id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1202.6573 | Francesc Rossell\'o | Gabriel Cardona, Arnau Mir, Francesc Rossello | Exact formulas for the variance of several balance indices under the
Yule model | 32 pages. The final version will appear in the J. Comp. Biol. v2
covers the Colless index, which did not appear in v1 | null | null | null | q-bio.PE math.PR q-bio.QM | http://creativecommons.org/licenses/publicdomain/ | One of the main applications of balance indices is in tests of null models of
evolutionary processes. The knowledge of an exact formula for a statistic of a
balance index, holding for any number n of leaves, is necessary in order to use
this statistic in tests of this kind involving trees of any size. In this paper
w... | [
{
"created": "Wed, 29 Feb 2012 15:28:47 GMT",
"version": "v1"
},
{
"created": "Fri, 19 Oct 2012 07:55:16 GMT",
"version": "v2"
}
] | 2012-10-22 | [
[
"Cardona",
"Gabriel",
""
],
[
"Mir",
"Arnau",
""
],
[
"Rossello",
"Francesc",
""
]
] | One of the main applications of balance indices is in tests of null models of evolutionary processes. The knowledge of an exact formula for a statistic of a balance index, holding for any number n of leaves, is necessary in order to use this statistic in tests of this kind involving trees of any size. In this paper we ... |
1310.3316 | Mike Steel Prof. | Benny Chor and Mike Steel | Tree split probabilities determine the branch lengths | 12 pages, 1 figure | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of aligned DNA sequence sites is generally modeled by a Markov
process operating along the edges of a phylogenetic tree. It is well known that
the probability distribution on the site patterns at the tips of the tree
determines the tree and its branch lengths. However, the number of patterns is
typicall... | [
{
"created": "Sat, 12 Oct 2013 00:13:38 GMT",
"version": "v1"
}
] | 2013-10-15 | [
[
"Chor",
"Benny",
""
],
[
"Steel",
"Mike",
""
]
] | The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree determines the tree and its branch lengths. However, the number of patterns is typically ... |
1611.03965 | Reza Ebrahimpour | Farzaneh Olianezhad, Maryam Tohidi-Moghaddam, Sajjad Zabbah, Reza
Ebrahimpour | Residual Information of Previous Decision Affects Evidence Accumulation
in Current Decision | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bias in perceptual decisions comes to pass when the advance knowledge
colludes with the current sensory evidence in support of the final choice. The
literature on decision making suggests two main hypotheses to account for this
kind of bias: internal bias signals are derived from (a) the residual of motor
response-re... | [
{
"created": "Sat, 12 Nov 2016 07:33:13 GMT",
"version": "v1"
},
{
"created": "Sat, 14 Oct 2017 11:26:03 GMT",
"version": "v2"
}
] | 2017-10-17 | [
[
"Olianezhad",
"Farzaneh",
""
],
[
"Tohidi-Moghaddam",
"Maryam",
""
],
[
"Zabbah",
"Sajjad",
""
],
[
"Ebrahimpour",
"Reza",
""
]
] | Bias in perceptual decisions comes to pass when the advance knowledge colludes with the current sensory evidence in support of the final choice. The literature on decision making suggests two main hypotheses to account for this kind of bias: internal bias signals are derived from (a) the residual of motor response-rela... |
1604.00385 | Stephen Plaza | Stephen M. Plaza and Stuart E. Berg | Large-Scale Electron Microscopy Image Segmentation in Spark | null | null | null | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The emerging field of connectomics aims to unlock the mysteries of the brain
by understanding the connectivity between neurons. To map this connectivity, we
acquire thousands of electron microscopy (EM) images with nanometer-scale
resolution. After aligning these images, the resulting dataset has the
potential to rev... | [
{
"created": "Fri, 1 Apr 2016 19:53:30 GMT",
"version": "v1"
}
] | 2016-04-04 | [
[
"Plaza",
"Stephen M.",
""
],
[
"Berg",
"Stuart E.",
""
]
] | The emerging field of connectomics aims to unlock the mysteries of the brain by understanding the connectivity between neurons. To map this connectivity, we acquire thousands of electron microscopy (EM) images with nanometer-scale resolution. After aligning these images, the resulting dataset has the potential to revea... |
0908.0230 | Marc Joyeux | Ana-Maria Florescu, Marc Joyeux and Benedicte Lafay | Modeling of two-dimensional DNA display | accepted in Electrophoresis | Electrophoresis 30 (2009) 3649 | 10.1002/elps.200900258 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | 2D display is a fast and economical way of visualizing polymorphism and
comparing genomes, which is based on the separation of DNA fragments in two
steps, according first to their size and then to their sequence composition. In
this paper, we present an exhaustive study of the numerical issues associated
with a model... | [
{
"created": "Mon, 3 Aug 2009 11:27:09 GMT",
"version": "v1"
},
{
"created": "Tue, 4 Aug 2009 06:56:40 GMT",
"version": "v2"
}
] | 2009-10-29 | [
[
"Florescu",
"Ana-Maria",
""
],
[
"Joyeux",
"Marc",
""
],
[
"Lafay",
"Benedicte",
""
]
] | 2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper, we present an exhaustive study of the numerical issues associated with a model a... |
0710.2739 | Dion Whitehead | Dion J. Whitehead, Claus O. Wilke, David Vernazobres, and Erich
Bornberg-Bauer | The look-ahead effect of phenotypic mutations | Submitted to "Genetics" | null | null | null | q-bio.PE | null | The evolution of complex molecular traits such as disulphide bridges often
requires multiple mutations. The intermediate steps in such evolutionary
trajectories are likely to be selectively neutral or deleterious. Therefore,
large populations and long times may be required to evolve such traits. We
propose that error... | [
{
"created": "Mon, 15 Oct 2007 08:47:00 GMT",
"version": "v1"
}
] | 2007-10-16 | [
[
"Whitehead",
"Dion J.",
""
],
[
"Wilke",
"Claus O.",
""
],
[
"Vernazobres",
"David",
""
],
[
"Bornberg-Bauer",
"Erich",
""
]
] | The evolution of complex molecular traits such as disulphide bridges often requires multiple mutations. The intermediate steps in such evolutionary trajectories are likely to be selectively neutral or deleterious. Therefore, large populations and long times may be required to evolve such traits. We propose that errors ... |
1510.04455 | Masafumi Oizumi | Masafumi Oizumi, Naotsugu Tsuchiya, and Shun-ichi Amari | A unified framework for information integration based on information
geometry | null | null | 10.1073/pnas.1603583113 | null | q-bio.NC cs.IT math.IT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a unified theoretical framework for quantifying spatio-temporal
interactions in a stochastic dynamical system based on information geometry. In
the proposed framework, the degree of interactions is quantified by the
divergence between the actual probability distribution of the system and a
constrained prob... | [
{
"created": "Thu, 15 Oct 2015 09:20:13 GMT",
"version": "v1"
}
] | 2016-12-08 | [
[
"Oizumi",
"Masafumi",
""
],
[
"Tsuchiya",
"Naotsugu",
""
],
[
"Amari",
"Shun-ichi",
""
]
] | We propose a unified theoretical framework for quantifying spatio-temporal interactions in a stochastic dynamical system based on information geometry. In the proposed framework, the degree of interactions is quantified by the divergence between the actual probability distribution of the system and a constrained probab... |
1912.02991 | Yuriy Shckorbatov G | Yuriy Shckorbatov | Chromatin Structure Changes in Human Disease: A Mini Review | 5 pages | null | null | null | q-bio.CB q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There are many experimental data indicating the correlations of the changes
in high level of organization of chromatin in human cells and changes in the
state of the whole organism related to disease, state of tiredness or aging. In
our previous work: arXiv.org-2018 (1812.00186) we analyzed the publications on
the to... | [
{
"created": "Fri, 6 Dec 2019 06:25:03 GMT",
"version": "v1"
}
] | 2019-12-09 | [
[
"Shckorbatov",
"Yuriy",
""
]
] | There are many experimental data indicating the correlations of the changes in high level of organization of chromatin in human cells and changes in the state of the whole organism related to disease, state of tiredness or aging. In our previous work: arXiv.org-2018 (1812.00186) we analyzed the publications on the topi... |
1304.0052 | Jingzhi Pu Jingzhi Pu | Yan Zhou, Pedro Ojeda-May, and Jingzhi Pu | H-loop Histidine Catalyzes ATP Hydrolysis in the E. coli ABC-Transporter
HlyB | null | Phys. Chem. Chem. Phys. 2013, 15, 15811-15815 | 10.1039/C3CP50965F | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Adenosine triphosphate (ATP)-binding cassette (ABC) transporters form a
family of molecular motor proteins that couple ATP hydrolysis to substrate
translocation across cell membranes. Each nucleotide binding domain of
ABC-transporters contains a highly conserved H-loop Histidine residue, whose
precise mechanistic rol... | [
{
"created": "Sat, 30 Mar 2013 00:28:58 GMT",
"version": "v1"
}
] | 2017-09-13 | [
[
"Zhou",
"Yan",
""
],
[
"Ojeda-May",
"Pedro",
""
],
[
"Pu",
"Jingzhi",
""
]
] | Adenosine triphosphate (ATP)-binding cassette (ABC) transporters form a family of molecular motor proteins that couple ATP hydrolysis to substrate translocation across cell membranes. Each nucleotide binding domain of ABC-transporters contains a highly conserved H-loop Histidine residue, whose precise mechanistic role ... |
1609.04856 | Ilya Nemenman | Xinxian Shao, Bruce R. Levin, Ilya Nemenman | Single variant bottleneck in the early dynamics of H. influenzae
bacteremia in neonatal rats questions the theory of independent action | 16 pages, 7 figures | null | 10.1088/1478-3975/aa731b | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | There is an abundance of information about the genetic basis, physiological
and molecular mechanisms of bacterial pathogenesis. In contrast, relatively
little is known about population dynamic processes, by which bacteria colonize
hosts and invade tissues and cells and thereby cause disease. In an article
published i... | [
{
"created": "Thu, 15 Sep 2016 20:48:58 GMT",
"version": "v1"
}
] | 2017-06-28 | [
[
"Shao",
"Xinxian",
""
],
[
"Levin",
"Bruce R.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | There is an abundance of information about the genetic basis, physiological and molecular mechanisms of bacterial pathogenesis. In contrast, relatively little is known about population dynamic processes, by which bacteria colonize hosts and invade tissues and cells and thereby cause disease. In an article published in ... |
1602.05847 | Fernando Vericat | C. Manuel Carlevaro, Ramiro M. Irastorza and Fernando Vericat | Chirality in a quaternionic representation of the genetic code | 17 pages, 9 figures. arXiv admin note: substantial text overlap with
arXiv:1505.04656 | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A quaternionic representation of the genetic code, previously reported by the
authors, is updated in order to incorporate chirality of nucleotide bases and
amino acids. The original representation assigns to each nucleotide base a
prime integer quaternion of norm 7 and involves a function that associates with
each co... | [
{
"created": "Wed, 30 Dec 2015 14:15:45 GMT",
"version": "v1"
}
] | 2016-02-19 | [
[
"Carlevaro",
"C. Manuel",
""
],
[
"Irastorza",
"Ramiro M.",
""
],
[
"Vericat",
"Fernando",
""
]
] | A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codo... |
1310.1334 | Yong Xu | Yong Xu, Xiaoqin Jin, Huiqing Zhang | The parallel logic gates in synthetic gene networks induced by
non-Gausssian noise | null | null | 10.1103/PhysRevE.88.052721 | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/3.0/ | The newly appeared idea of Logical Stochastic Resonance (LSR) is verified in
synthetic gene networks induced by non-Gaussian noise. We realize the switching
between two kinds of logic gates under optimal moderate noise intensity by
varying two different tunable parameters in a single gene network. Furthermore,
in ord... | [
{
"created": "Tue, 17 Sep 2013 05:30:19 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Xu",
"Yong",
""
],
[
"Jin",
"Xiaoqin",
""
],
[
"Zhang",
"Huiqing",
""
]
] | The newly appeared idea of Logical Stochastic Resonance (LSR) is verified in synthetic gene networks induced by non-Gaussian noise. We realize the switching between two kinds of logic gates under optimal moderate noise intensity by varying two different tunable parameters in a single gene network. Furthermore, in order... |
q-bio/0510036 | Gleb Basalyga | Gleb Basalyga and Emilio Salinas | When Response Variability Increases Neural Network Robustness to
Synaptic Noise | 26 pages, 7 figures, to appear in Neural Computation | null | null | null | q-bio.NC cond-mat.dis-nn | null | Cortical sensory neurons are known to be highly variable, in the sense that
responses evoked by identical stimuli often change dramatically from trial to
trial. The origin of this variability is uncertain, but it is usually
interpreted as detrimental noise that reduces the computational accuracy of
neural circuits. H... | [
{
"created": "Tue, 18 Oct 2005 20:38:33 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Basalyga",
"Gleb",
""
],
[
"Salinas",
"Emilio",
""
]
] | Cortical sensory neurons are known to be highly variable, in the sense that responses evoked by identical stimuli often change dramatically from trial to trial. The origin of this variability is uncertain, but it is usually interpreted as detrimental noise that reduces the computational accuracy of neural circuits. Her... |
1508.06232 | Stephen Plaza | Ting Zhao, Shin-ya Takemura, Gary B. Huang, Jane Anne Horne, William
T. Katz, Kazunori Shinomiya, Louis K. Scheffer, Ian A. Meinertzhagen,
Patricia K. Rivlin, Stephen M. Plaza | Large-scale EM Analysis of the Drosophila Antennal Lobe with
Automatically Computed Synapse Point Clouds | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The promise of extracting connectomes and performing useful analysis on large
electron microscopy (EM) datasets has been an elusive dream for many years.
