
]
] | Real-time forecasting of disease outbreaks requires standardized outputs generated in a timely manner. Development of pipelines to automate infectious disease forecasts can ensure that parameterization and software dependencies are common to any execution of the forecasting code. Here we present our implementation of a... |
1907.05017 | Anne Modat | Simon Dittami (LBI2M), Enrique Arboleda (SBR), Jean-Christophe Auguet
(UMR MARBEC), Arite Bigalke, Enora Briand (IFREMER Nantes), Paco C\'ardenas,
Ulisse Cardini, Johan Decelle, Ashwin Engelen (CCMAR), Damien Eveillard
(LS2N), Claire Gachon, Sarah Griffiths, Tilmann Harder, Ehsan Kayal (FR2424),
Elena Kazamia (... | A community perspective on the concept of marine holobionts:
state-of-the-art, challenges, and future directions | PeerJ Preprints, Computer Science Preprints., 2019 | null | 10.7287/peerj.preprints.27519v1 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Host-microbe interactions play crucial roles in marine ecosystems, but we
still have very little understanding of the mechanisms that govern these
relationships, the evolutionary processes that shape them, and their ecological
consequences. The holobiont concept is a renewed paradigm in biology that can
help describe... | [
{
"created": "Thu, 11 Jul 2019 06:40:52 GMT",
"version": "v1"
}
] | 2019-07-12 | [
[
"Dittami",
"Simon",
"",
"LBI2M"
],
[
"Arboleda",
"Enrique",
"",
"SBR"
],
[
"Auguet",
"Jean-Christophe",
"",
"UMR MARBEC"
],
[
"Bigalke",
"Arite",
"",
"IFREMER Nantes"
],
[
"Briand",
"Enora",
"",
"IFREMER Nantes"
],
... | Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe a... |
1705.01568 | Artem Novozhilov | Alexander S. Bratus, Artem S. Novozhilov, and Yuri S. Semenov | Adaptive Fitness Landscape for Replicator Systems: To Maximize or not to
Maximize | 13 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sewall Wright's adaptive landscape metaphor penetrates a significant part of
evolutionary thinking. Supplemented with Fisher's fundamental theorem of
natural selection and Kimura's maximum principle, it provides a unifying and
intuitive representation of the evolutionary process under the influence of
natural selecti... | [
{
"created": "Wed, 3 May 2017 18:12:01 GMT",
"version": "v1"
}
] | 2017-05-05 | [
[
"Bratus",
"Alexander S.",
""
],
[
"Novozhilov",
"Artem S.",
""
],
[
"Semenov",
"Yuri S.",
""
]
] | Sewall Wright's adaptive landscape metaphor penetrates a significant part of evolutionary thinking. Supplemented with Fisher's fundamental theorem of natural selection and Kimura's maximum principle, it provides a unifying and intuitive representation of the evolutionary process under the influence of natural selection... |
1104.4304 | Jason Graham | Jason M. Graham and Bruce P. Ayati and Prem S. Ramakrishnan and James
A. Martin | Towards a New Spatial Representation of Bone Remodeling | Math. Biosci. Eng., 9(2), 2012 | null | 10.3934/mbe.2012.9.281 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Irregular bone remodeling is associated with a number of bone diseases such
as osteoporosis and multiple myeloma.
Computational and mathematical modeling can aid in therapy and treatment as
well as understanding fundamental biology. Different approaches to modeling
give insight into different aspects of a phenomena... | [
{
"created": "Thu, 21 Apr 2011 16:25:42 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Mar 2012 15:24:19 GMT",
"version": "v2"
}
] | 2023-02-14 | [
[
"Graham",
"Jason M.",
""
],
[
"Ayati",
"Bruce P.",
""
],
[
"Ramakrishnan",
"Prem S.",
""
],
[
"Martin",
"James A.",
""
]
] | Irregular bone remodeling is associated with a number of bone diseases such as osteoporosis and multiple myeloma. Computational and mathematical modeling can aid in therapy and treatment as well as understanding fundamental biology. Different approaches to modeling give insight into different aspects of a phenomena so ... |
q-bio/0505045 | Georgy Karev | Faina S. Berezovskaya, Georgy P. Karev, and Terry W. Snell | Modeling the dynamics of natural rotifer populations: phase-parametric
analysis | 27 pages, 6 figures; submitted to "Ecological Complexity" | null | null | null | q-bio.SC q-bio.OT | null | A model of the dynamics of natural rotifer populations is described as a
discrete nonlinear map depending on three parameters, which reflect
characteristics of the population and environment. Model dynamics and their
change by variation of these parameters were investigated by methods of
bifurcation theory. A phase-p... | [
{
"created": "Tue, 24 May 2005 21:52:20 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Berezovskaya",
"Faina S.",
""
],
[
"Karev",
"Georgy P.",
""
],
[
"Snell",
"Terry W.",
""
]
] | A model of the dynamics of natural rotifer populations is described as a discrete nonlinear map depending on three parameters, which reflect characteristics of the population and environment. Model dynamics and their change by variation of these parameters were investigated by methods of bifurcation theory. A phase-par... |
1609.04314 | Sara Bernardi | Sara Bernardi, Ezio Venturino | An epidemiological model of viral infections in a Varroa-infested bee
colony: the case of a bee-dependent mite population size | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years the spread of the ectoparasitic mite Varroa destructor has
become the most serious threat to worldwide apiculture. In the model presented
here we extend the bee population dynamics with mite viral epidemiology
examined in an earlier paper by allowing a bee-dependent mite population size.
The results o... | [
{
"created": "Wed, 14 Sep 2016 15:35:02 GMT",
"version": "v1"
}
] | 2016-09-15 | [
[
"Bernardi",
"Sara",
""
],
[
"Venturino",
"Ezio",
""
]
] | In recent years the spread of the ectoparasitic mite Varroa destructor has become the most serious threat to worldwide apiculture. In the model presented here we extend the bee population dynamics with mite viral epidemiology examined in an earlier paper by allowing a bee-dependent mite population size. The results of ... |
2205.12334 | Shahab Mahdian | Shahab Mahdian, Michael A. Nitsche, Vahid Nejati | Gender differences in the neural structures of (non) emotional
perspective-taking: A tDCS study | this is an undergraduate research project | null | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | The perspective-taking in social cognition is an ability that makes
third-person judgments about the intentions, beliefs and thoughts of others. We
aimed to investigate gender differences in the neural structure differences in
(non) emotional perspective-taking ability.Thirty healthy adults (15 females
and 15 males) ... | [
{
"created": "Tue, 24 May 2022 19:34:34 GMT",
"version": "v1"
},
{
"created": "Wed, 20 Jul 2022 20:23:03 GMT",
"version": "v2"
}
] | 2022-07-22 | [
[
"Mahdian",
"Shahab",
""
],
[
"Nitsche",
"Michael A.",
""
],
[
"Nejati",
"Vahid",
""
]
] | The perspective-taking in social cognition is an ability that makes third-person judgments about the intentions, beliefs and thoughts of others. We aimed to investigate gender differences in the neural structure differences in (non) emotional perspective-taking ability.Thirty healthy adults (15 females and 15 males) re... |
2006.16326 | Babacar Mbaye Ndiaye | Vieux Medoune Ndiaye, Serigne Omar Sarr, Babacar Mbaye Ndiaye | Impact of contamination factors on the COVID-19 evolution in Senegal | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we perform an analysis of COVID-19 on one of the South
Saharan countries (hot zone), the Senegal (West Africa). Many questions remain
unanswered: why the African continent is not very contaminated compared to
other continents. Factors of cross immunity, temperature, population density,
youth, etc. ar... | [
{
"created": "Mon, 29 Jun 2020 19:16:43 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Ndiaye",
"Vieux Medoune",
""
],
[
"Sarr",
"Serigne Omar",
""
],
[
"Ndiaye",
"Babacar Mbaye",
""
]
] | In this article, we perform an analysis of COVID-19 on one of the South Saharan countries (hot zone), the Senegal (West Africa). Many questions remain unanswered: why the African continent is not very contaminated compared to other continents. Factors of cross immunity, temperature, population density, youth, etc. are ... |
2208.08361 | Tulio Pascoal | T\'ulio Pascoal, J\'er\'emie Decouchant, Antoine Boutet, Marcus V\"olp | I-GWAS: Privacy-Preserving Interdependent Genome-Wide Association
Studies | null | null | null | null | q-bio.GN cs.CR cs.DC cs.IR | http://creativecommons.org/licenses/by/4.0/ | Genome-wide Association Studies (GWASes) identify genomic variations that are
statistically associated with a trait, such as a disease, in a group of
individuals. Unfortunately, careless sharing of GWAS statistics might give rise
to privacy attacks. Several works attempted to reconcile secure processing with
privacy-... | [
{
"created": "Wed, 17 Aug 2022 15:52:43 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Sep 2022 09:38:31 GMT",
"version": "v2"
}
] | 2022-09-21 | [
[
"Pascoal",
"Túlio",
""
],
[
