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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2207.06518 | Peter Taylor | Thomas W. Owen, Gabrielle M. Schroeder, Vytene Janiukstyte, Gerard R.
Hall, Andrew McEvoy, Anna Miserocchi, Jane de Tisi, John S. Duncan, Fergus
Rugg-Gunn, Yujiang Wang, Peter N. Taylor | MEG abnormalities and mechanisms of surgical failure in neocortical
epilepsy | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Neocortical epilepsy surgery fails to achieve post-operative seizure freedom
in 30-40% of cases. It is not fully understood why surgery in some patients is
unsuccessful. Comparing interictal MEG bandpower from patients to normative
maps, which describe healthy spatial and population variability, we identify
patient s... | [
{
"created": "Wed, 13 Jul 2022 20:38:06 GMT",
"version": "v1"
},
{
"created": "Sat, 11 Feb 2023 15:53:13 GMT",
"version": "v2"
}
] | 2023-02-14 | [
[
"Owen",
"Thomas W.",
""
],
[
"Schroeder",
"Gabrielle M.",
""
],
[
"Janiukstyte",
"Vytene",
""
],
[
"Hall",
"Gerard R.",
""
],
[
"McEvoy",
"Andrew",
""
],
[
"Miserocchi",
"Anna",
""
],
[
"de Tisi",
"Jane",
"... | Neocortical epilepsy surgery fails to achieve post-operative seizure freedom in 30-40% of cases. It is not fully understood why surgery in some patients is unsuccessful. Comparing interictal MEG bandpower from patients to normative maps, which describe healthy spatial and population variability, we identify patient spe... |
q-bio/0309009 | Giuseppe Vitiello | Eliano Pessa and Giuseppe Vitiello | Quantum noise, entanglement and chaos in the quantum field theory of
mind/brain states | 15 pages | Mind and Matter 1, 59 (2003) | null | null | q-bio.OT q-bio.NC quant-ph | null | We review the dissipative quantum model of brain and present recent
developments related with the r\^ole of entanglement, quantum noise and chaos
in the model.
| [
{
"created": "Sun, 21 Sep 2003 21:54:17 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Pessa",
"Eliano",
""
],
[
"Vitiello",
"Giuseppe",
""
]
] | We review the dissipative quantum model of brain and present recent developments related with the r\^ole of entanglement, quantum noise and chaos in the model. |
2302.13340 | Anando Sen | Anando Sen, Victoria Hedley, John Owen, Ronald Cornet, Dipak Kalra,
Corinna Engel, Avril Palmeri, Joanne Lee, Jean-Christophe Roze, Joseph F
Standing, Adilia Warris, Claudia Pansieri, Rebecca Leary, Mark Turner, Volker
Straub | Standardizing Paediatric Clinical Data: The Development of the
conect4children (c4c) Cross Cutting Paediatric Data Dictionary | null | Journal of the Society of Clinical Data Management, Volume 2,
Issue 3, 2023 | 10.47912/jscdm.218 | null | q-bio.OT cs.DL | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Standardization of data items collected in paediatric clinical trials is an
important but challenging issue. The Clinical Data Interchange Standards
Consortium (CDISC) data standards are well understood by the pharmaceutical
industry but lack the implementation of some paediatric specific concepts. When
a paediatric ... | [
{
"created": "Sun, 26 Feb 2023 16:10:12 GMT",
"version": "v1"
}
] | 2023-02-28 | [
[
"Sen",
"Anando",
""
],
[
"Hedley",
"Victoria",
""
],
[
"Owen",
"John",
""
],
[
"Cornet",
"Ronald",
""
],
[
"Kalra",
"Dipak",
""
],
[
"Engel",
"Corinna",
""
],
[
"Palmeri",
"Avril",
""
],
[
"Lee",
... | Standardization of data items collected in paediatric clinical trials is an important but challenging issue. The Clinical Data Interchange Standards Consortium (CDISC) data standards are well understood by the pharmaceutical industry but lack the implementation of some paediatric specific concepts. When a paediatric co... |
1109.1495 | Carlo Amoruso Mr | Carlo Amoruso, Thibault Lagache, David Holcman | Modeling the early steps of cytoplasmic trafficking in viral infection
and gene delivery | 31 pages, 11 figures. To appear on SIAM | null | null | null | q-bio.SC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene delivery of nucleic acid to the cell nucleus is a fundamental step in
gene therapy. In this review of modeling drug and gene delivery, we focus on
the particular stage of plasmid DNA or virus cytoplasmic trafficking. A
challenging problem is to quantify the success of this limiting stage. We
present some models ... | [
{
"created": "Wed, 7 Sep 2011 15:49:00 GMT",
"version": "v1"
}
] | 2011-09-08 | [
[
"Amoruso",
"Carlo",
""
],
[
"Lagache",
"Thibault",
""
],
[
"Holcman",
"David",
""
]
] | Gene delivery of nucleic acid to the cell nucleus is a fundamental step in gene therapy. In this review of modeling drug and gene delivery, we focus on the particular stage of plasmid DNA or virus cytoplasmic trafficking. A challenging problem is to quantify the success of this limiting stage. We present some models an... |
2005.07171 | Dimitra Kosta | Muhammad Ardiyansyah, Dimitra Kosta, and Kaie Kubjas | The Model-Specific Markov Embedding Problem for Symmetric Group-Based
Models | 25 pages, 1 figure, 6 tables. An initial version of the main result
of this preprint appeared in the preprint arXiv:1705.09228. Following the
advice of referees, we divided the earlier preprint into two. The present
preprint supersedes the section on the embedding problem in arXiv:1705.09228.
A first version of... | null | null | null | q-bio.PE math.CO math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study model embeddability, which is a variation of the famous embedding
problem in probability theory, when apart from the requirement that the Markov
matrix is the matrix exponential of a rate matrix, we additionally ask that the
rate matrix follows the model structure. We provide a characterisation of model
embe... | [
{
"created": "Thu, 14 May 2020 17:41:24 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Apr 2021 17:46:40 GMT",
"version": "v2"
}
] | 2021-04-02 | [
[
"Ardiyansyah",
"Muhammad",
""
],
[
"Kosta",
"Dimitra",
""
],
[
"Kubjas",
"Kaie",
""
]
] | We study model embeddability, which is a variation of the famous embedding problem in probability theory, when apart from the requirement that the Markov matrix is the matrix exponential of a rate matrix, we additionally ask that the rate matrix follows the model structure. We provide a characterisation of model embedd... |
1902.04321 | Adam Barrett DPhil | Adam B. Barrett and Pedro A. M. Mediano | The Phi measure of integrated information is not well-defined for
general physical systems | 8 pages | Journal of Consciousness Studies, 26 (1-2). pp. 11-20. ISSN
1355-8250 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | According to the Integrated Information Theory of Consciousness,
consciousness is a fundamental observer-independent property of physical
systems, and the measure Phi of integrated information is identical to the
quantity or level of consciousness. For this to be plausible, there should be
no alternative formulae for... | [
{
"created": "Tue, 12 Feb 2019 10:40:06 GMT",
"version": "v1"
}
] | 2019-02-13 | [
[
"Barrett",
"Adam B.",
""
],
[
"Mediano",
"Pedro A. M.",
""
]
] | According to the Integrated Information Theory of Consciousness, consciousness is a fundamental observer-independent property of physical systems, and the measure Phi of integrated information is identical to the quantity or level of consciousness. For this to be plausible, there should be no alternative formulae for P... |
1908.09314 | Mamoru Sugamoto | Naoaki Fujimoto, Muneharu Onoue, Akio Sugamoto, Mamoru Sugamoto, and
Tsukasa Yumibayashi | Surround Inhibition Mechanism by Deep Learning | 5 pages, 4 figures | null | null | OUJ-FTC-3, OCHA-PP-356 | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the sensation of tones, visions and other stimuli, the "surround
inhibition mechanism" (or "lateral inhibition mechanism") is crucial. The
mechanism enhances the signals of the strongest tone, color and other stimuli,
by reducing and inhibiting the surrounding signals, since the latter signals
are less important. ... | [
{
"created": "Sun, 25 Aug 2019 12:41:56 GMT",
"version": "v1"
}
] | 2019-08-27 | [
[
"Fujimoto",
"Naoaki",
""
],
[
"Onoue",
"Muneharu",
""
],
[
"Sugamoto",
"Akio",
""
],
[
"Sugamoto",
"Mamoru",
""
],
[
"Yumibayashi",
"Tsukasa",
""
]
] | In the sensation of tones, visions and other stimuli, the "surround inhibition mechanism" (or "lateral inhibition mechanism") is crucial. The mechanism enhances the signals of the strongest tone, color and other stimuli, by reducing and inhibiting the surrounding signals, since the latter signals are less important. Th... |
2006.06767 | Steffen Werner | Steffen Werner, W Mathijs Rozemuller, Annabel Ebbing, Anna Alemany,
Joleen Traets, Jeroen S. van Zon, Alexander van Oudenaarden, Hendrik C.
Korswagen, Greg J. Stephens, and Thomas S. Shimizu | Functional modules from variable genes: Leveraging percolation to
analyze noisy, high-dimensional data | 13 pages, 8 figures | null | null | null | q-bio.GN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While measurement advances now allow extensive surveys of gene activity
(large numbers of genes across many samples), interpretation of these data is
often confounded by noise -- expression counts can differ strongly across
samples due to variation of both biological and experimental origin.
Complimentary to perturba... | [
{
"created": "Thu, 11 Jun 2020 19:45:08 GMT",
"version": "v1"
}
] | 2020-06-15 | [
[
"Werner",
"Steffen",
""
],
[
"Rozemuller",
"W Mathijs",
""
],
[
"Ebbing",
"Annabel",
""
],
[
"Alemany",
"Anna",
""
],
[
"Traets",
"Joleen",
""
],
[
"van Zon",
"Jeroen S.",
""
],
[
"van Oudenaarden",
"Alexander"... | While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to variation of both biological and experimental origin. Complimentary to perturbati... |
1109.4262 | Ilona Nagy | I. Nagy, J. T\'oth | Microscopic Reversibility or Detailed Balance in Ion Channel Models | null | null | null | null | q-bio.MN math.CA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mass action type deterministic kinetic models of ion channels are usually
constructed in such a way as to obey the principle of detailed balance (or,
microscopic reversibility) for two reasons: first, the authors aspire to have
models harmonizing with thermodynamics, second, the conditions to ensure
detailed balance ... | [
{
"created": "Tue, 20 Sep 2011 10:54:53 GMT",
"version": "v1"
}
] | 2011-09-21 | [
[
"Nagy",
"I.",
""
],
[
"Tóth",
"J.",
""
]
] | Mass action type deterministic kinetic models of ion channels are usually constructed in such a way as to obey the principle of detailed balance (or, microscopic reversibility) for two reasons: first, the authors aspire to have models harmonizing with thermodynamics, second, the conditions to ensure detailed balance re... |
1109.5402 | I. Emrah Nikerel | Oscar M.J.A. Stassen, Ruud J.J.Jorna, Bastiaan A. van den Berg, Rad
Haghi, Farzad Ehtemam, Steven M. Flipse, Marco J.L. de Groot, Janine A.
Kiers, I. Emrah Nikerel and Domenico Bellomo | Toward tunable RNA thermo-switches for temperature dependent gene
expression | 12 pages, 10 figures | null | null | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA thermometers are mRNA strands with a temperature dependent secondary
structure: depending on the spatial conformation, the mRNA strand can get
translated (on-state) or can be inaccessible for ribosomes binding (off-state).
