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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2401.15478 | Anthony Gitter | Daniel McNeela, Frederic Sala, Anthony Gitter | Product Manifold Representations for Learning on Biological Pathways | 28 pages, 19 figures | null | null | null | q-bio.QM cs.LG q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Machine learning models that embed graphs in non-Euclidean spaces have shown
substantial benefits in a variety of contexts, but their application has not
been studied extensively in the biological domain, particularly with respect to
biological pathway graphs. Such graphs exhibit a variety of complex network
structur... | [
{
"created": "Sat, 27 Jan 2024 18:46:19 GMT",
"version": "v1"
}
] | 2024-01-30 | [
[
"McNeela",
"Daniel",
""
],
[
"Sala",
"Frederic",
""
],
[
"Gitter",
"Anthony",
""
]
] | Machine learning models that embed graphs in non-Euclidean spaces have shown substantial benefits in a variety of contexts, but their application has not been studied extensively in the biological domain, particularly with respect to biological pathway graphs. Such graphs exhibit a variety of complex network structures... |
1712.02289 | Massimo Cencini Dr. | Massimo Cencini and Simone Pigolotti | Energetic funnel facilitates facilitated diffusion | 10 pages, Nucleic Acids Research in press. Supplementary information
available from the Journal (at
https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkx1220/4690584) | null | 10.1093/nar/gkx1220 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcription factors are able to associate to their binding sites on DNA
faster than the physical limit posed by diffusion. Such high association rates
can be achieved by alternating between three-dimensional diffusion and
one-dimensional sliding along the DNA chain, a mechanism dubbed Facilitated
Diffusion. By stud... | [
{
"created": "Wed, 6 Dec 2017 17:13:01 GMT",
"version": "v1"
}
] | 2017-12-07 | [
[
"Cencini",
"Massimo",
""
],
[
"Pigolotti",
"Simone",
""
]
] | Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism dubbed Facilitated Diffusion. By studyi... |
2203.02493 | Michael Beyeler | Ashley Bruce and Michael Beyeler | Greedy Optimization of Electrode Arrangement for Epiretinal Prostheses | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Visual neuroprostheses are the only FDA-approved technology for the treatment
of retinal degenerative blindness. Although recent work has demonstrated a
systematic relationship between electrode location and the shape of the
elicited visual percept, this knowledge has yet to be incorporated into retinal
prosthesis de... | [
{
"created": "Fri, 4 Mar 2022 18:45:43 GMT",
"version": "v1"
},
{
"created": "Thu, 30 Jun 2022 23:10:23 GMT",
"version": "v2"
}
] | 2022-07-04 | [
[
"Bruce",
"Ashley",
""
],
[
"Beyeler",
"Michael",
""
]
] | Visual neuroprostheses are the only FDA-approved technology for the treatment of retinal degenerative blindness. Although recent work has demonstrated a systematic relationship between electrode location and the shape of the elicited visual percept, this knowledge has yet to be incorporated into retinal prosthesis desi... |
1803.03189 | Gary Wilk | Gary Wilk, Rosemary Braun | Single nucleotide polymorphisms that modulate microRNA regulation of
gene expression in tumors | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-wide association studies (GWAS) have identified single nucleotide
polymorphisms (SNPs) associated with trait diversity and disease
susceptibility, yet the functional properties of many genetic variants and
their molecular interactions remains unclear. It has been hypothesized that
SNPs in microRNA binding site... | [
{
"created": "Thu, 8 Mar 2018 16:31:51 GMT",
"version": "v1"
},
{
"created": "Tue, 20 Mar 2018 14:13:43 GMT",
"version": "v2"
}
] | 2018-03-21 | [
[
"Wilk",
"Gary",
""
],
[
"Braun",
"Rosemary",
""
]
] | Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet the functional properties of many genetic variants and their molecular interactions remains unclear. It has been hypothesized that SNPs in microRNA binding sites ... |
2310.20031 | Nicol\`o Cogno | Nicol\`o Cogno, Cristian Axenie, Roman Bauer and Vasileios Vavourakis | Recipes for calibration and validation of agent-based models in cancer
biomedicine | null | null | null | null | q-bio.TO cs.MA | http://creativecommons.org/licenses/by/4.0/ | Computational models and simulations are not just appealing because of their
intrinsic characteristics across spatiotemporal scales, scalability, and
predictive power, but also because the set of problems in cancer biomedicine
that can be addressed computationally exceeds the set of those amenable to
analytical solut... | [
{
"created": "Mon, 30 Oct 2023 21:29:54 GMT",
"version": "v1"
}
] | 2023-11-01 | [
[
"Cogno",
"Nicolò",
""
],
[
"Axenie",
"Cristian",
""
],
[
"Bauer",
"Roman",
""
],
[
"Vavourakis",
"Vasileios",
""
]
] | Computational models and simulations are not just appealing because of their intrinsic characteristics across spatiotemporal scales, scalability, and predictive power, but also because the set of problems in cancer biomedicine that can be addressed computationally exceeds the set of those amenable to analytical solutio... |
2007.14941 | Sitabhra Sinha | Anand Pathak, Shakti N. Menon and Sitabhra Sinha | Mesoscopic architecture enhances communication across the Macaque
connectome revealing structure-function correspondence in the brain | 13 pages, 3 figures + 27 pages Supplementary Information | Phys. Rev. E 106, 054304 (2022) | 10.1103/PhysRevE.106.054304 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Analyzing the brain in terms of organizational structures at intermediate
scales provides an approach to negotiate the complexity arising from
interactions between its large number of components. Focusing on a wiring
diagram that spans the cortex, basal ganglia and thalamus of the Macaque brain,
we provide a mesoscop... | [
{
"created": "Wed, 29 Jul 2020 16:34:47 GMT",
"version": "v1"
}
] | 2023-01-10 | [
[
"Pathak",
"Anand",
""
],
[
"Menon",
"Shakti N.",
""
],
[
"Sinha",
"Sitabhra",
""
]
] | Analyzing the brain in terms of organizational structures at intermediate scales provides an approach to negotiate the complexity arising from interactions between its large number of components. Focusing on a wiring diagram that spans the cortex, basal ganglia and thalamus of the Macaque brain, we provide a mesoscopic... |
2012.12486 | Valentin Slepukhin | Valentin M. Slepukhin (1), Sufyan Ashhad (2), Jack L. Feldman (2),
Alex J. Levine (1,3 and 4) ((1) Department of Physics and Astronomy, UCLA,
(2) Systems Neurobiology Laboratory, Department of Neurobiology, David Geffen
School of Medicine, UCLA, (3) Department of Chemistry and Biochemistry, UCLA,
(4), Departmen... | Microcircuit synchronization and heavy tailed synaptic weight
distribution in preB\"otzinger Complex contribute to generation of breathing
rhythm | 47 pages, 10 figures | null | null | null | q-bio.NC cond-mat.dis-nn nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The preB\"otzinger Complex, the mammalian inspiratory rhythm generator,
encodes inspiratory time as motor pattern. Spike synchronization throughout
this sparsely connected network generates inspiratory bursts albeit with
variable latencies after preinspiratory activity onset in each breathing cycle.
Using preB\"otC r... | [
{
"created": "Wed, 23 Dec 2020 05:01:06 GMT",
"version": "v1"
}
] | 2020-12-24 | [
[
"Slepukhin",
"Valentin M.",
"",
"1,3 and 4"
],
[
"Ashhad",
"Sufyan",
"",
"1,3 and 4"
],
[
"Feldman",
"Jack L.",
"",
"1,3 and 4"
],
[
"Levine",
"Alex J.",
"",
"1,3 and 4"
]
] | The preB\"otzinger Complex, the mammalian inspiratory rhythm generator, encodes inspiratory time as motor pattern. Spike synchronization throughout this sparsely connected network generates inspiratory bursts albeit with variable latencies after preinspiratory activity onset in each breathing cycle. Using preB\"otC rhy... |
1602.00444 | Erik Henningsson | Stefan Diehl, Erik Henningsson, Anders Heyden | Efficient simulations of tubulin-driven axonal growth | Authors' accepted version, (post refereeing). The final publication
(in Journal of Computational Neuroscience) is available at Springer via
http://dx.doi.org/10.1007/s10827-016-0604-x | J. Comput. Neurosci. 41(1) (2016) 45--63 | 10.1007/s10827-016-0604-x | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This work concerns efficient and reliable numerical simulations of the
dynamic behaviour of a moving-boundary model for tubulin-driven axonal growth.
The model is nonlinear and consists of a coupled set of a partial differential
equation (PDE) and two ordinary differential equations. The PDE is defined on a
computati... | [
{
"created": "Mon, 1 Feb 2016 09:41:22 GMT",
"version": "v1"
},
{
"created": "Thu, 14 Apr 2016 13:01:33 GMT",
"version": "v2"
}
] | 2016-08-03 | [
[
"Diehl",
"Stefan",
""
],
[
"Henningsson",
"Erik",
""
],
[
"Heyden",
"Anders",
""
]
] | This work concerns efficient and reliable numerical simulations of the dynamic behaviour of a moving-boundary model for tubulin-driven axonal growth. The model is nonlinear and consists of a coupled set of a partial differential equation (PDE) and two ordinary differential equations. The PDE is defined on a computation... |
1212.1641 | Pravin Madhavan | Don Praveen Amarasinghe, Andrew Aylwin, Pravin Madhavan and Chris
Pettitt | Biomembranes report | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this report, we analyse and simulate a chemotaxis model given by a system
of stochastic reaction-diffusion equations posed on an evolving surface.
| [
{
"created": "Wed, 5 Dec 2012 17:07:01 GMT",
"version": "v1"
}
] | 2012-12-10 | [
[
"Amarasinghe",
"Don Praveen",
""
],
[
"Aylwin",
"Andrew",
""
],
[
"Madhavan",
"Pravin",
""
],
[
"Pettitt",
"Chris",
""
]
] | In this report, we analyse and simulate a chemotaxis model given by a system of stochastic reaction-diffusion equations posed on an evolving surface. |
1505.05616 | Marc-Andr\'e Delsuc | J.M.P. Vi\'eville and S. Barluenga and N. Winssinger and M-A. Delsuc | Duplex formation and secondary structure of {\gamma}-PNA observed by NMR
and CD | 13 pages, 6 figures, plus 30 pages of Supp. Mat | null | 10.1016/j.bpc.2015.09.002 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Peptide Nucleic Acids (PNA) are non-natural oligonucleotides mimics.
{\gamma}-PNA backbone are formed by standard nucleic acids nucleobases
connected by a neutral N-(2-aminoethyl)glycine backbone linked by a peptide
bond. In this study, we use Nuclear Magnetic Resonance (NMR) and Circular
Dichroism (CD) to explore th... | [
{
"created": "Thu, 21 May 2015 06:48:27 GMT",
"version": "v1"
},
{
"created": "Sat, 10 Oct 2015 21:33:21 GMT",
"version": "v2"
}
] | 2015-10-13 | [
[
"Viéville",
"J. M. P.",
""
],
[
"Barluenga",
"S.",
""
],
[
"Winssinger",
"N.",
""
],
[
"Delsuc",
"M-A.",
""
]
] | Peptide Nucleic Acids (PNA) are non-natural oligonucleotides mimics. {\gamma}-PNA backbone are formed by standard nucleic acids nucleobases connected by a neutral N-(2-aminoethyl)glycine backbone linked by a peptide bond. In this study, we use Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) to explore the ... |
2206.03454 | Bruno Travi Dr. | Bruno L. Travi | Current status of antihistamines repurposing for infectious diseases | This review article compiles information on antihistamine drugs that
have shown activity against multiple pathogens, including parasites,
bacteria, fungi, and viruses. submitted | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Objectives. This review gathers information on the potential role of
antihistamines as anti-infective agents and identifies gaps in research that
have impaired its applicability in human health. Methods. The literature search
encompassed MEDLINE, PubMed and Google Scholar from 1990 to 2022. Results. The
literature se... | [
{
"created": "Tue, 7 Jun 2022 17:18:52 GMT",
"version": "v1"
}
] | 2022-06-08 | [
[
"Travi",
"Bruno L.",
""
]
] | Objectives. This review gathers information on the potential role of antihistamines as anti-infective agents and identifies gaps in research that have impaired its applicability in human health. Methods. The literature search encompassed MEDLINE, PubMed and Google Scholar from 1990 to 2022. Results. The literature sear... |
2106.15428 | Richard Betzel | Farnaz Zamani Esfahlani, Youngheun Jo, Maria Grazia Puxeddu, Haily
Merritt, Jacob C. Tanner, Sarah Greenwell, Riya Patel, Joshua Faskowitz,
Richard F. Betzel | Modularity maximization as a flexible and generic framework for brain
network exploratory analysis | 18 pages, 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The modular structure of brain networks supports specialized information
processing, complex dynamics, and cost-efficient spatial embedding.