"Decouchant",
"Jérémie",
""
],
[
"Boutet",
"Antoine",
""
],
[
"Völp",
"Marcus",
""
]
] | Genome-wide Association Studies (GWASes) identify genomic variations that are statistically associated with a trait, such as a disease, in a group of individuals. Unfortunately, careless sharing of GWAS statistics might give rise to privacy attacks. Several works attempted to reconcile secure processing with privacy-pr... |
1507.02583 | Elsa Guillot | Elsa G. Guillot, Murray P. Cox | High Frequency Haplotypes are Expected Events, not Historical Figures | 8 pages, 1 figure, reply letter | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Cultural transmission of reproductive success states that successful men have
more children and pass this raised fecundity to their offspring. Balaresque and
colleagues found high frequency haplotypes in a Central Asian Y chromosome
dataset, which they attribute to cultural transmission of reproductive success
by pro... | [
{
"created": "Wed, 8 Jul 2015 09:43:28 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Sep 2015 15:49:58 GMT",
"version": "v2"
}
] | 2015-09-18 | [
[
"Guillot",
"Elsa G.",
""
],
[
"Cox",
"Murray P.",
""
]
] | Cultural transmission of reproductive success states that successful men have more children and pass this raised fecundity to their offspring. Balaresque and colleagues found high frequency haplotypes in a Central Asian Y chromosome dataset, which they attribute to cultural transmission of reproductive success by promi... |
1206.4361 | Stephen Wirkus | Erika T. Camacho, Stephen Wirkus | Tracing the Progression of Retinitis Pigmentosa via Photoreceptor
Interactions | 35 pages, 6 figures | null | null | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Retinitis pigmentosa (RP) is a group of inherited degenerative eye diseases
characterized by mutations in the genetic structure of the photoreceptors that
leads to the premature death of both rod and cone photoreceptors. Defects in
particular genes encoding proteins that are involved in either the
photoreceptor struc... | [
{
"created": "Tue, 19 Jun 2012 23:26:15 GMT",
"version": "v1"
}
] | 2012-06-21 | [
[
"Camacho",
"Erika T.",
""
],
[
"Wirkus",
"Stephen",
""
]
] | Retinitis pigmentosa (RP) is a group of inherited degenerative eye diseases characterized by mutations in the genetic structure of the photoreceptors that leads to the premature death of both rod and cone photoreceptors. Defects in particular genes encoding proteins that are involved in either the photoreceptor structu... |
1105.6282 | Davron Matrasulov | E.K. Ivanova, N.N. Turaeva, B.L. Oksengendler | Quantum theory of hydrogen key of point mutation in DNA | null | BioPhysics, Issue 2, (2011) 3 | null | null | q-bio.OT physics.bio-ph quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantum theory of hydrogen atoms distribution between two complementary
nucleotide bases in DNA double helix at moment of replication has been proposed
in this work. It bases on two mechanisms of proton tunneling: the
Andreev-Meyerovich mechanism with spontaneous phonon radiation and the
Kagan-Maximov (Flynn-Stoneham... | [
{
"created": "Sat, 28 May 2011 02:41:02 GMT",
"version": "v1"
}
] | 2011-06-01 | [
[
"Ivanova",
"E. K.",
""
],
[
"Turaeva",
"N. N.",
""
],
[
"Oksengendler",
"B. L.",
""
]
] | Quantum theory of hydrogen atoms distribution between two complementary nucleotide bases in DNA double helix at moment of replication has been proposed in this work. It bases on two mechanisms of proton tunneling: the Andreev-Meyerovich mechanism with spontaneous phonon radiation and the Kagan-Maximov (Flynn-Stoneham) ... |
1404.0444 | Stefano Schivo | Stefano Schivo (1), Jetse Scholma (2), Marcel Karperien (2), Janine N.
Post (2), Jaco van de Pol (1) and Rom Langerak (1) ((1) Formal Methods and
Tools, Faculty of EEMCS, University of Twente, Enschede, The Netherlands, (2)
Developmental BioEngineering, MIRA Institute for Biomedical Technology and
Technical Med... | Setting Parameters for Biological Models With ANIMO | null | EPTCS 145, 2014, pp. 35-47 | 10.4204/EPTCS.145.5 | null | q-bio.MN cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | ANIMO (Analysis of Networks with Interactive MOdeling) is a software for
modeling biological networks, such as e.g. signaling, metabolic or gene
networks. An ANIMO model is essentially the sum of a network topology and a
number of interaction parameters. The topology describes the interactions
between biological enti... | [
{
"created": "Wed, 2 Apr 2014 03:38:20 GMT",
"version": "v1"
}
] | 2014-04-03 | [
[
"Schivo",
"Stefano",
""
],
[
"Scholma",
"Jetse",
""
],
[
"Karperien",
"Marcel",
""
],
[
"Post",
"Janine N.",
""
],
[
"van de Pol",
"Jaco",
""
],
[
"Langerak",
"Rom",
""
]
] | ANIMO (Analysis of Networks with Interactive MOdeling) is a software for modeling biological networks, such as e.g. signaling, metabolic or gene networks. An ANIMO model is essentially the sum of a network topology and a number of interaction parameters. The topology describes the interactions between biological entiti... |
2111.07336 | Markus Kirkilionis | David Alonso, Steffen Bauer, Markus Kirkilionis, Lisa Maria Kreusser,
Luca Sbano | A Rule-Based Epidemiological Modelling Framework | 67 pages, 23 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Motivated by chemical reaction rules, we introduce a rule-based
epidemiological framework for the systematic mathematical modelling of future
pandemics. Here we stress that we do not have a specific model in mind, but a
whole collection of models which can be transformed into each other, or
represent different aspect... | [
{
"created": "Sun, 14 Nov 2021 13:11:38 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Nov 2021 16:42:09 GMT",
"version": "v2"
},
{
"created": "Wed, 22 May 2024 13:58:23 GMT",
"version": "v3"
}
] | 2024-05-24 | [
[
"Alonso",
"David",
""
],
[
"Bauer",
"Steffen",
""
],
[
"Kirkilionis",
"Markus",
""
],
[
"Kreusser",
"Lisa Maria",
""
],
[
"Sbano",
"Luca",
""
]
] | Motivated by chemical reaction rules, we introduce a rule-based epidemiological framework for the systematic mathematical modelling of future pandemics. Here we stress that we do not have a specific model in mind, but a whole collection of models which can be transformed into each other, or represent different aspects ... |
1512.00163 | Yoav Ram | Yoav Ram and Lilach Hadany | The probability of improvement in Fisher's geometric model: a
probabilistic approach | Post-print | Theoretical Population Biology 99 (February): 1-6 (2015) | 10.1016/j.tpb.2014.10.004 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Fisher developed his geometric model to support the micro-mutationalism
hypothesis which claims that small mutations are more likely to be beneficial
and therefore to contribute to evolution and adaptation. While others have
provided a general solution to the model using geometric approaches, we derive
an equivalent ... | [
{
"created": "Tue, 1 Dec 2015 07:04:10 GMT",
"version": "v1"
}
] | 2015-12-02 | [
[
"Ram",
"Yoav",
""
],
[
"Hadany",
"Lilach",
""
]
] | Fisher developed his geometric model to support the micro-mutationalism hypothesis which claims that small mutations are more likely to be beneficial and therefore to contribute to evolution and adaptation. While others have provided a general solution to the model using geometric approaches, we derive an equivalent ge... |
1004.4528 | Bernat Corominas-Murtra BCM | Ricard V. Sol\'e, Bernat Corominas-Murtra and Jordi Fortuny | Diversity, competition, extinction: the ecophysics of language change | 17 Pages. A review on current models from statistical Physics and
Theoretical Ecology applied to study language dynamics | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As early indicated by Charles Darwin, languages behave and change very much
like living species. They display high diversity, differentiate in space and
time, emerge and disappear. A large body of literature has explored the role of
information exchanges and communicative constraints in groups of agents under
selecti... | [
{
"created": "Wed, 21 Apr 2010 14:23:30 GMT",
"version": "v1"
}
] | 2010-04-27 | [
[
"Solé",
"Ricard V.",
""
],
[
"Corominas-Murtra",
"Bernat",
""
],
[
"Fortuny",
"Jordi",
""
]
] | As early indicated by Charles Darwin, languages behave and change very much like living species. They display high diversity, differentiate in space and time, emerge and disappear. A large body of literature has explored the role of information exchanges and communicative constraints in groups of agents under selective... |
2003.07283 | Tam\'as R\'obert Mezei | P\'eter L. Erd\H{o}s, Andrew Francis, Tam\'as R\'obert Mezei | Rooted NNI moves on tree-based phylogenetic networks | Fixed typos and references to labels in the last subsection | Discrete Applied Mathematics, Volume 294, 15 May 2021, Pages
205-213 | 10.1016/j.dam.2021.02.016 | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that the space of rooted tree-based phylogenetic networks is
connected under rooted nearest-neighbour interchange (rNNI) moves.