Tracing in even the smallest portions of neuropil requires copious human
annotation, the rate-limiting step for generating a connectome. While a
combination of impr... | [
{
"created": "Tue, 25 Aug 2015 17:48:55 GMT",
"version": "v1"
}
] | 2015-08-26 | [
[
"Zhao",
"Ting",
""
],
[
"Takemura",
"Shin-ya",
""
],
[
"Huang",
"Gary B.",
""
],
[
"Horne",
"Jane Anne",
""
],
[
"Katz",
"William T.",
""
],
[
"Shinomiya",
"Kazunori",
""
],
[
"Scheffer",
"Louis K.",
""
]... | The promise of extracting connectomes and performing useful analysis on large electron microscopy (EM) datasets has been an elusive dream for many years. Tracing in even the smallest portions of neuropil requires copious human annotation, the rate-limiting step for generating a connectome. While a combination of improv... |
2203.12101 | Josinaldo Menezes | J. Menezes, M. Tenorio, E. Rangel | Adaptive movement strategy may promote biodiversity in the
rock-paper-scissors model | 7 pages, 7 figures. arXiv admin note: text overlap with
arXiv:2203.06531 | Europhysics Letters,139, 57002 (2022) | 10.1209/0295-5075/ac817a | null | q-bio.PE nlin.AO nlin.PS physics.bio-ph physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the role of the adaptive movement strategy in promoting biodiversity
in cyclic models described by the rock-paper-scissors game rules. We assume
that individuals of one out of the species may adjust their movement to escape
hostile regions and stay longer in their comfort zones. Running a series of
stochasti... | [
{
"created": "Tue, 22 Mar 2022 23:50:55 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Dec 2022 19:31:20 GMT",
"version": "v2"
}
] | 2022-12-27 | [
[
"Menezes",
"J.",
""
],
[
"Tenorio",
"M.",
""
],
[
"Rangel",
"E.",
""
]
] | We study the role of the adaptive movement strategy in promoting biodiversity in cyclic models described by the rock-paper-scissors game rules. We assume that individuals of one out of the species may adjust their movement to escape hostile regions and stay longer in their comfort zones. Running a series of stochastic ... |
2005.09890 | Lars Ailo Bongo | Tengel Ekrem Skar, Einar Holsb{\o}, Kristian Svendsen, Lars Ailo Bongo | Interactive exploration of population scale pharmacoepidemiology
datasets | null | null | 10.1145/3388440.3414862 | null | q-bio.QM cs.CV | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population-scale drug prescription data linked with adverse drug reaction
(ADR) data supports the fitting of models large enough to detect drug use and
ADR patterns that are not detectable using traditional methods on smaller
datasets. However, detecting ADR patterns in large datasets requires tools for
scalable data... | [
{
"created": "Wed, 20 May 2020 07:34:50 GMT",
"version": "v1"
}
] | 2021-06-02 | [
[
"Skar",
"Tengel Ekrem",
""
],
[
"Holsbø",
"Einar",
""
],
[
"Svendsen",
"Kristian",
""
],
[
"Bongo",
"Lars Ailo",
""
]
] | Population-scale drug prescription data linked with adverse drug reaction (ADR) data supports the fitting of models large enough to detect drug use and ADR patterns that are not detectable using traditional methods on smaller datasets. However, detecting ADR patterns in large datasets requires tools for scalable data p... |
2306.15279 | Fabrice SARLEGNA | Najib Abi Chebel, Florence Gaunet, Pascale Chavet, Christine Assaiante
(LNC), Christophe Bourdin (ISM), Fabrice Sarlegna | Does visual experience influence arm proprioception and its
lateralization? Evidence from passive matching performance in
congenitally-blind and sighted adults | null | Neuroscience Letters, 2023, 137335, pp.137335 | 10.1016/j.neulet.2023.137335 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In humans, body segments' position and movement can be estimated from
multiple senses such as vision and proprioception. It has been suggested that
vision and proprioception can influence each other and that upper-limb
proprioception is asymmetrical, with proprioception of the non-dominant arm
being more accurate and... | [
{
"created": "Tue, 27 Jun 2023 08:10:52 GMT",
"version": "v1"
}
] | 2023-06-28 | [
[
"Chebel",
"Najib Abi",
"",
"LNC"
],
[
"Gaunet",
"Florence",
"",
"LNC"
],
[
"Chavet",
"Pascale",
"",
"LNC"
],
[
"Assaiante",
"Christine",
"",
"LNC"
],
[
"Bourdin",
"Christophe",
"",
"ISM"
],
[
"Sarlegna",
"F... | In humans, body segments' position and movement can be estimated from multiple senses such as vision and proprioception. It has been suggested that vision and proprioception can influence each other and that upper-limb proprioception is asymmetrical, with proprioception of the non-dominant arm being more accurate and/o... |
1911.00930 | Kaifu Gao | Kaifu Gao, Duc Duy Nguyen, Vishnu Sresht, Alan M. Mathiowetz, Meihua
Tu, and Guo-Wei Wei | Are 2D fingerprints still valuable for drug discovery? | null | null | 10.1039/D0CP00305K | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, molecular fingerprints extracted from three-dimensional (3D)
structures using advanced mathematics, such as algebraic topology, differential
geometry, and graph theory have been paired with efficient machine learning,
especially deep learning algorithms to outperform other methods in drug
discovery applicat... | [
{
"created": "Sun, 3 Nov 2019 17:06:26 GMT",
"version": "v1"
}
] | 2020-06-24 | [
[
"Gao",
"Kaifu",
""
],
[
"Nguyen",
"Duc Duy",
""
],
[
"Sresht",
"Vishnu",
""
],
[
"Mathiowetz",
"Alan M.",
""
],
[
"Tu",
"Meihua",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Recently, molecular fingerprints extracted from three-dimensional (3D) structures using advanced mathematics, such as algebraic topology, differential geometry, and graph theory have been paired with efficient machine learning, especially deep learning algorithms to outperform other methods in drug discovery applicatio... |
1609.08696 | David K. Lubensky | Meryl A. Spencer, Zahera Jabeen, David K. Lubensky | Vertex stability and topological transitions in vertex models of foams
and epithelia | 20 pages, 7 figures | null | null | null | q-bio.TO cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In computer simulations of dry foams and of epithelial tissues, vertex models
are often used to describe the shape and motion of individual cells. Although
these models have been widely adopted, relatively little is known about their
basic theoretical properties. For example, while fourfold vertices in real
foams are... | [
{
"created": "Tue, 27 Sep 2016 22:37:38 GMT",
"version": "v1"
}
] | 2016-09-29 | [
[
"Spencer",
"Meryl A.",
""
],
[
"Jabeen",
"Zahera",
""
],
[
"Lubensky",
"David K.",
""
]
] | In computer simulations of dry foams and of epithelial tissues, vertex models are often used to describe the shape and motion of individual cells. Although these models have been widely adopted, relatively little is known about their basic theoretical properties. For example, while fourfold vertices in real foams are a... |
2008.12106 | Irina Volinsky | Irina Volinsky, Alexander Domoshnitsky, Marina Bershadsky and Roman
Shklyar | Marchuk's models of infection diseases: new developments | null | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider mathematical models of infection diseases built by G.I. Marchuk
in his well known book on immunology. These models are in the form of systems
of ordinary delay differential equations. We add a distributed control in one
of the equations describing the dynamics of the antibody concentration rate.
Distribut... | [
{
"created": "Thu, 23 Jul 2020 18:47:53 GMT",
"version": "v1"
}
] | 2020-08-28 | [
[
"Volinsky",
"Irina",
""
],
[
"Domoshnitsky",
"Alexander",
""
],
[
"Bershadsky",
"Marina",
""
],
[
"Shklyar",
"Roman",
""
]
] | We consider mathematical models of infection diseases built by G.I. Marchuk in his well known book on immunology. These models are in the form of systems of ordinary delay differential equations. We add a distributed control in one of the equations describing the dynamics of the antibody concentration rate. Distributed... |
2312.11107 | Paul Sorba | Antonino Sciarrino and Paul Sorba | Hierarchy of codon usage frequencies from codon-anticodon interaction in
the crystal basis model | null | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Analyzing the codon usage frequencies of a specimen of 20 plants, for which
the codon-anticodon pattern is known, we have remarked that the hierarchy of
the usage frequencies present an almost "universal" behavior. Searching to
explain this behavior, we assume that the codon usage probability results from
the sum of ... | [
{
"created": "Mon, 18 Dec 2023 11:12:46 GMT",
"version": "v1"
}
] | 2023-12-19 | [
[
"Sciarrino",
"Antonino",
""
],
[
"Sorba",
"Paul",
""
]
] | Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of tw... |
2104.10771 | Joceline Lega | Adrienne C. Kinney, Sean Current, Joceline Lega | Aedes-AI: Neural Network Models of Mosquito Abundance | null | PLoS Comput Biol 17(11): e1009467 (2021) | 10.1371/journal.pcbi.1009467 | null | q-bio.PE cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We present artificial neural networks as a feasible replacement for a
mechanistic model of mosquito abundance. We develop a feed-forward neural
network, a long short-term memory recurrent neural network, and a gated
recurrent unit network. We evaluate the networks in their ability to replicate
the spatiotemporal feat... | [
{
"created": "Wed, 21 Apr 2021 21:28:03 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Aug 2021 21:38:14 GMT",
"version": "v2"
}
] | 2021-12-09 | [
[
"Kinney",
"Adrienne C.",
""
],
[
"Current",
"Sean",
""
],
[
"Lega",
"Joceline",
""
]
] | We present artificial neural networks as a feasible replacement for a mechanistic model of mosquito abundance. We develop a feed-forward neural network, a long short-term memory recurrent neural network, and a gated recurrent unit network. We evaluate the networks in their ability to replicate the spatiotemporal featur... |
q-bio/0507005 | Michael Stumpf | Michael P.H. Stumpf, Piers J. Ingram | Probability Models for Degree Distributions of Protein Interaction
Networks | null | Europhys.Lett., 71 (1), pp. 152-158 (2005) | 10.1209/epl/i2004-10531-8 | null | q-bio.MN | null | The degree distribution of many biological and technological networks has
been described as a power-law distribution. While the degree distribution does
not capture all aspects of a network, it has often been suggested that its
functional form contains important clues as to underlying evolutionary
processes that have... | [
{
"created": "Sun, 3 Jul 2005 08:40:55 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Stumpf",
"Michael P. H.",
""
],
[
"Ingram",
"Piers J.",
""
]
] | The degree distribution of many biological and technological networks has been described as a power-law distribution. While the degree distribution does not capture all aspects of a network, it has often been suggested that its functional form contains important clues as to underlying evolutionary processes that have s... |
1209.0128 | Casey Bergman | Martin Carr, Douda Bensasson, Casey M. Bergman | Evolutionary genomics of transposable elements in Saccharomyces
cerevisiae | 34 pages, 7 figures | Carr M, Bensasson D, Bergman CM (2012) Evolutionary Genomics of
Transposable Elements in Saccharomyces cerevisiae. PLoS ONE 7(11): e50978 | 10.1371/journal.pone.0050978 | null | q-bio.PE q-bio.GN | http://creativecommons.org/licenses/by/3.0/ | Saccharomyces cerevisiae is one of the premier model systems for studying the
genomics and evolution of transposable elements. The availability of the S.
cerevisiae genome led to many insights into its five known transposable element
families (Ty1-Ty5) in the years shortly after its completion. However,
subsequent ad... | [
{
"created": "Sat, 1 Sep 2012 19:56:01 GMT",
"version": "v1"
}
] | 2012-12-05 | [
[
"Carr",
"Martin",
""
],
[
"Bensasson",
"Douda",
""
],
[
"Bergman",
"Casey M.",
""
]
] | Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to many insights into its five known transposable element families (Ty1-Ty5) in the years shortly after its completion. However, subsequent adva... |
2403.01678 | Michael Plank | Michael J. Plank and Matthew J. Simpson | Structured methods for parameter inference and uncertainty
quantification for mechanistic models in the life sciences | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Parameter inference and uncertainty quantification are important steps when
relating mathematical models to real-world observations, and when estimating
uncertainty in model predictions. However, methods for doing this can be
computationally expensive, particularly when the number of unknown model
parameters is large... | [
{
"created": "Mon, 4 Mar 2024 02:13:58 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Apr 2024 23:51:08 GMT",
"version": "v2"
},
{
"created": "Mon, 8 Jul 2024 10:39:39 GMT",
"version": "v3"
}
] | 2024-07-09 | [
[
"Plank",
"Michael J.",
""
],
[
"Simpson",
"Matthew J.",
""
]
] | Parameter inference and uncertainty quantification are important steps when relating mathematical models to real-world observations, and when estimating uncertainty in model predictions. However, methods for doing this can be computationally expensive, particularly when the number of unknown model parameters is large. ... |
2212.07492 | Gianni De Fabritiis | Maciej Majewski, Adri\`a P\'erez, Philipp Th\"olke, Stefan Doerr,
Nicholas E. Charron, Toni Giorgino, Brooke E. Husic, Cecilia Clementi, Frank
No\'e and Gianni De Fabritiis | Machine Learning Coarse-Grained Potentials of Protein Thermodynamics | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A generalized understanding of protein dynamics is an unsolved scientific
problem, the solution of which is critical to the interpretation of the
structure-function relationships that govern essential biological processes.