These have been found in a number of microorganisms (mainly pathogens), where
they are used... | [
{
"created": "Sun, 25 Sep 2011 21:35:06 GMT",
"version": "v1"
}
] | 2011-09-27 | [
[
"Stassen",
"Oscar M. J. A.",
""
],
[
"Jorna",
"Ruud J. J.",
""
],
[
"Berg",
"Bastiaan A. van den",
""
],
[
"Haghi",
"Rad",
""
],
[
"Ehtemam",
"Farzad",
""
],
[
"Flipse",
"Steven M.",
""
],
[
"de Groot",
"Marco ... | RNA thermometers are mRNA strands with a temperature dependent secondary structure: depending on the spatial conformation, the mRNA strand can get translated (on-state) or can be inaccessible for ribosomes binding (off-state). These have been found in a number of microorganisms (mainly pathogens), where they are used t... |
2208.00417 | Wasiur R. KhudaBukhsh | Colin Klaus and Matthew Wascher and Wasiur R. KhudaBukhsh and Grzegorz
A. Rempala | Likelihood-Free Dynamical Survival Analysis Applied to the COVID-19
Epidemic in Ohio | 27 pages, 7 figures. Manuscript under submission for publication | null | null | null | q-bio.PE math.AP math.DS physics.soc-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Dynamical Survival Analysis (DSA) is a framework for modeling epidemics
based on mean field dynamics applied to individual (agent) level history of
infection and recovery. Recently, DSA has been shown to be an effective tool in
analyzing complex non-Markovian epidemic processes that are otherwise difficult
to han... | [
{
"created": "Sun, 31 Jul 2022 11:17:18 GMT",
"version": "v1"
}
] | 2022-08-02 | [
[
"Klaus",
"Colin",
""
],
[
"Wascher",
"Matthew",
""
],
[
"KhudaBukhsh",
"Wasiur R.",
""
],
[
"Rempala",
"Grzegorz A.",
""
]
] | The Dynamical Survival Analysis (DSA) is a framework for modeling epidemics based on mean field dynamics applied to individual (agent) level history of infection and recovery. Recently, DSA has been shown to be an effective tool in analyzing complex non-Markovian epidemic processes that are otherwise difficult to handl... |
q-bio/0507038 | Jaewook Joo | Jaewook Joo, Michelle Gunny, Marisa Cases, Peter Hudson, Reka Albert
and Eric Harvill | Bacteriophage-mediated competition in Bordetella bacteria | 10pages, 8 figures | Proceedings of the Royal Society B: Biological Sciences (2006) | 10.1098/rspb.2006.3512 | null | q-bio.PE | null | Apparent competition between species is believed to be one of the principle
driving forces that structure ecological communities, although the precise
mecha nisms have yet to be characterized. Here we develop a model system that
isolates phage-mediated interactions by neutralizing resource competition using
two genet... | [
{
"created": "Mon, 25 Jul 2005 21:51:45 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Joo",
"Jaewook",
""
],
[
"Gunny",
"Michelle",
""
],
[
"Cases",
"Marisa",
""
],
[
"Hudson",
"Peter",
""
],
[
"Albert",
"Reka",
""
],
[
"Harvill",
"Eric",
""
]
] | Apparent competition between species is believed to be one of the principle driving forces that structure ecological communities, although the precise mecha nisms have yet to be characterized. Here we develop a model system that isolates phage-mediated interactions by neutralizing resource competition using two genetic... |
2102.08524 | Nicolas Roth | Teresa Chouzouris, Nicolas Roth, Caglar Cakan, Klaus Obermayer | Applications of optimal nonlinear control to a whole-brain network of
FitzHugh-Nagumo oscillators | Main paper: 20 pages, 14 figures; supplemental material: 10 pages, 9
figures. For associated video files, see
https://github.com/rederoth/nonlinearControlFHN-videos | Phys. Rev. E 104, 024213 (2021) | 10.1103/PhysRevE.104.024213 | null | q-bio.NC cs.SY eess.SY nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We apply the framework of optimal nonlinear control to steer the dynamics of
a whole-brain network of FitzHugh-Nagumo oscillators. Its nodes correspond to
the cortical areas of an atlas-based segmentation of the human cerebral cortex,
and the inter-node coupling strengths are derived from Diffusion Tensor Imaging
dat... | [
{
"created": "Wed, 17 Feb 2021 01:38:56 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Mar 2021 17:29:26 GMT",
"version": "v2"
},
{
"created": "Fri, 3 Sep 2021 13:15:58 GMT",
"version": "v3"
}
] | 2021-09-08 | [
[
"Chouzouris",
"Teresa",
""
],
[
"Roth",
"Nicolas",
""
],
[
"Cakan",
"Caglar",
""
],
[
"Obermayer",
"Klaus",
""
]
] | We apply the framework of optimal nonlinear control to steer the dynamics of a whole-brain network of FitzHugh-Nagumo oscillators. Its nodes correspond to the cortical areas of an atlas-based segmentation of the human cerebral cortex, and the inter-node coupling strengths are derived from Diffusion Tensor Imaging data ... |
1609.04515 | Thomas R. Weikl | Michael Raatz and Thomas R. Weikl | Membrane tubulation by elongated and patchy nanoparticles | 11 pages, 6 figures | Adv. Mater. Interfaces 2016, 1600325 | 10.1002/admi.201600325 | null | q-bio.SC cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Advances in nanotechnology lead to an increasing interest in how
nanoparticles interact with biomembranes. Nanoparticles are wrapped
spontaneously by biomembranes if the adhesive interactions between the
particles and membranes compensate for the cost of membrane bending. In the
last years, the cooperative wrapping o... | [
{
"created": "Thu, 15 Sep 2016 05:38:50 GMT",
"version": "v1"
}
] | 2016-09-16 | [
[
"Raatz",
"Michael",
""
],
[
"Weikl",
"Thomas R.",
""
]
] | Advances in nanotechnology lead to an increasing interest in how nanoparticles interact with biomembranes. Nanoparticles are wrapped spontaneously by biomembranes if the adhesive interactions between the particles and membranes compensate for the cost of membrane bending. In the last years, the cooperative wrapping of ... |
0808.0750 | Raouf Ghomrasni | Raouf Ghomrasni and Lisa Bonney | SDE in Random Population Growth | 17 pages | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper we extend the recent work of C.A. Braumann \cite{B2007} to the
case of stochastic differential equation with random coefficients. Furthermore,
the relationship of the It\^o-Stratonovich stochastic calculus to studies of
random population growth is also explained.
| [
{
"created": "Wed, 6 Aug 2008 00:34:27 GMT",
"version": "v1"
}
] | 2008-08-07 | [
[
"Ghomrasni",
"Raouf",
""
],
[
"Bonney",
"Lisa",
""
]
] | In this paper we extend the recent work of C.A. Braumann \cite{B2007} to the case of stochastic differential equation with random coefficients. Furthermore, the relationship of the It\^o-Stratonovich stochastic calculus to studies of random population growth is also explained. |
2002.11195 | Ilya A. Surov Mr. | Ilya A. Surov | Quantum Cognitive Triad. Semantic geometry of context representation | 44 pages, 6 figures | null | 10.1007/s10699-020-09712-x | null | q-bio.NC cs.AI quant-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The paper describes an algorithm for semantic representation of behavioral
contexts relative to a dichotomic decision alternative. The contexts are
represented as quantum qubit states in two-dimensional Hilbert space visualized
as points on the Bloch sphere. The azimuthal coordinate of this sphere
functions as a one-... | [
{
"created": "Sat, 22 Feb 2020 17:29:10 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Dec 2020 14:43:28 GMT",
"version": "v2"
}
] | 2020-12-23 | [
[
"Surov",
"Ilya A.",
""
]
] | The paper describes an algorithm for semantic representation of behavioral contexts relative to a dichotomic decision alternative. The contexts are represented as quantum qubit states in two-dimensional Hilbert space visualized as points on the Bloch sphere. The azimuthal coordinate of this sphere functions as a one-di... |
0811.3034 | Elfi Kraka | S. Ranganathan, D. Izotov, E. Kraka, and D. Cremer | Description and Recognition of Regular and Distorted Secondary
Structures in Proteins Using the Automated Protein Structure Analysis Method | 49 pages, 6 figures, 2 schemes | null | null | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Automated Protein Structure Analysis (APSA) method, which describes the
protein backbone as a smooth line in 3-dimensional space and characterizes it
by curvature kappa and torsion tau as a function of arc length s, was applied
on 77 proteins to determine all secondary structural units via specific
kappa(s) and t... | [
{
"created": "Wed, 19 Nov 2008 00:22:37 GMT",
"version": "v1"
},
{
"created": "Mon, 24 Nov 2008 21:21:27 GMT",
"version": "v2"
}
] | 2008-11-24 | [
[
"Ranganathan",
"S.",
""
],
[
"Izotov",
"D.",
""
],
[
"Kraka",
"E.",
""
],
[
"Cremer",
"D.",
""
]
] | The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77 proteins to determine all secondary structural units via specific kappa(s) and tau... |
1901.00991 | Lin Yang | Xiaoliang Ma, Chengyu Hou, Liping Shi, Long Li, Jiacheng Li, Lin Ye,
Lin Yang, Xiaodong He | Physical Folding Codes for Proteins | 19 pages, 7 figures, 8 tables | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Exploring and understanding the protein-folding problem has been a
long-standing challenge in molecular biology. Here, using molecular dynamics
simulation, we reveal how parallel distributed adjacent planar peptide groups
of unfolded proteins fold reproducibly following explicit physical folding
codes in aqueous envi... | [
{
"created": "Fri, 4 Jan 2019 06:28:11 GMT",
"version": "v1"
}
] | 2019-01-11 | [
[
"Ma",
"Xiaoliang",
""
],
[
"Hou",
"Chengyu",
""
],
[
"Shi",
"Liping",
""
],
[
"Li",
"Long",
""
],
[
"Li",
"Jiacheng",
""
],
[
"Ye",
"Lin",
""
],
[
"Yang",
"Lin",
""
],
[
"He",
"Xiaodong",
""... | Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded proteins fold reproducibly following explicit physical folding codes in aqueous enviro... |
1807.02741 | Carina Curto | Carina Curto, Elizabeth Gross, Jack Jeffries, Katherine Morrison, Zvi
Rosen, Anne Shiu, and Nora Youngs | Algebraic signatures of convex and non-convex codes | 22 pages, 6 figures, 7 tables | null | null | null | q-bio.NC cs.DM math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A convex code is a binary code generated by the pattern of intersections of a
collection of open convex sets in some Euclidean space. Convex codes are
relevant to neuroscience as they arise from the activity of neurons that have
convex receptive fields. In this paper, we use algebraic methods to determine
if a code i... | [
{
"created": "Sun, 8 Jul 2018 02:43:04 GMT",
"version": "v1"
}
] | 2018-07-10 | [
[
"Curto",
"Carina",
""
],
[
"Gross",
"Elizabeth",
""
],
[
"Jeffries",
"Jack",
""
],
[
"Morrison",
"Katherine",
""
],
[
"Rosen",
"Zvi",
""
],
[
"Shiu",
"Anne",
""
],
[
"Youngs",
"Nora",
""
]
] | A convex code is a binary code generated by the pattern of intersections of a collection of open convex sets in some Euclidean space. Convex codes are relevant to neuroscience as they arise from the activity of neurons that have convex receptive fields. In this paper, we use algebraic methods to determine if a code is ... |
q-bio/0312043 | Peng-Ye Wang | Ping Xie, Shuo-Xing Dou, Peng-Ye Wang | Mechanism of unidirectional movement of kinesin motors | 22 pages, 6 figures | Chinese Physics, Vol.14, No.4 (2005) 734-743 | 10.1088/1009-1963/14/4/017 | null | q-bio.BM | null | Kinesin motors have been studied extensively both experimentally and
theoretically. However, the microscopic mechanism of the processive movement of
kinesin is still an open question. In this paper, we propose a hand-over-hand
model for the processivity of kinesin, which is based on chemical, mechanical,
and electric... | [
{
"created": "Tue, 30 Dec 2003 02:53:25 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Xie",
"Ping",
""
],
[
"Dou",
"Shuo-Xing",
""
],
[
"Wang",
"Peng-Ye",
""
]
] | Kinesin motors have been studied extensively both experimentally and theoretically. However, the microscopic mechanism of the processive movement of kinesin is still an open question. In this paper, we propose a hand-over-hand model for the processivity of kinesin, which is based on chemical, mechanical, and electrical... |
2405.05998 | Niki Kilbertus | Zhufeng Li and Sandeep S Cranganore and Nicholas Youngblut and Niki
Kilbertus | Whole Genome Transformer for Gene Interaction Effects in Microbiome
Habitat Specificity | null | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Leveraging the vast genetic diversity within microbiomes offers unparalleled
insights into complex phenotypes, yet the task of accurately predicting and
understanding such traits from genomic data remains challenging. We propose a
framework taking advantage of existing large models for gene vectorization to
predict h... | [
{
"created": "Thu, 9 May 2024 09:34:51 GMT",
"version": "v1"
},
{
"created": "Tue, 28 May 2024 10:59:16 GMT",
"version": "v2"
}
] | 2024-05-29 | [
[
"Li",
"Zhufeng",
""
],
[
"Cranganore",
"Sandeep S",
""
],
[
"Youngblut",
"Nicholas",
""
],
[
"Kilbertus",
"Niki",
""
]
] | Leveraging the vast genetic diversity within microbiomes offers unparalleled insights into complex phenotypes, yet the task of accurately predicting and understanding such traits from genomic data remains challenging. We propose a framework taking advantage of existing large models for gene vectorization to predict hab... |
1502.07110 | Gabor Szederkenyi | Antonio A. Alonso and Gabor Szederkenyi | Uniqueness of feasible equilibria for mass action law (MAL) kinetic
systems | null | Journal of Process Control, 48: 41-71, 2016 | 10.1016/j.jprocont.2016.10.002 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper studies the relations among system parameters, uniqueness, and
stability of equilibria, for kinetic systems given in the form of polynomial
ODEs. Such models are commonly used to describe the dynamics of nonnegative
systems, with a wide range of application fields such as chemistry, systems
biology, proces... | [
{
"created": "Wed, 25 Feb 2015 10:16:46 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Nov 2016 23:30:54 GMT",
"version": "v2"
}
] | 2016-11-14 | [
[
"Alonso",
"Antonio A.",
""
],
[
"Szederkenyi",
"Gabor",
""
]
] | This paper studies the relations among system parameters, uniqueness, and stability of equilibria, for kinetic systems given in the form of polynomial ODEs. Such models are commonly used to describe the dynamics of nonnegative systems, with a wide range of application fields such as chemistry, systems biology, process ... |
2210.01169 | Ying Tang | Ying Tang, Jiayu Weng, Pan Zhang | Neural-network solutions to stochastic reaction networks | null | null | null | null | q-bio.MN cs.LG nlin.AO | http://creativecommons.org/licenses/by/4.0/ | The stochastic reaction network in which chemical species evolve through a
set of reactions is widely used to model stochastic processes in physics,
chemistry and biology. To characterize the evolving joint probability
distribution in the state space of species counts requires solving a system of
ordinary differentia... | [
{
"created": "Thu, 29 Sep 2022 07:27:59 GMT",
"version": "v1"
},
{
"created": "Tue, 7 Feb 2023 05:21:30 GMT",
"version": "v2"
}
] | 2023-02-08 | [
[
"Tang",
"Ying",
""
],
[
"Weng",
"Jiayu",
""
],
[
"Zhang",
"Pan",
""
]
] | The stochastic reaction network in which chemical species evolve through a set of reactions is widely used to model stochastic processes in physics, chemistry and biology. To characterize the evolving joint probability distribution in the state space of species counts requires solving a system of ordinary differential ... |
2310.18377 | Ran Wang | Ran Wang and Zhe Sage Chen | Large-scale Foundation Models and Generative AI for BigData Neuroscience | null | null | null | null | q-bio.NC cs.AI cs.HC cs.LG cs.MM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent advances in machine learning have made revolutionary breakthroughs in
computer games, image and natural language understanding, and scientific
discovery. Foundation models and large-scale language models (LLMs) have
recently achieved human-like intelligence thanks to BigData. With the help of
self-supervised l... | [
{
"created": "Fri, 27 Oct 2023 00:44:40 GMT",
"version": "v1"
}
] | 2023-10-31 | [
[
"Wang",
"Ran",
""
],
[
"Chen",
"Zhe Sage",
""
]
] | Recent advances in machine learning have made revolutionary breakthroughs in computer games, image and natural language understanding, and scientific discovery. Foundation models and large-scale language models (LLMs) have recently achieved human-like intelligence thanks to BigData. With the help of self-supervised lea... |
1010.2538 | Adam Lipowski | Jacek Wendykier, Adam Lipowski, and Antonio Luis Ferreira | Coexistence and critical behaviour in a lattice model of competing
species | 11 pages, 14 figures | Phy. Rev. E 83, 031904 (2011) | 10.1103/PhysRevE.83.031904 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present paper we study a lattice model of two species competing for
the same resources. Monte Carlo simulations for d=1, 2, and 3 show that when
resources are easily available both species coexist. However, when the supply
of resources is on an intermediate level, the species with slower metabolism
becomes ext... | [
{
"created": "Tue, 12 Oct 2010 23:33:42 GMT",
"version": "v1"
},
{
"created": "Mon, 7 Mar 2011 21:14:35 GMT",
"version": "v2"
}
] | 2011-03-09 | [
[
"Wendykier",
"Jacek",
""
],
[
"Lipowski",
"Adam",
""
],
[
"Ferreira",
"Antonio Luis",
""
]
] | In the present paper we study a lattice model of two species competing for the same resources. Monte Carlo simulations for d=1, 2, and 3 show that when resources are easily available both species coexist. However, when the supply of resources is on an intermediate level, the species with slower metabolism becomes extin... |
1301.0170 | Yutaka Hori | Yutaka Hori and Shinji Hara | Noise-Induced Spatial Pattern Formation in Stochastic Reaction-Diffusion
Systems | null | Proceedings of IEEE Conference on Decision and Control, pp.