Inter-individual variation in modular structure has been linked to differences
in performance, disease, and development. There exist many data-driven methods
for detecting and c... | [
{
"created": "Tue, 29 Jun 2021 13:56:21 GMT",
"version": "v1"
}
] | 2021-06-30 | [
[
"Esfahlani",
"Farnaz Zamani",
""
],
[
"Jo",
"Youngheun",
""
],
[
"Puxeddu",
"Maria Grazia",
""
],
[
"Merritt",
"Haily",
""
],
[
"Tanner",
"Jacob C.",
""
],
[
"Greenwell",
"Sarah",
""
],
[
"Patel",
"Riya",
"... | The modular structure of brain networks supports specialized information processing, complex dynamics, and cost-efficient spatial embedding. Inter-individual variation in modular structure has been linked to differences in performance, disease, and development. There exist many data-driven methods for detecting and com... |
2308.14495 | Thomas Michelitsch | Teo Granger, Thomas Michelitsch, Bernard Collet, Michael Bestehorn,
Alejandro Riascos | Compartment model with retarded transition rates | Conference proceedings (Conference: From the nonlinear dynamical
systems theory to observational chaos, October 9-11, 2023 - Toulouse), 6
Pages, 3 Figures | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Our study is devoted to a four-compartment epidemic model of a constant
population of independent random walkers. Each walker is in one of four
compartments (S-susceptible, C-infected but not infectious (period of
incubation), I-infected and infectious, R-recovered and immune) characterizing
the states of health. The... | [
{
"created": "Mon, 28 Aug 2023 11:13:27 GMT",
"version": "v1"
}
] | 2023-08-29 | [
[
"Granger",
"Teo",
""
],
[
"Michelitsch",
"Thomas",
""
],
[
"Collet",
"Bernard",
""
],
[
"Bestehorn",
"Michael",
""
],
[
"Riascos",
"Alejandro",
""
]
] | Our study is devoted to a four-compartment epidemic model of a constant population of independent random walkers. Each walker is in one of four compartments (S-susceptible, C-infected but not infectious (period of incubation), I-infected and infectious, R-recovered and immune) characterizing the states of health. The w... |
q-bio/0505027 | Richard Kerner | Richard Kerner | Combinatorial rules of icosahedral capsid growth | New version with figures included | null | null | null | q-bio.QM | null | A model of growth of icosahedral viral capsids is proposed. It takes into
account the diversity of hexamers' compositions, leading to definite capsid
size. We show that the observed yield of capsid production implies a very high
level of self-organization of elementary building blocks. The exact number of
different p... | [
{
"created": "Sun, 15 May 2005 06:04:04 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Jun 2005 07:07:28 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Kerner",
"Richard",
""
]
] | A model of growth of icosahedral viral capsids is proposed. It takes into account the diversity of hexamers' compositions, leading to definite capsid size. We show that the observed yield of capsid production implies a very high level of self-organization of elementary building blocks. The exact number of different pro... |
2007.01363 | Armita Nourmohammad | Oskar H Schnaack, Armita Nourmohammad | Optimal evolutionary decision-making to store immune memory | null | null | null | null | q-bio.PE physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The adaptive immune system provides a diverse set of molecules that can mount
specific responses against a multitude of pathogens. Memory is a key feature of
adaptive immunity, which allows organisms to respond more readily upon
re-infections. However, differentiation of memory cells is still one of the
least underst... | [
{
"created": "Thu, 2 Jul 2020 20:03:11 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Apr 2021 23:14:52 GMT",
"version": "v2"
}
] | 2021-04-14 | [
[
"Schnaack",
"Oskar H",
""
],
[
"Nourmohammad",
"Armita",
""
]
] | The adaptive immune system provides a diverse set of molecules that can mount specific responses against a multitude of pathogens. Memory is a key feature of adaptive immunity, which allows organisms to respond more readily upon re-infections. However, differentiation of memory cells is still one of the least understoo... |
2205.13088 | Qi Li | Qi Li, Khalique Newaz, and Tijana Milenkovi\'c | Towards future directions in data-integrative supervised prediction of
human aging-related genes | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identification of human genes involved in the aging process is critical due
to the incidence of many diseases with age. A state-of-the-art approach for
this purpose infers a weighted dynamic aging-specific subnetwork by mapping
gene expression (GE) levels at different ages onto the protein-protein
interaction network... | [
{
"created": "Thu, 26 May 2022 00:07:06 GMT",
"version": "v1"
}
] | 2022-05-27 | [
[
"Li",
"Qi",
""
],
[
"Newaz",
"Khalique",
""
],
[
"Milenković",
"Tijana",
""
]
] | Identification of human genes involved in the aging process is critical due to the incidence of many diseases with age. A state-of-the-art approach for this purpose infers a weighted dynamic aging-specific subnetwork by mapping gene expression (GE) levels at different ages onto the protein-protein interaction network (... |
1308.1388 | Mark Howison | Mark Howison, Felipe Zapata, Erika J. Edwards, Casey W. Dunn | Bayesian genome assembly and assessment by Markov Chain Monte Carlo
sampling | 17 pages, 5 figures | PLoS ONE 9(6): e99497 (2014) | 10.1371/journal.pone.0099497 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most genome assemblers construct point estimates, choosing a genome sequence
from among many alternative hypotheses that are supported by the data. We
present a Markov Chain Monte Carlo approach to sequence assembly that instead
generates distributions of assembly hypotheses with posterior probabilities,
providing an... | [
{
"created": "Tue, 6 Aug 2013 19:40:08 GMT",
"version": "v1"
},
{
"created": "Tue, 15 Oct 2013 14:57:40 GMT",
"version": "v2"
}
] | 2014-06-30 | [
[
"Howison",
"Mark",
""
],
[
"Zapata",
"Felipe",
""
],
[
"Edwards",
"Erika J.",
""
],
[
"Dunn",
"Casey W.",
""
]
] | Most genome assemblers construct point estimates, choosing a genome sequence from among many alternative hypotheses that are supported by the data. We present a Markov Chain Monte Carlo approach to sequence assembly that instead generates distributions of assembly hypotheses with posterior probabilities, providing an e... |
2403.14801 | Junyoung Kim | Junyoung Kim (1), Jingye Yang (2 and 4), Kai Wang (2 and 3), Chunhua
Weng (1) and Cong Liu (1) ((1) Department of Biomedical Informatics, Columbia
University, New York, NY, USA, (2) Raymond G. Perelman Center for Cellular
and Molecular Therapeutics, Children's Hospital of Philadelphia,
Philadelphia, USA, (3) De... | Assessing the Utility of Large Language Models for Phenotype-Driven Gene
Prioritization in Rare Genetic Disorder Diagnosis | 56 pages, 6 figures, 6 tables, 2 supplementary tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phenotype-driven gene prioritization is a critical process in the diagnosis
of rare genetic disorders for identifying and ranking potential disease-causing
genes based on observed physical traits or phenotypes. While traditional
approaches rely on curated knowledge graphs with phenotype-gene relations,
recent advance... | [
{
"created": "Thu, 21 Mar 2024 19:29:44 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Apr 2024 20:55:34 GMT",
"version": "v2"
}
] | 2024-04-04 | [
[
"Kim",
"Junyoung",
"",
"2 and 4"
],
[
"Yang",
"Jingye",
"",
"2 and 4"
],
[
"Wang",
"Kai",
"",
"2 and 3"
],
[
"Weng",
"Chunhua",
""
],
[
"Liu",
"Cong",
""
]
] | Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches rely on curated knowledge graphs with phenotype-gene relations, recent advanceme... |
1707.08381 | Junqiu Wu | Ke Liu (1), Xiangyan Sun (3), Jun Ma (3), Zhenyu Zhou (3), Qilin Dong
(4), Shengwen Peng (3), Junqiu Wu (3), Suocheng Tan (3), G\"unter Blobel (2),
and Jie Fan (1) ((1) Accutar Biotechnology, (2) Laboratory of Cell Biology,
Howard Hughes Medical Institute, The Rockefeller University (3) Accutar
Biotechnology (S... | Prediction of amino acid side chain conformation using a deep neural
network | null | null | null | null | q-bio.BM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A deep neural network based architecture was constructed to predict amino
acid side chain conformation with unprecedented accuracy. Amino acid side chain
conformation prediction is essential for protein homology modeling and protein
design. Current widely-adopted methods use physics-based energy functions to
evaluate... | [
{
"created": "Wed, 26 Jul 2017 11:22:57 GMT",
"version": "v1"
}
] | 2017-07-27 | [
[
"Liu",
"Ke",
""
],
[
"Sun",
"Xiangyan",
""
],
[
"Ma",
"Jun",
""
],
[
"Zhou",
"Zhenyu",
""
],
[
"Dong",
"Qilin",
""
],
[
"Peng",
"Shengwen",
""
],
[
"Wu",
"Junqiu",
""
],
[
"Tan",
"Suocheng",
... | A deep neural network based architecture was constructed to predict amino acid side chain conformation with unprecedented accuracy. Amino acid side chain conformation prediction is essential for protein homology modeling and protein design. Current widely-adopted methods use physics-based energy functions to evaluate s... |
2209.04016 | Hue Sun Chan | Jonas Wess\'en, Suman Das, Tanmoy Pal, Hue Sun Chan | Analytical Formulation and Field-Theoretic Simulation of
Sequence-Specific Phase Separation of Proteinlike Heteropolymers with Short-
and Long-Spatial-Range Interactions | 54 pages, 13 figures, 168 references, with typographical errors in
previous versions corrected and clarifications added. Accepted for
publication in the Journal of Physical Chemistry B | The Journal of Physical Chemistry B 126, 9222-9245 (2022) | 10.1021/acs.jpcb.2c06181 | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | A theory for sequence dependent liquid-liquid phase separation (LLPS) of
intrinsically disordered proteins (IDPs) in the study of biomolecular
condensates is formulated by extending the random phase approximation (RPA) and
field-theoretic simulation (FTS) of heteropolymers with spatially long-range
Coulomb interactio... | [
{
"created": "Thu, 8 Sep 2022 19:56:35 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Oct 2022 21:55:44 GMT",
"version": "v2"
},
{
"created": "Tue, 8 Nov 2022 23:44:41 GMT",
"version": "v3"
}
] | 2022-11-28 | [
[
"Wessén",
"Jonas",
""
],
[
"Das",
"Suman",
""
],
[
"Pal",
"Tanmoy",
""
],
[
"Chan",
"Hue Sun",
""
]
] | A theory for sequence dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic simulation (FTS) of heteropolymers with spatially long-range Coulomb interactions... |
2402.05886 | Esteban Paduro | Eduardo Cerpa, Nathaly Corrales, Mat\'ias Courdurier, Leonel E.
Medina, Esteban Paduro | The impact of high frequency-based stability on the onset of action
potentials in neuron models | 32 pages, 3 figures | null | null | null | q-bio.NC math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper studies the phenomenon of conduction block in model neurons using
high-frequency biphasic stimulation (HFBS). The focus is investigating the
triggering of undesired onset action potentials when the HFBS is turned on. The
approach analyzes the transient behavior of an averaged system corresponding to
the Fi... | [
{
"created": "Thu, 8 Feb 2024 18:23:18 GMT",
"version": "v1"
}
] | 2024-02-09 | [
[
"Cerpa",
"Eduardo",
""
],
[
"Corrales",
"Nathaly",
""
],
[
"Courdurier",
"Matías",
""
],
[
"Medina",
"Leonel E.",
""
],
[
"Paduro",
"Esteban",
""
]
] | This paper studies the phenomenon of conduction block in model neurons using high-frequency biphasic stimulation (HFBS). The focus is investigating the triggering of undesired onset action potentials when the HFBS is turned on. The approach analyzes the transient behavior of an averaged system corresponding to the Fitz... |
1402.1445 | Eleonora Alfinito Dr. | E. Alfinito and L. Reggiani | Opsin vs opsin: new materials for biotechnological applications | 10 pages, 8 figures revised version with more figures | J. Appl. Phys. 116, 064901 (2014) | 10.1063/1.4892445 | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The need of new diagnostic methods satisfying, as an early detection, a low
invasive procedure and a cost-efficient value, is orienting the technological
research toward the use of bio-integrated devices, in particular bio-sensors.
The set of know-why necessary to achieve this goal is wide, from biochemistry
to elect... | [
{
"created": "Mon, 3 Feb 2014 16:04:28 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Jul 2014 14:52:25 GMT",
"version": "v2"
},
{
"created": "Sat, 9 Aug 2014 08:39:08 GMT",
"version": "v3"
}
] | 2015-06-18 | [
[
"Alfinito",
"E.",
""
],
[
"Reggiani",
"L.",
""
]
] | The need of new diagnostic methods satisfying, as an early detection, a low invasive procedure and a cost-efficient value, is orienting the technological research toward the use of bio-integrated devices, in particular bio-sensors. The set of know-why necessary to achieve this goal is wide, from biochemistry to electro... |
1302.5866 | Sungwoo Ahn | Sungwoo Ahn and Leonid L. Rubchinsky | Short desynchronization episodes prevail in synchronous dynamics of
human brain rhythms | 7 pages, 7 figures. The paper will appear in Chaos | Chaos 23(1):013138, 2013 | 10.1063/1.4794793 | null | q-bio.NC nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural synchronization is believed to be critical for many brain functions.
