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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1511.07222 | Sarah Beul | Sarah F. Beul, Helen Barbas, Claus C. Hilgetag | A predictive structural model of the primate connectome | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Anatomical connectivity imposes strong constraints on brain function, but
there is no general agreement about principles that govern its organization.
Based on extensive quantitative data we tested the power of three models to
predict connections of the primate cerebral cortex: architectonic similarity
(structural mo... | [
{
"created": "Mon, 23 Nov 2015 13:48:23 GMT",
"version": "v1"
},
{
"created": "Mon, 30 May 2016 12:03:05 GMT",
"version": "v2"
}
] | 2016-05-31 | [
[
"Beul",
"Sarah F.",
""
],
[
"Barbas",
"Helen",
""
],
[
"Hilgetag",
"Claus C.",
""
]
] | Anatomical connectivity imposes strong constraints on brain function, but there is no general agreement about principles that govern its organization. Based on extensive quantitative data we tested the power of three models to predict connections of the primate cerebral cortex: architectonic similarity (structural mode... |
2209.01034 | Alireza Modirshanechi | Alireza Modirshanechi, Johanni Brea, Wulfram Gerstner | A taxonomy of surprise definitions | To appear in the Journal of Mathematical Psychology | Journal of Mathematical Psychology Volume 110, September 2022,
102712 | 10.1016/j.jmp.2022.102712 | null | q-bio.NC stat.ML | http://creativecommons.org/licenses/by/4.0/ | Surprising events trigger measurable brain activity and influence human
behavior by affecting learning, memory, and decision-making. Currently there
is, however, no consensus on the definition of surprise. Here we identify 18
mathematical definitions of surprise in a unifying framework. We first propose
a technical c... | [
{
"created": "Fri, 2 Sep 2022 13:07:15 GMT",
"version": "v1"
}
] | 2022-09-26 | [
[
"Modirshanechi",
"Alireza",
""
],
[
"Brea",
"Johanni",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | Surprising events trigger measurable brain activity and influence human behavior by affecting learning, memory, and decision-making. Currently there is, however, no consensus on the definition of surprise. Here we identify 18 mathematical definitions of surprise in a unifying framework. We first propose a technical cla... |
1102.4026 | Pau Ru\'e | Pau Ru\'e and Jordi Garcia-Ojalvo | Gene circuit designs for noisy excitable dynamics | 9 pages, 10 figures | Mathematical Biosciences 231 (2011), pp. 90-97 | 10.1016/j.mbs.2011.02.013 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Certain cellular processes take the form of activity pulses that can be
interpreted in terms of noise-driven excitable dynamics. Here we present an
overview of different gene circuit architectures that exhibit excitable pulses
of protein expression, when subject to molecular noise. Different types of
excitable dynami... | [
{
"created": "Sat, 19 Feb 2011 21:12:48 GMT",
"version": "v1"
}
] | 2011-04-22 | [
[
"Rué",
"Pau",
""
],
[
"Garcia-Ojalvo",
"Jordi",
""
]
] | Certain cellular processes take the form of activity pulses that can be interpreted in terms of noise-driven excitable dynamics. Here we present an overview of different gene circuit architectures that exhibit excitable pulses of protein expression, when subject to molecular noise. Different types of excitable dynamics... |
1611.04812 | Krzysztof Gogolewski | K. Gogolewski, M. Startek, A. Gambin and A. Le Rouzic | Modelling the proliferation of transposable elements in populations
under environmental stress | 18 pages (wo references), 7 figures. The work was presented at RECOMB
2015 conference. To be published in Mobile DNA or Theoretical Population
Biology | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this article, we investigate the evolution of sexual diploid populations
which are hosts for active TE families. Our purpose is to explore the
relationship between the environmental change, that influences such population
and activity of those TEs that are present in genomes.
| [
{
"created": "Tue, 15 Nov 2016 12:59:01 GMT",
"version": "v1"
}
] | 2016-11-16 | [
[
"Gogolewski",
"K.",
""
],
[
"Startek",
"M.",
""
],
[
"Gambin",
"A.",
""
],
[
"Rouzic",
"A. Le",
""
]
] | In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of those TEs that are present in genomes. |
1903.11627 | Gabriel Birzu | Gabriel Birzu, Sakib Matin, Oskar Hallatschek and Kirill S. Korolev | Genetic drift in range expansions is very sensitive to density feedback
in dispersal and growth | 36 pages, 5 figures, and 1 table | null | null | null | q-bio.PE cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Theory predicts rapid genetic drift during invasions, yet many expanding
populations maintain high genetic diversity. We find that genetic drift is
dramatically suppressed when dispersal rates increase with the population
density because many more migrants from the diverse, high-density regions
arrive at the expansio... | [
{
"created": "Wed, 27 Mar 2019 18:07:14 GMT",
"version": "v1"
}
] | 2019-03-29 | [
[
"Birzu",
"Gabriel",
""
],
[
"Matin",
"Sakib",
""
],
[
"Hallatschek",
"Oskar",
""
],
[
"Korolev",
"Kirill S.",
""
]