| [
{
"created": "Mon, 16 Mar 2020 15:41:49 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Mar 2020 16:57:56 GMT",
"version": "v2"
}
] | 2021-07-06 | [
[
"Erdős",
"Péter L.",
""
],
[
"Francis",
"Andrew",
""
],
[
"Mezei",
"Tamás Róbert",
""
]
] | We show that the space of rooted tree-based phylogenetic networks is connected under rooted nearest-neighbour interchange (rNNI) moves. |
2110.12723 | Lizhen Huang | C He (1), C Lin (1), G Mo (1), B Xi (1), A Li (3), D Huang (1), Y Wan
(1), F Chen (1), Y Liang (3), Q Zuo (1), W Xu (1), D Feng (1), G Zhang (4), L
Han (1), C Ke (2), H Du (1), L Huang (1) | Rapid and Accurate Detection of SARS-CoV-2 Mutations using a
Cas12a-based Sensing Platform | 39 pages, 6 figures | null | null | null | q-bio.QM q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The increasing prevalence of SARS-CoV-2 variants with spike mutations has
raised concerns owing to higher transmission rates, disease severity, and
escape from neutralizing antibodies. Rapid and accurate detection of SARS-CoV-2
variants provides crucial information concerning the outbreaks of SARS-CoV-2
variants and ... | [
{
"created": "Mon, 25 Oct 2021 08:19:21 GMT",
"version": "v1"
}
] | 2021-10-26 | [
[
"He",
"C",
""
],
[
"Lin",
"C",
""
],
[
"Mo",
"G",
""
],
[
"Xi",
"B",
""
],
[
"Li",
"A",
""
],
[
"Huang",
"D",
""
],
[
"Wan",
"Y",
""
],
[
"Chen",
"F",
""
],
[
"Liang",
"Y",
"... | The increasing prevalence of SARS-CoV-2 variants with spike mutations has raised concerns owing to higher transmission rates, disease severity, and escape from neutralizing antibodies. Rapid and accurate detection of SARS-CoV-2 variants provides crucial information concerning the outbreaks of SARS-CoV-2 variants and po... |
2010.06477 | Vitali Nesterov | Vitali Nesterov, Mario Wieser, Volker Roth | 3DMolNet: A Generative Network for Molecular Structures | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | With the recent advances in machine learning for quantum chemistry, it is now
possible to predict the chemical properties of compounds and to generate novel
molecules. Existing generative models mostly use a string- or graph-based
representation, but the precise three-dimensional coordinates of the atoms are
usually ... | [
{
"created": "Thu, 8 Oct 2020 13:04:36 GMT",
"version": "v1"
}
] | 2020-10-14 | [
[
"Nesterov",
"Vitali",
""
],
[
"Wieser",
"Mario",
""
],
[
"Roth",
"Volker",
""
]
] | With the recent advances in machine learning for quantum chemistry, it is now possible to predict the chemical properties of compounds and to generate novel molecules. Existing generative models mostly use a string- or graph-based representation, but the precise three-dimensional coordinates of the atoms are usually no... |
2011.03443 | Amir Shanehsazzadeh | Amir Shanehsazzadeh, David Belanger, David Dohan | Is Transfer Learning Necessary for Protein Landscape Prediction? | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, there has been great interest in learning how to best represent
proteins, specifically with fixed-length embeddings. Deep learning has become a
popular tool for protein representation learning as a model's hidden layers
produce potentially useful vector embeddings. TAPE introduced a number of
benchmark task... | [
{
"created": "Sat, 31 Oct 2020 20:41:36 GMT",
"version": "v1"
}
] | 2020-11-09 | [
[
"Shanehsazzadeh",
"Amir",
""
],
[
"Belanger",
"David",
""
],
[
"Dohan",
"David",
""
]
] | Recently, there has been great interest in learning how to best represent proteins, specifically with fixed-length embeddings. Deep learning has become a popular tool for protein representation learning as a model's hidden layers produce potentially useful vector embeddings. TAPE introduced a number of benchmark tasks ... |
1402.5338 | Jian-Jun Shu | Jian-Jun Shu and Yajing Li | A statistical fat-tail test of predicting regulatory regions in the
Drosophila genome | null | Computers in Biology and Medicine, Vol. 42, No. 9, pp. 935-941,
2012 | 10.1016/j.compbiomed.2012.07.007 | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A statistical study of cis-regulatory modules (CRMs) is presented based on
the estimation of similar-word set distribution. It is observed that CRMs tend
to have a fat-tail distribution. A new statistical fat-tail test with two
kurtosis-based fatness coefficients is proposed to distinguish CRMs from
non-CRMs. As comp... | [
{
"created": "Fri, 21 Feb 2014 16:10:59 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Mar 2014 15:09:14 GMT",
"version": "v2"
},
{
"created": "Wed, 2 Aug 2023 12:31:30 GMT",
"version": "v3"
}
] | 2023-08-03 | [
[
"Shu",
"Jian-Jun",
""
],
[
"Li",
"Yajing",
""
]
] | A statistical study of cis-regulatory modules (CRMs) is presented based on the estimation of similar-word set distribution. It is observed that CRMs tend to have a fat-tail distribution. A new statistical fat-tail test with two kurtosis-based fatness coefficients is proposed to distinguish CRMs from non-CRMs. As compar... |
1312.2942 | Wes Maciejewski | Wes Maciejewski, Feng Fu, and Christoph Hauert | Evolutionary Game Dynamics in Populations with Heterogeneous Structures | null | PLOS Comp. Biol. 10 (4) e1003567 (2014) | 10.1371/journal.pcbi.1003567 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Evolutionary graph theory is a well established framework for modelling the
evolution of social behaviours in structured populations. An emerging consensus
in this field is that graphs that exhibit heterogeneity in the number of
connections between individuals are more conducive to the spread of cooperative
behaviour... | [
{
"created": "Tue, 10 Dec 2013 20:46:39 GMT",
"version": "v1"
}
] | 2018-11-20 | [
[
"Maciejewski",
"Wes",
""
],
[
"Fu",
"Feng",
""
],
[
"Hauert",
"Christoph",
""
]
] | Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours.... |
2302.04200 | Abdul Majiid | Madiha Hameed, Muhammad Bilal, Tuba Majid, Abdul Majid and Asifullah
Khan | Early Risk Prediction of Chronic Myeloid Leukemia with Protein Sequences
using Machine Learning-based Meta-Ensemble | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Leukemia, the cancer of blood cells, originates in the blood-forming cells of
the bone marrow. In Chronic Myeloid Leukemia (CML) conditions, the cells
partially become mature that look like normal white blood cells but do not
resist infection effectively. Early detection of CML is important for effective
treatment, b... | [
{
"created": "Wed, 8 Feb 2023 17:12:51 GMT",
"version": "v1"
}
] | 2023-02-09 | [
[
"Hameed",
"Madiha",
""
],
[
"Bilal",
"Muhammad",
""
],
[
"Majid",
"Tuba",
""
],
[
"Majid",
"Abdul",
""
],
[
"Khan",
"Asifullah",
""
]
] | Leukemia, the cancer of blood cells, originates in the blood-forming cells of the bone marrow. In Chronic Myeloid Leukemia (CML) conditions, the cells partially become mature that look like normal white blood cells but do not resist infection effectively. Early detection of CML is important for effective treatment, but... |
2112.00360 | Jana Massing | Jana C. Massing and Thilo Gross | Generalized Modeling: A survey and guide | 46 pages, 6 figures Subsection 6.3 (Normalization): minor corrections
in normalization of second equation of the two-variable system | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many current challenges involve understanding the complex dynamical interplay
between the constituents of systems. Typically, the number of such constituents
is high, but only limited data sources on them are available. Conventional
dynamical models of complex systems are rarely mathematically tractable and
their num... | [
{
"created": "Wed, 1 Dec 2021 09:13:06 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Dec 2021 11:10:59 GMT",
"version": "v2"
}
] | 2021-12-17 | [
[
"Massing",
"Jana C.",
""
],
[
"Gross",
"Thilo",
""
]
] | Many current challenges involve understanding the complex dynamical interplay between the constituents of systems. Typically, the number of such constituents is high, but only limited data sources on them are available. Conventional dynamical models of complex systems are rarely mathematically tractable and their numer... |
0802.3380 | Anthony Coolen | S. Rabello, A.C.C. Coolen, C.J. Perez-Vicente, and F. Fraternali | A solvable model of the genesis of amino-acid sequences via coupled
dynamics of folding and slow genetic variation | 51 pages, 13 figures, submitted to J. Phys. A | null | 10.1088/1751-8113/41/28/285004 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the coupled dynamics of primary and secondary structure formation
(i.e. slow genetic sequence selection and fast folding) in the context of a
solvable microscopic model that includes both short-range steric forces and and
long-range polarity-driven forces. Our solution is based on the diagonalization
of repl... | [
{
"created": "Fri, 22 Feb 2008 20:29:07 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Rabello",
"S.",
""
],
[
"Coolen",
"A. C. C.",
""
],
[
"Perez-Vicente",
"C. J.",
""
],
[
"Fraternali",
"F.",
""
]
] | We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and long-range polarity-driven forces. Our solution is based on the diagonalization of replic... |
2009.08868 | Qi Zhao | Qi Zhao, Zheng Zhao, Xiaoya Fan, Zhengwei Yuan, Qian Mao, Yudong Yao | Review of Machine-Learning Methods for RNA Secondary Structure
Prediction | 25 pages, 5 figures, 1 table | null | 10.1371/journal.pcbi.1009291 | null | q-bio.BM cs.LG stat.ML | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Secondary structure plays an important role in determining the function of
non-coding RNAs. Hence, identifying RNA secondary structures is of great value
to research. Computational prediction is a mainstream approach for predicting
RNA secondary structure. Unfortunately, even though new methods have been
proposed ove... | [
{
"created": "Tue, 1 Sep 2020 03:17:15 GMT",