1053-1058, 2012 | 10.1109/CDC.2012.6426152 | null | q-bio.QM cs.SY q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper is concerned with stochastic reaction-diffusion kinetics governed
by the reaction-diffusion master equation. Specifically, the primary goal of
this paper is to provide a mechanistic basis of Turing pattern formation that
is induced by intrinsic noise. To this end, we first derive an approximate
reaction-di... | [
{
"created": "Wed, 2 Jan 2013 05:38:34 GMT",
"version": "v1"
}
] | 2015-04-23 | [
[
"Hori",
"Yutaka",
""
],
[
"Hara",
"Shinji",
""
]
] | This paper is concerned with stochastic reaction-diffusion kinetics governed by the reaction-diffusion master equation. Specifically, the primary goal of this paper is to provide a mechanistic basis of Turing pattern formation that is induced by intrinsic noise. To this end, we first derive an approximate reaction-diff... |
2011.11335 | Sacha van Albada | Sacha Jennifer van Albada, Jari Pronold, Alexander van Meegen, Markus
Diesmann | Usage and Scaling of an Open-Source Spiking Multi-Area Model of Monkey
Cortex | null | null | 10.1007/978-3-030-82427-3_4 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | We are entering an age of `big' computational neuroscience, in which neural
network models are increasing in size and in numbers of underlying data sets.
Consolidating the zoo of models into large-scale models simultaneously
consistent with a wide range of data is only possible through the effort of
large teams, whic... | [
{
"created": "Mon, 23 Nov 2020 11:25:14 GMT",
"version": "v1"
}
] | 2022-10-17 | [
[
"van Albada",
"Sacha Jennifer",
""
],
[
"Pronold",
"Jari",
""
],
[
"van Meegen",
"Alexander",
""
],
[
"Diesmann",
"Markus",
""
]
] | We are entering an age of `big' computational neuroscience, in which neural network models are increasing in size and in numbers of underlying data sets. Consolidating the zoo of models into large-scale models simultaneously consistent with a wide range of data is only possible through the effort of large teams, which ... |
1403.4196 | Alison Hill | Alison L. Hill, Daniel I. S. Rosenbloom, Feng Fu, Martin A. Nowak,
Robert F. Siliciano | Predicting the outcomes of treatment to eradicate the latent reservoir
for HIV-1 | 8 pages main text (4 figures). In PNAS Early Edition
http://www.pnas.org/content/early/2014/08/05/1406663111. Ancillary files: SI,
24 pages SI (7 figures). File .htm opens a browser-based application to
calculate rebound times (see SI). Or, the .cdf file can be run with
Mathematica. The most up-to-date version ... | null | 10.1073/pnas.1406663111 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Massive research efforts are now underway to develop a cure for HIV
infection, allowing patients to discontinue lifelong combination antiretroviral
therapy (ART). New latency-reversing agents (LRAs) may be able to purge the
persistent reservoir of latent virus in resting memory CD4+ T cells, but the
degree of reservo... | [
{
"created": "Mon, 17 Mar 2014 18:25:16 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Aug 2014 20:50:42 GMT",
"version": "v2"
}
] | 2014-08-07 | [
[
"Hill",
"Alison L.",
""
],
[
"Rosenbloom",
"Daniel I. S.",
""
],
[
"Fu",
"Feng",
""
],
[
"Nowak",
"Martin A.",
""
],
[
"Siliciano",
"Robert F.",
""
]
] | Massive research efforts are now underway to develop a cure for HIV infection, allowing patients to discontinue lifelong combination antiretroviral therapy (ART). New latency-reversing agents (LRAs) may be able to purge the persistent reservoir of latent virus in resting memory CD4+ T cells, but the degree of reservoir... |
2301.01619 | Ankit Rao | Ankit Rao, Sooraj Sanjay, Majid Ahmadi, Anirudh Venugopalrao,
Navakanta Bhat, Bart Kooi, Srinivasan Raghavan, Pavan Nukala | Self-assembled neuromorphic networks at self-organized criticality in
Ag-hBN platform | null | null | null | null | q-bio.NC cond-mat.dis-nn cs.ET | http://creativecommons.org/licenses/by/4.0/ | Networks and systems which exhibit brain-like behavior can analyze
information from intrinsically noisy and unstructured data with very low power
consumption. Such characteristics arise due to the critical nature and complex
interconnectivity of the brain and its neuronal network. We demonstrate that a
system compris... | [
{
"created": "Wed, 7 Dec 2022 09:35:47 GMT",
"version": "v1"
}
] | 2023-01-05 | [
[
"Rao",
"Ankit",
""
],
[
"Sanjay",
"Sooraj",
""
],
[
"Ahmadi",
"Majid",
""
],
[
"Venugopalrao",
"Anirudh",
""
],
[
"Bhat",
"Navakanta",
""
],
[
"Kooi",
"Bart",
""
],
[
"Raghavan",
"Srinivasan",
""
],
[
... | Networks and systems which exhibit brain-like behavior can analyze information from intrinsically noisy and unstructured data with very low power consumption. Such characteristics arise due to the critical nature and complex interconnectivity of the brain and its neuronal network. We demonstrate that a system comprisin... |
2407.04232 | Jian-Sheng Kang | Shu-Ang Li, Xiao-Yan Meng, Su Zhang, Ying-Jie Zhang, Run-Zhou Yang,
Dian-Dian Wang, Yang Yang, Pei-Pei Liu, Jian-Sheng Kang | A Unified Intracellular pH Landscape with SITE-pHorin: a
Quantum-Entanglement-Enhanced pH Probe | 64 pages, 7 figures, the supplemental material contains 13
supplemental figures and 4 supplemental tables | null | null | null | q-bio.QM physics.bio-ph q-bio.BM q-bio.SC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | An accurate map of intracellular organelle pH is crucial for comprehending
cellular metabolism and organellar functions. However, a unified intracellular
pH spectrum using a single probe is still lack. Here, we developed a novel
quantum entanglement-enhanced pH-sensitive probe called SITE-pHorin, which
featured a wid... | [
{
"created": "Fri, 5 Jul 2024 03:19:49 GMT",
"version": "v1"
}
] | 2024-07-08 | [
[
"Li",
"Shu-Ang",
""
],
[
"Meng",
"Xiao-Yan",
""
],
[
"Zhang",
"Su",
""
],
[
"Zhang",
"Ying-Jie",
""
],
[
"Yang",
"Run-Zhou",
""
],
[
"Wang",
"Dian-Dian",
""
],
[
"Yang",
"Yang",
""
],
[
"Liu",
"... | An accurate map of intracellular organelle pH is crucial for comprehending cellular metabolism and organellar functions. However, a unified intracellular pH spectrum using a single probe is still lack. Here, we developed a novel quantum entanglement-enhanced pH-sensitive probe called SITE-pHorin, which featured a wide ... |
q-bio/0311009 | Lior Pachter | Lior Pachter, Bernd Sturmfels | Tropical Geometry of Statistical Models | 14 pages, 3 figures. Major revision. Applications now in companion
paper, "Parametric Inference for Biological Sequence Analysis" | null | 10.1073/pnas.0406010101 | null | q-bio.QM math.AG q-bio.GN | null | This paper presents a unified mathematical framework for inference in
graphical models, building on the observation that graphical models are
algebraic varieties.
From this geometric viewpoint, observations generated from a model are
coordinates of a point in the variety, and the sum-product algorithm is an
efficie... | [
{
"created": "Sat, 8 Nov 2003 23:32:48 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Jan 2004 03:38:20 GMT",
"version": "v2"
}
] | 2009-11-10 | [
[
"Pachter",
"Lior",
""
],
[
"Sturmfels",
"Bernd",
""
]
] | This paper presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient t... |
q-bio/0403028 | Popkov Vladislav | M. Barbi, C. Place, V. Popkov and M. Salerno | Base sequence dependent sliding of proteins on DNA | 12 pages, 3 figures | Phys. Rev. E 70, 041901 (2004) | 10.1103/PhysRevE.70.041901 | null | q-bio.BM cond-mat.soft physics.bio-ph | null | The possibility that the sliding motion of proteins on DNA is influenced by
the base sequence through a base pair reading interaction, is considered.
Referring to the case of the T7 RNA-polymerase, we show that the protein should
follow a noise-influenced sequence-dependent motion which deviate from the
standard rand... | [
{
"created": "Fri, 19 Mar 2004 19:38:18 GMT",
"version": "v1"
}
] | 2011-07-13 | [
[
"Barbi",
"M.",
""
],
[
"Place",
"C.",
""
],
[
"Popkov",
"V.",
""
],
[
"Salerno",
"M.",
""
]
] | The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random... |
1407.6117 | Areejit Samal | Joseph Xu Zhou, Areejit Samal, Aymeric Fouquier d'H\`erou\"el, Nathan
D. Price and Sui Huang | Relative Stability of Network States in Boolean Network Models of Gene
Regulation in Development | 24 pages, 6 figures, 1 table | Biosystems 142-143:15-24 (2016) | 10.1016/j.biosystems.2016.03.002 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Progress in cell type reprogramming has revived the interest in Waddington's
concept of the epigenetic landscape. Recently researchers developed the
quasi-potential theory to represent the Waddington's landscape. The
Quasi-potential U(x), derived from interactions in the gene regulatory network
(GRN) of a cell, quant... | [
{
"created": "Wed, 23 Jul 2014 07:06:27 GMT",
"version": "v1"
},
{
"created": "Mon, 12 Oct 2015 13:56:14 GMT",
"version": "v2"
}
] | 2016-05-09 | [
[
"Zhou",
"Joseph Xu",
""
],
[
"Samal",
"Areejit",
""
],
[
"d'Hèrouël",
"Aymeric Fouquier",
""
],
[
"Price",
"Nathan D.",
""
],
[
"Huang",
"Sui",
""
]
] | Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantif... |
1210.6979 | Ferdinando Giacco | Ferdinando Giacco and Silvia Scarpetta | Attractor networks and memory replay of phase coded spike patterns | arXiv admin note: text overlap with arXiv:1210.6789 | Frontiers in Artificial Intelligence and Applications, Volume 234,
2011, pag 265-274 | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse the storage and retrieval capacity in a recurrent neural network
of spiking integrate and fire neurons. In the model we distinguish between a
learning mode, during which the synaptic connections change according to a
Spike-Timing Dependent Plasticity (STDP) rule, and a recall mode, in which
connections str... | [
{
"created": "Thu, 25 Oct 2012 11:09:56 GMT",
"version": "v1"
}
] | 2012-10-29 | [
[
"Giacco",
"Ferdinando",
""
],
[
"Scarpetta",
"Silvia",
""
]
] | We analyse the storage and retrieval capacity in a recurrent neural network of spiking integrate and fire neurons. In the model we distinguish between a learning mode, during which the synaptic connections change according to a Spike-Timing Dependent Plasticity (STDP) rule, and a recall mode, in which connections stren... |
1106.0848 | Francisco-Jose Perez-Reche | Francisco J. Perez-Reche, Jonathan J. Ludlam, Sergei N. Taraskin, and
Christopher A. Gilligan | Synergy in spreading processes: from exploitative to explorative
foraging strategies | 16 pages, 15 figures. 4 pages for main text and 6 appendices
published as supplemental material at
http://link.aps.org/supplemental/10.1103/PhysRevLett.106.218701 | Phys. Rev. Lett. 106, 218701 (2011) | 10.1103/PhysRevLett.106.218701 | null | q-bio.PE cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An epidemiological model which incorporates synergistic effects that allow
the infectivity and/or susceptibility of hosts to be dependent on the number of
infected neighbours is proposed. Constructive synergy induces an exploitative
behaviour which results in a rapid invasion that infects a large number of
hosts. Int... | [
{
"created": "Sat, 4 Jun 2011 18:38:35 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Perez-Reche",
"Francisco J.",
""
],
[
"Ludlam",
"Jonathan J.",
""
],
[
"Taraskin",
"Sergei N.",
""
],
[
"Gilligan",
"Christopher A.",
""
]
] | An epidemiological model which incorporates synergistic effects that allow the infectivity and/or susceptibility of hosts to be dependent on the number of infected neighbours is proposed. Constructive synergy induces an exploitative behaviour which results in a rapid invasion that infects a large number of hosts. Inter... |
1503.02570 | Helio M. de Oliveira | H.M. de Oliveira and N.S. Santos-Magalhaes | The Genetic Code revisited: Inner-to-outer map, 2D-Gray map, and
World-map Genetic Representations | 6 pages, 5 figures | Lecture Notes in Computer Science, LNCS 3124, Heidelberg: Springer
Verlag, vol.1, pp.526-531, 2004 | 10.1007/b99377 | null | q-bio.OT cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How to represent the genetic code? Despite the fact that it is extensively
known, the DNA mapping into proteins remains as one of the relevant discoveries
of genetics. However, modern genomic signal processing usually requires
converting symbolic-DNA strings into complex-valued signals in order to take
full advantage... | [
{
"created": "Thu, 5 Mar 2015 18:31:43 GMT",
"version": "v1"
}
] | 2015-03-10 | [
[
"de Oliveira",
"H. M.",
""
],
[
"Santos-Magalhaes",
"N. S.",
""
]
] | How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting symbolic-DNA strings into complex-valued signals in order to take full advantage o... |
1503.06308 | Henrique Oliveira Prof Dr | Jo\~ao F. Alves and Henrique M. Oliveira | Similarity of general population matrices and pseudo-Leslie matrices | 14 pages | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A similarity transformation is obtained between general population matrices
models of the Usher or Lefkovitch types and a simpler model, the pseudo-Leslie
model. The pseudo Leslie model is a matrix that can be decomposed in a row
matrix, which is not necessarily non-negative and a subdiagonal positive
matrix. This te... | [
{
"created": "Sat, 21 Mar 2015 15:14:45 GMT",
"version": "v1"
}
] | 2015-03-29 | [
[
"Alves",
"João F.",
""
],
[
"Oliveira",
"Henrique M.",
""
]
] | A similarity transformation is obtained between general population matrices models of the Usher or Lefkovitch types and a simpler model, the pseudo-Leslie model. The pseudo Leslie model is a matrix that can be decomposed in a row matrix, which is not necessarily non-negative and a subdiagonal positive matrix. This tech... |
1307.6177 | Jose Fontanari | Jose F. Fontanari and Maurizio Serva | Nonlinear group survival in Kimura's model for the evolution of altruism | null | Mathematical Biosciences 249 (2014), 18-26 | 10.1016/j.mbs.2014.01.003 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Establishing the conditions that guarantee the spreading or the sustenance of
altruistic traits in a population is the main goal of intergroup selection
models. Of particular interest is the balance of the parameters associated to
group size, migration and group survival against the selective advantage of the
non-alt... | [
{
"created": "Tue, 23 Jul 2013 18:01:11 GMT",
"version": "v1"
},
{
"created": "Fri, 24 Jan 2014 11:08:39 GMT",
"version": "v2"
}
] | 2014-02-17 | [
[
"Fontanari",
"Jose F.",
""
],
[
"Serva",
"Maurizio",
""
]
] | Establishing the conditions that guarantee the spreading or the sustenance of altruistic traits in a population is the main goal of intergroup selection models. Of particular interest is the balance of the parameters associated to group size, migration and group survival against the selective advantage of the non-altru... |
2302.00582 | Alexander Jaffe | Alexander L. Jaffe, Cindy J. Castelle, and Jillian F. Banfield | Habitat transition in the evolution of bacteria and archaea | Accepted for publication in the Annual Review of Microbiology, Volume
77 | null | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Related groups of microbes are widely distributed across Earth's habitats,
implying numerous dispersal and adaptation events over evolutionary time.