It frequently exhibits temporal variability, but it is not known if this
variability has a specific temporal patterning. This study explores these
synchronization/desynchronization patterns. We employ recently developed
techniques to analyze ... | [
{
"created": "Sun, 24 Feb 2013 03:49:44 GMT",
"version": "v1"
}
] | 2013-03-11 | [
[
"Ahn",
"Sungwoo",
""
],
[
"Rubchinsky",
"Leonid L.",
""
]
] | Neural synchronization is believed to be critical for many brain functions. It frequently exhibits temporal variability, but it is not known if this variability has a specific temporal patterning. This study explores these synchronization/desynchronization patterns. We employ recently developed techniques to analyze th... |
1801.10189 | Jason Swedlow | Jan Ellenberg, Jason R Swedlow, Mary Barlow, Charles E Cook, Ardan
Patwardhan, Alvis Brazma, and Ewan Birney | Public archives for biological image data | 13 pages, 1 figure | null | 10.1038/s41592-018-0195-8 | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Public data archives are the backbone of modern biological and biomedical
research. While archives for biological molecules and structures are
well-established, resources for imaging data do not yet cover the full range of
spatial and temporal scales or application domains used by the scientific
community. In the las... | [
{
"created": "Tue, 30 Jan 2018 19:44:57 GMT",
"version": "v1"
}
] | 2018-11-05 | [
[
"Ellenberg",
"Jan",
""
],
[
"Swedlow",
"Jason R",
""
],
[
"Barlow",
"Mary",
""
],
[
"Cook",
"Charles E",
""
],
[
"Patwardhan",
"Ardan",
""
],
[
"Brazma",
"Alvis",
""
],
[
"Birney",
"Ewan",
""
]
] | Public data archives are the backbone of modern biological and biomedical research. While archives for biological molecules and structures are well-established, resources for imaging data do not yet cover the full range of spatial and temporal scales or application domains used by the scientific community. In the last ... |
1812.08357 | Sebastian Roch | Sebastien Roch | On the variance of internode distance under the multispecies coalescent | null | RECOMB-CG 2018 | null | null | q-bio.PE cs.CE math.PR math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider the problem of estimating species trees from unrooted gene tree
topologies in the presence of incomplete lineage sorting, a common phenomenon
that creates gene tree heterogeneity in multilocus datasets. One popular class
of reconstruction methods in this setting is based on internode distances, i.e.
the a... | [
{
"created": "Thu, 20 Dec 2018 04:48:19 GMT",
"version": "v1"
}
] | 2018-12-21 | [
[
"Roch",
"Sebastien",
""
]
] | We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of reconstruction methods in this setting is based on internode distances, i.e. the ave... |
2311.03821 | Veronica Centorrino | Veronica Centorrino, Anand Gokhale, Alexander Davydov, Giovanni Russo,
Francesco Bullo | Positive Competitive Networks for Sparse Reconstruction | 26 pages, 9 Figure, 1 Table | null | null | null | q-bio.NC cs.SY eess.SY math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose and analyze a continuous-time firing-rate neural network, the
positive firing-rate competitive network (\pfcn), to tackle sparse
reconstruction problems with non-negativity constraints. These problems, which
involve approximating a given input stimulus from a dictionary using a set of
sparse (active) neuro... | [
{
"created": "Tue, 7 Nov 2023 09:12:39 GMT",
"version": "v1"
},
{
"created": "Tue, 19 Dec 2023 16:00:46 GMT",
"version": "v2"
},
{
"created": "Fri, 22 Mar 2024 12:39:11 GMT",
"version": "v3"
}
] | 2024-03-25 | [
[
"Centorrino",
"Veronica",
""
],
[
"Gokhale",
"Anand",
""
],
[
"Davydov",
"Alexander",
""
],
[
"Russo",
"Giovanni",
""
],
[
"Bullo",
"Francesco",
""
]
] | We propose and analyze a continuous-time firing-rate neural network, the positive firing-rate competitive network (\pfcn), to tackle sparse reconstruction problems with non-negativity constraints. These problems, which involve approximating a given input stimulus from a dictionary using a set of sparse (active) neurons... |
1304.8077 | Claus Kadelka | Claus Kadelka, David Murrugarra, Reinhard Laubenbacher | Stabilizing Gene Regulatory Networks Through Feedforward Loops | 19 pages, 3 figures, (The following article has been accepted by
Chaos. After it is published, it will be found at http://chaos.aip.org) | null | 10.1063/1.4808248 | null | q-bio.MN math.DS nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The global dynamics of gene regulatory networks are known to show robustness
to perturbations in the form of intrinsic and extrinsic noise, as well as
mutations of individual genes. One molecular mechanism underlying this
robustness has been identified as the action of so-called microRNAs that
operate via feedforward... | [
{
"created": "Tue, 30 Apr 2013 17:16:38 GMT",
"version": "v1"
},
{
"created": "Thu, 23 May 2013 03:37:37 GMT",
"version": "v2"
}
] | 2015-06-15 | [
[
"Kadelka",
"Claus",
""
],
[
"Murrugarra",
"David",
""
],
[
"Laubenbacher",
"Reinhard",
""
]
] | The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has been identified as the action of so-called microRNAs that operate via feedforward l... |
1911.08509 | Dami\'an G. Hern\'andez | Dami\'an G. Hern\'andez, Samuel J. Sober and Ilya Nemenman | Unsupervised Bayesian Ising Approximation for revealing the neural
dictionary in songbirds | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The problem of deciphering how low-level patterns (action potentials in the
brain, amino acids in a protein, etc.) drive high-level biological features
(sensorimotor behavior, enzymatic function) represents the central challenge of
quantitative biology. The lack of general methods for doing so from the size of
datase... | [
{
"created": "Tue, 19 Nov 2019 19:11:49 GMT",
"version": "v1"
}
] | 2019-11-21 | [
[
"Hernández",
"Damián G.",
""
],
[
"Sober",
"Samuel J.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | The problem of deciphering how low-level patterns (action potentials in the brain, amino acids in a protein, etc.) drive high-level biological features (sensorimotor behavior, enzymatic function) represents the central challenge of quantitative biology. The lack of general methods for doing so from the size of datasets... |
1611.02332 | Peter Gawthrop | Peter J. Gawthrop and Edmund J. Crampin | Energy-based Analysis of Biomolecular Pathways | null | Proc. R. Soc. A 2017 473 20160825 | 10.1098/rspa.2016.0825 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Decomposition of biomolecular reaction networks into pathways is a powerful
approach to the analysis of metabolic and signalling networks. Current
approaches based on analysis of the stoichiometric matrix reveal information
about steady-state mass flows (reaction rates) through the network. In this
work we show how p... | [
{
"created": "Mon, 7 Nov 2016 22:49:56 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2017 09:34:08 GMT",
"version": "v2"
},
{
"created": "Tue, 23 May 2017 07:41:21 GMT",
"version": "v3"
}
] | 2018-08-14 | [
[
"Gawthrop",
"Peter J.",
""
],
[
"Crampin",
"Edmund J.",
""
]
] | Decomposition of biomolecular reaction networks into pathways is a powerful approach to the analysis of metabolic and signalling networks. Current approaches based on analysis of the stoichiometric matrix reveal information about steady-state mass flows (reaction rates) through the network. In this work we show how pat... |
1210.3561 | Miroslaw Rewekant PhD MD | S. Piekarski, M. Rewekant | On separation of time scales in pharmacokinetics | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A lot of criticism against the standard formulation of pharmacokinetics has
been raised by several authors. It seems that the natural reaction for that
criticism is to comment it from the point of view of the theory of conservation
laws. Simple example of balance equations for the intravenous administration of
drug h... | [
{
"created": "Fri, 12 Oct 2012 16:13:37 GMT",
"version": "v1"
}
] | 2012-10-15 | [
[
"Piekarski",
"S.",
""
],
[
"Rewekant",
"M.",
""
]
] | A lot of criticism against the standard formulation of pharmacokinetics has been raised by several authors. It seems that the natural reaction for that criticism is to comment it from the point of view of the theory of conservation laws. Simple example of balance equations for the intravenous administration of drug has... |
2209.09680 | Huw Day | Huw Day, N C Snaith | Stochastic Models for Replication Origin Spacings in Eukaryotic DNA
Replication | Reviewer feedback indicated we failed to acknowledge background
literature | null | null | null | q-bio.QM math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider eukaryotic DNA replication and in particular the role of
replication origins in this process. We focus on origins which are `active' -
that is, trigger themselves in the process before being read by the replication
forks of other origins. We initially consider the spacings of these active
replication orig... | [
{
"created": "Tue, 20 Sep 2022 12:31:46 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Nov 2022 14:03:53 GMT",
"version": "v2"
},
{
"created": "Sat, 8 Apr 2023 10:33:35 GMT",
"version": "v3"
}
] | 2023-04-11 | [
[
"Day",
"Huw",
""
],
[
"Snaith",
"N C",
""
]
] | We consider eukaryotic DNA replication and in particular the role of replication origins in this process. We focus on origins which are `active' - that is, trigger themselves in the process before being read by the replication forks of other origins. We initially consider the spacings of these active replication origin... |
2403.07925 | David C. Williams | David C. Williams and Neil Inala | Physics-informed generative model for drug-like molecule conformers | To appear in the Journal of Chemical Information and Modeling | null | 10.1021/acs.jcim.3c01816 | null | q-bio.BM cs.LG physics.chem-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We present a diffusion-based, generative model for conformer generation. Our
model is focused on the reproduction of bonded structure and is constructed
from the associated terms traditionally found in classical force fields to
ensure a physically relevant representation. Techniques in deep learning are
used to infer... | [
{
"created": "Thu, 29 Feb 2024 17:11:08 GMT",
"version": "v1"
},
{
"created": "Fri, 15 Mar 2024 00:21:25 GMT",
"version": "v2"
}
] | 2024-03-18 | [
[
"Williams",
"David C.",
""
],
[
"Inala",
"Neil",
""
]
] | We present a diffusion-based, generative model for conformer generation. Our model is focused on the reproduction of bonded structure and is constructed from the associated terms traditionally found in classical force fields to ensure a physically relevant representation. Techniques in deep learning are used to infer a... |
1803.04363 | Jingyi Zheng | Jingyi Zheng, Fushing Hsieh | Information of Epileptic Mechanism and its Systemic Change-points in a
Zebrafish's Brain-wide Calcium Imaging Video Data | 8 Pages, 11 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The epileptic mechanism is postulated as that an animal's neurons gradually
diminish their inhibition function coupled with enhanced excitation when an
epileptic event is approaching. Calcium imaging technique is designed to
directly record brain-wide neurons activity in order to discover the underlying
epileptic mec... | [
{
"created": "Wed, 14 Feb 2018 01:27:03 GMT",
"version": "v1"
}
] | 2018-03-13 | [
[
"Zheng",
"Jingyi",
""
],
[
"Hsieh",
"Fushing",
""
]
] | The epileptic mechanism is postulated as that an animal's neurons gradually diminish their inhibition function coupled with enhanced excitation when an epileptic event is approaching. Calcium imaging technique is designed to directly record brain-wide neurons activity in order to discover the underlying epileptic mecha... |
1712.06042 | Sergei Maslov | Akshit Goyal, Veronika Dubinkina, Sergei Maslov | Multiple stable states in microbial communities explained by the stable
marriage problem | 24 pages (including SI), 4 figures (+3 supplementary figures) | The ISME Journal 12, 2823-2834 (2018) | 10.1038/s41396-018-0222-x | null | q-bio.PE cs.GT physics.bio-ph q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experimental studies of microbial communities routinely reveal that they have
multiple stable states. While each of these states is generally resilient,
certain perturbations such as antibiotics, probiotics and diet shifts, result
in transitions to other states. Can we reliably both predict such stable states
as well... | [
{
"created": "Sun, 17 Dec 2017 01:33:57 GMT",
"version": "v1"
},
{
"created": "Tue, 3 Jul 2018 08:32:37 GMT",
"version": "v2"
}
] | 2019-02-15 | [
[
"Goyal",
"Akshit",
""
],
[
"Dubinkina",
"Veronika",
""
],
[
"Maslov",
"Sergei",
""
]
] | Experimental studies of microbial communities routinely reveal that they have multiple stable states. While each of these states is generally resilient, certain perturbations such as antibiotics, probiotics and diet shifts, result in transitions to other states. Can we reliably both predict such stable states as well a... |
0808.0043 | Jan Biro Dr | Jan C Biro | The Invention of Proteomic Code and mRNA Assisted Protein Folding | 24 pages including 2 tables and 6 figures | null | null | null | q-bio.BM q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background The theoretical requirements for a genetic code were well defined
and modeled by George Gamow and Francis Crick in the 50-es. Their models
failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in
1961, ignores many theoretical requirements for a perfect Code. Something is
simply missin... | [
{
"created": "Fri, 1 Aug 2008 00:06:50 GMT",
"version": "v1"
}
] | 2008-08-04 | [
[
"Biro",
"Jan C",
""
]
] | Background The theoretical requirements for a genetic code were well defined and modeled by George Gamow and Francis Crick in the 50-es. Their models failed. However the valid Genetic Code, provided by Nirenberg and Matthaei in 1961, ignores many theoretical requirements for a perfect Code. Something is simply missing ... |
1506.07906 | Aaron King | Clayton E. Cressler, Marguerite A. Butler, and Aaron A. King | Detecting adaptive evolution in phylogenetic comparative analysis using
the Ornstein-Uhlenbeck model | 38 pages, in press at Systematic Biology | null | 10.1093/sysbio/syv043 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic comparative analysis is an approach to inferring evolutionary
process from a combination of phylogenetic and phenotypic data. The last few
years have seen increasingly sophisticated models employed in the evaluation of
more and more detailed evolutionary hypotheses, including adaptive hypotheses
with mul... | [
{
"created": "Thu, 25 Jun 2015 21:57:02 GMT",
"version": "v1"
}
] | 2021-05-27 | [
[
"Cressler",
"Clayton E.",
""
],
[
"Butler",
"Marguerite A.",
""
],
[
"King",
"Aaron A.",
""
]
] | Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and more detailed evolutionary hypotheses, including adaptive hypotheses with multi... |
2009.02152 | Xiaoqi Zhang | Xiaoqi Zhang, Zheng Ji, Yanqiao Zheng, Xinyue Ye, Dong Li | Evaluating the effect of city lock-down on controlling COVID-19
propagation through deep learning and network science models | 27 pages, 9 figures | [J]. Cities, 2020: 102869 | 10.1016/j.cities.2020.102869 | null | q-bio.PE physics.soc-ph q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The special epistemic characteristics of the COVID-19, such as the long
incubation period and the infection through asymptomatic cases, put severe
challenge to the containment of its outbreak. By the end of March 2020, China
has successfully controlled the within-spreading of COVID-19 at a high cost of
locking down m... | [
{
"created": "Fri, 4 Sep 2020 12:39:12 GMT",
"version": "v1"
}
] | 2020-09-07 | [
[
"Zhang",
"Xiaoqi",
""
],
[
"Ji",
"Zheng",
""
],
[
"Zheng",
"Yanqiao",
""
],
[
"Ye",
"Xinyue",
""
],
[
"Li",
"Dong",
""
]
] | The special epistemic characteristics of the COVID-19, such as the long incubation period and the infection through asymptomatic cases, put severe challenge to the containment of its outbreak. By the end of March 2020, China has successfully controlled the within-spreading of COVID-19 at a high cost of locking down mos... |
2204.00067 | Muhammad Ammar Malik | Muhammad Ammar Malik, Alexander S. Lundervold and Tom Michoel | rfPhen2Gen: A machine learning based association study of brain imaging
phenotypes to genotypes | null | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Imaging genetic studies aim to find associations between genetic variants and
imaging quantitative traits. Traditional genome-wide association studies (GWAS)
are based on univariate statistical tests, but when multiple traits are
analyzed together they suffer from a multiple-testing problem and from not
taking into a... | [
{
"created": "Thu, 31 Mar 2022 20:15:22 GMT",
"version": "v1"
}
] | 2022-04-04 | [
[
"Malik",
"Muhammad Ammar",
""
],
[
"Lundervold",
"Alexander S.",
""
],
[
"Michoel",
"Tom",
""
]
] | Imaging genetic studies aim to find associations between genetic variants and imaging quantitative traits. Traditional genome-wide association studies (GWAS) are based on univariate statistical tests, but when multiple traits are analyzed together they suffer from a multiple-testing problem and from not taking into acc... |
2105.09998 | Eliana Paix\~ao | Eliana Celestino da Paixao do Rodrigues dos Santos | Distribuicao e diversidade de herbaceas de sub-bosque em uma floresta de
terra firme da amazonia meridional | Masters thesis, in Portuguese. 55 paginas e 9 figuras | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Environmental heterogeneity is a determining factor of the structure of
biological communities. Thus, understanding the distribution of species along
environmental gradients provides assistance to conservation. The goal of this
study was to determine the distribution pattern of the herbaceous community in
three areas... | [
{
"created": "Thu, 20 May 2021 19:17:11 GMT",
"version": "v1"
}
] | 2021-05-24 | [
[
"Santos",
"Eliana Celestino da Paixao do Rodrigues dos",
""
]
] | Environmental heterogeneity is a determining factor of the structure of biological communities. Thus, understanding the distribution of species along environmental gradients provides assistance to conservation. The goal of this study was to determine the distribution pattern of the herbaceous community in three areas o... |
2112.10548 | Jong Woo Kim | Jong Woo Kim (1), Niels Krausch (1), Judit Aizpuru (1), Tilman Barz
(2), Sergio Lucia (3), Ernesto C. Mart\'inez (4), Peter Neubauer (1), Mariano
Nicolas Cruz Bournazou (1 and 5) ((1) Technische Universit\"at Berlin, Chair
of Bioprocess Engineering, Strasse des 17. Juni 135, 10623 Berlin, Germany,
(2) AIT Austr... | Model predictive control guided with optimal experimental design for
pulse-based parallel cultivation | 6 pages, 4 figures, submitted to IFAC Conference | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Optimal experimental design for parameter precision attempts to maximize the
information content in experimental data for a most effective identification of
parametric model. With the recent developments in miniaturization and
parallelization of cultivation platforms for high-throughput screening of
optimal growth co... | [
{
"created": "Mon, 20 Dec 2021 14:20:42 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Kim",
"Jong Woo",
"",
"1 and 5"
],
[
"Krausch",
"Niels",
"",
"1 and 5"
],
[
"Aizpuru",
"Judit",
"",
"1 and 5"
],
[
"Barz",
"Tilman",
"",
"1 and 5"
],
[
"Lucia",
"Sergio",
"",
"1 and 5"
],
[
"Martínez",
"Er... | Optimal experimental design for parameter precision attempts to maximize the information content in experimental data for a most effective identification of parametric model. With the recent developments in miniaturization and parallelization of cultivation platforms for high-throughput screening of optimal growth cond... |
0807.1039 | Thierry Rabilloud | Thierry Rabilloud (BBSI) | Keynotes on membrane proteomics | null | Sub-cellular biochemistry 43 (2007) 3-11 | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This review article deals with the specificities of the proteomics analysis
of membrane proteins.