"version": "v1"
}
] | 2021-09-15 | [
[
"Zhao",
"Qi",
""
],
[
"Zhao",
"Zheng",
""
],
[
"Fan",
"Xiaoya",
""
],
[
"Yuan",
"Zhengwei",
""
],
[
"Mao",
"Qian",
""
],
[
"Yao",
"Yudong",
""
]
] | Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure. Unfortunately, even though new methods have been proposed over ... |
1502.03011 | Namiko Mitarai | Namiko Mitarai, Szabolcs Semsey, Kim Sneppen | Dynamic competition between transcription initiation and repression:
Role of nonequilibrium steps in cell-to-cell heterogeneity | 5 pages, 3 fiugres. Figure and text updated | Phys. Rev. E 92, 022710 (2015) | 10.1103/PhysRevE.92.022710 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcriptional repression may cause transcriptional noise by a competition
between repressor and RNA polymerase binding. Although promoter activity is
often governed by a single limiting step, we argue here that the size of the
noise strongly depends on whether this step is the initial equilibrium binding
or one of ... | [
{
"created": "Tue, 10 Feb 2015 17:43:53 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Apr 2015 16:37:56 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Aug 2015 14:57:13 GMT",
"version": "v3"
}
] | 2015-08-14 | [
[
"Mitarai",
"Namiko",
""
],
[
"Semsey",
"Szabolcs",
""
],
[
"Sneppen",
"Kim",
""
]
] | Transcriptional repression may cause transcriptional noise by a competition between repressor and RNA polymerase binding. Although promoter activity is often governed by a single limiting step, we argue here that the size of the noise strongly depends on whether this step is the initial equilibrium binding or one of th... |
2001.06948 | Thomas Caraco | Thomas Caraco | Antibiotics, duration of infectiousness, and transmission of disease | 22 pages of text, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Humans, domestic animals, orchard crops, and ornamental plants are commonly
treated with antibiotics in response to bacterial infection. By curing
infectious individuals, antibiotic therapy might limit the spread of contagious
disease among hosts. But antibiotic suppression of within-host pathogen density
might also ... | [
{
"created": "Mon, 20 Jan 2020 02:44:05 GMT",
"version": "v1"
}
] | 2020-01-22 | [
[
"Caraco",
"Thomas",
""
]
] | Humans, domestic animals, orchard crops, and ornamental plants are commonly treated with antibiotics in response to bacterial infection. By curing infectious individuals, antibiotic therapy might limit the spread of contagious disease among hosts. But antibiotic suppression of within-host pathogen density might also re... |
1302.6952 | Jonathan Touboul | Mathieu Galtier and Jonathan Touboul | Macroscopic equations governing noisy spiking neuronal populations | null | null | 10.1371/journal.pone.0078917 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | At functional scales, cortical behavior results from the complex interplay of
a large number of excitable cells operating in noisy environments. Such systems
resist to mathematical analysis, and computational neurosciences have largely
relied on heuristic partial (and partially justified) macroscopic models, which
su... | [
{
"created": "Wed, 27 Feb 2013 18:33:10 GMT",
"version": "v1"
}
] | 2014-03-05 | [
[
"Galtier",
"Mathieu",
""
],
[
"Touboul",
"Jonathan",
""
]
] | At functional scales, cortical behavior results from the complex interplay of a large number of excitable cells operating in noisy environments. Such systems resist to mathematical analysis, and computational neurosciences have largely relied on heuristic partial (and partially justified) macroscopic models, which succ... |
2405.14139 | Xinhao Fan | Xinhao Fan, Shreesh P Mysore | Contribute to balance, wire in accordance: Emergence of backpropagation
from a simple, bio-plausible neuroplasticity rule | null | null | null | null | q-bio.NC cs.LG cs.NE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Backpropagation (BP) has been pivotal in advancing machine learning and
remains essential in computational applications and comparative studies of
biological and artificial neural networks. Despite its widespread use, the
implementation of BP in the brain remains elusive, and its biological
plausibility is often ques... | [
{
"created": "Thu, 23 May 2024 03:28:52 GMT",
"version": "v1"
}
] | 2024-05-24 | [
[
"Fan",
"Xinhao",
""
],
[
"Mysore",
"Shreesh P",
""
]
] | Backpropagation (BP) has been pivotal in advancing machine learning and remains essential in computational applications and comparative studies of biological and artificial neural networks. Despite its widespread use, the implementation of BP in the brain remains elusive, and its biological plausibility is often questi... |
1507.03972 | Sergei Maslov | Purushottam Dixit, Tin Yau Pang, F. William Studier and Sergei Maslov | Recombinant transfer in the basic genome of E. coli | 29 pages (including SI), 4 figures | null | 10.1073/pnas.1510839112 | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli
representing six evolutionary groups has been derived and analyzed
computationally. A multiple-alignment of the 32 complete genome sequences was
filtered to remove mobile elements and identify the most reliable ~90% of the
aligned length of e... | [
{
"created": "Tue, 14 Jul 2015 19:23:29 GMT",
"version": "v1"
}
] | 2016-02-17 | [
[
"Dixit",
"Purushottam",
""
],
[
"Pang",
"Tin Yau",
""
],
[
"Studier",
"F. William",
""
],
[
"Maslov",
"Sergei",
""
]
] | An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of eac... |
q-bio/0607038 | Mathias Baumert | M Baumert, LM Brechtel, J Lock, A Voss, D Abbott | Scaling graphs of heart rate time series in athletes demonstrate the
VLF, LF and HF regions | null | 2006 Physiol. Meas. 27 N35-N39 | 10.1088/0967-3334/27/9/N01 | null | q-bio.QM | null | Scaling analysis of heart rate time series has emerged as an useful tool for
assessment of autonomic cardiac control. We investigate the heart rate time
series of ten athletes (five males and five females), by applying detrended
fluctuation analysis (DFA). High resolution ECGs are recorded under
standardized resting ... | [
{
"created": "Sat, 22 Jul 2006 00:44:22 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Baumert",
"M",
""
],
[
"Brechtel",
"LM",
""
],
[
"Lock",
"J",
""
],
[
"Voss",
"A",
""
],
[
"Abbott",
"D",
""
]
] | Scaling analysis of heart rate time series has emerged as an useful tool for assessment of autonomic cardiac control. We investigate the heart rate time series of ten athletes (five males and five females), by applying detrended fluctuation analysis (DFA). High resolution ECGs are recorded under standardized resting co... |
1304.3752 | Sergey Koren | Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono, Dayna
M Harhay, D. Scott Mcvey, Diana Radune, Nicholas H Bergman, and Adam M
Phillippy | Reducing assembly complexity of microbial genomes with single-molecule
sequencing | Published in Genome Biology: http://genomebiology.com/2013/14/9/R101/
Supplementary materials available from:
http://www.cbcb.umd.edu/software/PBcR/closure/index.html Reducing assembly
complexity of microbial genomes with single-molecule sequencing. Koren S,
Harhay GP, Smith TPL, Bono JL, Harhay DM, Mcvey SD, R... | null | 10.1186/gb-2013-14-9-r101 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The short reads output by first- and second-generation DNA
sequencing instruments cannot completely reconstruct microbial chromosomes.
Therefore, most genomes have been left unfinished due to the significant
resources required to manually close gaps in draft assemblies.
Third-generation, single-molecule s... | [
{
"created": "Sat, 13 Apr 2013 00:25:43 GMT",
"version": "v1"
},
{
"created": "Thu, 2 May 2013 17:10:52 GMT",
"version": "v2"
},
{
"created": "Tue, 30 Jul 2013 20:50:29 GMT",
"version": "v3"
},
{
"created": "Fri, 2 Aug 2013 20:50:26 GMT",
"version": "v4"
},
{
"cre... | 2013-11-18 | [
[
"Koren",
"Sergey",
""
],
[
"Harhay",
"Gregory P",
""
],
[
"Smith",
"Timothy PL",
""
],
[
"Bono",
"James L",
""
],
[
"Harhay",
"Dayna M",
""
],
[
"Mcvey",
"D. Scott",
""
],
[
"Radune",
"Diana",
""
],
[
... | Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule seq... |
1809.00083 | Haicang Zhang | Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Shiwei Sun, Yujuan
Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu | Predicting protein inter-residue contacts using composite likelihood
maximization and deep learning | null | null | null | null | q-bio.BM cs.LG stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate prediction of inter-residue contacts of a protein is important to
calcu- lating its tertiary structure. Analysis of co-evolutionary events among
residues has been proved effective to inferring inter-residue contacts. The
Markov ran- dom field (MRF) technique, although being widely used for contact
prediction... | [
{
"created": "Fri, 31 Aug 2018 23:38:41 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"Zhang",
"Haicang",
""
],
[
"Zhang",
"Qi",
""
],
[
"Ju",
"Fusong",
""
],
[
"Zhu",
"Jianwei",
""
],
[
"Sun",
"Shiwei",
""
],
[
"Gao",
"Yujuan",
""
],
[
"Xie",
"Ziwei",
""
],
[
"Deng",
"Minghua",
... | Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov ran- dom field (MRF) technique, although being widely used for contact prediction, ... |
2007.14391 | Jialei Chen | Jialei Chen, Zhaonan Liu, Kan Wang, Chen Jiang, Chuck Zhang, Ben Wang | A calibration-free method for biosensing in cell manufacturing | null | IISE Transactions, 2020 | 10.1080/24725854.2020.1856982 | null | q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chimeric antigen receptor T cell therapy has demonstrated innovative
therapeutic effectiveness in fighting cancers; however, it is extremely
expensive due to the intrinsic patient-to-patient variability in cell
manufacturing. We propose in this work a novel calibration-free statistical