However, to date, relatively little is known about the characteristics and
mechanisms of these habitat transitions, particularly for populations that
reside in animal mi... | [
{
"created": "Wed, 1 Feb 2023 16:56:06 GMT",
"version": "v1"
}
] | 2023-02-02 | [
[
"Jaffe",
"Alexander L.",
""
],
[
"Castelle",
"Cindy J.",
""
],
[
"Banfield",
"Jillian F.",
""
]
] | Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, to date, relatively little is known about the characteristics and mechanisms of these habitat transitions, particularly for populations that reside in animal micr... |
2111.00119 | Esteban Vargas Bernal | Esteban Vargas Bernal, Omar Saucedo, Joseph Hua Tien | Relating Eulerian and Lagrangian spatial models for vector-host diseases
dynamics through a fundamental matrix | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We explore the relationship between Eulerian and Lagrangian approaches for
modeling movement in vector-borne diseases for discrete space. In the Eulerian
approach we account for the movement of hosts explicitly through movement rates
captured by a graph Laplacian matrix $L$. In the Lagrangian approach we only
account... | [
{
"created": "Fri, 29 Oct 2021 23:31:22 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jan 2022 19:54:01 GMT",
"version": "v2"
}
] | 2022-01-25 | [
[
"Bernal",
"Esteban Vargas",
""
],
[
"Saucedo",
"Omar",
""
],
[
"Tien",
"Joseph Hua",
""
]
] | We explore the relationship between Eulerian and Lagrangian approaches for modeling movement in vector-borne diseases for discrete space. In the Eulerian approach we account for the movement of hosts explicitly through movement rates captured by a graph Laplacian matrix $L$. In the Lagrangian approach we only account f... |
2108.01620 | Amit Kumar Das | Amit Kumar Das | Stochastic gene transcription with non-competitive transcription
regulatory architecture | The article is substantially modified with new paragraphs,
equations,images and appendices, 29 pages, 63 figures, 2 tables | null | null | null | q-bio.MN cond-mat.soft cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The transcription factors, such as activators and repressors, can interact
with the promoter of gene either in a competitive or non-competitive way. In
this paper, we construct a stochastic model with non-competitive
transcriptional regulatory architecture and develop an analytical theory that
re-establishes the expe... | [
{
"created": "Tue, 3 Aug 2021 16:48:04 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Sep 2021 07:29:16 GMT",
"version": "v2"
},
{
"created": "Sat, 12 Feb 2022 13:34:03 GMT",
"version": "v3"
},
{
"created": "Thu, 26 May 2022 15:14:38 GMT",
"version": "v4"
}
] | 2022-05-27 | [
[
"Das",
"Amit Kumar",
""
]
] | The transcription factors, such as activators and repressors, can interact with the promoter of gene either in a competitive or non-competitive way. In this paper, we construct a stochastic model with non-competitive transcriptional regulatory architecture and develop an analytical theory that re-establishes the experi... |
2009.12693 | Abicumaran Uthamacumaran | Abicumaran Uthamacumaran | A Review of Complex Systems Approaches to Cancer Networks | 43 pages | Complex Systems, Vol. 29, Issue 4 (2020) | 10.25088/ComplexSystems.29.4.779 | null | q-bio.OT nlin.CD | http://creativecommons.org/licenses/by-sa/4.0/ | Cancers remain the lead cause of disease-related, pediatric death in North
America. The emerging field of complex systems has redefined cancer networks as
a computational system with intractable algorithmic complexity. Herein, a tumor
and its heterogeneous phenotypes are discussed as dynamical systems having
multiple... | [
{
"created": "Sat, 26 Sep 2020 21:40:48 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Nov 2020 01:05:58 GMT",
"version": "v2"
},
{
"created": "Sat, 20 Mar 2021 03:02:05 GMT",
"version": "v3"
},
{
"created": "Sun, 29 Aug 2021 08:21:41 GMT",
"version": "v4"
}
] | 2021-08-31 | [
[
"Uthamacumaran",
"Abicumaran",
""
]
] | Cancers remain the lead cause of disease-related, pediatric death in North America. The emerging field of complex systems has redefined cancer networks as a computational system with intractable algorithmic complexity. Herein, a tumor and its heterogeneous phenotypes are discussed as dynamical systems having multiple, ... |
q-bio/0512027 | Maria Barbi | Julien Mozziconacci, Christophe Lavelle, Maria Barbi, Annick Lesne and
Jean-Marc Victor | A Physical Model for the Condensation and Decondensation of Eukaryotic
Chromosomes | null | FEBS Letters 580 (2006) 368-372 | 10.1016/j.febslet.2005.12.053 | null | q-bio.SC | null | During the eukaryotic cell cycle, chromatin undergoes several conformational
changes, which are believed to play key roles in gene expression regulation
during interphase, and in genome replication and division during mitosis. In
this paper, we propose a scenario for chromatin structural reorganization
during mitosis... | [
{
"created": "Mon, 12 Dec 2005 17:05:58 GMT",
"version": "v1"
},
{
"created": "Mon, 3 Sep 2007 16:28:22 GMT",
"version": "v2"
}
] | 2007-09-03 | [
[
"Mozziconacci",
"Julien",
""
],
[
"Lavelle",
"Christophe",
""
],
[
"Barbi",
"Maria",
""
],
[
"Lesne",
"Annick",
""
],
[
"Victor",
"Jean-Marc",
""
]
] | During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this paper, we propose a scenario for chromatin structural reorganization during mitosis, ... |
1803.10753 | Milena \v{C}uki\'c Dr | Milena B. Cukic, Mirjana M. Platisa, Aleksandar Kalauzi, Joji Oommen,
Milos R. Ljubisavljevic | The comparison of Higuchi fractal dimension and Sample Entropy analysis
of sEMG: effects of muscle contraction intensity and TMS | 21 pages, 3 Figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The aim of the study was to examine how the complexity of surface
electromyogram (sEMG) signal, estimated by Higuchi fractal dimension (HFD) and
Sample Entropy (SampEn), change depending on muscle contraction intensity and
external perturbation of the corticospinal activity during muscle contraction
induced by single... | [
{
"created": "Wed, 28 Mar 2018 17:44:44 GMT",
"version": "v1"
}
] | 2018-03-29 | [
[
"Cukic",
"Milena B.",
""
],
[
"Platisa",
"Mirjana M.",
""
],
[
"Kalauzi",
"Aleksandar",
""
],
[
"Oommen",
"Joji",
""
],
[
"Ljubisavljevic",
"Milos R.",
""
]
] | The aim of the study was to examine how the complexity of surface electromyogram (sEMG) signal, estimated by Higuchi fractal dimension (HFD) and Sample Entropy (SampEn), change depending on muscle contraction intensity and external perturbation of the corticospinal activity during muscle contraction induced by single-p... |
2407.00050 | Zhangyang Gao | Zhangyang Gao, Cheng Tan, Stan Z. Li | FoldToken2: Learning compact, invariant and generative protein structure
language | null | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The equivalent nature of 3D coordinates has posed long term challenges in
protein structure representation learning, alignment, and generation. Can we
create a compact and invariant language that equivalently represents protein
structures? Towards this goal, we propose FoldToken2 to transfer equivariant
structures in... | [
{
"created": "Tue, 11 Jun 2024 09:24:51 GMT",
"version": "v1"
}
] | 2024-07-02 | [
[
"Gao",
"Zhangyang",
""
],
[
"Tan",
"Cheng",
""
],
[
"Li",
"Stan Z.",
""
]
] | The equivalent nature of 3D coordinates has posed long term challenges in protein structure representation learning, alignment, and generation. Can we create a compact and invariant language that equivalently represents protein structures? Towards this goal, we propose FoldToken2 to transfer equivariant structures into... |
1606.01315 | Vladimir Privman | Vladimir Privman | Theoretical Modeling Expressions for Networked Enzymatic Signal
Processing Steps as Logic Gates Optimized by Filtering | arXiv admin note: substantial text overlap with arXiv:1312.4235 | Int. J. Parallel Emergent Distrib. Syst. 32 (1), 30-43 (2017) | 10.1080/17445760.2016.1140167 | VP-269 | q-bio.MN cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe modeling approaches to a "network" of connected enzyme-catalyzed
reactions, with added (bio)chemical processes that introduce biochemical
filtering steps into the functioning of such a biocatalytic cascade.
Theoretical expressions are derived that allow simple, few-parameter modeling
of processes concaten... | [
{
"created": "Sat, 4 Jun 2016 01:07:27 GMT",
"version": "v1"
}
] | 2016-12-13 | [
[
"Privman",
"Vladimir",
""
]
] | We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical expressions are derived that allow simple, few-parameter modeling of processes concatenat... |
2008.12766 | Assad Oberai | Harisankar Ramaswamy, Assad A Oberai and Yannis C Yortsos | A comprehensive spatial-temporal infection model | null | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivated by analogies between the spreading of human-to-human infections and
of chemical processes, we develop a comprehensive model that accounts both for
infection and for transport. In this analogy, the three different populations
of infection models correspond to three chemical species. Areal densities
emerge as... | [
{
"created": "Fri, 28 Aug 2020 17:45:39 GMT",
"version": "v1"
},
{
"created": "Fri, 4 Dec 2020 21:03:25 GMT",
"version": "v2"
}
] | 2020-12-08 | [
[
"Ramaswamy",
"Harisankar",
""
],
[
"Oberai",
"Assad A",
""
],
[
"Yortsos",
"Yannis C",
""
]
] | Motivated by analogies between the spreading of human-to-human infections and of chemical processes, we develop a comprehensive model that accounts both for infection and for transport. In this analogy, the three different populations of infection models correspond to three chemical species. Areal densities emerge as t... |
1810.03666 | Giovanni Paolini | Emanuele Delucchi, Linard Hoessly, Giovanni Paolini | Impossibility results on stability of phylogenetic consensus methods | null | Systematic Biology 69 (3), pp. 557-565, 2020 | 10.1093/sysbio/syz071 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We answer two questions raised by Bryant, Francis and Steel in their work on
consensus methods in phylogenetics. Consensus methods apply to every practical
instance where it is desired to aggregate a set of given phylogenetic trees
(say, gene evolution trees) into a resulting, "consensus" tree (say, a species
tree). ... | [
{
"created": "Mon, 8 Oct 2018 19:12:22 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Nov 2023 14:24:19 GMT",
"version": "v2"
}
] | 2023-11-14 | [
[
"Delucchi",
"Emanuele",
""
],
[
"Hoessly",
"Linard",
""
],
[
"Paolini",
"Giovanni",
""
]
] | We answer two questions raised by Bryant, Francis and Steel in their work on consensus methods in phylogenetics. Consensus methods apply to every practical instance where it is desired to aggregate a set of given phylogenetic trees (say, gene evolution trees) into a resulting, "consensus" tree (say, a species tree). Va... |
2011.01877 | Camille Dunning | Camille Dunning | Exploring the Synchrony Between Body Temperature and HR, RR, and Aortic
Blood Pressure in Viral/Bacterial Disease Onsets with Signal Dynamics | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Signal-based early detection of illnesses has been a key topic in research
and hospital settings; it reduces technological costs and paves the way for
quick and effective patient-care operations. Elementary machine learning and
signal processing algorithms have proven to be sufficient in classifying the
onset of vira... | [
{
"created": "Fri, 30 Oct 2020 22:32:04 GMT",
"version": "v1"
}
] | 2020-11-04 | [
[
"Dunning",
"Camille",
""
]
] | Signal-based early detection of illnesses has been a key topic in research and hospital settings; it reduces technological costs and paves the way for quick and effective patient-care operations. Elementary machine learning and signal processing algorithms have proven to be sufficient in classifying the onset of viral ... |
1802.08849 | Petter Holme | Petter Holme, Liubov Tupikina | Epidemic extinction in networks: Insights from the 12,110 smallest
graphs | v2 has some minor bug fixes | null | 10.1088/1367-2630/aaf016 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate the expected time to extinction in the
susceptible-infectious-susceptible (SIS) model of disease spreading. Rather
than using stochastic simulations, or asymptotic calculations in network
models, we solve the extinction time exactly for all connected graphs with
three to eight vertices. This approach e... | [
{
"created": "Sat, 24 Feb 2018 14:11:08 GMT",
"version": "v1"
},
{
"created": "Thu, 15 Mar 2018 01:00:21 GMT",
"version": "v2"
},
{
"created": "Tue, 18 Sep 2018 10:40:13 GMT",
"version": "v3"
}
] | 2018-12-26 | [
[
"Holme",
"Petter",
""