| [
{
"created": "Mon, 7 Jul 2008 15:27:20 GMT",
"version": "v1"
}
] | 2008-07-08 | [
[
"Rabilloud",
"Thierry",
"",
"BBSI"
]
] | This review article deals with the specificities of the proteomics analysis of membrane proteins. |
2102.03373 | Stefano De Leo | Stefano De Leo, Manoel P. Araujo | A modelling study across the Italian regions: Lockdown, testing
strategy, colored zones, and skew-normal distributions. How a numerical index
of pandemic criticality could be useful in tackling the CoViD-19 | 25 pages, 10 figures, 3 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | As Europe is facing the second wave of the CoViD-19 pandemic, each country
should carefully review how it dealt with the first wave of outbreak. Lessons
from the first experience should be useful to avoid indiscriminate closures
and, above all, to determine universal (understandable) parameters to guide the
introduct... | [
{
"created": "Fri, 5 Feb 2021 19:00:37 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Feb 2021 12:45:45 GMT",
"version": "v2"
}
] | 2021-02-10 | [
[
"De Leo",
"Stefano",
""
],
[
"Araujo",
"Manoel P.",
""
]
] | As Europe is facing the second wave of the CoViD-19 pandemic, each country should carefully review how it dealt with the first wave of outbreak. Lessons from the first experience should be useful to avoid indiscriminate closures and, above all, to determine universal (understandable) parameters to guide the introductio... |
1403.3066 | Frederick Matsen IV | Connor O. McCoy, Trevor Bedford, Vladimir N. Minin, Philip Bradley,
Harlan Robins and Frederick A. Matsen IV | Quantifying evolutionary constraints on B cell affinity maturation | Previously entitled "Substitution and site-specific selection driving
B cell affinity maturation is consistent across individuals" | null | 10.1098/rstb.2014-0244 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The antibody repertoire of each individual is continuously updated by the
evolutionary process of B cell receptor mutation and selection. It has recently
become possible to gain detailed information concerning this process through
high-throughput sequencing. Here, we develop modern statistical molecular
evolution met... | [
{
"created": "Wed, 12 Mar 2014 19:01:41 GMT",
"version": "v1"
},
{
"created": "Wed, 9 Jul 2014 23:41:02 GMT",
"version": "v2"
},
{
"created": "Mon, 12 Jan 2015 22:45:43 GMT",
"version": "v3"
},
{
"created": "Fri, 8 May 2015 13:56:59 GMT",
"version": "v4"
}
] | 2015-05-11 | [
[
"McCoy",
"Connor O.",
""
],
[
"Bedford",
"Trevor",
""
],
[
"Minin",
"Vladimir N.",
""
],
[
"Bradley",
"Philip",
""
],
[
"Robins",
"Harlan",
""
],
[
"Matsen",
"Frederick A.",
"IV"
]
] | The antibody repertoire of each individual is continuously updated by the evolutionary process of B cell receptor mutation and selection. It has recently become possible to gain detailed information concerning this process through high-throughput sequencing. Here, we develop modern statistical molecular evolution metho... |
1911.11948 | Sang Woo Park | Sang Woo Park and Benjamin M. Bolker | A note on observation processes in epidemic models | 9 pages, 2 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Many disease models focus on characterizing the underlying transmission
mechanism but make simple, possibly naive assumptions about how infections are
reported. In this note, we use a simple deterministic
Susceptible-Infected-Removed (SIR) model to compare two common assumptions
about disease incidence reports: indiv... | [
{
"created": "Wed, 27 Nov 2019 04:37:51 GMT",
"version": "v1"
}
] | 2019-11-28 | [
[
"Park",
"Sang Woo",
""
],
[
"Bolker",
"Benjamin M.",
""
]
] | Many disease models focus on characterizing the underlying transmission mechanism but make simple, possibly naive assumptions about how infections are reported. In this note, we use a simple deterministic Susceptible-Infected-Removed (SIR) model to compare two common assumptions about disease incidence reports: individ... |
1010.3845 | Anna Melbinger | Anna Melbinger, Jonas Cremer, Erwin Frey | Evolutionary game theory in growing populations | 4 pages, 2 figures and 2 pages supplementary information | Phys. Rev. Lett. 105, 178101 (2010) | 10.1103/PhysRevLett.105.178101 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Existing theoretical models of evolution focus on the relative fitness
advantages of different mutants in a population while the dynamic behavior of
the population size is mostly left unconsidered. We here present a generic
stochastic model which combines the growth dynamics of the population and its
internal evoluti... | [
{
"created": "Tue, 19 Oct 2010 10:19:13 GMT",
"version": "v1"
}
] | 2010-10-20 | [
[
"Melbinger",
"Anna",
""
],
[
"Cremer",
"Jonas",
""
],
[
"Frey",
"Erwin",
""
]
] | Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We here present a generic stochastic model which combines the growth dynamics of the population and its internal evolution... |
2212.06505 | Katherine Benjamin | Katherine Benjamin, Aneesha Bhandari, Zhouchun Shang, Yanan Xing,
Yanru An, Nannan Zhang, Yong Hou, Ulrike Tillmann, Katherine R. Bull, Heather
A. Harrington | Multiscale topology classifies and quantifies cell types in subcellular
spatial transcriptomics | Main text: 8 pages, 4 figures. Supplement: 12 pages, 5 figures | null | null | null | q-bio.QM math.AT q-bio.GN stat.ME | http://creativecommons.org/licenses/by/4.0/ | Spatial transcriptomics has the potential to transform our understanding of
RNA expression in tissues. Classical array-based technologies produce
multiple-cell-scale measurements requiring deconvolution to recover single cell
information. However, rapid advances in subcellular measurement of RNA
expression at whole-t... | [
{
"created": "Tue, 13 Dec 2022 11:36:25 GMT",
"version": "v1"
}
] | 2022-12-14 | [
[
"Benjamin",
"Katherine",
""
],
[
"Bhandari",
"Aneesha",
""
],
[
"Shang",
"Zhouchun",
""
],
[
"Xing",
"Yanan",
""
],
[
"An",
"Yanru",
""
],
[
"Zhang",
"Nannan",
""
],
[
"Hou",
"Yong",
""
],
[
"Tillma... | Spatial transcriptomics has the potential to transform our understanding of RNA expression in tissues. Classical array-based technologies produce multiple-cell-scale measurements requiring deconvolution to recover single cell information. However, rapid advances in subcellular measurement of RNA expression at whole-tra... |
1111.6494 | Taiki Takahashi | Taiki Takahashi | Toward molecular neuroeconomics of obesity | null | null | null | null | q-bio.NC q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Because obesity is a risk factor for many serious illnesses such as diabetes,
better understandings of obesity and eating disorders have been attracting
attention in neurobiology, psychiatry, and neuroeconomics. This paper presents
future study directions by unifying (i) economic theory of addiction and
obesity (Beck... | [
{
"created": "Tue, 22 Nov 2011 22:41:59 GMT",
"version": "v1"
}
] | 2011-11-29 | [
[
"Takahashi",
"Taiki",
""
]
] | Because obesity is a risk factor for many serious illnesses such as diabetes, better understandings of obesity and eating disorders have been attracting attention in neurobiology, psychiatry, and neuroeconomics. This paper presents future study directions by unifying (i) economic theory of addiction and obesity (Becker... |
1101.1013 | Chris Adami | Evan D. Dorn, Kenneth H. Nealson, and Christoph Adami | Monomer abundance distribution patterns as a universal biosignature:
Examples from terrestrial and digital life | 35 pages, 5 figures. Supplementary material (two movie files)
available upon request. To appear in J. Mol. Evol | J. Molec. Evol.72:283-295, 2011 | null | null | q-bio.BM astro-ph.EP physics.bio-ph q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Organisms leave a distinctive chemical signature in their environment because
they synthesize those molecules that maximize their fitness. As a result, the
relative concentrations of related chemical monomers in life-bearing
environmental samples reflect, in part, those compounds' adaptive utility. In
contrast, rates... | [
{
"created": "Wed, 5 Jan 2011 15:51:02 GMT",
"version": "v1"
}
] | 2011-05-05 | [
[
"Dorn",
"Evan D.",
""
],
[
"Nealson",
"Kenneth H.",
""
],
[
"Adami",
"Christoph",
""
]
] | Organisms leave a distinctive chemical signature in their environment because they synthesize those molecules that maximize their fitness. As a result, the relative concentrations of related chemical monomers in life-bearing environmental samples reflect, in part, those compounds' adaptive utility. In contrast, rates o... |
1308.0879 | Takanobu Yamanobe | Takanobu Yamanobe | Global Dynamics of a Stochastic Neuronal Oscillator | 45 pages, 9 figures, authors homepage
http://niseiri.med.hokudai.ac.jp/yamanobe/indexeng.html | null | 10.1103/PhysRevE.88.052709 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Nonlinear oscillators have been used to model neurons that fire periodically
in the absence of input. These oscillators, which are called neuronal
oscillator, share some common response structures with other biological
oscillations. In this study, we analyze the dependence of the global dynamics
of an impulse-driven ... | [
{
"created": "Mon, 5 Aug 2013 03:42:36 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Yamanobe",
"Takanobu",
""
]
] | Nonlinear oscillators have been used to model neurons that fire periodically in the absence of input. These oscillators, which are called neuronal oscillator, share some common response structures with other biological oscillations. In this study, we analyze the dependence of the global dynamics of an impulse-driven st... |
2006.14752 | Shashank Reddy Vadyala | Shashank Reddy Vadyala, Sai Nethra Betgeri, Eric A. Sherer, Amod
Amritphale | Prediction of the Number of COVID-19 Confirmed Cases Based on
K-Means-LSTM | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | COVID-19 is a pandemic disease that began to rapidly spread in the US with
the first case detected on January 19, 2020, in Washington State. March 9,
2020, and then increased rapidly with total cases of 25,739 as of April 20,
2020. The Covid-19 pandemic is so unnerving that it is difficult to understand
how any perso... | [
{
"created": "Fri, 26 Jun 2020 01:42:07 GMT",
"version": "v1"
}
] | 2020-06-30 | [
[
"Vadyala",
"Shashank Reddy",
""
],
[
"Betgeri",
"Sai Nethra",
""
],
[
"Sherer",
"Eric A.",
""
],
[
"Amritphale",
"Amod",
""
]
] | COVID-19 is a pandemic disease that began to rapidly spread in the US with the first case detected on January 19, 2020, in Washington State. March 9, 2020, and then increased rapidly with total cases of 25,739 as of April 20, 2020. The Covid-19 pandemic is so unnerving that it is difficult to understand how any person ... |
2309.16685 | Truong Son Hy | Nhat Khang Ngo and Truong Son Hy | Target-aware Variational Auto-encoders for Ligand Generation with
Multimodal Protein Representation Learning | null | null | null | null | q-bio.BM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Without knowledge of specific pockets, generating ligands based on the global
structure of a protein target plays a crucial role in drug discovery as it
helps reduce the search space for potential drug-like candidates in the
pipeline. However, contemporary methods require optimizing tailored networks
for each protein... | [
{
"created": "Wed, 2 Aug 2023 12:08:17 GMT",
"version": "v1"
}
] | 2023-10-02 | [
[
"Ngo",
"Nhat Khang",
""
],
[
"Hy",
"Truong Son",
""
]
] | Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline. However, contemporary methods require optimizing tailored networks for each protein, ... |
2007.11183 | Shiyang Lai | Shiyang Lai, Tianqi Zhao, Ningyuan Fan | Inferring incubation period distribution of COVID-19 based on SEAIR
Model | 9 pages, 3 figures, 1 table | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To reduce the biases of traditional survey-based methods, this paper proposes
an epidemic model-based approach to inference the incubation period
distribution of COVID-19 utilizing the publicly reported confirmed case number.