framework to effectively recove... | [
{
"created": "Mon, 27 Jul 2020 22:37:56 GMT",
"version": "v1"
}
] | 2021-05-18 | [
[
"Chen",
"Jialei",
""
],
[
"Liu",
"Zhaonan",
""
],
[
"Wang",
"Kan",
""
],
[
"Jiang",
"Chen",
""
],
[
"Zhang",
"Chuck",
""
],
[
"Wang",
"Ben",
""
]
] | Chimeric antigen receptor T cell therapy has demonstrated innovative therapeutic effectiveness in fighting cancers; however, it is extremely expensive due to the intrinsic patient-to-patient variability in cell manufacturing. We propose in this work a novel calibration-free statistical framework to effectively recover ... |
1807.01479 | Johannes Zierenberg | Johannes Zierenberg and Jens Wilting and Viola Priesemann | Homeostatic plasticity and external input shape neural network dynamics | 14 pages, 8 figures, accepted at Phys. Rev. X | Phys. Rev. X 8, 031018 (2018) | 10.1103/PhysRevX.8.031018 | null | q-bio.NC cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In vitro and in vivo spiking activity clearly differ. Whereas networks in
vitro develop strong bursts separated by periods of very little spiking
activity, in vivo cortical networks show continuous activity. This is puzzling
considering that both networks presumably share similar single-neuron dynamics
and plasticity... | [
{
"created": "Wed, 4 Jul 2018 08:30:38 GMT",
"version": "v1"
}
] | 2018-07-24 | [
[
"Zierenberg",
"Johannes",
""
],
[
"Wilting",
"Jens",
""
],
[
"Priesemann",
"Viola",
""
]
] | In vitro and in vivo spiking activity clearly differ. Whereas networks in vitro develop strong bursts separated by periods of very little spiking activity, in vivo cortical networks show continuous activity. This is puzzling considering that both networks presumably share similar single-neuron dynamics and plasticity r... |
2404.05732 | Ehud Ahissar | Ehud Ahissar, Daniel Polani, Merav Ahissar | Mapping the Mind-Brain Duality to a Digital-Analog Perceptual Duality | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Could the abstract ideas of our minds originate from neuronal interactions
within our brains? To address this question, we examine interactions within
'brain-world' (BW) and 'brain-brain' (BB) domains, which represent the brain's
physical interactions with its environment and the mental interactions between
brains, r... | [
{
"created": "Tue, 20 Feb 2024 19:01:44 GMT",
"version": "v1"
}
] | 2024-04-10 | [
[
"Ahissar",
"Ehud",
""
],
[
"Polani",
"Daniel",
""
],
[
"Ahissar",
"Merav",
""
]
] | Could the abstract ideas of our minds originate from neuronal interactions within our brains? To address this question, we examine interactions within 'brain-world' (BW) and 'brain-brain' (BB) domains, which represent the brain's physical interactions with its environment and the mental interactions between brains, res... |
2401.07719 | Sebastien Benzekry | Benjamin Schneider (ISU), S\'ebastien Benzekry (COMPO), Jonathan
Mochel (ISU) | Comprehensive Joint Modeling of First-Line Therapeutics in Non-Small
Cell Lung Cancer | null | null | null | null | q-bio.CB q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | First-line antiproliferatives for non-small cell lung cancer (NSCLC) have a
relatively high failure rate due to high intrinsic resistance rates and
acquired resistance rates to therapy. 57% patients are diagnosed in late-stage
disease due to the tendency of early-stage NSCLC to be asymptomatic. For
patients first dia... | [
{
"created": "Mon, 15 Jan 2024 14:35:45 GMT",
"version": "v1"
}
] | 2024-01-17 | [
[
"Schneider",
"Benjamin",
"",
"ISU"
],
[
"Benzekry",
"Sébastien",
"",
"COMPO"
],
[
"Mochel",
"Jonathan",
"",
"ISU"
]
] | First-line antiproliferatives for non-small cell lung cancer (NSCLC) have a relatively high failure rate due to high intrinsic resistance rates and acquired resistance rates to therapy. 57% patients are diagnosed in late-stage disease due to the tendency of early-stage NSCLC to be asymptomatic. For patients first diagn... |
2403.03000 | Niklas Hohmann | Niklas Hohmann | Possible and Impossible Inferences From Reconstructed Evolutionary
Processes using Phylogenies as an Example | null | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by-sa/4.0/ | Our understanding of past evolutionary change is often based on
reconstructions based on incomplete data, raising fundamental questions about
the degree to which we can make reliable inferences about past evolutionary
processes. This was demonstrated by Louca and Pennell (2020), who showed that
each pure-birth proces... | [
{
"created": "Mon, 4 Mar 2024 16:48:14 GMT",
"version": "v1"
}
] | 2024-03-06 | [
[
"Hohmann",
"Niklas",
""
]
] | Our understanding of past evolutionary change is often based on reconstructions based on incomplete data, raising fundamental questions about the degree to which we can make reliable inferences about past evolutionary processes. This was demonstrated by Louca and Pennell (2020), who showed that each pure-birth process ... |
1809.01538 | Adeshina Adekunle | Adeshina I. Adekunle, Michael T. Meehan, Emma S. McBryde | Mathematical analysis of a Wolbachia invasive model with imperfect
maternal transmission and loss of Wolbachia infection | null | https://doi.org/10.1016/j.idm.2019.10.001 | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Arboviral infections, especially dengue, continue to cause significant health
burden in their endemic regions. One of the strategies to tackle these
infections is to replace the main vector agent, Ae. aegypti, with the ones
incapable of transmitting the virus. Wolbachia, an intracellular bacterium, has
shown promise ... | [
{
"created": "Tue, 4 Sep 2018 05:56:04 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Jun 2019 01:46:42 GMT",
"version": "v2"
}
] | 2019-10-22 | [
[
"Adekunle",
"Adeshina I.",
""
],
[
"Meehan",
"Michael T.",
""
],
[
"McBryde",
"Emma S.",
""
]
] | Arboviral infections, especially dengue, continue to cause significant health burden in their endemic regions. One of the strategies to tackle these infections is to replace the main vector agent, Ae. aegypti, with the ones incapable of transmitting the virus. Wolbachia, an intracellular bacterium, has shown promise in... |
1412.7972 | Antti Niemi | Jianfeng He, Jin Dai, Jing Li, Xubiao Peng, Antti J. Niemi | Aspects of structural landscape of human islet amyloid polypeptide | null | null | 10.1063/1.4905586 | null | q-bio.BM cond-mat.soft nlin.PS physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The human islet amyloid polypeptide (hIAPP) co-operates with insulin to
maintain glycemic balance. It also constitutes the amyloid plaques that
aggregate in the pancreas of type-II diabetic patients. We have performed
extensive in silico investigations to analyse the structural landscape of
monomeric hIAPP, which is ... | [
{
"created": "Fri, 26 Dec 2014 19:07:18 GMT",
"version": "v1"
}
] | 2015-06-23 | [
[
"He",
"Jianfeng",
""
],
[
"Dai",
"Jin",
""
],
[
"Li",
"Jing",
""
],
[
"Peng",
"Xubiao",
""
],
[
"Niemi",
"Antti J.",
""
]
] | The human islet amyloid polypeptide (hIAPP) co-operates with insulin to maintain glycemic balance. It also constitutes the amyloid plaques that aggregate in the pancreas of type-II diabetic patients. We have performed extensive in silico investigations to analyse the structural landscape of monomeric hIAPP, which is pr... |
1405.6411 | Artem Novozhilov S | Yuri S. Semenov, Alexander S. Bratus, Artem S. Novozhilov | On the behavior of the leading eigenvalue of Eigen's evolutionary
matrices | 37 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study general properties of the leading eigenvalue $\overline{w}(q)$ of
Eigen's evolutionary matrices depending on the probability $q$ of faithful
reproduction. This is a linear algebra problem that has various applications in
theoretical biology, including such diverse fields as the origin of life,
evolution of c... | [
{
"created": "Sun, 25 May 2014 18:02:25 GMT",
"version": "v1"
}
] | 2014-05-27 | [
[
"Semenov",
"Yuri S.",
""
],
[
"Bratus",
"Alexander S.",
""
],
[
"Novozhilov",
"Artem S.",
""
]
] | We study general properties of the leading eigenvalue $\overline{w}(q)$ of Eigen's evolutionary matrices depending on the probability $q$ of faithful reproduction. This is a linear algebra problem that has various applications in theoretical biology, including such diverse fields as the origin of life, evolution of can... |
2306.04582 | Carla Goldman | Pedro Ribeiro de Almeida, Vitor Hirata Sanches, Carla Goldman | Balancing the Benefits of Vaccination: an Envy-Free Strategy | 28 pages, 11 figures | null | null | null | q-bio.QM physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Covid-19 pandemic revealed the difficulties of vaccinating a population
under the circumstances marked by urgency and limited availability of doses
while balancing benefits associated with distinct guidelines satisfying
specific ethical criteria (J.W. Wu, S.D. John, E.Y. Adashi, Allocating Vaccines
in the Pandemi... | [
{
"created": "Wed, 7 Jun 2023 16:34:15 GMT",
"version": "v1"
}
] | 2023-06-08 | [
[
"de Almeida",
"Pedro Ribeiro",
""
],
[
"Sanches",
"Vitor Hirata",
""
],
[
"Goldman",
"Carla",
""
]
] | The Covid-19 pandemic revealed the difficulties of vaccinating a population under the circumstances marked by urgency and limited availability of doses while balancing benefits associated with distinct guidelines satisfying specific ethical criteria (J.W. Wu, S.D. John, E.Y. Adashi, Allocating Vaccines in the Pandemic:... |
1512.00424 | Vicente M. Reyes Ph.D. | Vicente M. Reyes | Implementation of the Spherical Coordinate Representation of Protein 3D
Structures and its Applications Using FORTRAN 77/90 Language | 36 pages, 10228 words total (27 pages/9384 words text, 9 pages/844
words figures+tables+legends), 7 figures total (fig. 1: panels A, B & C, fig.