],
[
"Tupikina",
"Liubov",
""
]
] | We investigate the expected time to extinction in the susceptible-infectious-susceptible (SIS) model of disease spreading. Rather than using stochastic simulations, or asymptotic calculations in network models, we solve the extinction time exactly for all connected graphs with three to eight vertices. This approach ena... |
1603.03767 | Samuel Johnson | Virginia Dom\'inguez-Garc\'ia and Samuel Johnson and Miguel A. Mu\~noz | Intervality and coherence in complex networks | null | null | 10.1063/1.4953163 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Food webs -- networks of predators and prey -- have long been known to
exhibit "intervality": species can generally be ordered along a single axis in
such a way that the prey of any given predator tend to lie on unbroken compact
intervals. Although the meaning of this axis -- identified with a "niche"
dimension -- ha... | [
{
"created": "Fri, 11 Mar 2016 10:53:09 GMT",
"version": "v1"
}
] | 2016-06-29 | [
[
"Domínguez-García",
"Virginia",
""
],
[
"Johnson",
"Samuel",
""
],
[
"Muñoz",
"Miguel A.",
""
]
] | Food webs -- networks of predators and prey -- have long been known to exhibit "intervality": species can generally be ordered along a single axis in such a way that the prey of any given predator tend to lie on unbroken compact intervals. Although the meaning of this axis -- identified with a "niche" dimension -- has ... |
1702.07319 | John Pearson | Shariq Iqbal and John Pearson | A Goal-Based Movement Model for Continuous Multi-Agent Tasks | New title; substantial simplifications of model | null | null | null | q-bio.NC cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite increasing attention paid to the need for fast, scalable methods to
analyze next-generation neuroscience data, comparatively little attention has
been paid to the development of similar methods for behavioral analysis. Just
as the volume and complexity of brain data have grown, behavioral paradigms in
systems... | [
{
"created": "Thu, 23 Feb 2017 18:09:14 GMT",
"version": "v1"
},
{
"created": "Tue, 31 Oct 2017 20:14:11 GMT",
"version": "v2"
}
] | 2017-11-02 | [
[
"Iqbal",
"Shariq",
""
],
[
"Pearson",
"John",
""
]
] | Despite increasing attention paid to the need for fast, scalable methods to analyze next-generation neuroscience data, comparatively little attention has been paid to the development of similar methods for behavioral analysis. Just as the volume and complexity of brain data have grown, behavioral paradigms in systems n... |
1501.01863 | Simon R. Schultz | Robin A. A. Ince, Simon R. Schultz and Stefano Panzeri | Estimating Information-Theoretic Quantities | 16 pages, 3 figures | Encyclopaedia of Computational Neuroscience 2014, pp 1-13 | 10.1007/978-1-4614-7320-6_140-1 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Information theory is a practical and theoretical framework developed for the
study of communication over noisy channels. Its probabilistic basis and
capacity to relate statistical structure to function make it ideally suited for
studying information flow in the nervous system. It has a number of useful
properties: i... | [
{
"created": "Thu, 8 Jan 2015 14:19:23 GMT",
"version": "v1"
}
] | 2015-01-09 | [
[
"Ince",
"Robin A. A.",
""
],
[
"Schultz",
"Simon R.",
""
],
[
"Panzeri",
"Stefano",
""
]
] | Information theory is a practical and theoretical framework developed for the study of communication over noisy channels. Its probabilistic basis and capacity to relate statistical structure to function make it ideally suited for studying information flow in the nervous system. It has a number of useful properties: it ... |
2303.08818 | Daeseok Lee | Daeseok Lee, Jeunghyun Byun and Bonggun Shin | Boosting Convolutional Neural Networks' Protein Binding Site Prediction
Capacity Using SE(3)-invariant transformers, Transfer Learning and
Homology-based Augmentation | Updates in version 2: author order change (making it clear that
Bonggun Shin is the corresponding author) | null | null | null | q-bio.QM cs.LG cs.NE q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Figuring out small molecule binding sites in target proteins, in the
resolution of either pocket or residue, is critical in many virtual and real
drug-discovery scenarios. Since it is not always easy to find such binding
sites based on domain knowledge or traditional methods, different deep learning
methods that pred... | [
{
"created": "Mon, 20 Feb 2023 05:02:40 GMT",
"version": "v1"
},
{
"created": "Tue, 18 Apr 2023 05:05:00 GMT",
"version": "v2"
}
] | 2023-04-19 | [
[
"Lee",
"Daeseok",
""
],
[
"Byun",
"Jeunghyun",
""
],
[
"Shin",
"Bonggun",
""
]
] | Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on domain knowledge or traditional methods, different deep learning methods that predic... |
2306.11232 | Haiping Huang | Haiping Huang | Eight challenges in developing theory of intelligence | 24 pages, 131 references, revised version to journal | Front. Comput. Neurosci. 18:1388166 (2024) | 10.3389/fncom.2024.1388166 | null | q-bio.NC cond-mat.stat-mech cs.AI cs.CL | http://creativecommons.org/licenses/by/4.0/ | A good theory of mathematical beauty is more practical than any current
observation, as new predictions of physical reality can be verified
self-consistently. This belief applies to the current status of understanding
deep neural networks including large language models and even the biological
intelligence. Toy model... | [
{
"created": "Tue, 20 Jun 2023 01:45:42 GMT",
"version": "v1"
},
{
"created": "Fri, 21 Jun 2024 08:26:30 GMT",
"version": "v2"
}
] | 2024-07-26 | [
[
"Huang",
"Haiping",
""
]
] | A good theory of mathematical beauty is more practical than any current observation, as new predictions of physical reality can be verified self-consistently. This belief applies to the current status of understanding deep neural networks including large language models and even the biological intelligence. Toy models ... |
1610.02301 | Sa\'ul Ares | Javier Munoz-Garcia and Saul Ares | Formation and maintenance of nitrogen fixing cell patterns in
filamentous cyanobacteria | null | Proc. Natl. Acad. Sci. USA 113, 6218-6223 (2016) | 10.1073/pnas.1524383113 | null | q-bio.CB nlin.PS q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cyanobacteria forming one-dimensional filaments are paradigmatic model
organisms of the transition between unicellular and multicellular living forms.
Under nitrogen limiting conditions, in filaments of the genus Anabaena, some
cells differentiate into heterocysts, which lose the possibility to divide but
are able to... | [
{
"created": "Fri, 7 Oct 2016 14:25:49 GMT",
"version": "v1"
}
] | 2016-10-10 | [
[
"Munoz-Garcia",
"Javier",
""
],
[
"Ares",
"Saul",
""
]
] | Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen limiting conditions, in filaments of the genus Anabaena, some cells differentiate into heterocysts, which lose the possibility to divide but are able to f... |
q-bio/0608003 | Leor Weinberger | Leor S. Weinberger, John C. Burnett, Jared E. Toettcher, Adam P.
Arkin, and David V. Schaffer | Supplemental Data: Stochastic Gene Expression in a Lentiviral Positive
Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity | Supplemental data for q-bio.MN/0608002 | null | null | null | q-bio.MN q-bio.CB | null | Supplemental data for "Stochastic Gene Expression in a Lentiviral Positive
Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity"
[q-bio.MN/0608002, Cell. 2005 Jul 29;122(2):169-82].
| [
{
"created": "Wed, 2 Aug 2006 19:21:27 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Weinberger",
"Leor S.",
""
],
[
"Burnett",
"John C.",
""
],
[
"Toettcher",
"Jared E.",
""
],
[
"Arkin",
"Adam P.",
""
],
[
"Schaffer",
"David V.",
""
]
] | Supplemental data for "Stochastic Gene Expression in a Lentiviral Positive Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity" [q-bio.MN/0608002, Cell. 2005 Jul 29;122(2):169-82]. |
1601.02948 | Yoram Burak | Noga Weiss Mosheiff, Haggai Agmon, Avraham Moriel, and Yoram Burak | An Efficient Coding Theory for a Dynamic Trajectory Predicts non-Uniform
Allocation of Grid Cells to Modules in the Entorhinal Cortex | 23 pages, 5 figures. Supplemental Information available from the
authors on request. A previous version of this work appeared in abstract form
(Program No. 727.02. 2015 Neuroscience Meeting Planner. Chicago, IL: Society
for Neuroscience, 2015. Online.) | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Grid cells in the entorhinal cortex encode the position of an animal in its
environment using spatially periodic tuning curves of varying periodicity.
Recent experiments established that these cells are functionally organized in
discrete modules with uniform grid spacing. Here we develop a theory for
efficient coding... | [
{
"created": "Tue, 12 Jan 2016 16:38:14 GMT",
"version": "v1"
}
] | 2016-01-13 | [
[
"Mosheiff",
"Noga Weiss",
""
],
[
"Agmon",
"Haggai",
""
],
[
"Moriel",
"Avraham",
""
],
[
"Burak",
"Yoram",
""
]
] | Grid cells in the entorhinal cortex encode the position of an animal in its environment using spatially periodic tuning curves of varying periodicity. Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing. Here we develop a theory for efficient coding o... |
2004.10177 | He Zhang | He Zhang, Liang Zhang, Ang Lin, Congcong Xu, Ziyu Li, Kaibo Liu,
Boxiang Liu, Xiaopin Ma, Fanfan Zhao, Weiguo Yao, Hangwen Li, David H.
Mathews, Yujian Zhang, and Liang Huang | Algorithm for Optimized mRNA Design Improves Stability and
Immunogenicity | 17 pages for main text; 24 pages of supporting information; 4+11=15
figures; 2 tables (both in supporting information) | Nature (621), 396-403, 2023 | 10.1038/s41586-023-06127-z | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer
from the critical issue of mRNA instability and degradation, which is a major
obstacle in the storage, distribution, and efficacy of the vaccine. Previous
work showed that optimizing secondary structure stability lengthens mRNA
half-life, whi... | [
{
"created": "Tue, 21 Apr 2020 17:35:45 GMT",
"version": "v1"
},
{
"created": "Tue, 5 May 2020 17:42:04 GMT",
"version": "v2"
},
{
"created": "Wed, 6 May 2020 17:31:10 GMT",
"version": "v3"
},
{
"created": "Wed, 13 May 2020 15:58:24 GMT",
"version": "v4"
},
{
"cre... | 2024-02-08 | [
[
"Zhang",
"He",
""
],
[
"Zhang",
"Liang",
""
],
[
"Lin",
"Ang",
""
],
[
"Xu",
"Congcong",
""
],
[
"Li",
"Ziyu",
""
],
[
"Liu",
"Kaibo",
""
],
[
"Liu",
"Boxiang",
""
],
[
"Ma",
"Xiaopin",
""
... | Messenger RNA (mRNA) vaccines are being used for COVID-19, but still suffer from the critical issue of mRNA instability and degradation, which is a major obstacle in the storage, distribution, and efficacy of the vaccine. Previous work showed that optimizing secondary structure stability lengthens mRNA half-life, which... |
0901.1572 | Sophie Querouil | Sophie Qu\'erouil (IMAR-DOP, CAVIAR), M. A. Silva (IMAR-DOP), I.
Cascao (IMAR-DOP), S. Magalhaes (IMAR-DOP), M. I. Seabra (IMAR-DOP), M. A.
Machete (IMAR-DOP), R. S. Santos (IMAR-DOP) | Why do dolphins form mixed-species associations in the Azores ? | null | Ethology 114, 12 (2008) 1183-1194 | 10.1111/j.1439-0310.2008.01570.x | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mixed-species associations are temporary associations between individuals of
different species that are often observed in birds, primates and cetaceans.
They have been interpreted as a strategy to reduce predation risk, enhance
foraging success and/or provide a social advantage. In the archipelago of the
Azores, four... | [
{
"created": "Mon, 12 Jan 2009 13:33:03 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Jul 2010 14:24:55 GMT",
"version": "v2"
}
] | 2010-07-26 | [
[
"Quérouil",
"Sophie",
"",
"IMAR-DOP, CAVIAR"
],
[
"Silva",
"M. A.",
"",
"IMAR-DOP"
],
[
"Cascao",
"I.",
"",
"IMAR-DOP"
],
[
"Magalhaes",
"S.",
"",
"IMAR-DOP"
],
[
"Seabra",
"M. I.",
"",
"IMAR-DOP"
],
[
"Machete... | Mixed-species associations are temporary associations between individuals of different species that are often observed in birds, primates and cetaceans. They have been interpreted as a strategy to reduce predation risk, enhance foraging success and/or provide a social advantage. In the archipelago of the Azores, four s... |
2003.08576 | Masaki Sasai | Bhaswati Bhattacharyya, Jin Wang and Masaki Sasai | Stochastic epigenetic dynamics of gene switching | null | Phys. Rev. E 102, 042408 (2020) | 10.1103/PhysRevE.102.042408 | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Epigenetic modifications of histones crucially affect the eukaryotic gene
activity, while the epigenetic histone state is largely determined by the
binding of specific factors such as the transcription factors (TFs) to DNA.