We construct an epidemic model, namely SEAIR, and take advantage of the dynamic
transmission... | [
{
"created": "Wed, 22 Jul 2020 03:31:45 GMT",
"version": "v1"
}
] | 2020-07-23 | [
[
"Lai",
"Shiyang",
""
],
[
"Zhao",
"Tianqi",
""
],
[
"Fan",
"Ningyuan",
""
]
] | To reduce the biases of traditional survey-based methods, this paper proposes an epidemic model-based approach to inference the incubation period distribution of COVID-19 utilizing the publicly reported confirmed case number. We construct an epidemic model, namely SEAIR, and take advantage of the dynamic transmission p... |
2012.10331 | Jacques P\'ecr\'eaux | Ma\"el Balluet, Florian Sizaire, Youssef El Habouz, Thomas Walter,
J\'er\'emy Pont, Baptiste Giroux, Otmane Bouchareb, Marc Tramier, Jacques
P\'ecr\'eaux | Neural network fast-classifies biological images using features selected
after their random-forests-importance to power smart microscopy | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial intelligence is nowadays used for cell detection and
classification in optical microscopy, during post-acquisition analysis. The
microscopes are now fully automated and next expected to be smart, to make
acquisition decisions based on the images. It calls for analysing them on the
fly. Biology further impo... | [
{
"created": "Fri, 18 Dec 2020 16:20:37 GMT",
"version": "v1"
}
] | 2021-10-18 | [
[
"Balluet",
"Maël",
""
],
[
"Sizaire",
"Florian",
""
],
[
"Habouz",
"Youssef El",
""
],
[
"Walter",
"Thomas",
""
],
[
"Pont",
"Jérémy",
""
],
[
"Giroux",
"Baptiste",
""
],
[
"Bouchareb",
"Otmane",
""
],
... | Artificial intelligence is nowadays used for cell detection and classification in optical microscopy, during post-acquisition analysis. The microscopes are now fully automated and next expected to be smart, to make acquisition decisions based on the images. It calls for analysing them on the fly. Biology further impose... |
2408.02988 | Amir Heydari | Amir Heydari, Abbas Ahmadi, Tae Hyung Kim, Berkin Bilgic | Fast Whole-Brain MR Multi-Parametric Mapping with Scan-Specific
Self-Supervised Networks | null | null | null | null | q-bio.QM physics.med-ph | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Quantification of tissue parameters using MRI is emerging as a powerful tool
in clinical diagnosis and research studies. The need for multiple long scans
with different acquisition parameters prohibits quantitative MRI from reaching
widespread adoption in routine clinical and research exams. Accelerated
parameter map... | [
{
"created": "Tue, 6 Aug 2024 06:43:06 GMT",
"version": "v1"
}
] | 2024-08-07 | [
[
"Heydari",
"Amir",
""
],
[
"Ahmadi",
"Abbas",
""
],
[
"Kim",
"Tae Hyung",
""
],
[
"Bilgic",
"Berkin",
""
]
] | Quantification of tissue parameters using MRI is emerging as a powerful tool in clinical diagnosis and research studies. The need for multiple long scans with different acquisition parameters prohibits quantitative MRI from reaching widespread adoption in routine clinical and research exams. Accelerated parameter mappi... |
2005.04796 | Steven Frank | Steven A. Frank | Metabolic heat in microbial conflict and cooperation | V3: Added new figure, more references, some editing. V2: Add several
key references, comments about heat diffusion as single-cell scale | Frontiers in Ecology and Evolution 8:275 (2020) | 10.3389/fevo.2020.00275 | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Many microbes live in habitats below their optimum temperature. Retention of
metabolic heat by aggregation or insulation would boost growth. Generation of
excess metabolic heat may also provide benefit. A cell that makes excess
metabolic heat pays the cost of production, whereas the benefit may be shared
by neighbors... | [
{
"created": "Sun, 10 May 2020 22:06:40 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Jul 2020 18:49:58 GMT",
"version": "v2"
},
{
"created": "Thu, 30 Jul 2020 16:15:28 GMT",
"version": "v3"
}
] | 2020-10-22 | [
[
"Frank",
"Steven A.",
""
]
] | Many microbes live in habitats below their optimum temperature. Retention of metabolic heat by aggregation or insulation would boost growth. Generation of excess metabolic heat may also provide benefit. A cell that makes excess metabolic heat pays the cost of production, whereas the benefit may be shared by neighbors w... |
1506.06988 | Christoph Adami | Christoph Adami and Thomas LaBar | From Entropy to Information: Biased Typewriters and the Origin of Life | 19 pages, 8 figures in "From Matter to Life: Information and
Causality", S.I. Walker, P.C.W. Davies, and G. F. R. Ellis, eds., (Cambridge
University Press, 2017) pp. 130-154 | null | null | null | q-bio.PE cs.IT math.IT nlin.AO q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The origin of life can be understood mathematically to be the origin of
information that can replicate. The likelihood that entropy spontaneously
becomes information can be calculated from first principles, and depends
exponentially on the amount of information that is necessary for replication.
We do not know what t... | [
{
"created": "Tue, 23 Jun 2015 13:36:54 GMT",
"version": "v1"
},
{
"created": "Fri, 6 Jan 2017 16:46:56 GMT",
"version": "v2"
}
] | 2017-01-09 | [
[
"Adami",
"Christoph",
""
],
[
"LaBar",
"Thomas",
""
]
] | The origin of life can be understood mathematically to be the origin of information that can replicate. The likelihood that entropy spontaneously becomes information can be calculated from first principles, and depends exponentially on the amount of information that is necessary for replication. We do not know what the... |
0812.4295 | Georgy Karev | G.P. Karev | How to explore replicator equations? | 7 pages; Proceedings of the 6th International Conference on
Differential Equations and Dynamical Systems, Baltimore MD, 2008 | null | null | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/publicdomain/ | Replicator equations (RE) are among the basic tools in mathematical theory of
selection and evolution. We develop a method for reducing a wide class of the
RE, which in general are systems of differential equations in Banach space to
escort systems of ODEs that in many cases can be explored analytically. The
method h... | [
{
"created": "Mon, 22 Dec 2008 21:26:17 GMT",
"version": "v1"
}
] | 2008-12-24 | [
[
"Karev",
"G. P.",
""
]
] | Replicator equations (RE) are among the basic tools in mathematical theory of selection and evolution. We develop a method for reducing a wide class of the RE, which in general are systems of differential equations in Banach space to escort systems of ODEs that in many cases can be explored analytically. The method has... |
0905.0042 | Dmitry Fedosov | Dmitry A. Fedosov, Bruce Caswell, George E. Karniadakis | General coarse-grained red blood cell models: I. Mechanics | 16 pages, 7 figures | null | null | null | q-bio.CB cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a rigorous procedure to derive coarse-grained red blood cell (RBC)
models, which lead to accurate mechanical properties of realistic RBCs. Based
on a semi-analytic theory linear and non-linear elastic properties of the RBC
membrane can be matched with those obtained in optical tweezers stretching
experimen... | [
{
"created": "Fri, 1 May 2009 03:43:01 GMT",
"version": "v1"
}
] | 2009-05-04 | [
[
"Fedosov",
"Dmitry A.",
""
],
[
"Caswell",
"Bruce",
""
],
[
"Karniadakis",
"George E.",
""
]
] | We present a rigorous procedure to derive coarse-grained red blood cell (RBC) models, which lead to accurate mechanical properties of realistic RBCs. Based on a semi-analytic theory linear and non-linear elastic properties of the RBC membrane can be matched with those obtained in optical tweezers stretching experiments... |
q-bio/0510052 | Ariel Schwartz | Ariel S. Schwartz, Eugene W. Myers, Lior Pachter | Alignment Metric Accuracy | null | null | null | null | q-bio.QM math.ST stat.TH | null | We propose a metric for the space of multiple sequence alignments that can be
used to compare two alignments to each other. In the case where one of the
alignments is a reference alignment, the resulting accuracy measure improves
upon previous approaches, and provides a balanced assessment of the fidelity of
both mat... | [
{
"created": "Thu, 27 Oct 2005 22:49:50 GMT",
"version": "v1"
}
] | 2011-11-09 | [
[
"Schwartz",
"Ariel S.",
""
],
[
"Myers",
"Eugene W.",
""
],
[
"Pachter",
"Lior",
""
]
] | We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon previous approaches, and provides a balanced assessment of the fidelity of both match... |
2109.00852 | Kok Yew Ng Dr | Niamh McCallan and Scot Davidson and Kok Yew Ng and Pardis Biglarbeigi
and Dewar Finlay and Boon Leong Lan and James McLaughlin | Seizure Classification of EEG based on Wavelet Signal Denoising Using a
Novel Channel Selection Algorithm | 8 pages, 6 figures, accepted for publication at the 13th Asia Pacific
Signal and Information Processing Association Annual Summit and Conference
(APSIPA ASC) | 2021 Asia-Pacific Signal and Information Processing Association
Annual Summit and Conference (APSIPA ASC), 2021, pp. 1269-1276 | null | null | q-bio.PE q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epilepsy is a disorder of the nervous system that can affect people of any
age group. With roughly 50 million people worldwide diagnosed with the
disorder, it is one of the most common neurological disorders. The EEG is an
indispensable tool for diagnosis of epileptic seizures in an ideal case, as
brain waves from an... | [
{
"created": "Thu, 2 Sep 2021 11:41:33 GMT",
"version": "v1"
}
] | 2022-02-21 | [
[
"McCallan",
"Niamh",
""
],
[
"Davidson",
"Scot",
""
],
[
"Ng",
"Kok Yew",
""
],
[
"Biglarbeigi",
"Pardis",
""
],
[
"Finlay",
"Dewar",
""
],
[
"Lan",
"Boon Leong",
""
],
[
"McLaughlin",
"James",
""
]
] | Epilepsy is a disorder of the nervous system that can affect people of any age group. With roughly 50 million people worldwide diagnosed with the disorder, it is one of the most common neurological disorders. The EEG is an indispensable tool for diagnosis of epileptic seizures in an ideal case, as brain waves from an e... |
2312.12628 | Geoffrey Van Dover | Geoffrey van Dover, Josh Javor, Jourdan Ewoldt, Ha Eun Lee, Mikhail
Zhernenkov, Guillaume Freychet, Patryk Wasik, Dana Brown, David Bishop,
Christopher Chen | Structural maturation of myofilaments in engineered 3D cardiac
microtissues characterized using small angle X-ray scattering | null | null | null | null | q-bio.TO | http://creativecommons.org/publicdomain/zero/1.0/ | Understanding the structural and functional development of human-induced
pluripotent stem-cell-derived cardiomyocytes is essential to engineering
cardiac tissue that enables pharmaceutical testing, modeling diseases, and
designing therapies. Here we use a method not commonly applied to biological
materials, small ang... | [
{
"created": "Tue, 19 Dec 2023 22:16:33 GMT",
"version": "v1"
}
] | 2023-12-21 | [
[
"van Dover",
"Geoffrey",
""
],
[
"Javor",
"Josh",
""
],
[
"Ewoldt",
"Jourdan",
""
],
[
"Lee",
"Ha Eun",
""
],
[
"Zhernenkov",
"Mikhail",
""
],
[
"Freychet",
"Guillaume",
""
],
[
"Wasik",
"Patryk",
""
],
... | Understanding the structural and functional development of human-induced pluripotent stem-cell-derived cardiomyocytes is essential to engineering cardiac tissue that enables pharmaceutical testing, modeling diseases, and designing therapies. Here we use a method not commonly applied to biological materials, small angle... |
1809.00809 | Angus McLure | Angus McLure, Kathryn Glass | Some simple rules for estimating reproduction numbers in the presence of
reservoir exposure or imported cases | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The basic reproduction number ($R_0$) is a threshold parameter for disease
extinction or survival in isolated populations. However no human population is
fully isolated from other human or animal populations. We use compartmental
models to derive simple rules for the basic reproduction number for populations
with loc... | [
{
"created": "Tue, 4 Sep 2018 06:57:33 GMT",
"version": "v1"
}
] | 2018-09-05 | [
[
"McLure",
"Angus",
""
],
[
"Glass",
"Kathryn",
""
]
] | The basic reproduction number ($R_0$) is a threshold parameter for disease extinction or survival in isolated populations. However no human population is fully isolated from other human or animal populations. We use compartmental models to derive simple rules for the basic reproduction number for populations with local... |
1703.03777 | Wieland Brendel | Wieland Brendel, Ralph Bourdoukan, Pietro Vertechi, Christian K.