Here, we approach this problem by constructing coarse-grained molecular
potentials based on art... | [
{
"created": "Wed, 14 Dec 2022 20:23:11 GMT",
"version": "v1"
}
] | 2022-12-16 | [
[
"Majewski",
"Maciej",
""
],
[
"Pérez",
"Adrià",
""
],
[
"Thölke",
"Philipp",
""
],
[
"Doerr",
"Stefan",
""
],
[
"Charron",
"Nicholas E.",
""
],
[
"Giorgino",
"Toni",
""
],
[
"Husic",
"Brooke E.",
""
],
... | A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artif... |
1505.03785 | Silvia Bartolucci | Silvia Bartolucci, Alessia Annibale | A dynamical model of the adaptive immune system: effects of cells
promiscuity, antigens and B-B interactions | 40 pages, 26 figures | null | 10.1088/1742-5468/2015/08/P08017 | null | q-bio.CB cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse a minimal model for the primary response in the adaptive immune
system comprising three different players: antigens, T and B cells. We assume
B-T interactions to be diluted and sampled locally from heterogeneous degree
distributions, which mimic B cells receptors' promiscuity. We derive dynamical
equations... | [
{
"created": "Thu, 14 May 2015 16:25:22 GMT",
"version": "v1"
}
] | 2015-09-30 | [
[
"Bartolucci",
"Silvia",
""
],
[
"Annibale",
"Alessia",
""
]
] | We analyse a minimal model for the primary response in the adaptive immune system comprising three different players: antigens, T and B cells. We assume B-T interactions to be diluted and sampled locally from heterogeneous degree distributions, which mimic B cells receptors' promiscuity. We derive dynamical equations f... |
1302.3869 | Daniele Marinazzo | Daniele Marinazzo, Mario Pellicoro, Guorong Wu, Leonardo Angelini,
Jesus M Cortes, Sebastiano Stramaglia | Information transfer of an Ising model on a brain network | null | null | null | null | q-bio.NC cond-mat.dis-nn physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We implement the Ising model on a structural connectivity matrix describing
the brain at a coarse scale. Tuning the model temperature to its critical
value, i.e. at the susceptibility peak, we find a maximal amount of total
information transfer between the spin variables. At this point the amount of
information that ... | [
{
"created": "Fri, 15 Feb 2013 20:32:22 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Mar 2013 20:45:14 GMT",
"version": "v2"
},
{
"created": "Wed, 3 Jul 2013 15:39:50 GMT",
"version": "v3"
},
{
"created": "Sun, 1 Sep 2013 14:38:18 GMT",
"version": "v4"
}
] | 2013-09-03 | [
[
"Marinazzo",
"Daniele",
""
],
[
"Pellicoro",
"Mario",
""
],
[
"Wu",
"Guorong",
""
],
[
"Angelini",
"Leonardo",
""
],
[
"Cortes",
"Jesus M",
""
],
[
"Stramaglia",
"Sebastiano",
""
]
] | We implement the Ising model on a structural connectivity matrix describing the brain at a coarse scale. Tuning the model temperature to its critical value, i.e. at the susceptibility peak, we find a maximal amount of total information transfer between the spin variables. At this point the amount of information that ca... |
1508.06549 | Alexander Teplukhin | V. I. Poltev, E. Rodriguez, T. I. Grokhlina, A. V. Teplukhin, A.
Deriabina, and E. Gonzalez | Computational Study of Molecular Mechanisms of Caffeine Actions | Proceedings of the International Conference on Applied Computer
Science, Malta, September 15-17, 2010, pp. 51-55 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Caffeine (CAF) is one of the most widely and regularly consumed biologically
active substances. We use computer simulation approach to the study of CAF
activity by searching for its possible complexes with biopolymer fragments. The
principal CAF target at physiologically important concentrations refers to
adenosine r... | [
{
"created": "Wed, 26 Aug 2015 16:08:24 GMT",
"version": "v1"
}
] | 2015-08-27 | [
[
"Poltev",
"V. I.",
""
],
[
"Rodriguez",
"E.",
""
],
[
"Grokhlina",
"T. I.",
""
],
[
"Teplukhin",
"A. V.",
""
],
[
"Deriabina",
"A.",
""
],
[
"Gonzalez",
"E.",
""
]
] | Caffeine (CAF) is one of the most widely and regularly consumed biologically active substances. We use computer simulation approach to the study of CAF activity by searching for its possible complexes with biopolymer fragments. The principal CAF target at physiologically important concentrations refers to adenosine rec... |
2004.14920 | Cesar Castilho | Marcilio Ferreira dos Santos and Cesar Castilho | Deterministic Critical Community Size For The SIR System and Viral
Strain Selection | null | null | null | null | q-bio.PE math.DS physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper the concept of Critical Community Size (CCS) for the
deterministic SIR model is introduced and its consequences for the disease
dynamics are stressed. The disease can fade out after an outburst. Also the
principle of competitive exclusion holds no longer true. This is exemplified
for the dynamics of two... | [
{
"created": "Wed, 29 Apr 2020 17:05:57 GMT",
"version": "v1"
}
] | 2020-05-01 | [
[
"Santos",
"Marcilio Ferreira dos",
""
],
[
"Castilho",
"Cesar",
""
]
] | In this paper the concept of Critical Community Size (CCS) for the deterministic SIR model is introduced and its consequences for the disease dynamics are stressed. The disease can fade out after an outburst. Also the principle of competitive exclusion holds no longer true. This is exemplified for the dynamics of two c... |
2305.09189 | Christopher Miles | Pei Tan, Christopher E Miles | Intrinsic statistical separation of subpopulations in heterogeneous
collective motion via dimensionality reduction | 9 pages, 7 figures; v2: based on a great reviewer's suggestion, all
numerical experiments to start after equilibration and figures updated
accordingly | null | 10.1103/PhysRevE.109.014403 | null | q-bio.QM nlin.AO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Collective motion of locally interacting agents is found ubiquitously
throughout nature. The inability to probe individuals has driven longstanding
interest in the development of methods for inferring the underlying
interactions. In the context of heterogeneous collectives, where the population
consists of individual... | [
{
"created": "Tue, 16 May 2023 05:55:00 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Nov 2023 18:38:53 GMT",
"version": "v2"
}
] | 2024-01-23 | [
[
"Tan",
"Pei",
""
],
[
"Miles",
"Christopher E",
""
]
] | Collective motion of locally interacting agents is found ubiquitously throughout nature. The inability to probe individuals has driven longstanding interest in the development of methods for inferring the underlying interactions. In the context of heterogeneous collectives, where the population consists of individuals ... |
1505.00452 | Loren Coquille | Martina Baar, Loren Coquille, Hannah Mayer, Michael H\"olzel, Meri
Rogava, Thomas T\"uting, Anton Bovier | A stochastic individual-based model for immunotherapy of cancer | null | Scientific Reports, 6, 24169 (2016) | 10.1038/srep24169 | null | q-bio.PE math.PR q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose an extension of a standard stochastic individual-based model in
population dynamics which broadens the range of biological applications. Our
primary motivation is modelling of immunotherapy of malignant tumours. In this
context the different actors, T-cells, cytokines or cancer cells, are modelled
as singl... | [
{
"created": "Sun, 3 May 2015 17:05:18 GMT",
"version": "v1"
},
{
"created": "Mon, 27 Jul 2015 11:20:06 GMT",
"version": "v2"
},
{
"created": "Fri, 15 Apr 2016 14:13:34 GMT",
"version": "v3"
}
] | 2016-04-18 | [
[
"Baar",
"Martina",
""
],
[
"Coquille",
"Loren",
""
],
[
"Mayer",
"Hannah",
""
],
[
"Hölzel",
"Michael",
""
],
[
"Rogava",
"Meri",
""
],
[
"Tüting",
"Thomas",
""
],
[
"Bovier",
"Anton",
""
]
] | We propose an extension of a standard stochastic individual-based model in population dynamics which broadens the range of biological applications. Our primary motivation is modelling of immunotherapy of malignant tumours. In this context the different actors, T-cells, cytokines or cancer cells, are modelled as single ... |
2406.18531 | Nghi Nguyen | Duy Duong-Tran, Nghi Nguyen, Shizhuo Mu, Jiong Chen, Jingxuan Bao,
Frederick Xu, Sumita Garai, Jose Cadena-Pico, Alan David Kaplan, Tianlong
Chen, Yize Zhao, Li Shen, and Joaqu\'in Go\~ni | A principled framework to assess the information-theoretic fitness of
brain functional sub-circuits | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | In systems and network neuroscience, many common practices in brain
connectomic analysis are often not properly scrutinized. One such practice is
mapping a predetermined set of sub-circuits, like functional networks (FNs),
onto subjects' functional connectomes (FCs) without adequately assessing the
information-theore... | [
{
"created": "Wed, 26 Jun 2024 17:57:27 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Jul 2024 23:01:08 GMT",
"version": "v2"
}
] | 2024-07-25 | [
[
"Duong-Tran",
"Duy",
""
],
[
"Nguyen",
"Nghi",
""
],
[
"Mu",
"Shizhuo",
""
],
[
"Chen",
"Jiong",
""
],
[
"Bao",
"Jingxuan",
""
],
[
"Xu",
"Frederick",
""
],
[
"Garai",
"Sumita",
""
],
[
"Cadena-Pico... | In systems and network neuroscience, many common practices in brain connectomic analysis are often not properly scrutinized. One such practice is mapping a predetermined set of sub-circuits, like functional networks (FNs), onto subjects' functional connectomes (FCs) without adequately assessing the information-theoreti... |
2205.05014 | Cristian Staii | Ilya Yurchenko, Matthew Farwell, Donovan D. Brady and Cristian Staii | Neuronal Growth and Formation of Neuron Networks on Directional Surfaces | 34 pages, 10 figures | Biomimetics 6(2), 41 (2021) | null | null | q-bio.CB physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | The formation of neuron networks is a process of fundamental importance for
understanding the development of the nervous system and for creating biomimetic
devices for tissue engineering and neural repair. The basic process that
controls the network formation is the growth of an axon from the cell body and
its extens... | [
{
"created": "Tue, 10 May 2022 16:31:12 GMT",
"version": "v1"
},
{
"created": "Fri, 13 May 2022 02:42:17 GMT",
"version": "v2"
}
] | 2022-05-16 | [
[
"Yurchenko",
"Ilya",
""
],
[
"Farwell",
"Matthew",
""
],
[
"Brady",
"Donovan D.",
""
],
[
"Staii",
"Cristian",
""
]
] | The formation of neuron networks is a process of fundamental importance for understanding the development of the nervous system and for creating biomimetic devices for tissue engineering and neural repair. The basic process that controls the network formation is the growth of an axon from the cell body and its extensio... |
2204.11026 | Jiahao Ma | Jiahao Ma, Guotong Xu, Le Ao, Siqi Chen, Jingze Liu | Bioinformatic analysis for structure and function of Glutamine
synthetase(GS) | 8 pages, 8 figures | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | Objective: To predict structure and function of Glutamine synthetase (GS)
from Pseudoalteromonas sp. by bioinformatics technology, and to provide a
theoretical basis for further study. Methods: Open reading frame (ORF) of GS
sequence from Pseudoalteromonas sp. was obtained by ORF finder and was
translated into amino ... | [
{
"created": "Sat, 23 Apr 2022 09:02:20 GMT",
"version": "v1"
}
] | 2022-04-26 | [
[
"Ma",
"Jiahao",
""
],
[
"Xu",
"Guotong",
""
],
[
"Ao",
"Le",
""
],
[
"Chen",
"Siqi",
""
],
[
"Liu",
"Jingze",
""
]
] | Objective: To predict structure and function of Glutamine synthetase (GS) from Pseudoalteromonas sp. by bioinformatics technology, and to provide a theoretical basis for further study. Methods: Open reading frame (ORF) of GS sequence from Pseudoalteromonas sp. was obtained by ORF finder and was translated into amino ac... |
1310.0889 | Nobu C. Shirai | Nobu C. Shirai and Macoto Kikuchi | Structural flexibility of intrinsically disordered proteins induces
stepwise target recognition | 9 pages, 14 figures, 1 table | J. Chem. Phys. 139, 225103 (2013) | 10.1063/1.4838476 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | An intrinsically disordered protein (IDP) lacks a stable three-dimensional
structure, while it folds into a specific structure when it binds to a target
molecule. In some IDP-target complexes, not all target binding surfaces are
exposed on the outside, and intermediate states are observed in their binding
processes. ... | [
{
"created": "Thu, 3 Oct 2013 03:45:18 GMT",
"version": "v1"
},
{
"created": "Tue, 12 Nov 2013 14:05:10 GMT",
"version": "v2"
}
] | 2013-12-12 | [
[
"Shirai",
"Nobu C.",
""
],
[
"Kikuchi",
"Macoto",
""
]
] | An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on the outside, and intermediate states are observed in their binding processes. We... |
1211.6198 | Chao Yang Mr. | Chao Yang, Zengyou He and Weichuan Yu | Running PeptideProphet Separately on Replicates Improves Peptide
Identification Results | Due to an error | null | null | null | q-bio.QM q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Limited spectrum coverage is a problem in shotgun proteomics. Replicates are
generated to improve the spectrum coverage. When integrating peptide
identification results obtained from replicates, the state-of-the-art algorithm
PeptideProphet combines Peptide-Spectrum Matches (PSMs) before building the
statistical mode... | [
{
"created": "Tue, 27 Nov 2012 02:42:15 GMT",
"version": "v1"
},
{
"created": "Thu, 29 Nov 2012 01:49:07 GMT",
"version": "v2"
},
{
"created": "Sun, 2 Dec 2012 06:14:12 GMT",
"version": "v3"
}
] | 2012-12-04 | [
[
"Yang",
"Chao",
""
],
[
"He",
"Zengyou",
""
],
[
"Yu",
"Weichuan",
""
]
] | Limited spectrum coverage is a problem in shotgun proteomics. Replicates are generated to improve the spectrum coverage. When integrating peptide identification results obtained from replicates, the state-of-the-art algorithm PeptideProphet combines Peptide-Spectrum Matches (PSMs) before building the statistical model ... |
1106.0236 | Alessia Annibale | A. Annibale and A.C.C. Coolen | What you see is not what you get: how sampling affects macroscopic
features of biological networks | 26 pages, 8 figures | null | null | null | q-bio.QM cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use mathematical methods from the theory of tailored random graphs to