Here, the way how the TFs and the histone state are dynamically correlated is
not obvious when... | [
{
"created": "Thu, 19 Mar 2020 05:14:24 GMT",
"version": "v1"
},
{
"created": "Sat, 17 Oct 2020 00:04:18 GMT",
"version": "v2"
}
] | 2020-10-28 | [
[
"Bhattacharyya",
"Bhaswati",
""
],
[
"Wang",
"Jin",
""
],
[
"Sasai",
"Masaki",
""
]
] | Epigenetic modifications of histones crucially affect the eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way how the TFs and the histone state are dynamically correlated is not obvious when t... |
1206.0344 | Andrew Vlasic | Andrew Vlasic | Long-Run Analysis of the Stochastic Replicator Dynamics in the Presence
of Random Jumps | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A further generalization of the stochastic replicator dynamic derived by
Fudenberg and Harris \cite{FH92} is considered. In particular, a Poissonian
integral is introduced to the fitness to simulate the affects of anomalous
events. For the two strategy population, an estimation of the long run behavior
of the dynamic... | [
{
"created": "Sat, 2 Jun 2012 04:30:21 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Jan 2014 20:46:57 GMT",
"version": "v2"
}
] | 2014-01-30 | [
[
"Vlasic",
"Andrew",
""
]
] | A further generalization of the stochastic replicator dynamic derived by Fudenberg and Harris \cite{FH92} is considered. In particular, a Poissonian integral is introduced to the fitness to simulate the affects of anomalous events. For the two strategy population, an estimation of the long run behavior of the dynamic i... |
1110.0433 | Matthias Keil | Matthias S. Keil | Computation of Object Approach by a Biophysical Model of a Wide-Field
Visual Neuron: Dynamics, Peaks, and Fits | A revised version of this paper with the title "Emergence of
Multiplication in a Biophysical Model of a Wide-Field Visual Neuron for
Computing Object Approaches: Dynamics, Peaks, & Fits" has been accepted in
Advances in Neural Information Processing Systems, NIPS 2011, Granda, Spain | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Many species show avoidance reactions in response to looming object
approaches. In locusts, the corresponding escape behavior correlates with the
activity of the lobula giant movement detector (LGMD) neuron. During an object
approach, its firing rate was reported to gradually increase until a peak is
reached, and the... | [
{
"created": "Mon, 3 Oct 2011 18:00:00 GMT",
"version": "v1"
}
] | 2011-10-04 | [
[
"Keil",
"Matthias S.",
""
]
] | Many species show avoidance reactions in response to looming object approaches. In locusts, the corresponding escape behavior correlates with the activity of the lobula giant movement detector (LGMD) neuron. During an object approach, its firing rate was reported to gradually increase until a peak is reached, and then ... |
1803.01123 | Chen Jia | Chen Jia, Hong Qian, Min Chen, Michael Q. Zhang | Relaxation rates of gene expression kinetics reveal the feedback signs
of autoregulatory gene networks | 17 pages | null | 10.1063/1.5009749 | null | q-bio.MN cond-mat.stat-mech q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The transient response to a stimulus and subsequent recovery to a steady
state are the fundamental characteristics of a living organism. Here we study
the relaxation kinetics of autoregulatory gene networks based on the chemical
master equation model of single-cell stochastic gene expression with nonlinear
feedback r... | [
{
"created": "Sat, 3 Mar 2018 08:18:42 GMT",
"version": "v1"
}
] | 2018-03-06 | [
[
"Jia",
"Chen",
""
],
[
"Qian",
"Hong",
""
],
[
"Chen",
"Min",
""
],
[
"Zhang",
"Michael Q.",
""
]
] | The transient response to a stimulus and subsequent recovery to a steady state are the fundamental characteristics of a living organism. Here we study the relaxation kinetics of autoregulatory gene networks based on the chemical master equation model of single-cell stochastic gene expression with nonlinear feedback reg... |
1407.2480 | Alain Destexhe | Claude Bedard and Alain Destexhe | Generalized cable formalism to calculate the magnetic field of single
neurons and neuronal populations | Physical Review E (in press); 24 pages, 16 figures | Physical Review E 90: 042723 (2014) | 10.1103/PhysRevE.90.042723 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neurons generate magnetic fields which can be recorded with macroscopic
techniques such as magneto-encephalography. The theory that accounts for the
genesis of neuronal magnetic fields involves dendritic cable structures in
homogeneous resistive extracellular media. Here, we generalize this model by
considering dendr... | [
{
"created": "Wed, 9 Jul 2014 13:53:23 GMT",
"version": "v1"
},
{
"created": "Fri, 10 Oct 2014 21:37:23 GMT",
"version": "v2"
}
] | 2014-11-04 | [
[
"Bedard",
"Claude",
""
],
[
"Destexhe",
"Alain",
""
]
] | Neurons generate magnetic fields which can be recorded with macroscopic techniques such as magneto-encephalography. The theory that accounts for the genesis of neuronal magnetic fields involves dendritic cable structures in homogeneous resistive extracellular media. Here, we generalize this model by considering dendrit... |
1206.6071 | Pascal Buenzli | Pascal R. Buenzli, C. David L. Thomas, John G. Clement, Peter Pivonka | Endocortical bone loss in osteoporosis: The role of bone surface
availability | 13 pages, 3 figures. V2: minor stylistic improvements in
text/figures; more accurately referenced subsection "Internal mechanical
stress distribution"; some improved remarks in the Discussion section | Int J Numer Meth Biomed Engng (2013) 29:1307-1322 | 10.1002/cnm.2567 | null | q-bio.TO physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Age-related bone loss and postmenopausal osteoporosis are disorders of bone
remodelling, in which less bone is reformed than resorbed. Yet, this
dysregulation of bone remodelling does not occur equally in all bone regions.
Loss of bone is more pronounced near and at the endocortex, leading to cortical
wall thinning a... | [
{
"created": "Tue, 26 Jun 2012 18:26:45 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Aug 2012 17:32:39 GMT",
"version": "v2"
}
] | 2014-05-21 | [
[
"Buenzli",
"Pascal R.",
""
],
[
"Thomas",
"C. David L.",
""
],
[
"Clement",
"John G.",
""
],
[
"Pivonka",
"Peter",
""
]
] | Age-related bone loss and postmenopausal osteoporosis are disorders of bone remodelling, in which less bone is reformed than resorbed. Yet, this dysregulation of bone remodelling does not occur equally in all bone regions. Loss of bone is more pronounced near and at the endocortex, leading to cortical wall thinning and... |
2312.11584 | Zhi Jin | Zhi Jin, Sheng Xu, Xiang Zhang, Tianze Ling, Nanqing Dong, Wanli
Ouyang, Zhiqiang Gao, Cheng Chang, Siqi Sun | ContraNovo: A Contrastive Learning Approach to Enhance De Novo Peptide
Sequencing | This paper has been accepted by AAAI 2024 | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | De novo peptide sequencing from mass spectrometry (MS) data is a critical
task in proteomics research. Traditional de novo algorithms have encountered a
bottleneck in accuracy due to the inherent complexity of proteomics data. While
deep learning-based methods have shown progress, they reduce the problem to a
transla... | [
{
"created": "Mon, 18 Dec 2023 12:49:46 GMT",
"version": "v1"
}
] | 2023-12-20 | [
[
"Jin",
"Zhi",
""
],
[
"Xu",
"Sheng",
""
],
[
"Zhang",
"Xiang",
""
],
[
"Ling",
"Tianze",
""
],
[
"Dong",
"Nanqing",
""
],
[
"Ouyang",
"Wanli",
""
],
[
"Gao",
"Zhiqiang",
""
],
[
"Chang",
"Cheng"... | De novo peptide sequencing from mass spectrometry (MS) data is a critical task in proteomics research. Traditional de novo algorithms have encountered a bottleneck in accuracy due to the inherent complexity of proteomics data. While deep learning-based methods have shown progress, they reduce the problem to a translati... |
2301.10774 | Cheng Tan | Cheng Tan, Yijie Zhang, Zhangyang Gao, Bozhen Hu, Siyuan Li, Zicheng
Liu, Stan Z. Li | RDesign: Hierarchical Data-efficient Representation Learning for
Tertiary Structure-based RNA Design | 30 pages, 28 figures, 16 tables | null | null | null | q-bio.BM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | While artificial intelligence has made remarkable strides in revealing the
relationship between biological macromolecules' primary sequence and tertiary
structure, designing RNA sequences based on specified tertiary structures
remains challenging. Though existing approaches in protein design have
thoroughly explored ... | [
{
"created": "Wed, 25 Jan 2023 17:19:49 GMT",
"version": "v1"
},
{
"created": "Wed, 17 May 2023 13:59:04 GMT",
"version": "v2"
},
{
"created": "Thu, 7 Mar 2024 02:07:37 GMT",
"version": "v3"
}
] | 2024-03-08 | [
[
"Tan",
"Cheng",
""
],
[
"Zhang",
"Yijie",
""
],
[
"Gao",
"Zhangyang",
""
],
[
"Hu",
"Bozhen",
""
],
[
"Li",
"Siyuan",
""
],
[
"Liu",
"Zicheng",
""
],
[
"Li",
"Stan Z.",
""
]
] | While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored st... |
1412.1525 | Jeremy Sumner | Michael D. Woodhams, Jes\'us Fern\'andez-S\'anchez, and Jeremy G.
Sumner | A new hierarchy of phylogenetic models consistent with heterogeneous
substitution rates | 20 pages. Supplementary files available via email | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When the process underlying DNA substitutions varies across evolutionary
history, the standard Markov models underlying standard phylogenetic methods
are mathematically inconsistent. The most prominent example is the general time
reversible model (GTR) together with some, but not all, of its submodels. To
rectify thi... | [
{
"created": "Thu, 4 Dec 2014 00:43:03 GMT",
"version": "v1"
}
] | 2014-12-05 | [
[
"Woodhams",
"Michael D.",
""
],
[
"Fernández-Sánchez",
"Jesús",
""
],
[
"Sumner",
"Jeremy G.",
""
]
] | When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible model (GTR) together with some, but not all, of its submodels. To rectify this ... |
1010.4726 | Peter Thomas PhD | Edward K. Agarwala, Hillel J. Chiel, Peter J. Thomas | Information Maximization Fails to Maximize Expected Utility in a Simple
Foraging Model | 52 pages, 14 figures | null | null | null | q-bio.OT cs.IT math.IT physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Information theory has explained the organization of many biological
phenomena, from the physiology of sensory receptive fields to the variability
of certain DNA sequence ensembles. Some scholars have proposed that information
should provide the central explanatory principle in biology, in the sense that
any behavior... | [
{
"created": "Fri, 22 Oct 2010 14:33:46 GMT",
"version": "v1"
}
] | 2010-10-25 | [
[
"Agarwala",
"Edward K.",
""
],
[
"Chiel",
"Hillel J.",
""
],
[
"Thomas",
"Peter J.",
""
]
] | Information theory has explained the organization of many biological phenomena, from the physiology of sensory receptive fields to the variability of certain DNA sequence ensembles. Some scholars have proposed that information should provide the central explanatory principle in biology, in the sense that any behavioral... |
q-bio/0701004 | Feng Yang | Feng Yang, Feng Qi, and Daniel A. Beard | Directionality is an inherent property of biochemical networks | A short version of the previous one, more concise and previse. It
includes 5 pages, 5 figures and 1 table | null | null | null | q-bio.MN | null | Thermodynamic constraints on reactions directions are inherent in the
structure of a given biochemical network. However, concrete procedures for
determining feasible reaction directions for large-scale metabolic networks are
not well established. This work introduces a systematic approach to compute
reaction directio... | [
{
"created": "Tue, 2 Jan 2007 22:26:38 GMT",
"version": "v1"
},
{
"created": "Thu, 1 Feb 2007 18:06:05 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Yang",
"Feng",
""
],
[
"Qi",
"Feng",
""
],
[
"Beard",
"Daniel A.",
""
]
] | Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well established. This work introduces a systematic approach to compute reaction directions... |
1710.10153 | Kelly Iarosz | E.L. Lameu, E.E.N. Macau, F.S. Borges, K.C. Iarosz, I.L. Caldas, R.R.
Borges, P.R. Protachevicz, R.L. Viana, A.M. Batista | Alterations in brain connectivity due to plasticity and synaptic delay | null | null | 10.1140/epjst/e2018-00090-6 | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brain plasticity refers to brain's ability to change neuronal connections, as
a result of environmental stimuli, new experiences, or damage. In this work, we
study the effects of the synaptic delay on both the coupling strengths and
synchronisation in a neuronal network with synaptic plasticity. We build a
network of... | [
{
"created": "Fri, 27 Oct 2017 14:21:21 GMT",
"version": "v1"
}
] | 2018-11-14 | [
[
"Lameu",
"E. L.",
""
],
[
"Macau",
"E. E. N.",
""
],
[
"Borges",
"F. S.",
""
],
[
"Iarosz",
"K. C.",
""
],
[
"Caldas",
"I. L.",
""
],
[
"Borges",
"R. R.",
""
],
[
"Protachevicz",
"P. R.",
""
],
[
"V... | Brain plasticity refers to brain's ability to change neuronal connections, as a result of environmental stimuli, new experiences, or damage. In this work, we study the effects of the synaptic delay on both the coupling strengths and synchronisation in a neuronal network with synaptic plasticity. We build a network of H... |
1305.6717 | Hiroshi Toyoizumi | Hiroshi Toyizumi, Jeremy Field | Dyanamics of Social Queues | null | null | null | null | q-bio.PE math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Queues formed by social wasps to inherit the dominant position in the nest
are analyzed by using a transient quasi-birth-and-death process. We show that
the extended nest life time due to division of labor between queen and helpers
has a big impact for the nest productivity.
| [
{
"created": "Wed, 29 May 2013 08:10:04 GMT",
"version": "v1"
}
] | 2013-05-30 | [
[
"Toyizumi",
"Hiroshi",
""
],
[
"Field",
"Jeremy",
""
]
] | Queues formed by social wasps to inherit the dominant position in the nest are analyzed by using a transient quasi-birth-and-death process. We show that the extended nest life time due to division of labor between queen and helpers has a big impact for the nest productivity. |
1204.1564 | Jose Fontanari | Paulo F. C. Tilles and Jose F. Fontanari | Minimal model of associative learning for cross-situational lexicon
acquisition | null | J. Math. Psych. 56, 396-403 (2012) | 10.1016/j.jmp.2012.11.002 | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An explanation for the acquisition of word-object mappings is the associative
learning in a cross-situational scenario. Here we present analytical results of
the performance of a simple associative learning algorithm for acquiring a
one-to-one mapping between $N$ objects and $N$ words based solely on the
co-occurrenc... | [
{
"created": "Fri, 6 Apr 2012 20:57:07 GMT",
"version": "v1"
},
{
"created": "Fri, 1 Jun 2012 12:04:12 GMT",
"version": "v2"
},
{
"created": "Wed, 22 Aug 2012 12:15:10 GMT",
"version": "v3"
},
{
"created": "Mon, 17 Dec 2012 16:58:04 GMT",
"version": "v4"
}
] | 2012-12-18 | [
[
"Tilles",
"Paulo F. C.",
""
],
[
"Fontanari",
"Jose F.",
""
]
] | An explanation for the acquisition of word-object mappings is the associative learning in a cross-situational scenario. Here we present analytical results of the performance of a simple associative learning algorithm for acquiring a one-to-one mapping between $N$ objects and $N$ words based solely on the co-occurrence ... |
1512.05143 | Igor Florinsky | I. V. Florinsky, E. V. Selezneva, A. I. Kulikova | GIS-based support for the complex botanical studies at the Molnieboi
Spur, Altai | 10 pages, 7 figures (corrected text, references added) | null | null | null | q-bio.QM physics.geo-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Molnieboi Spur is located at the northwestern margin of the Katun Range,
the high-mountain part of the Altai Mountains. Unique geological and
geophysical characteristics of the Molnieboi Spur made it an attractive target
for complex botanical studies including botanical, soil, geological,
geochemical, geophysical... | [
{
"created": "Wed, 16 Dec 2015 12:20:42 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Dec 2015 11:16:14 GMT",
"version": "v2"
},
{
"created": "Fri, 18 Dec 2015 20:21:09 GMT",
"version": "v3"
},
{
"created": "Mon, 21 Dec 2015 21:13:11 GMT",
"version": "v4"
}
] | 2015-12-23 | [
[
"Florinsky",
"I. V.",
""
],
[
"Selezneva",
"E. V.",
""
],
[
"Kulikova",
"A. I.",
""
]
] | The Molnieboi Spur is located at the northwestern margin of the Katun Range, the high-mountain part of the Altai Mountains. Unique geological and geophysical characteristics of the Molnieboi Spur made it an attractive target for complex botanical studies including botanical, soil, geological, geochemical, geophysical, ... |
1704.05906 | Eugene Postnikov | Eugene B. Postnikov, Maria O. Tsoy, Maxim A. Kurochkin, Dmitry E.