Machens, Sophie Den\'eve | Learning to represent signals spike by spike | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A key question in neuroscience is at which level functional meaning emerges
from biophysical phenomena. In most vertebrate systems, precise functions are
assigned at the level of neural populations, while single-neurons are deemed
unreliable and redundant. Here we challenge this view and show that many
single-neuron ... | [
{
"created": "Fri, 10 Mar 2017 17:41:36 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Mar 2017 15:59:59 GMT",
"version": "v2"
}
] | 2017-03-17 | [
[
"Brendel",
"Wieland",
""
],
[
"Bourdoukan",
"Ralph",
""
],
[
"Vertechi",
"Pietro",
""
],
[
"Machens",
"Christian K.",
""
],
[
"Denéve",
"Sophie",
""
]
] | A key question in neuroscience is at which level functional meaning emerges from biophysical phenomena. In most vertebrate systems, precise functions are assigned at the level of neural populations, while single-neurons are deemed unreliable and redundant. Here we challenge this view and show that many single-neuron qu... |
1911.04835 | Hongyi Li Dr. | Li Hongyi, Yin Yajun, Yang Chongqing, Chen Min, Wang Fang, Ma Chao, Li
Hua, Kong Yiya, Ji Fusui, Hu Jun | Active interfacial dynamic transport of fluid in fibrous connective
tissues and a hypothesis of interstitial fluid circulatory system | 15 pages, 2 figures, 18 conferences | Cell Proliferation. 2020;00:e12760 | 10.1111/cpr.12760 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fluid in interstitial spaces accounts for ~20% of an adult body weight. Does
it circulate around the body like vascular circulations besides a diffusive and
short-ranged transport? This bold conjecture has been debated for decades. As a
conventional physiological concept, interstitial space was the space between
cell... | [
{
"created": "Tue, 12 Nov 2019 13:21:19 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Nov 2019 08:20:48 GMT",
"version": "v2"
}
] | 2021-07-06 | [
[
"Hongyi",
"Li",
""
],
[
"Yajun",
"Yin",
""
],
[
"Chongqing",
"Yang",
""
],
[
"Min",
"Chen",
""
],
[
"Fang",
"Wang",
""
],
[
"Chao",
"Ma",
""
],
[
"Hua",
"Li",
""
],
[
"Yiya",
"Kong",
""
],... | Fluid in interstitial spaces accounts for ~20% of an adult body weight. Does it circulate around the body like vascular circulations besides a diffusive and short-ranged transport? This bold conjecture has been debated for decades. As a conventional physiological concept, interstitial space was the space between cells ... |
2105.10578 | Rowan Swiers | Cheng Ye, Rowan Swiers, Stephen Bonner, Ian Barrett | A Knowledge Graph-Enhanced Tensor Factorisation Model for Discovering
Drug Targets | 16 pages, 4 figures, IEEE/ACM Transactions on Computational Biology
and Bioinformatics | null | 10.1109/TCBB.2022.3197320 | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | The drug discovery and development process is a long and expensive one,
costing over 1 billion USD on average per drug and taking 10-15 years. To
reduce the high levels of attrition throughout the process, there has been a
growing interest in applying machine learning methodologies to various stages
of drug discovery... | [
{
"created": "Thu, 20 May 2021 16:19:00 GMT",
"version": "v1"
},
{
"created": "Thu, 22 Jul 2021 14:51:10 GMT",
"version": "v2"
},
{
"created": "Fri, 19 Aug 2022 14:08:55 GMT",
"version": "v3"
}
] | 2022-08-22 | [
[
"Ye",
"Cheng",
""
],
[
"Swiers",
"Rowan",
""
],
[
"Bonner",
"Stephen",
""
],
[
"Barrett",
"Ian",
""
]
] | The drug discovery and development process is a long and expensive one, costing over 1 billion USD on average per drug and taking 10-15 years. To reduce the high levels of attrition throughout the process, there has been a growing interest in applying machine learning methodologies to various stages of drug discovery a... |
1911.02551 | Tal Galili | Tal Galili, Alan OCallaghan, Jonathan Sidi, Carson Sievert | heatmaply: an R package for creating interactive cluster heatmaps for
online publishing | 3 pages | Bioinformatics 34.9 (2017): 1600-1602 | 10.1093/bioinformatics/btx657 | null | q-bio.QM stat.CO | http://creativecommons.org/licenses/by/4.0/ | Summary: heatmaply is an R package for easily creating interactive cluster
heatmaps that can be shared online as a stand-alone HTML file. Interactivity
includes a tooltip display of values when hovering over cells, as well as the
ability to zoom in to specific sections of the figure from the data matrix, the
side den... | [
{
"created": "Mon, 4 Nov 2019 13:33:44 GMT",
"version": "v1"
}
] | 2019-11-07 | [
[
"Galili",
"Tal",
""
],
[
"OCallaghan",
"Alan",
""
],
[
"Sidi",
"Jonathan",
""
],
[
"Sievert",
"Carson",
""
]
] | Summary: heatmaply is an R package for easily creating interactive cluster heatmaps that can be shared online as a stand-alone HTML file. Interactivity includes a tooltip display of values when hovering over cells, as well as the ability to zoom in to specific sections of the figure from the data matrix, the side dendr... |
2404.17952 | Yujiang Wang | Heather Woodhouse, Gerard Hall, Callum Simpson, Csaba Kozma, Frances
Turner, Gabrielle M. Schroeder, Beate Diehl, John S. Duncan, Jiajie Mo, Kai
Zhang, Aswin Chari, Martin Tisdall, Friederike Moeller, Chris Petkov, Matthew
A. Howard, George M. Ibrahim, Elizabeth Donner, Nebras M. Warsi, Raheel
Ahmed, Peter N. T... | Multi-centre normative brain mapping of intracranial EEG lifespan
patterns in the human brain | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Understanding healthy human brain function is crucial to identify
and map pathological tissue within it. Whilst previous studies have mapped
intracranial EEG (icEEG) from non-epileptogenic brain regions, these maps do
not consider the effects of age and sex. Further, most existing work on icEEG
has often ... | [
{
"created": "Sat, 27 Apr 2024 16:18:37 GMT",
"version": "v1"
}
] | 2024-04-30 | [
[
"Woodhouse",
"Heather",
""
],
[
"Hall",
"Gerard",
""
],
[
"Simpson",
"Callum",
""
],
[
"Kozma",
"Csaba",
""
],
[
"Turner",
"Frances",
""
],
[
"Schroeder",
"Gabrielle M.",
""
],
[
"Diehl",
"Beate",
""
],
... | Background: Understanding healthy human brain function is crucial to identify and map pathological tissue within it. Whilst previous studies have mapped intracranial EEG (icEEG) from non-epileptogenic brain regions, these maps do not consider the effects of age and sex. Further, most existing work on icEEG has often su... |
2112.13210 | Isaac Ronald Ward | Isaac Ronald Ward, Ling Wang, Juan lu, Mohammed Bennamoun, Girish
Dwivedi, Frank M Sanfilippo | Explainable Artificial Intelligence for Pharmacovigilance: What Features
Are Important When Predicting Adverse Outcomes? | Comput Methods Programs Biomed. 2021 Nov;212:106415. Epub 2021 Sep 26 | null | 10.1016/j.cmpb.2021.106415 | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Explainable Artificial Intelligence (XAI) has been identified as a viable
method for determining the importance of features when making predictions using
Machine Learning (ML) models. In this study, we created models that take an
individual's health information (e.g. their drug history and comorbidities) as
inputs, a... | [
{
"created": "Sat, 25 Dec 2021 09:00:08 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Ward",
"Isaac Ronald",
""
],
[
"Wang",
"Ling",
""
],
[
"lu",
"Juan",
""
],
[
"Bennamoun",
"Mohammed",
""
],
[
"Dwivedi",
"Girish",
""
],
[
"Sanfilippo",
"Frank M",
""
]
] | Explainable Artificial Intelligence (XAI) has been identified as a viable method for determining the importance of features when making predictions using Machine Learning (ML) models. In this study, we created models that take an individual's health information (e.g. their drug history and comorbidities) as inputs, and... |
2407.04025 | Ilenna Jones Dr | Ilenna Simone Jones and Konrad Paul Kording | Efficient optimization of ODE neuron models using gradient descent | 25 pages, 4 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuroscientists fit morphologically and biophysically detailed neuron
simulations to physiological data, often using evolutionary algorithms.
However, such gradient-free approaches are computationally expensive, making
convergence slow when neuron models have many parameters. Here we introduce a
gradient-based algori... | [
{
"created": "Thu, 4 Jul 2024 16:10:27 GMT",
"version": "v1"
},
{
"created": "Sat, 20 Jul 2024 19:49:09 GMT",
"version": "v2"
}
] | 2024-07-23 | [
[
"Jones",
"Ilenna Simone",
""
],
[
"Kording",
"Konrad Paul",
""
]
] | Neuroscientists fit morphologically and biophysically detailed neuron simulations to physiological data, often using evolutionary algorithms. However, such gradient-free approaches are computationally expensive, making convergence slow when neuron models have many parameters. Here we introduce a gradient-based algorith... |
2210.16292 | Leonardo Martini | Leonardo Martini, Adriano Fazzone, Michele Gentili, Luca Becchetti,
Brian Hobbs | Network Based Approach to Gene Prioritization at Genome-Wide Association
Study Loci | null | null | null | null | q-bio.QM q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Motivation: Genome-wide association studies (GWAS) have successfully
identified thousands of genetic risk loci for complex traits and diseases. Most
of these GWAS loci lie in regulatory regions of the genome and the gene through
which each GWAS risk locus exerts its effects is not always clear. Many
computational met... | [
{
"created": "Fri, 28 Oct 2022 17:41:57 GMT",
"version": "v1"
}
] | 2022-10-31 | [
[
"Martini",
"Leonardo",
""
],
[
"Fazzone",
"Adriano",
""
],
[
"Gentili",
"Michele",
""
],
[
"Becchetti",
"Luca",
""
],
[
"Hobbs",
"Brian",
""
]
] | Motivation: Genome-wide association studies (GWAS) have successfully identified thousands of genetic risk loci for complex traits and diseases. Most of these GWAS loci lie in regulatory regions of the genome and the gene through which each GWAS risk locus exerts its effects is not always clear. Many computational metho... |
1209.5032 | Betul Kacar | Betul Kacar, Eric Gaucher | Towards the Recapitulation of Ancient History in the Laboratory:
Combining Synthetic Biology with Experimental Evolution | 8 pages, 4 figures | Artificial Life XIII: Proceedings of the Thirteenth International
Conference on the Synthesis and Simulation of Living Systems. pp 11-18.
Cambridge, MA: MIT Press 2012 | null | null | q-bio.PE q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One way to understand the role history plays on evolutionary trajectories is
by giving ancient life a second opportunity to evolve. Our ability to
empirically perform such an experiment, however, is limited by current
experimental designs. Combining ancestral sequence reconstruction with
synthetic biology allows us t... | [
{
"created": "Sun, 23 Sep 2012 02:15:22 GMT",
"version": "v1"
}
] | 2012-09-25 | [
[
"Kacar",
"Betul",
""
],
[
"Gaucher",
"Eric",
""
]
] | One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to ... |
1403.3626 | Bahram Houchmandzadeh | Bahram Houchmandzadeh (LIPhy) | Noise driven emergence of cooperative behavior | null | null | null | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperative behaviors are defined as the production of common goods
benefitting all members of the community at the producer's cost. They could
seem to be in contradiction with natural selection, as non-cooperators have an
increased fitness compared to cooperators. Understanding the emergence of
cooperation has neces... | [
{
"created": "Fri, 14 Mar 2014 16:12:18 GMT",
"version": "v1"
}
] | 2014-03-17 | [
[
"Houchmandzadeh",
"Bahram",
"",
"LIPhy"
]
] | Cooperative behaviors are defined as the production of common goods benefitting all members of the community at the producer's cost. They could seem to be in contradiction with natural selection, as non-cooperators have an increased fitness compared to cooperators. Understanding the emergence of cooperation has necessi... |
2007.16069 | Ivan Gutierrez-Sagredo | Angel Ballesteros, Alfonso Blasco, Ivan Gutierrez-Sagredo | Exact closed-form solution of a modified SIR model | 17 pages. New section added | null | null | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The exact analytical solution in closed form of a modified SIR system where
recovered individuals are removed from the population is presented. In this
dynamical system the populations $S(t)$ and $R(t)$ of susceptible and recovered
individuals are found to be generalized logistic functions, while infective
ones $I(t)... | [
{
"created": "Fri, 31 Jul 2020 13:38:40 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Oct 2020 10:28:09 GMT",
"version": "v2"
},
{
"created": "Tue, 10 Nov 2020 10:57:22 GMT",
"version": "v3"
}
] | 2020-11-11 | [
[
"Ballesteros",
"Angel",
""
],
[
"Blasco",
"Alfonso",
""
],
[
"Gutierrez-Sagredo",
"Ivan",
""
]
] | The exact analytical solution in closed form of a modified SIR system where recovered individuals are removed from the population is presented. In this dynamical system the populations $S(t)$ and $R(t)$ of susceptible and recovered individuals are found to be generalized logistic functions, while infective ones $I(t)$ ... |
1302.1752 | Dmitry Karabanov | D.P. Karabanov | Genetical adaptation of common kilka Clupeonella cultriventris
(Nordmann, 1840) (Actinopterygii: Clupeidae) | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is the first time, when genetic diversity and the common kilka population
structure were investigated throughout the areal. Data about the species
condition at the Upper Volga basins were updated accordingly to modern
condition. Physiological and ecological adaptations to northern water basins
were evaluated. Sign... | [
{
"created": "Thu, 7 Feb 2013 14:10:29 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Feb 2013 11:14:26 GMT",
"version": "v2"
}
] | 2013-02-13 | [
[
"Karabanov",
"D. P.",
""
]
] | It is the first time, when genetic diversity and the common kilka population structure were investigated throughout the areal. Data about the species condition at the Upper Volga basins were updated accordingly to modern condition. Physiological and ecological adaptations to northern water basins were evaluated. Signif... |
2103.00677 | Vikas Srivastava | Thomas Usherwood, Zachary LaJoie and Vikas Srivastava (corresponding
author) | Modeling and prediction of COVID-19 in the United States considering
population behavior and vaccination | 11 pages, 7 figures | A model and predictions for COVID-19 considering population
behavior and vaccination. Sciietific Reports 11, 12051 (2021) | 10.1038/s41598-021-91514-7 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | COVID-19 has devastated the entire global community. Vaccines present an
opportunity to mitigate the pandemic; however, the effect of vaccination
coupled with the behavioral response of the population is not well understood.