study systematically the effects of sampling on topological features of large
biological signalling networks. Our aim in doing so is to increase our
quantitative understanding of the relation between true biological networks and
the imperfect an... | [
{
"created": "Wed, 1 Jun 2011 16:35:14 GMT",
"version": "v1"
}
] | 2011-06-02 | [
[
"Annibale",
"A.",
""
],
[
"Coolen",
"A. C. C.",
""
]
] | We use mathematical methods from the theory of tailored random graphs to study systematically the effects of sampling on topological features of large biological signalling networks. Our aim in doing so is to increase our quantitative understanding of the relation between true biological networks and the imperfect and ... |
2003.05666 | Liu Hong | Wuyue Yang, Dongyan Zhang, Liangrong Peng, Changjing Zhuge, Liu Hong | Rational evaluation of various epidemic models based on the COVID-19
data of China | 25 pages, 5 figures, 2 tables | null | null | null | q-bio.PE math.DS q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, based on the Akaike information criterion, root mean square
error and robustness coefficient, a rational evaluation of various epidemic
models/methods, including seven empirical functions, four statistical inference
methods and five dynamical models, on their forecasting abilities is carried
out. With ... | [
{
"created": "Thu, 12 Mar 2020 08:58:39 GMT",
"version": "v1"
},
{
"created": "Wed, 15 Sep 2021 03:45:26 GMT",
"version": "v2"
}
] | 2021-09-16 | [
[
"Yang",
"Wuyue",
""
],
[
"Zhang",
"Dongyan",
""
],
[
"Peng",
"Liangrong",
""
],
[
"Zhuge",
"Changjing",
""
],
[
"Hong",
"Liu",
""
]
] | In this paper, based on the Akaike information criterion, root mean square error and robustness coefficient, a rational evaluation of various epidemic models/methods, including seven empirical functions, four statistical inference methods and five dynamical models, on their forecasting abilities is carried out. With re... |
1402.6397 | Jamie Oaks | Jamie R. Oaks, Charles W. Linkem and Jeet Sukumaran | Implications of uniformly distributed, empirically informed priors for
phylogeographical model selection: A reply to Hickerson et al | 24 pages, 4 figures, 1 table, 14 pages of supporting information with
10 supporting figures | null | 10.1111/evo.12523 | null | q-bio.PE stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Establishing that a set of population-splitting events occurred at the same
time can be a potentially persuasive argument that a common process affected
the populations. Oaks et al. (2013) assessed the ability of an
approximate-Bayesian method (msBayes) to estimate such a pattern of
simultaneous divergence across tax... | [
{
"created": "Wed, 26 Feb 2014 02:29:29 GMT",
"version": "v1"
},
{
"created": "Mon, 24 Nov 2014 22:41:08 GMT",
"version": "v2"
}
] | 2014-11-26 | [
[
"Oaks",
"Jamie R.",
""
],
[
"Linkem",
"Charles W.",
""
],
[
"Sukumaran",
"Jeet",
""
]
] | Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Oaks et al. (2013) assessed the ability of an approximate-Bayesian method (msBayes) to estimate such a pattern of simultaneous divergence across taxa,... |
2408.05579 | Claus Metzner | Claus Metzner, Achim Schilling, Andreas Maier and Patrick Krauss | Recurrence Resonance -- Noise-Enhanced Dynamics in Recurrent Neural
Networks | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | In specific motifs of three recurrently connected neurons with probabilistic
response, the spontaneous information flux, defined as the mutual information
between subsequent states, has been shown to increase by adding ongoing white
noise of some optimal strength to each of the neurons
\cite{krauss2019recurrence}. Ho... | [
{
"created": "Sat, 10 Aug 2024 15:14:41 GMT",
"version": "v1"
}
] | 2024-08-13 | [
[
"Metzner",
"Claus",
""
],
[
"Schilling",
"Achim",
""
],
[
"Maier",
"Andreas",
""
],
[
"Krauss",
"Patrick",
""
]
] | In specific motifs of three recurrently connected neurons with probabilistic response, the spontaneous information flux, defined as the mutual information between subsequent states, has been shown to increase by adding ongoing white noise of some optimal strength to each of the neurons \cite{krauss2019recurrence}. Howe... |
2107.10901 | Saba Moeinizade | Saba Moeinizade, Guiping Hu, Lizhi Wang | A reinforcement learning approach to resource allocation in genomic
selection | 18 pages,5 figures | null | null | null | q-bio.GN cs.AI cs.LG math.OC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Genomic selection (GS) is a technique that plant breeders use to select
individuals to mate and produce new generations of species. Allocation of
resources is a key factor in GS. At each selection cycle, breeders are facing
the choice of budget allocation to make crosses and produce the next generation
of breeding pa... | [
{
"created": "Thu, 22 Jul 2021 19:55:16 GMT",
"version": "v1"
}
] | 2021-07-26 | [
[
"Moeinizade",
"Saba",
""
],
[
"Hu",
"Guiping",
""
],
[
"Wang",
"Lizhi",
""
]
] | Genomic selection (GS) is a technique that plant breeders use to select individuals to mate and produce new generations of species. Allocation of resources is a key factor in GS. At each selection cycle, breeders are facing the choice of budget allocation to make crosses and produce the next generation of breeding pare... |
1907.13472 | Jean-Marc Ginoux | Jean-Marc Ginoux (LIS), Heikki Ruskeep\"a\"a, Matja\v{z} Perc, Roomila
Naeck, V\'eronique Di Costanzo, Moez Bouchouicha (LIS), Farhat Fnaiech,
Mounir Sayadi, Takoua Hamdi | Is type 1 diabetes a chaotic phenomenon? | null | Chaos, Solitons & Fractals 111, 198-205 (2018) | 10.1016/j.chaos.2018.03.033 | null | q-bio.OT nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A database of ten type 1 diabetes patients wearing a continuous glucose
monitoring device has enabled to record their blood glucose continuous
variations every minute all day long during fourteen consecutive days. These
recordings represent, for each patient, a time series consisting of 1 value of
glycaemia per minut... | [
{
"created": "Mon, 29 Jul 2019 13:09:02 GMT",
"version": "v1"
}
] | 2019-08-07 | [
[
"Ginoux",
"Jean-Marc",
"",
"LIS"
],
[
"Ruskeepää",
"Heikki",
"",
"LIS"
],
[
"Perc",
"Matjaž",
"",
"LIS"
],
[
"Naeck",
"Roomila",
"",
"LIS"
],
[
"Di Costanzo",
"Véronique",
"",
"LIS"
],
[
"Bouchouicha",
"Moe... | A database of ten type 1 diabetes patients wearing a continuous glucose monitoring device has enabled to record their blood glucose continuous variations every minute all day long during fourteen consecutive days. These recordings represent, for each patient, a time series consisting of 1 value of glycaemia per minute ... |
1906.08238 | Sebastian Salassi | Sebastian Salassi, Ester Canepa, Riccardo Ferrando and Giulia Rossi | Anionic nanoparticle-lipid membrane interactions: the protonation of
anionic ligands at the membrane surface reduces membrane disruption | null | RSC Adv., 2019, 9, 13992 | 10.1039/c9ra02462j | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical
tools with applications to diagnosis and therapy, thanks to their
biocompatibility and versatility. Here we show how the NP surface
functionalization can drive the mechanism of interaction with lipid membranes.
In particular, we show that the sp... | [
{
"created": "Thu, 30 May 2019 13:14:28 GMT",
"version": "v1"
}
] | 2019-06-20 | [
[
"Salassi",
"Sebastian",
""
],
[
"Canepa",
"Ester",
""
],
[
"Ferrando",
"Riccardo",
""
],
[
"Rossi",
"Giulia",
""
]
] | Monolayer-protected gold nanoparticles (Au NPs) are promising biomedical tools with applications to diagnosis and therapy, thanks to their biocompatibility and versatility. Here we show how the NP surface functionalization can drive the mechanism of interaction with lipid membranes. In particular, we show that the spon... |
q-bio/0605003 | Zhao Jing | Jing Zhao, Hong Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li | Hierarchical modularity of nested bow-ties in metabolic networks | 26 pages, 9 figures | BMC Bioinformatics 2006, 7:386 | null | null | q-bio.MN | null | The exploration of the structural topology and the organizing principles of
genome-based large-scale metabolic networks is essential for studying possible
relations between structure and functionality of metabolic networks.
Topological analysis of graph models has often been applied to study the
structural characteri... | [
{
"created": "Sun, 30 Apr 2006 05:43:36 GMT",
"version": "v1"
},
{
"created": "Thu, 31 Aug 2006 12:20:53 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Zhao",
"Jing",
""
],
[
"Yu",
"Hong",
""
],
[
"Luo",
"Jian-Hua",
""
],
[
"Cao",
"Zhi-Wei",
""
],
[
"Li",
"Yi-Xue",
""
]
] | The exploration of the structural topology and the organizing principles of genome-based large-scale metabolic networks is essential for studying possible relations between structure and functionality of metabolic networks. Topological analysis of graph models has often been applied to study the structural characterist... |
1308.5342 | Michael Harvey | Brian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C.
Glenn, Robb T. Brumfield | Target capture and massively parallel sequencing of ultraconserved
elements (UCEs) for comparative studies at shallow evolutionary time scales | 53 pages, 2 tables, 4 figures, 5 supplemental tables, 11 supplemental
figures | (2014) Systematic Biology 63: 83-95 | 10.1093/sysbio/syt061 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Comparative genetic studies of non-model organisms are transforming rapidly
due to major advances in sequencing technology. A limiting factor in these
studies has been the identification and screening of orthologous loci across an
evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic
markers t... | [
{
"created": "Sat, 24 Aug 2013 14:56:21 GMT",
"version": "v1"
}
] | 2017-03-28 | [
[
"Smith",
"Brian Tilston",
""
],
[
"Harvey",
"Michael G.",
""
],
[
"Faircloth",
"Brant C.",
""
],
[
"Glenn",
"Travis C.",
""
],
[
"Brumfield",
"Robb T.",
""
]
] | Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers tar... |
1611.04425 | Yuan Zhi Pan | Xue Lan Liao, Guo Qin Wen, Qing Lin Liu, Xue Yang Li Meng Xi Wu and
Yuan Zhi Pan | The Drought-Stress Response of a Drought Resistant Impatiens Processed
in PEG-6000 Solution in a Simulation Test | 19 pages,6 figures,1 table | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Premise of the Study: Impatiens is a commonly seen garden flower, renowned
for its strong adaptability and long history of cultivation. However, seldom
has any research touched on its physiological resistance mechanism. In this
experiment, the impatiens is selected from those which experienced aerospace
mutation and ... | [
{
"created": "Mon, 14 Nov 2016 15:46:26 GMT",
"version": "v1"
}
] | 2016-11-15 | [
[
"Liao",
"Xue Lan",
""
],
[
"Wen",
"Guo Qin",
""
],
[
"Liu",
"Qing Lin",
""
],
[
"Wu",
"Xue Yang Li Meng Xi",
""
],
[
"Pan",
"Yuan Zhi",
""
]
] | Premise of the Study: Impatiens is a commonly seen garden flower, renowned for its strong adaptability and long history of cultivation. However, seldom has any research touched on its physiological resistance mechanism. In this experiment, the impatiens is selected from those which experienced aerospace mutation and th... |
2404.16769 | Martina Conte | Giulia Chiari, Martina Conte, and Marcello Delitala | Multi-scale modeling of Snail-mediated response to hypoxia in tumor
progression | 30 pages, 8 figures | null | null | null | q-bio.CB | http://creativecommons.org/licenses/by/4.0/ | Tumor cell migration within the microenvironment is a crucial aspect for
cancer progression and, in this context, hypoxia has a significant role. An
inadequate oxygen supply acts as an environmental stressor inducing migratory
bias and phenotypic changes. In this paper, we propose a novel multi-scale
mathematical mod... | [
{
"created": "Thu, 25 Apr 2024 17:23:29 GMT",
"version": "v1"
}
] | 2024-04-26 | [
[
"Chiari",
"Giulia",
""
],
[
"Conte",
"Martina",
""
],
[
"Delitala",
"Marcello",
""
]
] | Tumor cell migration within the microenvironment is a crucial aspect for cancer progression and, in this context, hypoxia has a significant role. An inadequate oxygen supply acts as an environmental stressor inducing migratory bias and phenotypic changes. In this paper, we propose a novel multi-scale mathematical model... |
1704.05407 | Sergei Maslov | Sergei Maslov and Kim Sneppen | Severe population collapses and species extinctions in multi-host
epidemic dynamics | null | Phys. Rev. E 96, 022412 (2017) | 10.1103/PhysRevE.96.022412 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most infectious diseases including more than half of known human pathogens
are not restricted to just one host, yet much of the mathematical modeling of
infections has been limited to a single species. We investigate consequences of
a single epidemic propagating in multiple species and compare and contrast it
with th... | [
{
"created": "Tue, 18 Apr 2017 16:12:25 GMT",
"version": "v1"
}
] | 2017-08-30 | [
[
"Maslov",
"Sergei",
""
],
[
"Sneppen",
"Kim",
""
]
] | Most infectious diseases including more than half of known human pathogens are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a single epidemic propagating in multiple species and compare and contrast it with the ... |
2303.00933 | Fabian Filipp | Fabian V. Filipp | Spatial cancer systems biology resolves heterotypic interactions and
identifies disruption of spatial hierarchy as a pathological driver event | 7 pages, 2 figures | null | null | null | q-bio.GN q-bio.CB q-bio.MN q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Spatially annotated single-cell datasets provide unprecedented opportunities
to dissect cell-cell communication in development and disease. Heterotypic
signaling includes interactions between different cell types and is well
established in tissue development and spatial organization. Epithelial
organization requires ... | [
{
"created": "Thu, 2 Mar 2023 03:14:06 GMT",
"version": "v1"
}
] | 2023-03-03 | [
[
"Filipp",
"Fabian V.",
""
]
] | Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in tissue development and spatial organization. Epithelial organization requires se... |
1912.05370 | Yves Dumont | Michael Chapwanya, Yves Dumont (UMR AMAP) | Application of Mathematical Epidemiology to crop vector-borne diseases.