Postnov | A fast method for the detection of vascular structure in images, based
on the continuous wavelet transform with the Morlet wavelet having a low
central frequency | 6 pages, 3 figures | Proc. SPIE (2017) 10337 | 10.1117/12.2268427 | null | q-bio.QM math.NA | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A manual measurement of blood vessels diameter is a conventional component of
routine visual assessment of microcirculation, say, during optical
capillaroscopy. However, many modern optical methods for blood flow
measurements demand the reliable procedure for a fully automated detection of
vessels and estimation of t... | [
{
"created": "Wed, 19 Apr 2017 19:29:48 GMT",
"version": "v1"
}
] | 2017-04-21 | [
[
"Postnikov",
"Eugene B.",
""
],
[
"Tsoy",
"Maria O.",
""
],
[
"Kurochkin",
"Maxim A.",
""
],
[
"Postnov",
"Dmitry E.",
""
]
] | A manual measurement of blood vessels diameter is a conventional component of routine visual assessment of microcirculation, say, during optical capillaroscopy. However, many modern optical methods for blood flow measurements demand the reliable procedure for a fully automated detection of vessels and estimation of the... |
1403.2051 | Vyacheslav Yukalov | V.I. Yukalov, E.P. Yukalova, and D. Sornette | Population dynamics with nonlinear delayed carrying capacity | Latex file, 24 pages | Int. J. Bifur. Chaos 24 (2014) 1450021 | 10.1142/S0218127414500217 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a class of evolution equations describing population dynamics in
the presence of a carrying capacity depending on the population with delay. In
an earlier work, we presented an exhaustive classification of the logistic
equation where the carrying capacity is linearly dependent on the population
with a tim... | [
{
"created": "Sun, 9 Mar 2014 12:23:55 GMT",
"version": "v1"
}
] | 2015-06-19 | [
[
"Yukalov",
"V. I.",
""
],
[
"Yukalova",
"E. P.",
""
],
[
"Sornette",
"D.",
""
]
] | We consider a class of evolution equations describing population dynamics in the presence of a carrying capacity depending on the population with delay. In an earlier work, we presented an exhaustive classification of the logistic equation where the carrying capacity is linearly dependent on the population with a time ... |
2306.10040 | Giulia Chiari | Giulia Chiari, Giada Fiandaca, Marcello Edoardo Delitala | Hypoxia-related radiotherapy resistance in tumours: treatment efficacy
investigation in an eco-evolutionary perspective | null | Front. Appl. Math. Stat., 13 July 2023 Sec. Mathematical Biology | 10.3389/fams.2023.1193191 | null | q-bio.PE physics.med-ph q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In the study of therapeutic strategies for the treatment of cancer,
eco-evolutionary dynamics are of particular interest, since characteristics of
the tumour population, interaction with the environment and effects of the
treatment, influence the geometric and epigenetic characterization of the
tumour with direct con... | [
{
"created": "Sat, 10 Jun 2023 08:40:28 GMT",
"version": "v1"
},
{
"created": "Tue, 27 Jun 2023 09:33:11 GMT",
"version": "v2"
}
] | 2023-07-19 | [
[
"Chiari",
"Giulia",
""
],
[
"Fiandaca",
"Giada",
""
],
[
"Delitala",
"Marcello Edoardo",
""
]
] | In the study of therapeutic strategies for the treatment of cancer, eco-evolutionary dynamics are of particular interest, since characteristics of the tumour population, interaction with the environment and effects of the treatment, influence the geometric and epigenetic characterization of the tumour with direct conse... |
q-bio/0403044 | Markus Kollmann | H.H. von Gr\"unberg and M. Kollmann | Variations in Substitution Rate in Human and Mouse Genomes | 4 pages, 3 Figs | null | 10.1103/PhysRevLett.93.208102 | null | q-bio.GN q-bio.PE | null | We present a method to quantify spatial fluctuations of the substitution rate
on different length scales throughout genomes of eukaryotes. The fluctuations
on large length scales are found to be predominantly a consequence of a
coarse-graining effect of fluctuations on shorter length scales. This is
verified for both... | [
{
"created": "Wed, 31 Mar 2004 13:55:28 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"von Grünberg",
"H. H.",
""
],
[
"Kollmann",
"M.",
""
]
] | We present a method to quantify spatial fluctuations of the substitution rate on different length scales throughout genomes of eukaryotes. The fluctuations on large length scales are found to be predominantly a consequence of a coarse-graining effect of fluctuations on shorter length scales. This is verified for both t... |
2010.08359 | Julien Yann Dutheil | Julien Y. Dutheil | Towards more realistic models of genomes in populations: the
Markov-modulated sequentially Markov coalescent | 24 pages, 5 figures | Probabilistic Structures in Evolution (E. Baake and A.
Wakolbinger, eds.), EMS Press, Berlin, 2021, pp. 383-408 | null | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | The development of coalescent theory paved the way to statistical inference
from population genetic data. In the genomic era, however, coalescent models
are limited due to the complexity of the underlying ancestral recombination
graph. The sequentially Markov coalescent (SMC) is a heuristic that enables the
modelling... | [
{
"created": "Fri, 16 Oct 2020 12:56:21 GMT",
"version": "v1"
}
] | 2021-06-30 | [
[
"Dutheil",
"Julien Y.",
""
]
] | The development of coalescent theory paved the way to statistical inference from population genetic data. In the genomic era, however, coalescent models are limited due to the complexity of the underlying ancestral recombination graph. The sequentially Markov coalescent (SMC) is a heuristic that enables the modelling o... |
2007.08782 | Yukihiro Murakami | Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long
and Yukihiro Murakami | Distinguishing level-1 phylogenetic networks on the basis of data
generated by Markov processes | 24 pages, 10 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks can represent evolutionary events that cannot be
described by phylogenetic trees. These networks are able to incorporate
reticulate evolutionary events such as hybridization, introgression, and
lateral gene transfer. Recently, network-based Markov models of DNA sequence
evolution have been intro... | [
{
"created": "Fri, 17 Jul 2020 07:15:33 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Nov 2020 17:12:19 GMT",
"version": "v2"
},
{
"created": "Wed, 7 Jul 2021 09:33:45 GMT",
"version": "v3"
}
] | 2021-07-08 | [
[
"Gross",
"Elizabeth",
""
],
[
"van Iersel",
"Leo",
""
],
[
"Janssen",
"Remie",
""
],
[
"Jones",
"Mark",
""
],
[
"Long",
"Colby",
""
],
[
"Murakami",
"Yukihiro",
""
]
] | Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introdu... |
1709.07193 | Thu Thuy | Charles Burdet (DEBRC, IAME), Sakina Sayah-Jeanne, Thu Thuy Nguyen
(IAME), Christine Miossec, Nathalie Saint-Lu, Mark Pulse, William Weiss,
Antoine Andremont (IAME), France Mentr\'e (IAME, DEBRC), Jean De Gunzburg | Protection of hamsters from mortality by reducing fecal moxifloxacin
concentration with DAV131A in a model of moxifloxacin-induced Clostridium
difficile colitis | null | Antimicrobial Agents and Chemotherapy, American Society for
Microbiology, 2017 | 10.1128/AAC.00543-17 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | BackgroundLowering the gut exposure to antibiotics during treatments can
prevent microbiota disruption. We evaluated the effect of an activated
charcoal-based adsorbent, DAV131A, on fecal free moxifloxacin concentration and
mortality in a hamster model of moxifloxacin-induced C. difficile
infection.Methods215 hamster... | [
{
"created": "Thu, 21 Sep 2017 08:04:55 GMT",
"version": "v1"
}
] | 2017-09-22 | [
[
"Burdet",
"Charles",
"",
"DEBRC, IAME"
],
[
"Sayah-Jeanne",
"Sakina",
"",
"IAME"
],
[
"Nguyen",
"Thu Thuy",
"",
"IAME"
],
[
"Miossec",
"Christine",
"",
"IAME"
],
[
"Saint-Lu",
"Nathalie",
"",
"IAME"
],
[
"Pulse... | BackgroundLowering the gut exposure to antibiotics during treatments can prevent microbiota disruption. We evaluated the effect of an activated charcoal-based adsorbent, DAV131A, on fecal free moxifloxacin concentration and mortality in a hamster model of moxifloxacin-induced C. difficile infection.Methods215 hamsters ... |
1707.04129 | Gerard Rinkus | Gerard J. Rinkus | A cortical sparse distributed coding model linking mini- and
macrocolumn-scale functionality | 13 pages, 5 figures | Frontiers in Neuroanatomy (2010) 4:17 | 10.3389/fnana.2010.00017 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | No generic function for the minicolumn, i.e., one that would apply equally
well to all cortical areas and species, has yet been proposed. I propose that
the minicolumn does have a generic functionality, which only becomes clear when
seen in the context of the function of the higher-level, subsuming unit, the
macrocol... | [
{
"created": "Thu, 13 Jul 2017 13:56:51 GMT",
"version": "v1"
}
] | 2017-07-14 | [
[
"Rinkus",
"Gerard J.",
""
]
] | No generic function for the minicolumn, i.e., one that would apply equally well to all cortical areas and species, has yet been proposed. I propose that the minicolumn does have a generic functionality, which only becomes clear when seen in the context of the function of the higher-level, subsuming unit, the macrocolum... |
2102.03276 | Daniel Charlebois | Kevin S. Farquhar, Samira Rasouli Koohi, and Daniel A. Charlebois | Does Non-Genetic Heterogeneity Facilitate the Development of Genetic
Drug Resistance? | 11 pages, 2 figures | BioEssays, 43: e2100043 (2021) | 10.1002/bies.202100043 | null | q-bio.PE physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Non-genetic forms of antimicrobial drug resistance can result from
cell-to-cell variability that is not encoded in the genetic material. Data from
recent studies also suggest that non-genetic mechanisms can facilitate the
development of genetic drug resistance. In this Perspective article, we
speculate on how the int... | [
{
"created": "Fri, 5 Feb 2021 16:31:58 GMT",
"version": "v1"
}
] | 2022-06-23 | [
[
"Farquhar",
"Kevin S.",
""
],
[
"Koohi",
"Samira Rasouli",
""
],
[
"Charlebois",
"Daniel A.",
""
]
] | Non-genetic forms of antimicrobial drug resistance can result from cell-to-cell variability that is not encoded in the genetic material. Data from recent studies also suggest that non-genetic mechanisms can facilitate the development of genetic drug resistance. In this Perspective article, we speculate on how the inter... |
1210.4948 | Michael Courtney | Joshua Courtney, Jessica Abbott, Kerri Schmidt, and Michael Courtney | Plump Cutthroat Trout and Thin Rainbow Trout in a Lentic Ecosystem | 7 pages, 2 tables, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Much has been written about introduced rainbow trout
(Oncorhynchus mykiss) interbreeding and outcompeting cutthroat trout
(Oncorhynchus clarkii). However, the specific mechanisms by which rainbow trout
and their hybrids outcompete cutthroat trout have not been thoroughly explored,
and the published data i... | [
{
"created": "Wed, 17 Oct 2012 20:15:28 GMT",
"version": "v1"
}
] | 2012-10-19 | [
[
"Courtney",
"Joshua",
""
],
[
"Abbott",
"Jessica",
""
],
[
"Schmidt",
"Kerri",
""
],
[
"Courtney",
"Michael",
""
]
] | Background: Much has been written about introduced rainbow trout (Oncorhynchus mykiss) interbreeding and outcompeting cutthroat trout (Oncorhynchus clarkii). However, the specific mechanisms by which rainbow trout and their hybrids outcompete cutthroat trout have not been thoroughly explored, and the published data is ... |
1211.4251 | Claus O. Wilke | Matthew Z. Tien, Austin G. Meyer, Dariya K. Sydykova, Stephanie J.
Spielman, and Claus O. Wilke | Maximum allowed solvent accessibilites of residues in proteins | 16 pages, 4 figures | PLoS ONE 8(11): e80635 | 10.1371/journal.pone.0080635 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The relative solvent accessibility (RSA) of a residue in a protein measures
the extent of burial or exposure of that residue in the 3D structure. RSA is
frequently used to describe a protein's biophysical or evolutionary properties.
To calculate RSA, a residue's solvent accessibility (ASA) needs to be
normalized by a... | [
{
"created": "Sun, 18 Nov 2012 19:51:45 GMT",
"version": "v1"
},
{
"created": "Thu, 10 Jan 2013 18:18:55 GMT",
"version": "v2"
},
{
"created": "Wed, 25 Sep 2013 22:56:13 GMT",
"version": "v3"
}
] | 2013-11-28 | [
[
"Tien",
"Matthew Z.",
""
],
[
"Meyer",
"Austin G.",
""
],
[
"Sydykova",
"Dariya K.",
""
],
[
"Spielman",
"Stephanie J.",
""
],
[
"Wilke",
"Claus O.",
""
]
] | The relative solvent accessibility (RSA) of a residue in a protein measures the extent of burial or exposure of that residue in the 3D structure. RSA is frequently used to describe a protein's biophysical or evolutionary properties. To calculate RSA, a residue's solvent accessibility (ASA) needs to be normalized by a s... |
2104.06857 | Ioannis Kontoyiannis | Jussi Taipale, Ioannis Kontoyiannis, and Sten Linnarsson | Population-scale testing can suppress the spread of infectious disease | This paper is based, in part, on an earlier manuscript, that appears
as medRxiv 2020.04.27.20078329. This is a significantly extended version,
including a new and more extensive mathematical analysis. The present
manuscript was written in September 2020. The form included here includes
some additional bibliogra... | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | Major advances in public health have resulted from disease prevention.
However, prevention of a new infectious disease by vaccination or
pharmaceuticals is made difficult by the slow process of vaccine and drug
development. We propose an additional intervention that allows rapid control of
emerging infectious disease... | [
{
"created": "Wed, 14 Apr 2021 13:48:38 GMT",
"version": "v1"
}
] | 2021-04-15 | [
[
"Taipale",
"Jussi",
""
],
[
"Kontoyiannis",
"Ioannis",
""
],
[
"Linnarsson",
"Sten",
""
]
] | Major advances in public health have resulted from disease prevention. However, prevention of a new infectious disease by vaccination or pharmaceuticals is made difficult by the slow process of vaccine and drug development. We propose an additional intervention that allows rapid control of emerging infectious diseases,... |
1304.0399 | Fernando Fabian Montani | Fernando Montani, Emilia B. Deleglise, Osvaldo A. Rosso | Efficiency characterization of a large neuronal network: a causal
information approach | 26 pages, 3 Figures; Physica A, in press | null | 10.1016/j.physa.2013.12.053 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | When inhibitory neurons constitute about 40% of neurons they could have an
important antinociceptive role, as they would easily regulate the level of
activity of other neurons. We consider a simple network of cortical spiking
neurons with axonal conduction delays and spike timing dependent plasticity,
representative ... | [
{
"created": "Mon, 1 Apr 2013 17:36:49 GMT",
"version": "v1"
},
{
"created": "Sun, 26 Jan 2014 14:53:37 GMT",
"version": "v2"
}
] | 2014-01-28 | [
[
"Montani",
"Fernando",
""
],
[
"Deleglise",
"Emilia B.",
""
],
[
"Rosso",
"Osvaldo A.",
""
]
] | When inhibitory neurons constitute about 40% of neurons they could have an important antinociceptive role, as they would easily regulate the level of activity of other neurons. We consider a simple network of cortical spiking neurons with axonal conduction delays and spike timing dependent plasticity, representative of... |
2209.08694 | Ketevi A. Assamagan | Dephney Mathebula, Abigail Amankwah, Kossi Amouzouvi, K\'et\'evi A.