We propose a model that incorporates two important dynamically varying
population behaviors: ... | [
{
"created": "Mon, 1 Mar 2021 01:13:29 GMT",
"version": "v1"
}
] | 2021-10-26 | [
[
"Usherwood",
"Thomas",
"",
"corresponding\n author"
],
[
"LaJoie",
"Zachary",
"",
"corresponding\n author"
],
[
"Srivastava",
"Vikas",
"",
"corresponding\n author"
]
] | COVID-19 has devastated the entire global community. Vaccines present an opportunity to mitigate the pandemic; however, the effect of vaccination coupled with the behavioral response of the population is not well understood. We propose a model that incorporates two important dynamically varying population behaviors: le... |
2004.01295 | Ram\'on Enrique Ramayo Gonz\'alez | Ram\'on E. R. Gonz\'alez | Different scenarios in the Dynamics of SARS-Cov-2 Infection: an adapted
ODE model | 11 pages, 7 figures and 8 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A mathematical model to calculate the transmissibility of SARS-Cov-2 in Wuhan
City was developed and published recently by Tian-Mu Chen et al., Infectious
Diseases of Poverty, 2020, https://doi.org/10.1186/s40249-020-00640-3. This
paper improves this model in order to study the effect of different scenarios
that incl... | [
{
"created": "Thu, 2 Apr 2020 22:47:39 GMT",
"version": "v1"
}
] | 2020-04-06 | [
[
"González",
"Ramón E. R.",
""
]
] | A mathematical model to calculate the transmissibility of SARS-Cov-2 in Wuhan City was developed and published recently by Tian-Mu Chen et al., Infectious Diseases of Poverty, 2020, https://doi.org/10.1186/s40249-020-00640-3. This paper improves this model in order to study the effect of different scenarios that includ... |
1409.1096 | Colin Gillespie | Colin S. Gillespie, Andrew Golightly | Diagnostics for assessing the linear noise and moment closure
approximations | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Solving the chemical master equation exactly is typically not possible, so
instead we must rely on simulation based methods. Unfortunately, drawing exact
realisations, results in simulating every reaction that occurs. This will
preclude the use of exact simulators for models of any realistic size and so
approximate a... | [
{
"created": "Wed, 3 Sep 2014 14:11:59 GMT",
"version": "v1"
},
{
"created": "Tue, 30 Aug 2016 12:50:54 GMT",
"version": "v2"
}
] | 2016-08-31 | [
[
"Gillespie",
"Colin S.",
""
],
[
"Golightly",
"Andrew",
""
]
] | Solving the chemical master equation exactly is typically not possible, so instead we must rely on simulation based methods. Unfortunately, drawing exact realisations, results in simulating every reaction that occurs. This will preclude the use of exact simulators for models of any realistic size and so approximate alg... |
1312.2120 | Xi Huo | Xi Huo | Modeling of Contact Tracing in Epidemic Populations Structured by
Disease Age | null | null | null | null | q-bio.PE math.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider an age-structured epidemic model with two basic public health
interventions: (i) identifying and isolating symptomatic cases, and (ii)
tracing and quarantine of the contacts of identified infectives. The dynamics
of the infected population are modeled by a nonlinear infection-age-dependent
partial differe... | [
{
"created": "Sat, 7 Dec 2013 18:02:46 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Mar 2014 20:46:37 GMT",
"version": "v2"
}
] | 2014-03-13 | [
[
"Huo",
"Xi",
""
]
] | We consider an age-structured epidemic model with two basic public health interventions: (i) identifying and isolating symptomatic cases, and (ii) tracing and quarantine of the contacts of identified infectives. The dynamics of the infected population are modeled by a nonlinear infection-age-dependent partial different... |
1308.3824 | Fabio Pichierri | Fabio Pichierri | Protein conformational dynamics and electronic structure | 11 pages, 4 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantum mechanical calculations are performed on 116 conformers of the
protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results
indicate that the heat of formation (HOF), dipole moment, energy of the
frontier orbitals HOMO and LUMO, and HOMO-LUMO gap fluctuate within their
corresponding ranges. Thi... | [
{
"created": "Sun, 18 Aug 2013 02:38:09 GMT",
"version": "v1"
}
] | 2013-08-20 | [
[
"Pichierri",
"Fabio",
""
]
] | Quantum mechanical calculations are performed on 116 conformers of the protein ubiquitin (Lange et al., Science 2008, 320, 1471-1475). The results indicate that the heat of formation (HOF), dipole moment, energy of the frontier orbitals HOMO and LUMO, and HOMO-LUMO gap fluctuate within their corresponding ranges. This ... |
1908.06733 | Christian R\"over | Moreno Ursino, Christian R\"over, Sarah Zohar and Tim Friede | Random-effects meta-analysis of phase I dose-finding studies using
stochastic process priors | 23 pages, 6 figures, 7 tables | The Annals of Applied Statistics, 15(1):174-193, 2021 | 10.1214/20-AOAS1390 | null | q-bio.QM stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phase I dose-finding studies aim at identifying the maximal tolerated dose
(MTD). It is not uncommon that several dose-finding studies are conducted,
although often with some variation in the administration mode or dose panel.
For instance, sorafenib (BAY 43-900) was used as monotherapy in at least 29
phase I trials ... | [
{
"created": "Thu, 1 Aug 2019 07:16:40 GMT",
"version": "v1"
}
] | 2021-03-24 | [
[
"Ursino",
"Moreno",
""
],
[
"Röver",
"Christian",
""
],
[
"Zohar",
"Sarah",
""
],
[
"Friede",
"Tim",
""
]
] | Phase I dose-finding studies aim at identifying the maximal tolerated dose (MTD). It is not uncommon that several dose-finding studies are conducted, although often with some variation in the administration mode or dose panel. For instance, sorafenib (BAY 43-900) was used as monotherapy in at least 29 phase I trials ac... |
2111.10695 | Antony Sagayaraj | Toni Sagayaraj, Carsten Eickhoff | Image-Like Graph Representations for Improved Molecular Property
Prediction | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Research into deep learning models for molecular property prediction has
primarily focused on the development of better Graph Neural Network (GNN)
architectures. Though new GNN variants continue to improve performance, their
modifications share a common theme of alleviating problems intrinsic to their
fundamental gra... | [
{
"created": "Sat, 20 Nov 2021 22:39:11 GMT",
"version": "v1"
}
] | 2021-11-23 | [
[
"Sagayaraj",
"Toni",
""
],
[
"Eickhoff",
"Carsten",
""
]
] | Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications share a common theme of alleviating problems intrinsic to their fundamental graph... |
2008.03493 | R\'emi Eyraud | Philipp O. Tsvetkov, R\'emi Eyraud, St\'ephane Ayache, Anton A.
Bougaev, Soazig Malesinski, Hamed Benazha, Svetlana Gorokhova, Christophe
Buffat, Caroline Dehais, Marc Sanson, Franck Bielle, Dominique
Figarella-Branger, Olivier Chinot, Emeline Tabouret, Fran\c{c}ois Devred | An AI-powered blood test to detect cancer using nanoDSF | null | null | null | null | q-bio.QM cs.LG q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe a novel cancer diagnostic method based on plasma denaturation
profiles obtained by a non-conventional use of Differential Scanning
Fluorimetry. We show that 84 glioma patients and 63 healthy controls can be
automatically classified using denaturation profiles with the help of machine
learning algorithms w... | [
{
"created": "Sat, 8 Aug 2020 11:20:53 GMT",
"version": "v1"
}
] | 2020-08-11 | [
[
"Tsvetkov",
"Philipp O.",
""
],
[
"Eyraud",
"Rémi",
""
],
[
"Ayache",
"Stéphane",
""
],
[
"Bougaev",
"Anton A.",
""
],
[
"Malesinski",
"Soazig",
""
],
[
"Benazha",
"Hamed",
""
],
[
"Gorokhova",
"Svetlana",
... | We describe a novel cancer diagnostic method based on plasma denaturation profiles obtained by a non-conventional use of Differential Scanning Fluorimetry. We show that 84 glioma patients and 63 healthy controls can be automatically classified using denaturation profiles with the help of machine learning algorithms wit... |
1502.06172 | Carina Curto | Chad Giusti, Eva Pastalkova, Carina Curto, Vladimir Itskov | Clique topology reveals intrinsic geometric structure in neural
correlations | 29 pages, 4 figures, 13 supplementary figures (last two authors
contributed equally) | PNAS, vol. 112 no. 44, pp. 13455-13460, 2015 | 10.1073/pnas.1506407112 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Detecting meaningful structure in neural activity and connectivity data is
challenging in the presence of hidden nonlinearities, where traditional
eigenvalue-based methods may be misleading. We introduce a novel approach to
matrix analysis, called clique topology, that extracts features of the data
invariant under no... | [
{
"created": "Sun, 22 Feb 2015 03:17:24 GMT",
"version": "v1"
}
] | 2015-11-24 | [
[
"Giusti",
"Chad",
""
],
[
"Pastalkova",
"Eva",
""
],
[
"Curto",
"Carina",
""
],
[
"Itskov",
"Vladimir",
""
]
] | Detecting meaningful structure in neural activity and connectivity data is challenging in the presence of hidden nonlinearities, where traditional eigenvalue-based methods may be misleading. We introduce a novel approach to matrix analysis, called clique topology, that extracts features of the data invariant under nonl... |
1304.7945 | Dmytro Grytskyy | Dmytro Grytskyy, Tom Tetzlaff, Markus Diesmann, Moritz Helias | A unified view on weakly correlated recurrent networks | null | null | 10.3389/fncom.2013.00131 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The diversity of neuron models used in contemporary theoretical neuroscience
to investigate specific properties of covariances raises the question how these
models relate to each other. In particular it is hard to distinguish between
generic properties and peculiarities due to the abstracted model. Here we
present a ... | [
{
"created": "Tue, 30 Apr 2013 10:28:31 GMT",
"version": "v1"
},
{
"created": "Fri, 13 Sep 2013 14:24:45 GMT",
"version": "v2"
}
] | 2022-05-17 | [
[
"Grytskyy",
"Dmytro",
""
],
[
"Tetzlaff",
"Tom",
""
],
[
"Diesmann",
"Markus",
""
],
[
"Helias",
"Moritz",
""
]
] | The diversity of neuron models used in contemporary theoretical neuroscience to investigate specific properties of covariances raises the question how these models relate to each other. In particular it is hard to distinguish between generic properties and peculiarities due to the abstracted model. Here we present a un... |
2101.00613 | Jozef Cernak | Jozef \v{C}ern\'ak | The questionable impact of population-wide public testing in reducing
SARS-CoV-2 infection prevalence in the Slovak Republic | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mina and Andersen, authors of the Perspectives in Science: COVID-19 Testing:
One Size Does Not Fit All have referred to results and adopted conclusions from
recently published governmental report Pavelka et al. "The effectiveness of
population wide, rapid antigen test based screening in reducing SARS-CoV-2
infection ... | [
{
"created": "Sun, 3 Jan 2021 12:14:21 GMT",
"version": "v1"
}
] | 2021-01-05 | [
[
"Černák",
"Jozef",
""
]
] | Mina and Andersen, authors of the Perspectives in Science: COVID-19 Testing: One Size Does Not Fit All have referred to results and adopted conclusions from recently published governmental report Pavelka et al. "The effectiveness of population wide, rapid antigen test based screening in reducing SARS-CoV-2 infection pr... |
1404.2147 | Ana Nunes | Tom\'as Aquino, Diogo Bolster and Ana Nunes | Characterization of the Endemic Equilibrium and Response to Mutant
Injection in a Multi-strain Disease Model | 20 pages, 5 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Starting from common assumptions, we build a rate equation model for
multi-strain disease dynamics in terms of immune repertoire classes. We then
move to a strain-level description where a low-order closure reminiscent of a
pair approximation can be applied. We characterize the endemic equilibrium of
the ensuing mode... | [
{
"created": "Tue, 8 Apr 2014 14:24:22 GMT",
"version": "v1"
}
] | 2014-04-09 | [
[
"Aquino",
"Tomás",
""
],
[
"Bolster",
"Diogo",
""
],
[
"Nunes",
"Ana",
""
]
] | Starting from common assumptions, we build a rate equation model for multi-strain disease dynamics in terms of immune repertoire classes. We then move to a strain-level description where a low-order closure reminiscent of a pair approximation can be applied. We characterize the endemic equilibrium of the ensuing model ... |
q-bio/0405003 | Ravasz Maria | Maria Ravasz, Gyorgy Szabo, Attila Szolnoki | Spreading of families in cyclic predator-prey models | to be published in PRE | Phys. Rev. E 70, 012901 (2004) | 10.1103/PhysRevE.70.012901 | null | q-bio.PE cond-mat.stat-mech | null | We study the spreading of families in two-dimensional multispecies
predator-prey systems, in which species cyclically dominate each other. In each
time step randomly chosen individuals invade one of the nearest sites of the
square lattice eliminating their prey. Initially all individuals get a
family-name which will ... | [
{
"created": "Wed, 5 May 2004 17:06:58 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Ravasz",
"Maria",
""
],
[
"Szabo",
"Gyorgy",
""
],
[
"Szolnoki",
"Attila",
""
]
] | We study the spreading of families in two-dimensional multispecies predator-prey systems, in which species cyclically dominate each other. In each time step randomly chosen individuals invade one of the nearest sites of the square lattice eliminating their prey. Initially all individuals get a family-name which will be... |
1307.6071 | Yong-Jung Kim | Changwook Yoon and Yong-Jung Kim | Bacterial chemotaxis without gradient-sensing | 19 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Models for chemotaxis are based on gradient sensing of individual organisms.