The cassava mosaic virus disease case | Infectious Diseases and our Planet, In press | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this chapter, an application of Mathematical Epidemiology to crop
vector-borne diseases is presented to investigate the interactions between
crops, vectors, and virus. The main illustrative example is the cassava mosaic
disease (CMD). The CMD virus has two routes of infection: through vectors and
also through infe... | [
{
"created": "Wed, 11 Dec 2019 14:56:29 GMT",
"version": "v1"
}
] | 2019-12-12 | [
[
"Chapwanya",
"Michael",
"",
"UMR AMAP"
],
[
"Dumont",
"Yves",
"",
"UMR AMAP"
]
] | In this chapter, an application of Mathematical Epidemiology to crop vector-borne diseases is presented to investigate the interactions between crops, vectors, and virus. The main illustrative example is the cassava mosaic disease (CMD). The CMD virus has two routes of infection: through vectors and also through infect... |
2112.10068 | Somali Chaterji | Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik,
and Somali Chaterji | Lerna: Transformer Architectures for Configuring Error Correction Tools
for Short- and Long-Read Genome Sequencing | 26 pages, 5 figures, 10 tables. Accepted to BMC Bioinformatics | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by/4.0/ | Sequencing technologies are prone to errors, making error correction (EC)
necessary for downstream applications. EC tools need to be manually configured
for optimal performance. We find that the optimal parameters (e.g., k-mer size)
are both tool- and dataset-dependent. Moreover, evaluating the performance
(i.e., Ali... | [
{
"created": "Sun, 19 Dec 2021 05:59:26 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Sharma",
"Atul",
""
],
[
"Jain",
"Pranjal",
""
],
[
"Mahgoub",
"Ashraf",
""
],
[
"Zhou",
"Zihan",
""
],
[
"Mahadik",
"Kanak",
""
],
[
"Chaterji",
"Somali",
""
]
] | Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Align... |
1210.5497 | Mary Rorick | David V. Foster, Mary M. Rorick, Tanja Gesell, Laura Feeney and Jacob
G. Foster | Dynamic Landscapes: A Model of Context and Contingency in Evolution | null | null | null | null | q-bio.PE q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The basic mechanics of evolution have been understood since Darwin. But
debate continues over whether macroevolutionary phenomena are driven primary by
the fitness structure of genotype space or by ecological interaction. In this
paper we propose a simple, abstract model capturing some key features of
fitness-landsca... | [
{
"created": "Fri, 19 Oct 2012 18:49:51 GMT",
"version": "v1"
}
] | 2012-10-22 | [
[
"Foster",
"David V.",
""
],
[
"Rorick",
"Mary M.",
""
],
[
"Gesell",
"Tanja",
""
],
[
"Feeney",
"Laura",
""
],
[
"Foster",
"Jacob G.",
""
]
] | The basic mechanics of evolution have been understood since Darwin. But debate continues over whether macroevolutionary phenomena are driven primary by the fitness structure of genotype space or by ecological interaction. In this paper we propose a simple, abstract model capturing some key features of fitness-landscape... |
2003.09348 | Pradeep Sarin | Ishant Tiwari, Pradeep Sarin, Punit Parmananda | Predictive modelling of disease propagation in a mobile, connected
community | Updated with full model calculations. Submited to PRL | null | 10.1063/5.0021113 | null | q-bio.PE nlin.CG physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present numerical results obtained from the modelling of a stochastic,
highly connected and mobile community. The spread of attributes like health,
disease among the community members is simulated using cellular automata on a
planar 2 dimensional bounded space. With remarkably few assumptions, we are
able to predi... | [
{
"created": "Thu, 19 Mar 2020 16:08:29 GMT",
"version": "v1"
},
{
"created": "Fri, 1 May 2020 09:13:04 GMT",
"version": "v2"
}
] | 2020-08-26 | [
[
"Tiwari",
"Ishant",
""
],
[
"Sarin",
"Pradeep",
""
],
[
"Parmananda",
"Punit",
""
]
] | We present numerical results obtained from the modelling of a stochastic, highly connected and mobile community. The spread of attributes like health, disease among the community members is simulated using cellular automata on a planar 2 dimensional bounded space. With remarkably few assumptions, we are able to predict... |
2302.05789 | Ivana Pajic-Lijakovic Dr. | Ivana Pajic-Lijakovic and Milan Milivojevic | Physics of collective cell migration | 21 pages, 3 figures, 2 tables | null | null | null | q-bio.CB q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Movement of cell clusters along extracellular matrices (ECM) during tissue
development, wound healing, and early stage of cancer invasion involve various
inter-connected migration modes such as: (1) cell movement within clusters, (2)
cluster extension (wetting) and compression (de-wetting), and (3) directional
cluste... | [
{
"created": "Sat, 11 Feb 2023 21:47:57 GMT",
"version": "v1"
}
] | 2023-02-14 | [
[
"Pajic-Lijakovic",
"Ivana",
""
],
[
"Milivojevic",
"Milan",
""
]
] | Movement of cell clusters along extracellular matrices (ECM) during tissue development, wound healing, and early stage of cancer invasion involve various inter-connected migration modes such as: (1) cell movement within clusters, (2) cluster extension (wetting) and compression (de-wetting), and (3) directional cluster ... |
1903.10478 | Benjamin Allen | Benjamin Allen, Gabor Lippner, Martin A. Nowak | Evolutionary Games on Isothermal Graphs | 40 pages, 6 figures | null | 10.1038/s41467-019-13006-7 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Population structure affects the outcome of natural selection. Static
population structures can be described by graphs, where individuals occupy the
nodes, and interactions occur along the edges. General conditions for
evolutionary success on any weighted graph were recently derived, for weak
selection, in terms of c... | [
{
"created": "Mon, 25 Mar 2019 17:26:34 GMT",
"version": "v1"
}
] | 2020-01-08 | [
[
"Allen",
"Benjamin",
""
],
[
"Lippner",
"Gabor",
""
],
[
"Nowak",
"Martin A.",
""
]
] | Population structure affects the outcome of natural selection. Static population structures can be described by graphs, where individuals occupy the nodes, and interactions occur along the edges. General conditions for evolutionary success on any weighted graph were recently derived, for weak selection, in terms of coa... |
2311.07791 | Jesse Meyer | Yuming Jiang, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin
A. Neely, Germ\'an L. Rosano, Norbert Volkmar, Amanda Momenzadeh, Trenton M.
Peters-Clarke, Susan B. Egbert, Simion Kreimer, Emma H. Doud, Oliver M.
Crook, Amit Kumar Yadav, Muralidharan Vanuopadath, Mart\'in L. Mayta, Anna G.
Duboff, Nicholas... | Comprehensive Overview of Bottom-up Proteomics using Mass Spectrometry | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Proteomics is the large scale study of protein structure and function from
biological systems through protein identification and quantification. "Shotgun
proteomics" or "bottom-up proteomics" is the prevailing strategy, in which
proteins are hydrolyzed into peptides that are analyzed by mass spectrometry.
Proteomics ... | [
{
"created": "Mon, 13 Nov 2023 22:58:30 GMT",
"version": "v1"
}
] | 2023-11-15 | [
[
"Jiang",
"Yuming",
""
],
[
"Rex",
"Devasahayam Arokia Balaya",
""
],
[
"Schuster",
"Dina",
""
],
[
"Neely",
"Benjamin A.",
""
],
[
"Rosano",
"Germán L.",
""
],
[
"Volkmar",
"Norbert",
""
],
[
"Momenzadeh",
"Ama... | Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics st... |
1807.00215 | Peter Clote | Peter Clote | On the scale-free nature of RNA secondary structure networks | 4 tables, 11 figures, 26 pages | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A network is scale-free if its connectivity density function is proportional
to a power-law distribution. Scale-free networks may provide an explanation for
the robustness observed in certain physical and biological phenomena, since the
presence of a few highly connected hub nodes and a large number of small-
degree ... | [
{
"created": "Sat, 30 Jun 2018 18:12:14 GMT",
"version": "v1"
}
] | 2018-07-03 | [
[
"Clote",
"Peter",
""
]
] | A network is scale-free if its connectivity density function is proportional to a power-law distribution. Scale-free networks may provide an explanation for the robustness observed in certain physical and biological phenomena, since the presence of a few highly connected hub nodes and a large number of small- degree no... |
2403.00033 | Jun-En Ding | Jun-En Ding, Shihao Yang, Anna Zilverstand, and Feng Liu | Identification of Craving Maps among Marijuana Users via the Analysis of
Functional Brain Networks with High-Order Attention Graph Neural Networks | null | null | null | null | q-bio.NC cs.LG eess.SP | http://creativecommons.org/licenses/by/4.0/ | The excessive consumption of marijuana can induce substantial psychological
and social consequences. In this investigation, we propose an elucidative
framework termed high-order graph attention neural networks (HOGANN) for the
classification of Marijuana addiction, coupled with an analysis of localized
brain network ... | [
{
"created": "Thu, 29 Feb 2024 04:01:38 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Mar 2024 15:00:58 GMT",
"version": "v2"
},
{
"created": "Sun, 17 Mar 2024 03:59:44 GMT",
"version": "v3"
},
{
"created": "Tue, 26 Mar 2024 04:58:01 GMT",
"version": "v4"
}
] | 2024-03-27 | [
[
"Ding",
"Jun-En",
""
],
[
"Yang",
"Shihao",
""
],
[
"Zilverstand",
"Anna",
""
],
[
"Liu",
"Feng",
""
]
] | The excessive consumption of marijuana can induce substantial psychological and social consequences. In this investigation, we propose an elucidative framework termed high-order graph attention neural networks (HOGANN) for the classification of Marijuana addiction, coupled with an analysis of localized brain network co... |
1109.4160 | Monica Skoge | Monica Skoge, Yigal Meir, and Ned S. Wingreen | Dynamics of cooperativity in chemical sensing among cell-surface
receptors | 5 pages, 2 figures | null | 10.1103/PhysRevLett.107.178101 | Phys. Rev. Lett. 107 (2011) 178101 | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperative interactions among sensory receptors provide a general mechanism
to increase the sensitivity of signal transduction. In particular, bacterial
chemotaxis receptors interact cooperatively to produce an ultrasensitive
response to chemoeffector concentrations. However, cooperativity between
receptors in large... | [
{
"created": "Mon, 19 Sep 2011 20:11:36 GMT",
"version": "v1"
}
] | 2011-10-19 | [
[
"Skoge",
"Monica",
""
],
[
"Meir",
"Yigal",
""
],
[
"Wingreen",
"Ned S.",
""
]
] | Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to chemoeffector concentrations. However, cooperativity between receptors in large m... |
2012.02113 | Tom Leinster | Tom Leinster | Entropy and Diversity: The Axiomatic Approach | Book, viii + 442 pages. Version 3: small number of minor corrections | Cambridge University Press 2021, ISBN 9781108965576 (paperback),
9781108832700 (hardback) | null | null | q-bio.PE cs.IT math.CA math.CT math.IT q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This book brings new mathematical rigour to the ongoing vigorous debate on
how to quantify biological diversity. The question "what is diversity?" has
surprising mathematical depth, and breadth too: this book involves parts of
mathematics ranging from information theory, functional equations and
probability theory to... | [
{
"created": "Thu, 3 Dec 2020 17:47:44 GMT",
"version": "v1"
},
{
"created": "Tue, 22 Jun 2021 18:51:20 GMT",
"version": "v2"
},
{
"created": "Sat, 22 Oct 2022 22:46:41 GMT",
"version": "v3"
}
] | 2022-10-25 | [
[
"Leinster",
"Tom",
""
]
] | This book brings new mathematical rigour to the ongoing vigorous debate on how to quantify biological diversity. The question "what is diversity?" has surprising mathematical depth, and breadth too: this book involves parts of mathematics ranging from information theory, functional equations and probability theory to c... |
2005.11201 | Jos\'e-Miguel Ponciano PhD | Jos\'e Miguel Ponciano and Juan Adolfo Ponciano and Juan Pablo G\'omez
and Robert D. Holt and Jason K. Blackburn | Poverty levels, societal and individual heterogeneities explain the
SARS-CoV-2 pandemic growth in Latin America | 22 pages, 5 figures, Supplementary Material not uploaded | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but
poverty and weak public health institutions hamper gathering the kind of
refined data needed to inform classical SEIR models of epidemics. We present an
alternative approach that draws on advances in statistical ecology and
conservation biol... | [
{
"created": "Fri, 22 May 2020 14:23:42 GMT",
"version": "v1"
}
] | 2020-05-25 | [
[
"Ponciano",
"José Miguel",
""
],
[
"Ponciano",
"Juan Adolfo",
""
],
[
"Gómez",
"Juan Pablo",
""
],
[
"Holt",
"Robert D.",
""
],
[
"Blackburn",
"Jason K.",
""
]
] | Latin America is experiencing severe impacts of the SARS-CoV-2 pandemic, but poverty and weak public health institutions hamper gathering the kind of refined data needed to inform classical SEIR models of epidemics. We present an alternative approach that draws on advances in statistical ecology and conservation biolog... |
2010.15055 | Sara Zein | Sara A. Zein, Marie-Claude Bordage, Ziad Francis, Giovanni Macetti,
Alessandro Genoni, Claude Dal Cappello, Wook-Geun Shin, Sebastien Incerti | Electron transport in DNA bases: An extension of the Geant4-DNA Monte
Carlo toolkit | 23 pages, 12 figures, 1 table | null | 10.1016/j.nimb.2020.11.021 | null | q-bio.BM physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to
include electron interactions with the four DNA bases using a set of cross
sections recently implemented in Geant-DNA CPA100 models and available for
liquid water. Electron interaction cross sections for elastic scattering,
ionisation, and el... | [
{
"created": "Wed, 21 Oct 2020 17:39:06 GMT",
"version": "v1"
}
] | 2021-02-24 | [
[
"Zein",
"Sara A.",
""
],
[
"Bordage",
"Marie-Claude",
""
],
[
"Francis",
"Ziad",
""
],
[
"Macetti",
"Giovanni",
""
],
[
"Genoni",
"Alessandro",
""
],
[
"Cappello",
"Claude Dal",
""
],
[
"Shin",
"Wook-Geun",
... | The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water. Electron interaction cross sections for elastic scattering, ionisation, and elec... |
1210.0104 | Andrew Mugler | Andrew Mugler, Pieter Rein ten Wolde | The macroscopic effects of microscopic heterogeneity | 20 pages, 5 figures. To appear in Advances in Chemical Physics | Advances in Chemical Physics (2013) 153, 373-396 | 10.1002/9781118571767.ch5 | null | q-bio.MN q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Over the past decade, advances in super-resolution microscopy and
particle-based modeling have driven an intense interest in investigating
spatial heterogeneity at the level of single molecules in cells. Remarkably, it
is becoming clear that spatiotemporal correlations between just a few molecules
can have profound e... | [
{
"created": "Sat, 29 Sep 2012 13:22:21 GMT",
"version": "v1"
},
{
"created": "Wed, 3 Oct 2012 09:41:24 GMT",
"version": "v2"
}
] | 2013-11-19 | [
[
"Mugler",
"Andrew",
""
],
[
"Wolde",
"Pieter Rein ten",
""
]
] | Over the past decade, advances in super-resolution microscopy and particle-based modeling have driven an intense interest in investigating spatial heterogeneity at the level of single molecules in cells. Remarkably, it is becoming clear that spatiotemporal correlations between just a few molecules can have profound eff... |
2310.12005 | Morten Gram Pedersen | Francesco Montefusco and Morten Gram Pedersen | Geometric slow-fast analysis of a hybrid pituitary cell model with
stochastic ion channel dynamics | 15 pages, 8 figures | null | null | null | q-bio.QM math.DS | http://creativecommons.org/licenses/by-nc-sa/4.0/ | To obtain explicit understanding of the behavior of dynamical systems,
geometrical methods and slow-fast analysis have proved to be highly useful.