Assamagan, Somi\'ealo Azote, Jesutofunmi Ayo Fajemisin, Jean Baptiste Fankam
Fankam, Aluwani Guga, Moses Kamwela, Toivo S. Mabote, Mulape M Kanduza,
Francisco Fenias Macucule, Azwinndini Muronga, Ann Njeri, Michael Oluwole,
Cl\'audio Mois\'es P... | Modelling the impact of vaccination on the COVID-19 pandemic in African
countries | 40 pages, 10 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The rapid development of vaccines to combat the spread of COVID-19 disease
caused by the SARS-CoV-2 virus is a great scientific achievement. Before the
development of the COVID-19 vaccines, most studies capitalized on the available
data that did not include pharmaceutical measures. Such studies focused on the
impact ... | [
{
"created": "Mon, 19 Sep 2022 01:00:57 GMT",
"version": "v1"
},
{
"created": "Wed, 21 Sep 2022 19:59:51 GMT",
"version": "v2"
},
{
"created": "Sun, 30 Oct 2022 09:12:01 GMT",
"version": "v3"
},
{
"created": "Thu, 10 Nov 2022 12:14:20 GMT",
"version": "v4"
}
] | 2022-11-11 | [
[
"Mathebula",
"Dephney",
""
],
[
"Amankwah",
"Abigail",
""
],
[
"Amouzouvi",
"Kossi",
""
],
[
"Assamagan",
"Kétévi A.",
""
],
[
"Azote",
"Somiéalo",
""
],
[
"Fajemisin",
"Jesutofunmi Ayo",
""
],
[
"Fankam",
"Jea... | The rapid development of vaccines to combat the spread of COVID-19 disease caused by the SARS-CoV-2 virus is a great scientific achievement. Before the development of the COVID-19 vaccines, most studies capitalized on the available data that did not include pharmaceutical measures. Such studies focused on the impact of... |
2110.06882 | Paul Bressloff | Paul C Bressloff | Queuing model of axonal transport | 34 pages, 9 figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The motor-driven intracellular transport of vesicles to synaptic targets in
the axons and dendrites of neurons plays a crucial role in normal cell
function. Moreover, stimulus-dependent regulation of active transport is an
important component of long-term synaptic plasticity, whereas the disruption of
vesicular trans... | [
{
"created": "Wed, 13 Oct 2021 17:16:24 GMT",
"version": "v1"
}
] | 2021-10-14 | [
[
"Bressloff",
"Paul C",
""
]
] | The motor-driven intracellular transport of vesicles to synaptic targets in the axons and dendrites of neurons plays a crucial role in normal cell function. Moreover, stimulus-dependent regulation of active transport is an important component of long-term synaptic plasticity, whereas the disruption of vesicular transpo... |
2006.05357 | Tomas Veloz | Tomas Veloz, Pedro Maldonado, Samuel Ropert, Cesar Ravello, Soraya
Mora, Alejandra Barrios, Tomas Villaseca, Cesar Valdenegro, Tomas Perez-Acle | On the interplay between mobility and hospitalization capacity during
the COVID-19 pandemic: The SEIRHUD model | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Measures to reduce the impact of the COVID-19 pandemic require a mix of
logistic, political and social capacity. Depending on the country, different
approaches to increase hospitalization capacity or to properly apply lock-downs
are observed. In order to better understand the impact of these measures we
have develope... | [
{
"created": "Tue, 9 Jun 2020 15:42:51 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Jun 2020 02:34:19 GMT",
"version": "v2"
}
] | 2020-06-12 | [
[
"Veloz",
"Tomas",
""
],
[
"Maldonado",
"Pedro",
""
],
[
"Ropert",
"Samuel",
""
],
[
"Ravello",
"Cesar",
""
],
[
"Mora",
"Soraya",
""
],
[
"Barrios",
"Alejandra",
""
],
[
"Villaseca",
"Tomas",
""
],
[
... | Measures to reduce the impact of the COVID-19 pandemic require a mix of logistic, political and social capacity. Depending on the country, different approaches to increase hospitalization capacity or to properly apply lock-downs are observed. In order to better understand the impact of these measures we have developed ... |
1807.03781 | Stefano Corni | Giorgia Brancolini, Maria Celeste Maschio, Cristina Cantarutti,
Alessandra Corazza, Federico Fogolari, Vittorio Bellotti, Stefano Corni,
Gennaro Esposito | Citrate stabilized gold nanoparticles interfere with amyloid fibril
formation: D76N and {\Delta}N6 \b{eta}2-microglobulin variants | Published by RSC, under a Creative Commons Attribution 3.0 Unported
Licence | Nanoscale, 2018, 10, 4793 | 10.1039/c7nr06808e | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein aggregation including the formation of dimers and multimers in
solution, underlies an array of human diseases such as systemic amyloidosis
which is a fatal disease caused by misfolding of native globular proteins
damaging the structure and function of affected organs. Different kind of
interactors can interfe... | [
{
"created": "Tue, 10 Jul 2018 12:53:58 GMT",
"version": "v1"
}
] | 2018-07-12 | [
[
"Brancolini",
"Giorgia",
""
],
[
"Maschio",
"Maria Celeste",
""
],
[
"Cantarutti",
"Cristina",
""
],
[
"Corazza",
"Alessandra",
""
],
[
"Fogolari",
"Federico",
""
],
[
"Bellotti",
"Vittorio",
""
],
[
"Corni",
"... | Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the structure and function of affected organs. Different kind of interactors can interfere... |
2109.09740 | Gabriele Corso | Gabriele Corso, Rex Ying, Michal P\'andy, Petar Veli\v{c}kovi\'c, Jure
Leskovec, Pietro Li\`o | Neural Distance Embeddings for Biological Sequences | Advances in Neural Information Processing Systems (NeurIPS 2021) | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The development of data-dependent heuristics and representations for
biological sequences that reflect their evolutionary distance is critical for
large-scale biological research. However, popular machine learning approaches,
based on continuous Euclidean spaces, have struggled with the discrete
combinatorial formula... | [
{
"created": "Mon, 20 Sep 2021 17:30:58 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Oct 2021 19:49:08 GMT",
"version": "v2"
}
] | 2021-10-13 | [
[
"Corso",
"Gabriele",
""
],
[
"Ying",
"Rex",
""
],
[
"Pándy",
"Michal",
""
],
[
"Veličković",
"Petar",
""
],
[
"Leskovec",
"Jure",
""
],
[
"Liò",
"Pietro",
""
]
] | The development of data-dependent heuristics and representations for biological sequences that reflect their evolutionary distance is critical for large-scale biological research. However, popular machine learning approaches, based on continuous Euclidean spaces, have struggled with the discrete combinatorial formulati... |
1505.00569 | Igor Sazonov Dr | Igor Sazonov and Mark Kelbert | Randomized migration processes between two epidemic centers | 27 pages, 10 figures (17 plots) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epidemic dynamics in a stochastic network of interacting epidemic centers is
considered. The epidemic and migration processes are modelled by Markov's
chains. Explicit formulas for probability distribution of the migration process
are derived. Dependence of outbreak parameters on initial parameters,
population, coupl... | [
{
"created": "Mon, 4 May 2015 09:42:06 GMT",
"version": "v1"
}
] | 2015-05-05 | [
[
"Sazonov",
"Igor",
""
],
[
"Kelbert",
"Mark",
""
]
] | Epidemic dynamics in a stochastic network of interacting epidemic centers is considered. The epidemic and migration processes are modelled by Markov's chains. Explicit formulas for probability distribution of the migration process are derived. Dependence of outbreak parameters on initial parameters, population, couplin... |
2004.12472 | Bing Liu | Bing Liu | A Model Checking-based Analysis Framework for Systems Biology Models | To appear in the Proceedings of the 57th Design Automation Conference
(DAC) | null | null | null | q-bio.QM cs.FL | http://creativecommons.org/licenses/by/4.0/ | Biological systems are often modeled as a system of ordinary differential
equations (ODEs) with time-invariant parameters. However, cell signaling events
or pharmacological interventions may alter the cellular state and induce
multi-mode dynamics of the system. Such systems are naturally modeled as hybrid
automata, w... | [
{
"created": "Sun, 26 Apr 2020 20:31:39 GMT",
"version": "v1"
}
] | 2020-04-28 | [
[
"Liu",
"Bing",
""
]
] | Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode dynamics of the system. Such systems are naturally modeled as hybrid automata, whi... |
2210.13423 | Sara Mohammad Taheri Mrs | Sara Mohammad-Taheri and Vartika Tewari and Rohan Kapre and Ehsan
Rahiminasab and Karen Sachs and Charles Tapley Hoyt and Jeremy Zucker and
Olga Vitek | Experimental design for causal query estimation in partially observed
biomolecular networks | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Estimating a causal query from observational data is an essential task in the
analysis of biomolecular networks. Estimation takes as input a network
topology, a query estimation method, and observational measurements on the
network variables. However, estimations involving many variables can be
experimentally expensi... | [
{
"created": "Mon, 24 Oct 2022 17:39:07 GMT",
"version": "v1"
},
{
"created": "Mon, 28 Nov 2022 22:00:23 GMT",
"version": "v2"
}
] | 2022-11-30 | [
[
"Mohammad-Taheri",
"Sara",
""
],
[
"Tewari",
"Vartika",
""
],
[
"Kapre",
"Rohan",
""
],
[
"Rahiminasab",
"Ehsan",
""
],
[
"Sachs",
"Karen",
""
],
[
"Hoyt",
"Charles Tapley",
""
],
[
"Zucker",
"Jeremy",
""
... | Estimating a causal query from observational data is an essential task in the analysis of biomolecular networks. Estimation takes as input a network topology, a query estimation method, and observational measurements on the network variables. However, estimations involving many variables can be experimentally expensive... |
1311.3214 | Wes Maciejewski | Wes Maciejewski and Gregory J. Puleo | Environmental Evolutionary Graph Theory | null | Journal of Theoretical Biology, (2014), vol.360, pp.117-128 | 10.1016/j.jtbi.2014.06.040 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the influence of an environment on the evolution of its
resident population is a major challenge in evolutionary biology. Great
progress has been made in homogeneous population structures while heterogeneous
structures have received relatively less attention. Here we present a
structured population mode... | [
{
"created": "Wed, 13 Nov 2013 17:08:31 GMT",
"version": "v1"
}
] | 2014-07-30 | [
[
"Maciejewski",
"Wes",
""
],
[
"Puleo",
"Gregory J.",
""
]
] | Understanding the influence of an environment on the evolution of its resident population is a major challenge in evolutionary biology. Great progress has been made in homogeneous population structures while heterogeneous structures have received relatively less attention. Here we present a structured population model ... |
0811.3040 | Andre Brown | Andre E. X. Brown, Alina Hategan, Daniel Safer, Yale E. Goldman,
Dennis E. Discher | Cross-correlated TIRF/AFM shows Self-assembled Synthetic Myosin
Filaments are Asymmetric - Implications for Motile Filaments | 25 pages, 8 figures. Accepted in Biophysical Journal | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Myosin-II's rod-like tail drives filament assembly with a head arrangement
that should generate equal and opposite contractile forces on actin--if one
assumes that the filament is a symmetric bipole. Self-assembled myosin
filaments are shown here to be asymmetric in physiological buffer based on
cross-correlated imag... | [
{
"created": "Wed, 19 Nov 2008 01:09:39 GMT",
"version": "v1"
}
] | 2008-11-20 | [
[
"Brown",
"Andre E. X.",
""
],
[
"Hategan",
"Alina",
""
],
[
"Safer",
"Daniel",
""
],
[
"Goldman",
"Yale E.",
""
],
[
"Discher",
"Dennis E.",
""
]
] | Myosin-II's rod-like tail drives filament assembly with a head arrangement that should generate equal and opposite contractile forces on actin--if one assumes that the filament is a symmetric bipole. Self-assembled myosin filaments are shown here to be asymmetric in physiological buffer based on cross-correlated images... |
2202.06635 | Josip Mesari\'c | Josip Mesari\'c | Novel prediction methods for virtual drug screening | Review article | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Drug development is an expensive and time-consuming process where thousands
of chemical compounds are being tested in order to find those possessing
drug-like properties while being safe and effective. One of key parts of the
early drug discovery process has become virtual drug screening -- a method used
to narrow do... | [
{
"created": "Mon, 14 Feb 2022 11:41:39 GMT",
"version": "v1"
}
] | 2022-02-15 | [
[
"Mesarić",
"Josip",
""
]
] | Drug development is an expensive and time-consuming process where thousands of chemical compounds are being tested in order to find those possessing drug-like properties while being safe and effective. One of key parts of the early drug discovery process has become virtual drug screening -- a method used to narrow down... |
2004.14297 | Sebastian Dominguez | D. S. Ryan, S. Dom\'inguez, S. A. Ross, N. Nigam, J. M. Wakeling | The energy of muscle contraction. II. Transverse compression and work | 20 pages, 7 figures. Manuscript submitted to Frontiers in Physiology | null | 10.3389/fphys.2020.538522 | null | q-bio.TO q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this study we reproduced this compression-induced reduction in muscle
force through the use of a three-dimensional finite element model of
contracting muscle. The model used the principle of minimum total energy and
allowed for the redistribution of energy through different strain
energy-densities; this allowed us... | [
{
"created": "Tue, 28 Apr 2020 06:18:27 GMT",
"version": "v1"
}
] | 2021-01-13 | [
[
"Ryan",
"D. S.",
""
],
[
"Domínguez",
"S.",
""
],
[
"Ross",
"S. A.",
""
],
[
"Nigam",
"N.",
""
],
[
"Wakeling",
"J. M.",
""
]
] | In this study we reproduced this compression-induced reduction in muscle force through the use of a three-dimensional finite element model of contracting muscle. The model used the principle of minimum total energy and allowed for the redistribution of energy through different strain energy-densities; this allowed us t... |
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