2: panels A, B, C & D), 6 tables total (tbl. 1, tbl. 2, tbl. 3: panels A, B &
C, tbl. 4) | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We previously described the representation of protein 3D structures in
spherical coordinates (rho, phi, theta) and two of its applications: separation
of the outer layer (OL) from the inner core (IC) of proteins, and assessment of
protein surface protrusions and invaginations (Reyes, V.M., 2011& 2009). Here
we presen... | [
{
"created": "Mon, 30 Nov 2015 08:12:59 GMT",
"version": "v1"
}
] | 2015-12-02 | [
[
"Reyes",
"Vicente M.",
""
]
] | We previously described the representation of protein 3D structures in spherical coordinates (rho, phi, theta) and two of its applications: separation of the outer layer (OL) from the inner core (IC) of proteins, and assessment of protein surface protrusions and invaginations (Reyes, V.M., 2011& 2009). Here we present ... |
1304.6966 | Zhandong Liu | Ying-Wooi Wan, Claire M. Mach, Genevera Allen, Matthew L. Anderson,
Zhandong Liu | On the Reproducibility of TCGA Ovarian Cancer MicroRNA Profiles | null | null | 10.1371/journal.pone.0087782 | null | q-bio.GN stat.AP | http://creativecommons.org/licenses/publicdomain/ | Dysregulated microRNA (miRNA) expression is a well-established feature of
human cancer. However, the role of specific miRNAs in determining cancer
outcomes remains unclear. Using Level 3 expression data from the Cancer Genome
Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival
in 469 ovari... | [
{
"created": "Thu, 25 Apr 2013 17:34:52 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Nov 2013 22:47:49 GMT",
"version": "v2"
}
] | 2014-03-05 | [
[
"Wan",
"Ying-Wooi",
""
],
[
"Mach",
"Claire M.",
""
],
[
"Allen",
"Genevera",
""
],
[
"Anderson",
"Matthew L.",
""
],
[
"Liu",
"Zhandong",
""
]
] | Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA), we identified 61 miRNAs that are associated with overall survival in 469 ovarian... |
2103.00867 | Tatjana Pyragiene | Kestutis Pyragas, Augustinas P. Fedaravi\v{c}ius, Tatjana Pyragien\.e | Suppression of synchronous spiking in two interacting populations of
excitatory and inhibitory quadratic integrate-and-fire neurons | 11 figures | Phys. Rev. E 104, 014203 (2021) | 10.1103/PhysRevE.104.014203 | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Collective oscillations and their suppression by external stimulation are
analyzed in a large-scale neural network consisting of two interacting
populations of excitatory and inhibitory quadratic integrate-and-fire neurons.
In the limit of an infinite number of neurons, the microscopic model of this
network can be re... | [
{
"created": "Mon, 1 Mar 2021 09:36:54 GMT",
"version": "v1"
},
{
"created": "Mon, 5 Jul 2021 08:00:33 GMT",
"version": "v2"
}
] | 2021-07-14 | [
[
"Pyragas",
"Kestutis",
""
],
[
"Fedaravičius",
"Augustinas P.",
""
],
[
"Pyragienė",
"Tatjana",
""
]
] | Collective oscillations and their suppression by external stimulation are analyzed in a large-scale neural network consisting of two interacting populations of excitatory and inhibitory quadratic integrate-and-fire neurons. In the limit of an infinite number of neurons, the microscopic model of this network can be redu... |
2407.00040 | Alwani Liyana Ahmad | Alwani Liyana Ahmad, Jose Sanchez-Bornot, Roberto C. Sotero, Damien
Coyle, Zamzuri Idris, and Ibrahima Faye | A Machine Learning Approach for Identifying Anatomical Biomarkers of
Early Mild Cognitive Impairment | 34 pages, 6 figures, 7 tables | null | null | null | q-bio.NC cs.LG eess.SP | http://creativecommons.org/licenses/by/4.0/ | Alzheimer Disease poses a significant challenge, necessitating early
detection for effective intervention. MRI is a key neuroimaging tool due to its
ease of use and cost effectiveness. This study analyzes machine learning
methods for MRI based biomarker selection and classification to distinguish
between healthy cont... | [
{
"created": "Wed, 29 May 2024 06:12:05 GMT",
"version": "v1"
},
{
"created": "Fri, 9 Aug 2024 02:00:05 GMT",
"version": "v2"
}
] | 2024-08-12 | [
[
"Ahmad",
"Alwani Liyana",
""
],
[
"Sanchez-Bornot",
"Jose",
""
],
[
"Sotero",
"Roberto C.",
""
],
[
"Coyle",
"Damien",
""
],
[
"Idris",
"Zamzuri",
""
],
[
"Faye",
"Ibrahima",
""
]
] | Alzheimer Disease poses a significant challenge, necessitating early detection for effective intervention. MRI is a key neuroimaging tool due to its ease of use and cost effectiveness. This study analyzes machine learning methods for MRI based biomarker selection and classification to distinguish between healthy contro... |
q-bio/0612039 | Maksim Kouza M | Maksim Kouza, Mai Suan Li, Edward P. O'Brien Jr., Chin-Kun Hu and D.
Thirumalai | Effect of finite size on cooperativity and rates of protein folding | 17 pages, 3 figures, 2 tables | J. Phys. Chem. A 110, 671 (2006) | 10.1021/jp053770b | null | q-bio.BM | null | We analyze the dependence of cooperativity of the thermal denaturation
transition and folding rates of globular proteins on the number of amino acid
residues, $N$, using lattice models with side chains,off-lattice Go models and
the available experimental data. A dimensionless measure of cooperativity,
$\Omega_c$ ($0 ... | [
{
"created": "Thu, 21 Dec 2006 15:14:45 GMT",
"version": "v1"
}
] | 2016-09-28 | [
[
"Kouza",
"Maksim",
""
],
[
"Li",
"Mai Suan",
""
],
[
"O'Brien",
"Edward P.",
"Jr."
],
[
"Hu",
"Chin-Kun",
""
],
[
"Thirumalai",
"D.",
""
]
] | We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, $N$, using lattice models with side chains,off-lattice Go models and the available experimental data. A dimensionless measure of cooperativity, $\Omega_c$ ($0 < ... |
2308.08524 | Carsten Conradi | Carsten Conradi and Maya Mincheva | In distributive phosphorylation catalytic constants enable non-trivial
dynamics | null | null | null | null | q-bio.MN math.DS | http://creativecommons.org/licenses/by/4.0/ | Ordered distributive double phosphorylation is a recurrent motif in
intracellular signaling and control. It is either sequential (where the site
phosphorylated last is dephosphorylated first) or cyclic (where the site
phosphorylated first is dephosphorylated first). Sequential distributive double
phosphorylation has ... | [
{
"created": "Wed, 16 Aug 2023 17:20:52 GMT",
"version": "v1"
},
{
"created": "Thu, 8 Feb 2024 18:05:49 GMT",
"version": "v2"
}
] | 2024-02-09 | [
[
"Conradi",
"Carsten",
""
],
[
"Mincheva",
"Maya",
""
]
] | Ordered distributive double phosphorylation is a recurrent motif in intracellular signaling and control. It is either sequential (where the site phosphorylated last is dephosphorylated first) or cyclic (where the site phosphorylated first is dephosphorylated first). Sequential distributive double phosphorylation has be... |
1903.07551 | Eryu Xia | Eryu Xia, Yiqin Yu, Enliang Xu, Jing Mei, Wen Sun | From Risk Prediction Models to Risk Assessment Service: A Formulation of
Development Paradigm | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Risk assessment services fulfil the task of generating a risk report from
personal information and are developed for purposes like disease prognosis,
resource utilization prioritization, and informing clinical interventions. A
major component of a risk assessment service is a risk prediction model. For a
model to be ... | [
{
"created": "Fri, 1 Mar 2019 02:54:46 GMT",
"version": "v1"
}
] | 2019-03-19 | [
[
"Xia",
"Eryu",
""
],
[
"Yu",
"Yiqin",
""
],
[
"Xu",
"Enliang",
""
],
[
"Mei",
"Jing",
""
],
[
"Sun",
"Wen",
""
]
] | Risk assessment services fulfil the task of generating a risk report from personal information and are developed for purposes like disease prognosis, resource utilization prioritization, and informing clinical interventions. A major component of a risk assessment service is a risk prediction model. For a model to be ea... |
1807.06740 | Zachary Kilpatrick PhD | Nikhil Krishnan and Zachary P. Kilpatrick | Optimizing a jump-diffusion model of a starving forager | 8 pages, 5 figures | Phys. Rev. E 98, 052406 (2018) | 10.1103/PhysRevE.98.052406 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the movement of a starving forager on a one-dimensional periodic
lattice, where each location contains one unit of food. As the forager lands on
sites with food, it consumes the food, leaving the sites empty. If the forager
lands consecutively on $s$ empty sites, then it will starve. The forager has
two mo... | [
{
"created": "Wed, 18 Jul 2018 02:23:27 GMT",
"version": "v1"
}
] | 2018-11-28 | [
[
"Krishnan",
"Nikhil",
""
],
[
"Kilpatrick",
"Zachary P.",
""
]
] | We analyze the movement of a starving forager on a one-dimensional periodic lattice, where each location contains one unit of food. As the forager lands on sites with food, it consumes the food, leaving the sites empty. If the forager lands consecutively on $s$ empty sites, then it will starve. The forager has two mode... |
2202.07473 | Ahmed Hafez | Ahmed Hafez, Beatriz Soriano, Aya A. Elsayed, Ricardo Futami, Raquel
Ceprian, Ricardo Ramos-Ruiz, Genis Martinez, Francisco J. Roig, Miguel A.