Such methods are standard for smooth dynamical systems, and increasingly used
for continuous, non-smooth dynamical systems. However, they are much less used
for random dyn... | [
{
"created": "Wed, 18 Oct 2023 14:39:34 GMT",
"version": "v1"
}
] | 2023-10-19 | [
[
"Montefusco",
"Francesco",
""
],
[
"Pedersen",
"Morten Gram",
""
]
] | To obtain explicit understanding of the behavior of dynamical systems, geometrical methods and slow-fast analysis have proved to be highly useful. Such methods are standard for smooth dynamical systems, and increasingly used for continuous, non-smooth dynamical systems. However, they are much less used for random dynam... |
q-bio/0411014 | Arnaud Buhot | Avraham Halperin, Arnaud Buhot, and Ekaterina B. Zhulina | Hybridization Isotherms of DNA Microarrays and the Quantification of
Mutation Studies | To be published in Clinical Chemistry Nov. 2004. 15 pages and 8
figures | Clin. Chem. 50, 2254-2262, (2004). | null | null | q-bio.BM cond-mat.soft q-bio.GN | null | Background: Diagnostic DNA arrays for detection of point mutations as markers
for cancer usually function in the presence of a large excess of wild type DNA.
This excess can give rise to false positives due to competitive hybridization
of the wild type target at the mutation spot. The analysis of the DNA array
data i... | [
{
"created": "Wed, 3 Nov 2004 14:19:34 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Halperin",
"Avraham",
""
],
[
"Buhot",
"Arnaud",
""
],
[
"Zhulina",
"Ekaterina B.",
""
]
] | Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of the wild type target at the mutation spot. The analysis of the DNA array data is ... |
2312.01272 | Hongyan Du | Hongyan Du, Guo-Wei Wei, Tingjun Hou | Multiscale Topology in Interactomic Network: From Transcriptome to
Antiaddiction Drug Repurposing | null | null | null | null | q-bio.BM cs.LG q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The escalating drug addiction crisis in the United States underscores the
urgent need for innovative therapeutic strategies. This study embarked on an
innovative and rigorous strategy to unearth potential drug repurposing
candidates for opioid and cocaine addiction treatment, bridging the gap between
transcriptomic d... | [
{
"created": "Sun, 3 Dec 2023 04:01:38 GMT",
"version": "v1"
}
] | 2023-12-05 | [
[
"Du",
"Hongyan",
""
],
[
"Wei",
"Guo-Wei",
""
],
[
"Hou",
"Tingjun",
""
]
] | The escalating drug addiction crisis in the United States underscores the urgent need for innovative therapeutic strategies. This study embarked on an innovative and rigorous strategy to unearth potential drug repurposing candidates for opioid and cocaine addiction treatment, bridging the gap between transcriptomic dat... |
2308.12354 | Nikolai Schapin | Nikolai Schapin, Maciej Majewski, Alejandro Varela, Carlos Arroniz,
Gianni De Fabritiis | Machine Learning Small Molecule Properties in Drug Discovery | 46 pages, 1 figure | null | null | null | q-bio.BM cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Machine learning (ML) is a promising approach for predicting small molecule
properties in drug discovery. Here, we provide a comprehensive overview of
various ML methods introduced for this purpose in recent years. We review a
wide range of properties, including binding affinities, solubility, and ADMET
(Absorption, ... | [
{
"created": "Wed, 2 Aug 2023 22:18:41 GMT",
"version": "v1"
}
] | 2023-08-25 | [
[
"Schapin",
"Nikolai",
""
],
[
"Majewski",
"Maciej",
""
],
[
"Varela",
"Alejandro",
""
],
[
"Arroniz",
"Carlos",
""
],
[
"De Fabritiis",
"Gianni",
""
]
] | Machine learning (ML) is a promising approach for predicting small molecule properties in drug discovery. Here, we provide a comprehensive overview of various ML methods introduced for this purpose in recent years. We review a wide range of properties, including binding affinities, solubility, and ADMET (Absorption, Di... |
q-bio/0512005 | Wilfred Ndifon | W. Ndifon and A. Nkwanta | An RNA foldability metric; implications for the design of rapidly
foldable RNA sequences | To appear in Biophysical Chemistry | null | 10.1016/j.bpc.2005.11.012 | null | q-bio.BM physics.bio-ph | null | Evidence is presented suggesting, for the first time, that the protein
foldability metric sigma=(T_theta - T_f)/T_theta, where T_theta and T_f are,
respectively, the collapse and folding transition temperatures, could be used
also to measure the foldability of RNA sequences. The importance of sigma is
discussed in th... | [
{
"created": "Fri, 2 Dec 2005 00:54:57 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Ndifon",
"W.",
""
],
[
"Nkwanta",
"A.",
""
]
] | Evidence is presented suggesting, for the first time, that the protein foldability metric sigma=(T_theta - T_f)/T_theta, where T_theta and T_f are, respectively, the collapse and folding transition temperatures, could be used also to measure the foldability of RNA sequences. The importance of sigma is discussed in the ... |
1902.05235 | Shunfu Mao | Shunfu Mao and Yihan Jiang and Edwin Basil Mathew and Sreeram Kannan | BOAssembler: a Bayesian Optimization Framework to Improve RNA-Seq
Assembly Performance | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | High throughput sequencing of RNA (RNA-Seq) can provide us with millions of
short fragments of RNA transcripts from a sample. How to better recover the
original RNA transcripts from those fragments (RNA-Seq assembly) is still a
difficult task. For example, RNA-Seq assembly tools typically require
hyper-parameter tuni... | [
{
"created": "Thu, 14 Feb 2019 06:18:34 GMT",
"version": "v1"
}
] | 2019-02-15 | [
[
"Mao",
"Shunfu",
""
],
[
"Jiang",
"Yihan",
""
],
[
"Mathew",
"Edwin Basil",
""
],
[
"Kannan",
"Sreeram",
""
]
] | High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult task. For example, RNA-Seq assembly tools typically require hyper-parameter tuning... |
1206.1401 | Jesus Fernandez | Jes\'us Fern\'andez-S\'anchez, Jeremy G. Sumner, Peter D. Jarvis, and
Michael D. Woodhams | Lie Markov models with purine/pyrimidine symmetry | 32 pages | null | null | null | q-bio.PE math.GR math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Continuous-time Markov chains are a standard tool in phylogenetic inference.
If homogeneity is assumed, the chain is formulated by specifying
time-independent rates of substitutions between states in the chain. In
applications, there are usually extra constraints on the rates, depending on
the situation. If a model i... | [
{
"created": "Thu, 7 Jun 2012 05:08:38 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Jun 2013 15:14:45 GMT",
"version": "v2"
}
] | 2013-06-26 | [
[
"Fernández-Sánchez",
"Jesús",
""
],
[
"Sumner",
"Jeremy G.",
""
],
[
"Jarvis",
"Peter D.",
""
],
[
"Woodhams",
"Michael D.",
""
]
] | Continuous-time Markov chains are a standard tool in phylogenetic inference. If homogeneity is assumed, the chain is formulated by specifying time-independent rates of substitutions between states in the chain. In applications, there are usually extra constraints on the rates, depending on the situation. If a model is ... |
1605.08001 | Hande Topa | Hande Topa and Antti Honkela | Analysis of differential splicing suggests different modes of short-term
splicing regulation | 20 pages, 5 figures. To be published in the conference proceedings of
Intelligent Systems for Molecular Biology (ISMB) 2016 | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Motivation: Alternative splicing is an important mechanism in which the
regions of pre-mRNAs are differentially joined in order to form different
transcript isoforms. Alternative splicing is involved in the regulation of
normal physiological functions but also linked to the development of diseases
such as cancer. We ... | [
{
"created": "Wed, 25 May 2016 18:43:54 GMT",
"version": "v1"
}
] | 2016-05-26 | [
[
"Topa",
"Hande",
""
],
[
"Honkela",
"Antti",
""
]
] | Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal physiological functions but also linked to the development of diseases such as cancer. We an... |
2102.12860 | Laura Wadkin PhD | L E Wadkin, S Orozco-Fuentes, I Neganova, M Lako, N G Parker, A
Shukurov | A mathematical modelling framework for the regulation of intra-cellular
OCT4 in human pluripotent stem cells | null | null | null | null | q-bio.SC physics.bio-ph q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Human pluripotent stem cells (hPSCs) have promising clinical applications in
regenerative medicine, drug-discovery and personalised medicine due to their
potential to differentiate into all cell types, a property know as
pluripotency. A deeper understanding of how pluripotency is regulated is
required to assist in co... | [
{
"created": "Thu, 25 Feb 2021 13:58:12 GMT",
"version": "v1"
}
] | 2021-02-26 | [
[
"Wadkin",
"L E",
""
],
[
"Orozco-Fuentes",
"S",
""
],
[
"Neganova",
"I",
""
],
[
"Lako",
"M",
""
],
[
"Parker",
"N G",
""
],
[
"Shukurov",
"A",
""
]
] | Human pluripotent stem cells (hPSCs) have promising clinical applications in regenerative medicine, drug-discovery and personalised medicine due to their potential to differentiate into all cell types, a property know as pluripotency. A deeper understanding of how pluripotency is regulated is required to assist in cont... |
1602.08802 | Randal Olson | Randal S. Olson, Arend Hintze, Fred C. Dyer, Jason H. Moore, Christoph
Adami | Exploring the coevolution of predator and prey morphology and behavior | 8 pages, 8 figures, submitted to Artificial Life 2016 conference | Proceedings Artificial Life 15 (C. Gershenson, T. Froese, J.M.