The key contribution of Keller and Segel is showing that erratic movements of
individuals may result in an accurate chemotaxis phenomenon as a group. In this
paper we provide another option to understand chemotactic behavior when
individuals... | [
{
"created": "Tue, 23 Jul 2013 13:35:37 GMT",
"version": "v1"
},
{
"created": "Mon, 29 Jul 2013 23:18:35 GMT",
"version": "v2"
}
] | 2013-07-31 | [
[
"Yoon",
"Changwook",
""
],
[
"Kim",
"Yong-Jung",
""
]
] | Models for chemotaxis are based on gradient sensing of individual organisms. The key contribution of Keller and Segel is showing that erratic movements of individuals may result in an accurate chemotaxis phenomenon as a group. In this paper we provide another option to understand chemotactic behavior when individuals d... |
2212.09749 | Rakib Hassan Pran | Rakib Hassan Pran | Statistical Comparison among Brain Networks with Popular Network
Measurement Algorithms | 22 pages, 38 figures, 19 tables | null | null | null | q-bio.NC cs.SI stat.CO | http://creativecommons.org/licenses/by/4.0/ | In this research, a number of popular network measurement algorithms have
been applied to several brain networks (based on applicability of algorithms)
for finding out statistical correlation among these popular network
measurements which will help scientists to understand these popular network
measurement algorithms... | [
{
"created": "Sat, 22 Oct 2022 21:27:58 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Mar 2023 16:41:37 GMT",
"version": "v2"
}
] | 2023-03-30 | [
[
"Pran",
"Rakib Hassan",
""
]
] | In this research, a number of popular network measurement algorithms have been applied to several brain networks (based on applicability of algorithms) for finding out statistical correlation among these popular network measurements which will help scientists to understand these popular network measurement algorithms a... |
1403.6074 | Anjan Nandi | Anjan K. Nandi, Anindita Bhadra, Annagiri Sumana, Sujata A. Deshpande
and Raghavendra Gadagkar | The Evolution of Complexity in Social Organization - A Model Using
Dominance-Subordinate Behaviour in Two Social Wasp Species | 13 pages, 6 figures, 2 tables | Journal of theoretical biology 327 (2013): 34-44 | 10.1016/j.jtbi.2013.01.010 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dominance and subordinate behaviours are important ingredients in the social
organizations of group living animals. Behavioural observations on the two
eusocial species \textit{Ropalidia marginata} and \textit{Ropalidia
cyathiformis} suggest varying complexities in their social systems. The queen
of R. cyathiformis i... | [
{
"created": "Mon, 24 Mar 2014 18:34:54 GMT",
"version": "v1"
}
] | 2014-03-25 | [
[
"Nandi",
"Anjan K.",
""
],
[
"Bhadra",
"Anindita",
""
],
[
"Sumana",
"Annagiri",
""
],
[
"Deshpande",
"Sujata A.",
""
],
[
"Gadagkar",
"Raghavendra",
""
]
] | Dominance and subordinate behaviours are important ingredients in the social organizations of group living animals. Behavioural observations on the two eusocial species \textit{Ropalidia marginata} and \textit{Ropalidia cyathiformis} suggest varying complexities in their social systems. The queen of R. cyathiformis is ... |
2111.14053 | John Kevin Cava | John Kevin Cava, John Vant, Nicholas Ho, Ankita Shukla, Pavan Turaga,
Ross Maciejewski, and Abhishek Singharoy | Towards Conditional Generation of Minimal Action Potential Pathways for
Molecular Dynamics | Accepted to ELLIS ML4Molecules Workshop 2021 | null | null | null | q-bio.BM cs.AI cs.LG physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | In this paper, we utilized generative models, and reformulate it for problems
in molecular dynamics (MD) simulation, by introducing an MD potential energy
component to our generative model. By incorporating potential energy as
calculated from TorchMD into a conditional generative framework, we attempt to
construct a ... | [
{
"created": "Sun, 28 Nov 2021 05:17:47 GMT",
"version": "v1"
},
{
"created": "Wed, 5 Jan 2022 20:41:24 GMT",
"version": "v2"
}
] | 2022-01-07 | [
[
"Cava",
"John Kevin",
""
],
[
"Vant",
"John",
""
],
[
"Ho",
"Nicholas",
""
],
[
"Shukla",
"Ankita",
""
],
[
"Turaga",
"Pavan",
""
],
[
"Maciejewski",
"Ross",
""
],
[
"Singharoy",
"Abhishek",
""
]
] | In this paper, we utilized generative models, and reformulate it for problems in molecular dynamics (MD) simulation, by introducing an MD potential energy component to our generative model. By incorporating potential energy as calculated from TorchMD into a conditional generative framework, we attempt to construct a lo... |
1608.04059 | Kriti Sen Sharma | Kriti Sen Sharma | Scout-It: Interior tomography using modified scout acquisition | null | null | null | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Global scout views have been previously used to reduce interior
reconstruction artifacts in high-resolution micro-CT and C-arm systems. However
these methods cannot be directly used in the all-important domain of clinical
CT. This is because when the CT scan is truncated, the scout views are also
truncated. However m... | [
{
"created": "Sun, 14 Aug 2016 04:42:30 GMT",
"version": "v1"
}
] | 2016-08-16 | [
[
"Sharma",
"Kriti Sen",
""
]
] | Global scout views have been previously used to reduce interior reconstruction artifacts in high-resolution micro-CT and C-arm systems. However these methods cannot be directly used in the all-important domain of clinical CT. This is because when the CT scan is truncated, the scout views are also truncated. However man... |
1609.06480 | Shihua Zhang | Wenwen Min, Juan Liu, Shihua Zhang | Network-regularized Sparse Logistic Regression Models for Clinical Risk
Prediction and Biomarker Discovery | 10 pages, 3 figures | null | null | null | q-bio.GN cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular profiling data (e.g., gene expression) has been used for clinical
risk prediction and biomarker discovery. However, it is necessary to integrate
other prior knowledge like biological pathways or gene interaction networks to
improve the predictive ability and biological interpretability of biomarkers.
Here, ... | [
{
"created": "Wed, 21 Sep 2016 09:47:32 GMT",
"version": "v1"
}
] | 2016-09-22 | [
[
"Min",
"Wenwen",
""
],
[
"Liu",
"Juan",
""
],
[
"Zhang",
"Shihua",
""
]
] | Molecular profiling data (e.g., gene expression) has been used for clinical risk prediction and biomarker discovery. However, it is necessary to integrate other prior knowledge like biological pathways or gene interaction networks to improve the predictive ability and biological interpretability of biomarkers. Here, we... |
1910.06392 | Muhammad Usman | Muhammad Usman and Jeong A Lee | AFP-CKSAAP: Prediction of Antifreeze Proteins Using Composition of
k-Spaced Amino Acid Pairs with Deep Neural Network | Accepted for oral presentation at 19th 2019 IEEE International
Conference on Bioinformatics and Bioengineering (IC-BIBE 2019) Copyright (c)
2019 IEEE | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Antifreeze proteins (AFPs) are the sub-set of ice binding proteins
indispensable for the species living in extreme cold weather. These proteins
bind to the ice crystals, hindering their growth into large ice lattice that
could cause physical damage. There are variety of AFPs found in numerous
organisms and due to the... | [
{
"created": "Wed, 11 Sep 2019 03:13:14 GMT",
"version": "v1"
}
] | 2019-10-16 | [
[
"Usman",
"Muhammad",
""
],
[
"Lee",
"Jeong A",
""
]
] | Antifreeze proteins (AFPs) are the sub-set of ice binding proteins indispensable for the species living in extreme cold weather. These proteins bind to the ice crystals, hindering their growth into large ice lattice that could cause physical damage. There are variety of AFPs found in numerous organisms and due to the h... |
1312.1057 | Thierry Rabilloud | Thierry Rabilloud (LCBM) | How to use 2D gel electrophoresis in plant proteomics | null | Methods in Molecular Biology -Clifton then Totowa- 1072 (2014)
43-50 | 10.1007/978-1-62703-631-3_4 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Two-dimensional electrophoresis has nurtured the birth of proteomics. It is
however no longer the exclusive setup used in proteomics, with the development
of shotgun proteomics techniques that appear more fancy and fashionable
nowadays.Nevertheless, 2D gel-based proteomics still has valuable features, and
sometimes u... | [
{
"created": "Wed, 4 Dec 2013 08:53:08 GMT",
"version": "v1"
}
] | 2013-12-05 | [
[
"Rabilloud",
"Thierry",
"",
"LCBM"
]
] | Two-dimensional electrophoresis has nurtured the birth of proteomics. It is however no longer the exclusive setup used in proteomics, with the development of shotgun proteomics techniques that appear more fancy and fashionable nowadays.Nevertheless, 2D gel-based proteomics still has valuable features, and sometimes uni... |
1411.0573 | Enrico Bibbona | Enrico Bibbona | Stochastic Chemical Kinetics. Theory and (Mostly) Systems Biological
Applications, P. Erdi, G. Lente. Springer (2014) | null | null | 10.1016/j.biosystems.2014.10.004 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Book review of Stochastic Chemical Kinetics. Theory and (Mostly) Systems
Biological Applications, P. Erdi, G. Lente. Springer (2014)
| [
{
"created": "Fri, 31 Oct 2014 16:47:58 GMT",
"version": "v1"
}
] | 2014-11-04 | [
[
"Bibbona",
"Enrico",
""
]
] | Book review of Stochastic Chemical Kinetics. Theory and (Mostly) Systems Biological Applications, P. Erdi, G. Lente. Springer (2014) |
0910.0835 | Thierry Mora | Thierry Mora, Howard Yu and Ned S. Wingreen | Modeling torque versus speed, shot noise, and rotational diffusion of
the bacterial flagellar motor | null | Phys. Rev. Lett. 103, 248102 (2009) | 10.1103/PhysRevLett.103.248102 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a minimal physical model for the flagellar motor that enables
bacteria to swim. Our model explains the experimentally measured torque-speed
relationship of the proton-driven E. coli motor at various pH and temperature
conditions. In particular, the dramatic drop of torque at high rotation speeds
(the "knee... | [
{
"created": "Mon, 5 Oct 2009 19:59:53 GMT",
"version": "v1"
}
] | 2009-12-11 | [
[
"Mora",
"Thierry",
""
],
[
"Yu",
"Howard",
""
],
[
"Wingreen",
"Ned S.",
""
]
] | We present a minimal physical model for the flagellar motor that enables bacteria to swim. Our model explains the experimentally measured torque-speed relationship of the proton-driven E. coli motor at various pH and temperature conditions. In particular, the dramatic drop of torque at high rotation speeds (the "knee")... |
1909.02456 | Anton Bovier | Anton Bovier | Stochastic models for adaptive dynamics: Scaling limits and diversity | 19 page, This is a review paper that will appear in "Probabilistic
Structures in Evolution", ed. by E. Baake and A. Wakolbinger | in: Probabilistic Structures in Evolution (E. Baake and A.
Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 127--150 | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | I discuss the so-called stochastic individual based model of adaptive
dynamics and in particular how different scaling limits can be obtained by
taking limits of large populations, small mutation rate, and small effect of
single mutations together with appropriate time rescaling. In particular, one
derives the trait ... | [
{
"created": "Thu, 5 Sep 2019 14:42:10 GMT",
"version": "v1"
}
] | 2021-07-06 | [
[
"Bovier",
"Anton",
""
]
] | I discuss the so-called stochastic individual based model of adaptive dynamics and in particular how different scaling limits can be obtained by taking limits of large populations, small mutation rate, and small effect of single mutations together with appropriate time rescaling. In particular, one derives the trait su... |
2303.00240 | Hongsong Feng | Hongsong Feng, Jian Jiang, Guo-Wei Wei | Machine-learning Repurposing of DrugBank Compounds for Opioid Use
Disorder | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Opioid use disorder (OUD) is a chronic and relapsing condition that involves
the continued and compulsive use of opioids despite harmful consequences. The
development of medications with improved efficacy and safety profiles for OUD
treatment is urgently needed. Drug repurposing is a promising option for drug
discove... | [
{
"created": "Wed, 1 Mar 2023 05:23:06 GMT",
"version": "v1"
}
] | 2023-03-02 | [
[
"Feng",
"Hongsong",
""
],
[
"Jiang",
"Jian",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Opioid use disorder (OUD) is a chronic and relapsing condition that involves the continued and compulsive use of opioids despite harmful consequences. The development of medications with improved efficacy and safety profiles for OUD treatment is urgently needed. Drug repurposing is a promising option for drug discovery... |
q-bio/0310016 | David Biron | D. Biron, P. Libros, D. Sagi, D. Mirelman and E. Moses | Cytokinesis: the initial linear phase crosses over to a multiplicity of
non-linear endings | null | null | null | null | q-bio.CB | null | We investigate the final stage of cytokinesis in two types of amoeba,
pointing out the existence of biphasic furrow contraction. The first phase is
characterized by a constant contraction rate, is better studied, and seems
universal to a large extent. The second phase is more diverse. In Dictyostelium
discoideum the ... | [
{
"created": "Tue, 14 Oct 2003 15:32:38 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Biron",
"D.",
""
],
[
"Libros",
"P.",
""
],
[
"Sagi",
"D.",
""
],
[
"Mirelman",
"D.",
""
],
[
"Moses",
"E.",
""
]
] | We investigate the final stage of cytokinesis in two types of amoeba, pointing out the existence of biphasic furrow contraction. The first phase is characterized by a constant contraction rate, is better studied, and seems universal to a large extent. The second phase is more diverse. In Dictyostelium discoideum the tr... |
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