Torres-Font, Fernando Naya-Catal\`a, Josep Alvar Calduch-Giner, Lucia
Trilla-Fuertes, Angelo Gamez-Pozo, Vicente Arnau, Jose M. Sempere, Jaume
Perez-S\'anchez, Toni Gaba... | Client applications and Server Side docker for management of RNASeq
and/or VariantSeq workflows and pipelines of the GPRO Suite | null | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The GPRO suite is an in-progress bioinformatic project for -omic data
analyses. As part of the continued growth of this project, we introduce a
client side & server side solution for comparative transcriptomics and analysis
of variants. The client side consists of two Java applications called "RNASeq"
and "VariantSeq... | [
{
"created": "Mon, 14 Feb 2022 12:00:35 GMT",
"version": "v1"
},
{
"created": "Mon, 23 May 2022 13:28:45 GMT",
"version": "v2"
},
{
"created": "Mon, 8 Aug 2022 06:39:41 GMT",
"version": "v3"
},
{
"created": "Sat, 19 Nov 2022 12:29:58 GMT",
"version": "v4"
}
] | 2022-11-22 | [
[
"Hafez",
"Ahmed",
""
],
[
"Soriano",
"Beatriz",
""
],
[
"Elsayed",
"Aya A.",
""
],
[
"Futami",
"Ricardo",
""
],
[
"Ceprian",
"Raquel",
""
],
[
"Ramos-Ruiz",
"Ricardo",
""
],
[
"Martinez",
"Genis",
""
],
... | The GPRO suite is an in-progress bioinformatic project for -omic data analyses. As part of the continued growth of this project, we introduce a client side & server side solution for comparative transcriptomics and analysis of variants. The client side consists of two Java applications called "RNASeq" and "VariantSeq" ... |
2104.02794 | Janaki Raghavan | R. Janaki and A. S. Vytheeswaran | The interplay of inhibitory and electrical synapses results in complex
persistent activity | Main text: 10 pages, 5 figures; Supplementary Information: 2 pages, 3
figures | null | null | null | q-bio.NC nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inhibitory neurons play a crucial role in maintaining persistent neuronal
activity. Although connected extensively through electrical synapses
(gap-junctions), these neurons also exhibit interactions through chemical
synapses in certain regions of the brain. When the coupling is sufficiently
strong, the effects of th... | [
{
"created": "Tue, 6 Apr 2021 21:25:58 GMT",
"version": "v1"
}
] | 2021-04-08 | [
[
"Janaki",
"R.",
""
],
[
"Vytheeswaran",
"A. S.",
""
]
] | Inhibitory neurons play a crucial role in maintaining persistent neuronal activity. Although connected extensively through electrical synapses (gap-junctions), these neurons also exhibit interactions through chemical synapses in certain regions of the brain. When the coupling is sufficiently strong, the effects of thes... |
1502.00156 | Ulrich S. Schwarz | Johanna E. Baschek, Heinrich C. R. Klein and Ulrich S. Schwarz
(Heidelberg University) | Stochastic dynamics of virus capsid formation: direct versus
hierarchical self-assembly | Revtex, 31 pages, 9 EPS figures | BMC Biophysics 5:22 (2012) | 10.1186/2046-1682-5-22 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In order to replicate within their cellular host, many viruses have developed
self-assembly strategies for their capsids which are sufficiently robust as to
be reconstituted in vitro. Mathematical models for virus self-assembly usually
assume that the bonds leading to cluster formation have constant reactivity
over t... | [
{
"created": "Sat, 31 Jan 2015 19:47:54 GMT",
"version": "v1"
}
] | 2015-02-03 | [
[
"Baschek",
"Johanna E.",
"",
"Heidelberg University"
],
[
"Klein",
"Heinrich C. R.",
"",
"Heidelberg University"
],
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg University"
]
] | In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the... |
q-bio/0505003 | William Bialek | William Bialek and Rob R. de Ruyter van Steveninck | Features and dimensions: Motion estimation in fly vision | 18 pages, 11 figures, some in color | null | null | null | q-bio.NC | null | We characterize the computation of motion in the fly visual system as a
mapping from the high dimensional space of signals in the retinal photodetector
array to the probability of generating an action potential in a motion
sensitive neuron. Our approach to this problem identifies a low dimensional
subspace of signals... | [
{
"created": "Mon, 2 May 2005 22:02:58 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Bialek",
"William",
""
],
[
"van Steveninck",
"Rob R. de Ruyter",
""
]
] | We characterize the computation of motion in the fly visual system as a mapping from the high dimensional space of signals in the retinal photodetector array to the probability of generating an action potential in a motion sensitive neuron. Our approach to this problem identifies a low dimensional subspace of signals w... |
1606.01319 | Vladimir Privman | Sergii Domanskyi, Vladimir Privman | Modeling and Modifying Response of Biochemical Processes for
Biocomputing and Biosensing Signal Processing | arXiv admin note: text overlap with arXiv:1305.5803, arXiv:1411.2185 | Ch. 3 in Advances in Unconventional Computing, Vol. 2: Prototypes,
Models and Algorithms, pages 61-83, edited by A. Adamatzky, Vol. 23 of
Emergence, Complexity and Computation (Springer Nature, Basel, Switzerland,
2017) | 10.1007/978-3-319-33921-4_3 | VP-271 | q-bio.MN cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Processes involving multi-input multi-step reaction cascades are used in
developing novel biosensing, biocomputing, and decision making systems. In
various applications different changes in responses of the constituent
processing steps (reactions) in a cascade are desirable in order to allow
control of the system's r... | [
{
"created": "Sat, 4 Jun 2016 02:28:35 GMT",
"version": "v1"
}
] | 2016-08-16 | [
[
"Domanskyi",
"Sergii",
""
],
[
"Privman",
"Vladimir",
""
]
] | Processes involving multi-input multi-step reaction cascades are used in developing novel biosensing, biocomputing, and decision making systems. In various applications different changes in responses of the constituent processing steps (reactions) in a cascade are desirable in order to allow control of the system's res... |
1903.02890 | Kelin Xia | Zhenyu Meng, D Vijay Anand, Yunpeng Lu, Jie Wu, Kelin Xia | Weighted persistent homology for biomolecular data analysis | 27 pages; 18 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we systematically review weighted persistent homology (WPH)
models and their applications in biomolecular data analysis. Essentially, the
weight value, which reflects physical, chemical and biological properties, can
be assigned to vertices (atom centers), edges (bonds), or higher order
simplexes (clus... | [
{
"created": "Thu, 7 Mar 2019 13:09:33 GMT",
"version": "v1"
}
] | 2019-03-08 | [
[
"Meng",
"Zhenyu",
""
],
[
"Anand",
"D Vijay",
""
],
[
"Lu",
"Yunpeng",
""
],
[
"Wu",
"Jie",
""
],
[
"Xia",
"Kelin",
""
]
] | In this paper, we systematically review weighted persistent homology (WPH) models and their applications in biomolecular data analysis. Essentially, the weight value, which reflects physical, chemical and biological properties, can be assigned to vertices (atom centers), edges (bonds), or higher order simplexes (cluste... |
1710.10080 | Daan Brinks | Miao-Ping Chien, Daan Brinks, Yoav Adam, William Bloxham, Simon
Kheifets, Adam E. Cohen | Two-photon photoactivated voltage imaging in tissue with an
Archaerhodopsin-derived reporter | null | null | null | null | q-bio.QM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Robust voltage imaging in tissue remains a technical challenge. Existing
combinations of genetically encoded voltage indicators (GEVIs) and microscopy
techniques cannot simultaneously achieve sufficiently high voltage sensitivity,
background rejection, and time resolution for high-resolution mapping of
sub-cellular v... | [
{
"created": "Fri, 27 Oct 2017 11:21:30 GMT",
"version": "v1"
}
] | 2017-10-30 | [
[
"Chien",
"Miao-Ping",
""
],
[
"Brinks",
"Daan",
""
],
[
"Adam",
"Yoav",
""
],
[
"Bloxham",
"William",
""
],
[
"Kheifets",
"Simon",
""
],
[
"Cohen",
"Adam E.",
""
]
] | Robust voltage imaging in tissue remains a technical challenge. Existing combinations of genetically encoded voltage indicators (GEVIs) and microscopy techniques cannot simultaneously achieve sufficiently high voltage sensitivity, background rejection, and time resolution for high-resolution mapping of sub-cellular vol... |
0805.4316 | Vasily Ogryzko V | Vasily Ogryzko | On two quantum approaches to adaptive mutations in bacteria | 35 pages, 6 figures, 3 tables, 1 Appendix. This version was accepted
in the NeuroQuantology Journal. Format has been adjusted accordingly,
together with a number of clarifying modifications | null | null | null | q-bio.PE q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I compare two quantum-theoretical approaches to the phenomenon of adaptive
mutations, termed here Q-cell and Q-genome. I use 'fluctuation trapping' model
as a general framework. I introduce notions of R-error and D-error and argue
that the 'fluctuation trapping' model has to employ a correlation between the
R- and D-... | [
{
"created": "Wed, 28 May 2008 11:59:22 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Jul 2008 11:15:56 GMT",
"version": "v2"
},
{
"created": "Thu, 31 Jul 2008 14:36:46 GMT",
"version": "v3"
},
{
"created": "Mon, 7 Sep 2009 15:33:37 GMT",
"version": "v4"
}
] | 2009-09-07 | [
[
"Ogryzko",
"Vasily",
""
]
] | I compare two quantum-theoretical approaches to the phenomenon of adaptive mutations, termed here Q-cell and Q-genome. I use 'fluctuation trapping' model as a general framework. I introduce notions of R-error and D-error and argue that the 'fluctuation trapping' model has to employ a correlation between the R- and D- e... |