Sisqueiros, W. Aguilar, E.J. Izquierdo, H. Sayama, eds.) MIT Press
(Cambridge, MA, 2016), pp. 250-258 | 10.7551/978-0-262-33936-0-ch045 | null | q-bio.PE cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A common idiom in biology education states, "Eyes in the front, the animal
hunts. Eyes on the side, the animal hides." In this paper, we explore one
possible explanation for why predators tend to have forward-facing, high-acuity
visual systems. We do so using an agent-based computational model of evolution,
where pre... | [
{
"created": "Mon, 29 Feb 2016 02:48:19 GMT",
"version": "v1"
}
] | 2016-12-07 | [
[
"Olson",
"Randal S.",
""
],
[
"Hintze",
"Arend",
""
],
[
"Dyer",
"Fred C.",
""
],
[
"Moore",
"Jason H.",
""
],
[
"Adami",
"Christoph",
""
]
] | A common idiom in biology education states, "Eyes in the front, the animal hunts. Eyes on the side, the animal hides." In this paper, we explore one possible explanation for why predators tend to have forward-facing, high-acuity visual systems. We do so using an agent-based computational model of evolution, where preda... |
2106.03663 | Raffaella Mulas | Raffaella Mulas and Michael J. Casey | Estimating cellular redundancy in networks of genetic expression | null | Mathematical Biosciences (2021) | 10.1016/j.mbs.2021.108713 | null | q-bio.MN math.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Networks of genetic expression can be modelled by hypergraphs with the
additional structure that real coefficients are given to each vertex-edge
incidence. The spectra, i.e. the multiset of the eigenvalues, of such
hypergraphs, are known to encode structural information of the data. We show
how these spectra can be u... | [
{
"created": "Mon, 7 Jun 2021 14:41:23 GMT",
"version": "v1"
},
{
"created": "Thu, 23 Sep 2021 06:34:41 GMT",
"version": "v2"
}
] | 2021-09-24 | [
[
"Mulas",
"Raffaella",
""
],
[
"Casey",
"Michael J.",
""
]
] | Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to encode structural information of the data. We show how these spectra can be use... |
1109.3351 | Ulrich Gerland | Nico Geisel and Ulrich Gerland | Physical limits on cooperative protein-DNA binding and the kinetics of
combinatorial transcription regulation | manuscript and supplementary material combined into a single
document; to be published in Biophysical Journal | null | 10.1016/j.bpj.2011.08.041 | null | q-bio.BM physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Much of the complexity observed in gene regulation originates from
cooperative protein-DNA binding. While studies of the target search of proteins
for their specific binding sites on the DNA have revealed design principles for
the quantitative characteristics of protein-DNA interactions, no such
principles are known ... | [
{
"created": "Thu, 15 Sep 2011 13:37:40 GMT",
"version": "v1"
}
] | 2015-05-30 | [
[
"Geisel",
"Nico",
""
],
[
"Gerland",
"Ulrich",
""
]
] | Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative characteristics of protein-DNA interactions, no such principles are known fo... |
1604.04883 | Steven Frank | Steven A. Frank | The invariances of power law size distributions | Added appendix discussing the lognormal distribution, updated to
match version 2 of published version at F1000Research | F1000Research 2016, 5:2074 | 10.12688/f1000research.9452.2 | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | Size varies. Small things are typically more frequent than large things. The
logarithm of frequency often declines linearly with the logarithm of size. That
power law relation forms one of the common patterns of nature. Why does the
complexity of nature reduce to such a simple pattern? Why do things as
different as t... | [
{
"created": "Sun, 17 Apr 2016 15:23:53 GMT",
"version": "v1"
},
{
"created": "Thu, 25 Aug 2016 20:23:55 GMT",
"version": "v2"
},
{
"created": "Mon, 7 Nov 2016 18:34:25 GMT",
"version": "v3"
}
] | 2016-11-08 | [
[
"Frank",
"Steven A.",
""
]
] | Size varies. Small things are typically more frequent than large things. The logarithm of frequency often declines linearly with the logarithm of size. That power law relation forms one of the common patterns of nature. Why does the complexity of nature reduce to such a simple pattern? Why do things as different as tre... |
1805.04329 | Matteo Cinelli | M. Cinelli, and I. Echegoyen, and M. Oliveira, and S. Orellana, and T.
Gili | Altered Modularity and Disproportional Integration in Functional
Networks are Markers of Abnormal Brain Organization in Schizophrenia | This work is the output of the Complexity72h workshop, held at IMT
School in Lucca, 7-11 May 2018. https://complexity72h.weebly.com/ | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modularity plays an important role in brain networks' architecture and
influences its dynamics and the ability to integrate and segregate different
modules of cerebral regions. Alterations in community structure are associated
with several clinical disorders, specially schizophrenia, although its time
evolution is no... | [
{
"created": "Fri, 11 May 2018 11:25:30 GMT",
"version": "v1"
}
] | 2018-05-14 | [
[
"Cinelli",
"M.",
""
],
[
"Echegoyen",
"I.",
""
],
[
"Oliveira",
"M.",
""
],
[
"Orellana",
"S.",
""
],
[
"Gili",
"T.",
""
]
] | Modularity plays an important role in brain networks' architecture and influences its dynamics and the ability to integrate and segregate different modules of cerebral regions. Alterations in community structure are associated with several clinical disorders, specially schizophrenia, although its time evolution is not ... |
1809.04877 | Fereshteh Lagzi | Fereshteh Lagzi, Fatihcan M. Atay, Stefan Rotter | Bifurcation analysis of the dynamics of interacting populations of
spiking networks | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the collective dynamics of hierarchically structured networks of
densely connected spiking neurons. These networks of sub-networks may represent
interactions between cell assemblies or different nuclei in the brain. The
dynamical activity pattern that results from these interactions depends on the
strength... | [
{
"created": "Thu, 13 Sep 2018 10:29:29 GMT",
"version": "v1"
}
] | 2018-09-14 | [
[
"Lagzi",
"Fereshteh",
""
],
[
"Atay",
"Fatihcan M.",
""
],
[
"Rotter",
"Stefan",
""
]
] | We analyze the collective dynamics of hierarchically structured networks of densely connected spiking neurons. These networks of sub-networks may represent interactions between cell assemblies or different nuclei in the brain. The dynamical activity pattern that results from these interactions depends on the strength o... |
2004.14482 | Simon Wood | Simon N. Wood, Ernst C. Wit, Matteo Fasiolo and Peter J. Green | COVID-19 and the difficulty of inferring epidemiological parameters from
clinical data | Version accepted by the Lancet Infectious Diseases. See previous
version for less terse presentation | null | 10.1016/S1473-3099(20)30437-0 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Knowing the infection fatality ratio (IFR) is of crucial importance for
evidence-based epidemic management: for immediate planning; for balancing the
life years saved against the life years lost due to the consequences of
management; and for evaluating the ethical issues associated with the tacit
willingness to pay s... | [
{
"created": "Tue, 28 Apr 2020 14:46:27 GMT",
"version": "v1"
},
{
"created": "Tue, 5 May 2020 12:43:30 GMT",
"version": "v2"
}
] | 2020-08-11 | [
[
"Wood",
"Simon N.",
""
],
[
"Wit",
"Ernst C.",
""
],
[
"Fasiolo",
"Matteo",
""
],
[
"Green",
"Peter J.",
""
]
] | Knowing the infection fatality ratio (IFR) is of crucial importance for evidence-based epidemic management: for immediate planning; for balancing the life years saved against the life years lost due to the consequences of management; and for evaluating the ethical issues associated with the tacit willingness to pay sub... |
2012.07691 | Thiago B. Burghi | Thiago B. Burghi, Maarten Schoukens, Rodolphe Sepulchre | System identification of biophysical neuronal models | Slightly extended pre-print of the paper to be presented at the 59th
Conference on Decision and Control, held remotely between December 14-18,
2020 | Proceedings of the 2020 59th IEEE Conference on Decision and
Control (CDC), Jeju, South Korea | 10.1109/CDC42340.2020.9304363 | null | q-bio.NC cs.LG cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | After sixty years of quantitative biophysical modeling of neurons, the
identification of neuronal dynamics from input-output data remains a
challenging problem, primarily due to the inherently nonlinear nature of
excitable behaviors. By reformulating the problem in terms of the
identification of an operator with fadi... | [
{
"created": "Mon, 14 Dec 2020 16:41:27 GMT",
"version": "v1"
}
] | 2024-02-29 | [
[
"Burghi",
"Thiago B.",
""
],
[
"Schoukens",
"Maarten",
""
],
[
"Sepulchre",
"Rodolphe",
""
]
] | After sixty years of quantitative biophysical modeling of neurons, the identification of neuronal dynamics from input-output data remains a challenging problem, primarily due to the inherently nonlinear nature of excitable behaviors. By reformulating the problem in terms of the identification of an operator with fading... |
2109.04431 | Alexander Stewart | Mark Jayson Cortez, Alan Eric Akil, Kre\v{s}imir Josi\'c and Alexander
J. Stewart | Incorporating Computational Challenges into a Multidisciplinary Course
on Stochastic Processes | null | null | null | null | q-bio.OT math.HO | http://creativecommons.org/licenses/by/4.0/ | Quantitative methods and mathematical modeling are playing an increasingly
important role across disciplines. As a result, interdisciplinary mathematics
courses are increasing in popularity. However, teaching such courses at an
advanced level can be challenging. Students often arrive with different
mathematical backg... | [
{
"created": "Thu, 9 Sep 2021 17:23:21 GMT",
"version": "v1"
}
] | 2021-09-10 | [
[
"Cortez",
"Mark Jayson",
""
],
[
"Akil",
"Alan Eric",
""
],
[
"Josić",
"Krešimir",
""
],
[
"Stewart",
"Alexander J.",
""
]
] | Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced level can be challenging. Students often arrive with different mathematical backgro... |
2007.14236 | Bruno Golosio | Bruno Golosio, Gianmarco Tiddia, Chiara De Luca, Elena Pastorelli,
Francesco Simula, Pier Stanislao Paolucci | Fast simulations of highly-connected spiking cortical models using GPUs | null | Front. Comput. Neurosci. 15:627620 2021 | 10.3389/fncom.2021.627620 | null | q-bio.NC cs.DC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Over the past decade there has been a growing interest in the development of
parallel hardware systems for simulating large-scale networks of spiking
neurons. Compared to other highly-parallel systems, GPU-accelerated solutions
have the advantage of a relatively low cost and a great versatility, thanks
also to the po... | [
{
"created": "Tue, 28 Jul 2020 13:58:50 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Jul 2020 15:43:02 GMT",
"version": "v2"
},
{
"created": "Mon, 9 Nov 2020 17:13:33 GMT",
"version": "v3"
}
] | 2021-02-22 | [
[
"Golosio",
"Bruno",
""
],
[
"Tiddia",
"Gianmarco",
""
],
[
"De Luca",
"Chiara",
""
],
[
"Pastorelli",
"Elena",
""
],
[
"Simula",
"Francesco",
""
],
[
"Paolucci",
"Pier Stanislao",
""
]
] | Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the advantage of a relatively low cost and a great versatility, thanks also to the poss... |
1203.0873 | Jing Kang Dr. | Jing Kang, Jianhua Wu, Anteo Smerieri and Jianfeng Feng | Weber's law implies neural discharge more regular than a Poisson process | 13 pages, 8 figures; European Journal of Neuroscience 2010 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Weber's law is one of the basic laws in psychophysics, but the link between
this psychophysical behavior and the neuronal response has not yet been
established. In this paper, we carried out an analysis on the spike train
statistics when Weber's law holds, and found that the efferent spike train of a
single neuron is... | [
{
"created": "Mon, 5 Mar 2012 11:51:23 GMT",
"version": "v1"
}
] | 2012-03-06 | [
[
"Kang",
"Jing",
""
],
[
"Wu",
"Jianhua",
""
],
[
"Smerieri",
"Anteo",
""
],
[
"Feng",
"Jianfeng",
""
]
] | Weber's law is one of the basic laws in psychophysics, but the link between this psychophysical behavior and the neuronal response has not yet been established. In this paper, we carried out an analysis on the spike train statistics when Weber's law holds, and found that the efferent spike train of a single neuron is l... |
2003.14333 | Bing He | Bing He, Lana Garmire | Prediction of repurposed drugs for treating lung injury in COVID-19 | null | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Coronavirus disease (COVID-19) is an infectious disease discovered in 2019
and currently in outbreak across the world. Lung injury with severe respiratory
failure is the leading cause of death in COVID-19, brought by severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there still lacks
efficient tr... | [
{
"created": "Mon, 30 Mar 2020 03:36:44 GMT",
"version": "v1"
},
{
"created": "Sun, 3 May 2020 05:34:24 GMT",
"version": "v2"
}
] | 2020-05-05 | [
[
"He",
"Bing",
""
],
[
"Garmire",
"Lana",
""
]
] | Coronavirus disease (COVID-19) is an infectious disease discovered in 2019 and currently in outbreak across the world. Lung injury with severe respiratory failure is the leading cause of death in COVID-19, brought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there still lacks efficient trea... |
1311.1651 | Rafael Guariento Dettogni | Rafael D Guariento | Population Density as an Equalizing (or Misbalancing) Mechanism for
Species Coexistence | 26 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Despite the general acknowledgment of the role of niche and fitness
differences in community dynamics, species abundance has been coined as a
relevant feature not just regarding niche perspectives, but also according to
neutral perspectives. Here we explore a minimum probabilistic stochastic model
to evaluate the rol... | [
{
"created": "Thu, 7 Nov 2013 12:11:03 GMT",
"version": "v1"
}
] | 2013-11-08 | [
[
"Guariento",
"Rafael D",
""
]
] | Despite the general acknowledgment of the role of niche and fitness differences in community dynamics, species abundance has been coined as a relevant feature not just regarding niche perspectives, but also according to neutral perspectives. Here we explore a minimum probabilistic stochastic model to evaluate the role ... |
1201.3216 | Giuseppe Jurman | A. Barla and S. Riccadonna and S. Masecchia and M. Squillario and M.
Filosi and G. Jurman and C. Furlanello | Evaluating sources of variability in pathway profiling | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A bioinformatics platform is introduced aimed at identifying models of
disease-specific pathways, as well as a set of network measures that can
quantify changes in terms of global structure or single link disruptions.The
approach integrates a network comparison framework with machine learning
molecular profiling. <CA... | [
{
"created": "Mon, 16 Jan 2012 11:19:45 GMT",
"version": "v1"
}
] | 2012-01-17 | [
[
"Barla",
"A.",
""
],
[
"Riccadonna",
"S.",
""
],
[
"Masecchia",
"S.",
""
],
[
"Squillario",
"M.",
""
],
[
"Filosi",
"M.",
""
],
[
"Jurman",
"G.",
""
],
[
"Furlanello",
"C.",
""
]
] | A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates a network comparison framework with machine learning molecular profiling. <CA>T... |
1112.5704 | Tetsuhiro Hatakeyama | Tetsuhiro S. Hatakeyama, Kunihiko Kaneko | Generic temperature compensation of biological clocks by autonomous
regulation of catalyst concentration | 21 pages, 12 figures | null | 10.1073/pnas.1120711109 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular
organisms, often exhibit intrinsic temperature compensation; the period of
circadian oscillators is maintained constant over a range of physiological
temperatures, despite the expected Arrhenius form for the reaction coefficient.
Observation... | [
{
"created": "Sat, 24 Dec 2011 07:33:50 GMT",
"version": "v1"
}
] | 2014-07-21 | [
[
"Hatakeyama",
"Tetsuhiro S.",
""
],
[
"Kaneko",
"Kunihiko",
""
]
] | Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations ... |
1812.10841 | Daisuke Kihara | Atilla Sit and Daisuke Kihara | Three-Dimensional Krawtchouk Descriptors for Protein Local Surface Shape
Comparison | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Direct comparison of three-dimensional (3D) objects is computationally
expensive due to the need for translation, rotation, and scaling of the objects
to evaluate their similarity. In applications of 3D object comparison, often
identifying specific local regions of objects is of particular interest. We
have recently ... | [
{
"created": "Thu, 27 Dec 2018 22:41:14 GMT",
"version": "v1"
}
] | 2018-12-31 | [
[
"Sit",
"Atilla",
""
],
[
"Kihara",
"Daisuke",
""
]
] | Direct comparison of three-dimensional (3D) objects is computationally expensive due to the need for translation, rotation, and scaling of the objects to evaluate their similarity. In applications of 3D object comparison, often identifying specific local regions of objects is of particular interest. We have recently de... |
1710.05639 | Xiang-Yi Li | Xiaoquan Yu, Xiang-Yi Li | Applications of WKB and Fokker-Planck methods in analyzing population
extinction driven by weak demographic fluctuations | null | Yu, X. & Li, XY. Bull Math Biol (2018).
https://doi.org/10.1007/s11538-018-0483-6 | 10.1007/s11538-018-0483-6 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In large but finite populations, weak demographic stochasticity due to random
birth and death events can lead to population extinction. The process is
analogous to the escaping problem of trapped particles under random forces.
Methods widely used in studying such physical systems, for instance,
Wentzel-Kramers-Brillo... | [
{
"created": "Mon, 16 Oct 2017 12:01:26 GMT",
"version": "v1"
},
{
"created": "Tue, 17 Oct 2017 10:06:25 GMT",
"version": "v2"
},
{
"created": "Sat, 21 Jul 2018 07:36:21 GMT",
"version": "v3"
}
] | 2018-11-28 | [
[
"Yu",
"Xiaoquan",
""
],
[
"Li",
"Xiang-Yi",
""
]
] | In large but finite populations, weak demographic stochasticity due to random birth and death events can lead to population extinction. The process is analogous to the escaping problem of trapped particles under random forces. Methods widely used in studying such physical systems, for instance, Wentzel-Kramers-Brilloui... |
2112.13153 | Leonid Hanin | Leonid Hanin (1), Liyang Xie (2), Rainer Sachs (2) ((1) Idaho State
University, Pocatello, Idaho, USA, (2) University of California, Berkeley,
Berkeley, California, USA) | Mathematical Properties of Incremental Effect Additivity and Other
Synergy Theories | 53 pages including 14 figures and supplementary materials | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synergy theories for multi-component agent mixtures use 1-agent dose-effect
relations, assumed known from analyzing previous 1-agent experiments, to
calculate baseline Neither-Synergy-Nor-Antagonism mixture dose-effect
relations. The most commonly used synergy theory, Simple Effect Additivity, is
not self-consistent ... | [
{
"created": "Fri, 24 Dec 2021 22:38:56 GMT",
"version": "v1"
}
] | 2021-12-28 | [
[
"Hanin",
"Leonid",
""
],
[
"Xie",
"Liyang",
""
],
[
"Sachs",
"Rainer",
""
]
] | Synergy theories for multi-component agent mixtures use 1-agent dose-effect relations, assumed known from analyzing previous 1-agent experiments, to calculate baseline Neither-Synergy-Nor-Antagonism mixture dose-effect relations. The most commonly used synergy theory, Simple Effect Additivity, is not self-consistent ma... |
2007.01979 | Ronal Arela-Bobadilla | Ronal Arela-Bobadilla | Excess deaths hidden 100 days after the quarantine in Peru by COVID-19 | in Spanish | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objective: To make an estimate of the excess deaths caused by COVID-19 in the
non-violent mortality of Peru, controlling for the effect of quarantine.
Methods: Analysis of longitudinal data from the departments of Peru using
official public information from the National Death Information System and the
Ministry of He... | [
{
"created": "Sat, 4 Jul 2020 01:16:56 GMT",
"version": "v1"
}
] | 2020-07-07 | [
[
"Arela-Bobadilla",
"Ronal",
""
]
] | Objective: To make an estimate of the excess deaths caused by COVID-19 in the non-violent mortality of Peru, controlling for the effect of quarantine. Methods: Analysis of longitudinal data from the departments of Peru using official public information from the National Death Information System and the Ministry of Heal... |
2211.12412 | Jay Stotsky | Jay A. Stotsky and Hans G. Othmer | The Role of Cytonemes and Diffusive Transport in the Establishment of
Morphogen Gradients | 36 pages, 16 figures | null | null | null | q-bio.CB math.PR | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spatial distributions of morphogens provide positional information in
developing systems, but how the distributions are established and maintained
remains an open problem. Transport by diffusion has been the
traditional mechanism, but recent experimental work has shown that cells can
also communicate by filop... | [
{
"created": "Tue, 22 Nov 2022 17:16:25 GMT",
"version": "v1"
}
] | 2022-11-23 | [
[
"Stotsky",
"Jay A.",
""
],
[
"Othmer",
"Hans G.",
""
]
] | Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but recent experimental work has shown that cells can also communicate by filopodia-like ... |
q-bio/0512007 | Ping Ao | X. Zhu, L. Yin, L. Hood, D. Galas, and P. Ao | Efficiency, Robustness and Stochasticity of Gene Regulatory Networks in
Systems Biology: lambda Switch as a Working Example | 40 pages | null | null | null | q-bio.SC cond-mat.other nlin.AO q-bio.MN q-bio.OT | null | Phage lambda is one of the most studied biological models in modern molecular
biology. Over the past 50 years quantitative experimental knowledge on this
biological model has been accumulated at all levels: physics, chemistry,
genomics, proteomics, functions, and more. All its components have been known
to a great de... | [
{
"created": "Fri, 2 Dec 2005 17:14:59 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Feb 2006 03:23:29 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Zhu",
"X.",
""
],
[
"Yin",
"L.",
""
],
[
"Hood",
"L.",
""
],
[
"Galas",
"D.",
""
],
[
"Ao",
"P.",
""
]
] | Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics, proteomics, functions, and more. All its components have been known to a great deta... |
1505.02072 | Andrew Lover | Andrew A. Lover | Epidemiology of Latency and Relapse in Plasmodium vivax Malaria | PhD thesis (2015); 128 pages | null | null | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Malaria is a major contributor to health burdens throughout the regions where
it is endemic. Historically, it was believed that there was limited morbidity
and essentially no mortality associated with Plasmodium vivax; however,
evidence from diverse settings now suggests that infections with P. vivax can
be both seve... | [
{
"created": "Fri, 8 May 2015 15:57:46 GMT",
"version": "v1"
}
] | 2015-05-11 | [
[
"Lover",
"Andrew A.",
""
]
] | Malaria is a major contributor to health burdens throughout the regions where it is endemic. Historically, it was believed that there was limited morbidity and essentially no mortality associated with Plasmodium vivax; however, evidence from diverse settings now suggests that infections with P. vivax can be both severe... |
2009.10018 | Madhav Marathe | Aniruddha Adiga, Jiangzhuo Chen, Madhav Marathe, Henning Mortveit,
Srinivasan Venkatramanan, Anil Vullikanti | Data-driven modeling for different stages of pandemic response | null | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Some of the key questions of interest during the COVID-19 pandemic (and all
outbreaks) include: where did the disease start, how is it spreading, who is at
risk, and how to control the spread. There are a large number of complex
factors driving the spread of pandemics, and, as a result, multiple modeling
techniques p... | [
{
"created": "Mon, 21 Sep 2020 16:48:59 GMT",
"version": "v1"
}
] | 2020-09-22 | [
[
"Adiga",
"Aniruddha",
""
],
[
"Chen",
"Jiangzhuo",
""
],
[
"Marathe",
"Madhav",
""
],
[
"Mortveit",
"Henning",
""
],
[
"Venkatramanan",
"Srinivasan",
""
],
[
"Vullikanti",
"Anil",
""
]
] | Some of the key questions of interest during the COVID-19 pandemic (and all outbreaks) include: where did the disease start, how is it spreading, who is at risk, and how to control the spread. There are a large number of complex factors driving the spread of pandemics, and, as a result, multiple modeling techniques pla... |
1608.06222 | Bienvenue Kouwaye | Gilles Cottrell (UPD5 Pharmacie), Bienvenue Kouwaye (SAMM, UAC),
Charlotte Pierrat (ENEC, MERIT), Agn\`es Le Port (UPD5 Pharmacie, MERIT,
UPD5), Boura\"ima Aziz (MERIT), No\"el Fonton, Achille Massougbodji (UAC,
MERIT), Vincent Corbel (MIVEGEC, MERIT), Mahouton Norbert Hounkonnou, Andr\'e
Garcia (UPD5 Pharmacie... | Modeling the Influence of Local Environmental Factors on Malaria
Transmission in Benin and Its Implications for Cohort Study | PLoS ONE, Public Library of Science, 2012 | null | 10.1371/journal.pone.0028812.g005 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Malaria remains endemic in tropical areas, especially in Africa. For the
evaluation of new tools and to further ourunderstanding of host-parasite
interactions, knowing the environmental risk of transmission-even at a very
local scale-isessential. The aim of this study was to assess how malaria
transmission is influen... | [
{
"created": "Fri, 19 Aug 2016 16:25:30 GMT",
"version": "v1"
}
] | 2016-08-23 | [
[
"Cottrell",
"Gilles",
"",
"UPD5 Pharmacie"
],
[
"Kouwaye",
"Bienvenue",
"",
"SAMM, UAC"
],
[
"Pierrat",
"Charlotte",
"",
"ENEC, MERIT"
],
[
"Port",
"Agnès Le",
"",
"UPD5 Pharmacie, MERIT,\n UPD5"
],
[
"Aziz",
"Bouraïma",
... | Malaria remains endemic in tropical areas, especially in Africa. For the evaluation of new tools and to further ourunderstanding of host-parasite interactions, knowing the environmental risk of transmission-even at a very local scale-isessential. The aim of this study was to assess how malaria transmission is influence... |
1507.03053 | Francis Manno | Francis AM Manno III | Memetic evolution of art to distinct aesthetics | short theory article, 3 pages, 3 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Humans have been using symbolic representation (i.e. art) as a creative
cultural form indisputably for at least 80,000 years. A description of the
processes central to the evolution of art from sculpted earthen forms early in
human existence to paintings in museums of the modern world is absent in
scholarly literatur... | [
{
"created": "Sat, 11 Jul 2015 01:41:26 GMT",
"version": "v1"
}
] | 2015-07-14 | [
[
"Manno",
"Francis AM",
"III"
]
] | Humans have been using symbolic representation (i.e. art) as a creative cultural form indisputably for at least 80,000 years. A description of the processes central to the evolution of art from sculpted earthen forms early in human existence to paintings in museums of the modern world is absent in scholarly literature.... |
2201.09916 | Rainer Engelken | Rainer Engelken, Alessandro Ingrosso, Ramin Khajeh, Sven Goedeke, L.
F. Abbott | Input correlations impede suppression of chaos and learning in balanced
rate networks | null | null | 10.1371/journal.pcbi.1010590 | null | q-bio.NC cond-mat.dis-nn cs.LG nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural circuits exhibit complex activity patterns, both spontaneously and
evoked by external stimuli. Information encoding and learning in neural
circuits depend on how well time-varying stimuli can control spontaneous
network activity. We show that in firing-rate networks in the balanced state,
external control of r... | [
{
"created": "Mon, 24 Jan 2022 19:20:49 GMT",
"version": "v1"
}
] | 2023-01-11 | [
[
"Engelken",
"Rainer",
""
],
[
"Ingrosso",
"Alessandro",
""
],
[
"Khajeh",
"Ramin",
""
],
[
"Goedeke",
"Sven",
""
],
[
"Abbott",
"L. F.",
""
]
] | Neural circuits exhibit complex activity patterns, both spontaneously and evoked by external stimuli. Information encoding and learning in neural circuits depend on how well time-varying stimuli can control spontaneous network activity. We show that in firing-rate networks in the balanced state, external control of rec... |
1711.09558 | Jasper Zuallaert | Jasper Zuallaert, Mijung Kim, Yvan Saeys, Wesley De Neve | Interpretable Convolutional Neural Networks for Effective Translation
Initiation Site Prediction | Presented at International Workshop on Deep Learning in
Bioinformatics, Biomedicine, and Healthcare Informatics (DLB2H 2017) --- in
conjunction with the IEEE International Conference on Bioinformatics and
Biomedicine (BIBM 2017) | null | null | null | q-bio.GN cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Thanks to rapidly evolving sequencing techniques, the amount of genomic data
at our disposal is growing increasingly large. Determining the gene structure
is a fundamental requirement to effectively interpret gene function and
regulation. An important part in that determination process is the
identification of transl... | [
{
"created": "Mon, 27 Nov 2017 06:37:37 GMT",
"version": "v1"
}
] | 2017-11-28 | [
[
"Zuallaert",
"Jasper",
""
],
[
"Kim",
"Mijung",
""
],
[
"Saeys",
"Yvan",
""
],
[
"De Neve",
"Wesley",
""
]
] | Thanks to rapidly evolving sequencing techniques, the amount of genomic data at our disposal is growing increasingly large. Determining the gene structure is a fundamental requirement to effectively interpret gene function and regulation. An important part in that determination process is the identification of translat... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.