2210.01546 | Jai Sharma | Jai Sharma, Vidhyacharan Bhaskar | An RNA Sequencing Analysis of Glaucoma Genesis in Mice | 6 pages, 6 figures | null | null | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Glaucoma is the leading cause of irreversible blindness in people over the
age of 60, accounting for 6.6 to 8% of all blindness in 2010, but there is
still much to be learned about the genetic origins of the eye disease. With the
modern development of Next-Generation Sequencing (NGS) technologies, scientists
are star... | [
{
"created": "Sun, 2 Oct 2022 10:16:31 GMT",
"version": "v1"
}
] | 2022-10-05 | [
[
"Sharma",
"Jai",
""
],
[
"Bhaskar",
"Vidhyacharan",
""
]
] | Glaucoma is the leading cause of irreversible blindness in people over the age of 60, accounting for 6.6 to 8% of all blindness in 2010, but there is still much to be learned about the genetic origins of the eye disease. With the modern development of Next-Generation Sequencing (NGS) technologies, scientists are starti... |
0708.1598 | HC Paul Lee | Sing-Guan Kong, Hong-Da Chen, Wen-Lang Fan, Jan Wigger, Andrew Torda,
and HC Lee | Genomes: at the edge of chaos with maximum information capacity | 4 pages, 3 figures, paper | null | null | null | q-bio.GN | null | We propose an order index, phi, which quantifies the notion of ``life at the
edge of chaos'' when applied to genome sequences. It maps genomes to a number
from 0 (random and of infinite length) to 1 (fully ordered) and applies
regardless of sequence length. The 786 complete genomic sequences in GenBank
were found to ... | [
{
"created": "Sun, 12 Aug 2007 07:45:19 GMT",
"version": "v1"
}
] | 2007-08-14 | [
[
"Kong",
"Sing-Guan",
""
],
[
"Chen",
"Hong-Da",
""
],
[
"Fan",
"Wen-Lang",
""
],
[
"Wigger",
"Jan",
""
],
[
"Torda",
"Andrew",
""
],
[
"Lee",
"HC",
""
]
] | We propose an order index, phi, which quantifies the notion of ``life at the edge of chaos'' when applied to genome sequences. It maps genomes to a number from 0 (random and of infinite length) to 1 (fully ordered) and applies regardless of sequence length. The 786 complete genomic sequences in GenBank were found to ha... |
2305.06808 | Glen Pridham | Rebecca Tobin, Glen Pridham, Andrew D. Rutenberg | Modelling disease impact: lifespan reduction is greatest for young
adults in an exogenous damage model of disease | null | Sci. Rep. 13 (2023) 1-10 | 10.1038/s41598-023-43005-0 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We model the effects of disease and other exogenous damage during human
aging. Even when the exogenous damage is repaired at the end of acute disease,
propagated secondary damage remains. We consider both short-term mortality
effects due to (acute) exogenous damage and long-term mortality effects due to
propagated da... | [
{
"created": "Thu, 11 May 2023 14:01:41 GMT",
"version": "v1"
},
{
"created": "Sat, 29 Jul 2023 13:59:37 GMT",
"version": "v2"
}
] | 2023-09-29 | [
[
"Tobin",
"Rebecca",
""
],
[
"Pridham",
"Glen",
""
],
[
"Rutenberg",
"Andrew D.",
""
]
] | We model the effects of disease and other exogenous damage during human aging. Even when the exogenous damage is repaired at the end of acute disease, propagated secondary damage remains. We consider both short-term mortality effects due to (acute) exogenous damage and long-term mortality effects due to propagated dama... |
0805.0819 | Luis Trevisan | Luis Augusto Trevisan and Fabiano Meira de Moura Luz | Prey-predator modeling of CO2 atmospheric concentration | Key words:Prey Predator model, Photosynthesis rate, CO2 concentration | null | null | null | q-bio.OT q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work we propose a mathematical model, based in a modified version of
the Lotka-Volterra prey-predator equations, to predict the increasing in CO2
atmospheric concentration. We consider how the photosynthesis rate has changed
with the increase of CO2 and how this affects plant reproduction and CO2
absorptions ... | [
{
"created": "Wed, 7 May 2008 01:13:32 GMT",
"version": "v1"
}
] | 2008-05-08 | [
[
"Trevisan",
"Luis Augusto",
""
],
[
"Luz",
"Fabiano Meira de Moura",
""
]
] | In this work we propose a mathematical model, based in a modified version of the Lotka-Volterra prey-predator equations, to predict the increasing in CO2 atmospheric concentration. We consider how the photosynthesis rate has changed with the increase of CO2 and how this affects plant reproduction and CO2 absorptions ra... |
1602.06584 | Lionel Roques | Mamadou Ciss, Sylvain Poggi, Mohamed-Mahmoud Memmah, Pierre Franck,
Marie Gosme, Nicolas Parisey and Lionel Roques | A model-based approach to assess the effectiveness of pest biocontrol by
natural enemies | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Main goal: The aim of this note is to propose a modeling approach for
assessing the effectiveness of pest biocontrol by natural enemies in
diversified agricultural landscapes including several pesticide-based
management strategies. Our approach combines a stochastic landscape model with
a spatially-explicit model of ... | [
{
"created": "Sun, 21 Feb 2016 21:28:05 GMT",
"version": "v1"
}
] | 2016-02-23 | [
[
"Ciss",
"Mamadou",
""
],
[
"Poggi",
"Sylvain",
""
],
[
"Memmah",
"Mohamed-Mahmoud",
""
],
[
"Franck",
"Pierre",
""
],
[
"Gosme",
"Marie",
""
],
[
"Parisey",
"Nicolas",
""
],
[
"Roques",
"Lionel",
""
]
] | Main goal: The aim of this note is to propose a modeling approach for assessing the effectiveness of pest biocontrol by natural enemies in diversified agricultural landscapes including several pesticide-based management strategies. Our approach combines a stochastic landscape model with a spatially-explicit model of po... |
2010.07437 | Axel Wism\"uller | Axel Wism\"uller and Larry Stockmaster | Tracking Results and Utilization of Artificial Intelligence (tru-AI) in
Radiology: Early-Stage COVID-19 Pandemic Observations | 9 pages, 1 figure, 1 table | null | null | null | q-bio.QM cs.LG q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: To introduce a method for tracking results and utilization of
Artificial Intelligence (tru-AI) in radiology. By tracking both large-scale
utilization and AI results data, the tru-AI approach is designed to calculate
surrogates for measuring important disease-related observational quantities
over time, such... | [
{
"created": "Wed, 14 Oct 2020 23:37:15 GMT",
"version": "v1"
}
] | 2020-10-16 | [
[
"Wismüller",
"Axel",
""
],
[
"Stockmaster",
"Larry",
""
]
] | Objective: To introduce a method for tracking results and utilization of Artificial Intelligence (tru-AI) in radiology. By tracking both large-scale utilization and AI results data, the tru-AI approach is designed to calculate surrogates for measuring important disease-related observational quantities over time, such a... |
1211.0937 | Bernhard Mehlig | M. Rafajlovic, A. Eriksson, A. Rimark, S. H. Saltin, G. Charrier, M.
Panova, C. Andr\'e, K. Johannesson, and B. Mehlig | The effect of multiple paternity on genetic diversity during and after
colonisation | 7 pages, 5 figures, electronic supplementary material | PLoS ONE 8(10) e75587 (2013) | 10.1371/journal.pone.0075587 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In metapopulations, genetic variation of local populations is influenced by
the genetic content of the founders, and of migrants following establishment.
We analyse the effect of multiple paternity on genetic diversity using a model
in which the highly promiscuous marine snail Littorina saxatilis expands from a
mainl... | [
{
"created": "Mon, 5 Nov 2012 17:23:36 GMT",
"version": "v1"
}
] | 2013-10-30 | [
[
"Rafajlovic",
"M.",
""
],
[
"Eriksson",
"A.",
""
],
[
"Rimark",
"A.",
""
],
[
"Saltin",
"S. H.",
""
],
[
"Charrier",
"G.",
""
],
[
"Panova",
"M.",
""
],
[
"André",
"C.",
""
],
[
"Johannesson",
"... | In metapopulations, genetic variation of local populations is influenced by the genetic content of the founders, and of migrants following establishment. We analyse the effect of multiple paternity on genetic diversity using a model in which the highly promiscuous marine snail Littorina saxatilis expands from a mainlan... |
2006.16735 | Erik Aurell | Hong-Li Zeng, Eugenio Mauri, Vito Dichio, Simona Cocco, Remi Monasson,
Erik Aurell | Inferring epistasis from genomic data with comparable mutation and
outcrossing rate | 16 pages, 9 figures. Substantial revision from second version,
previous suggestions and comments gratefully acknowledged | null | 10.1088/1742-5468/ac0f64 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a population evolving due to mutation, selection and
recombination, where selection includes single-locus terms (additive fitness)
and two-loci terms (pairwise epistatic fitness). We further consider the
problem of inferring fitness in the evolutionary dynamics from one or several
snap-shots of the distri... | [
{
"created": "Tue, 30 Jun 2020 12:45:19 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Dec 2020 15:21:04 GMT",
"version": "v2"
},
{
"created": "Tue, 4 May 2021 07:50:49 GMT",
"version": "v3"
}
] | 2021-09-01 | [
[
"Zeng",
"Hong-Li",
""
],
[
"Mauri",
"Eugenio",
""
],
[
"Dichio",
"Vito",
""
],
[
"Cocco",
"Simona",
""
],
[
"Monasson",
"Remi",
""
],
[
"Aurell",
"Erik",
""
]
] | We consider a population evolving due to mutation, selection and recombination, where selection includes single-locus terms (additive fitness) and two-loci terms (pairwise epistatic fitness). We further consider the problem of inferring fitness in the evolutionary dynamics from one or several snap-shots of the distribu... |
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