] | Theory predicts rapid genetic drift during invasions, yet many expanding populations maintain high genetic diversity. We find that genetic drift is dramatically suppressed when dispersal rates increase with the population density because many more migrants from the diverse, high-density regions arrive at the expansion ... |
1709.03813 | Muniba Faiza | Muniba Faiza, Tariq Abdullah, Prof. Yonghua Wang | Dithymoquinone as a novel inhibitor for
3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) to prevent renal
failure | 27 pages, 4 figures, and 2 tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is a major
endogenous ligand found in the human serum albumin (HSA) of renal failure
patients. It gets accumulated in the HSA and its concentration in sera of
patients may reflect the chronicity of renal failure [1-4]. It is considered
uremic toxin due to its d... | [
{
"created": "Sun, 23 Jul 2017 10:53:26 GMT",
"version": "v1"
}
] | 2017-09-13 | [
[
"Faiza",
"Muniba",
""
],
[
"Abdullah",
"Tariq",
""
],
[
"Wang",
"Prof. Yonghua",
""
]
] | 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is a major endogenous ligand found in the human serum albumin (HSA) of renal failure patients. It gets accumulated in the HSA and its concentration in sera of patients may reflect the chronicity of renal failure [1-4]. It is considered uremic toxin due to its dam... |
1811.08578 | Bernard Marius 't Hart | Ahmed A. Mostafa, Bernard Marius 't Hart, Denise Y.P. Henriques | Motor Learning Without Moving: Hand Localization after Passive Training | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | An accurate estimate of limb position is necessary for movement. Where we
localize our unseen hand after a reach depends on felt hand position, or
proprioception, but often only predicted sensory consequences based on
efference copies of motor commands are considered. Both signals should
contribute, so here we use pa... | [
{
"created": "Wed, 21 Nov 2018 02:58:11 GMT",
"version": "v1"
}
] | 2018-11-22 | [
[
"Mostafa",
"Ahmed A.",
""
],
[
"Hart",
"Bernard Marius 't",
""
],
[
"Henriques",
"Denise Y. P.",
""
]
] | An accurate estimate of limb position is necessary for movement. Where we localize our unseen hand after a reach depends on felt hand position, or proprioception, but often only predicted sensory consequences based on efference copies of motor commands are considered. Both signals should contribute, so here we use pass... |
1809.07550 | Jens Wilting | Jens Wilting, Jonas Dehning, Joao Pinheiro Neto, Lucas Rudelt, Michael
Wibral, Johannes Zierenberg, Viola Priesemann | Dynamic Adaptive Computation: Tuning network states to task requirements | 6 pages + references, 2 figures | Frontiers in systems neuroscience 12 (2018) | 10.3389/fnsys.2018.00055 | null | q-bio.NC nlin.AO | http://creativecommons.org/licenses/by-sa/4.0/ | Neural circuits are able to perform computations under very diverse
conditions and requirements. The required computations impose clear constraints
on their fine-tuning: a rapid and maximally informative response to stimuli in
general requires decorrelated baseline neural activity. Such network dynamics
is known as a... | [
{
"created": "Thu, 20 Sep 2018 10:00:18 GMT",
"version": "v1"
}
] | 2019-10-22 | [
[
"Wilting",
"Jens",
""
],
[
"Dehning",
"Jonas",
""
],
[
"Neto",
"Joao Pinheiro",
""
],
[
"Rudelt",
"Lucas",
""
],
[
"Wibral",
"Michael",
""
],
[
"Zierenberg",
"Johannes",
""
],
[
"Priesemann",
"Viola",
""
... | Neural circuits are able to perform computations under very diverse conditions and requirements. The required computations impose clear constraints on their fine-tuning: a rapid and maximally informative response to stimuli in general requires decorrelated baseline neural activity. Such network dynamics is known as asy... |
2212.02229 | Dominic Masters | Dominic Masters, Josef Dean, Kerstin Klaser, Zhiyi Li, Sam
Maddrell-Mander, Adam Sanders, Hatem Helal, Deniz Beker, Ladislav
Ramp\'a\v{s}ek and Dominique Beaini | GPS++: An Optimised Hybrid MPNN/Transformer for Molecular Property
Prediction | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by-sa/4.0/ | This technical report presents GPS++, the first-place solution to the Open
Graph Benchmark Large-Scale Challenge (OGB-LSC 2022) for the PCQM4Mv2 molecular
property prediction task. Our approach implements several key principles from
the prior literature. At its core our GPS++ method is a hybrid MPNN/Transformer
model... | [
{
"created": "Fri, 18 Nov 2022 18:11:27 GMT",
"version": "v1"
},
{
"created": "Tue, 6 Dec 2022 16:53:52 GMT",
"version": "v2"
}
] | 2022-12-07 | [
[
"Masters",
"Dominic",
""
],
[
"Dean",
"Josef",
""
],
[
"Klaser",
"Kerstin",
""
],
[
"Li",
"Zhiyi",
""
],
[
"Maddrell-Mander",
"Sam",
""
],
[
"Sanders",
"Adam",
""
],
[
"Helal",
"Hatem",
""
],
[
"Bek... | This technical report presents GPS++, the first-place solution to the Open Graph Benchmark Large-Scale Challenge (OGB-LSC 2022) for the PCQM4Mv2 molecular property prediction task. Our approach implements several key principles from the prior literature. At its core our GPS++ method is a hybrid MPNN/Transformer model t... |
0706.0643 | Dietrich Stauffer | Dietrich Stauffer, Christian Schulze, Dieter W. Heermann | Superdiffusion in a Model for Diffusion in a Molecularly Crowded
Environment | 8 pages including 4 figures | null | null | null | q-bio.SC | null | We present a model for diffusion in a molecularly crowded environment. The
model consists of random barriers in percolation network. Random walks in the
presence of slowly moving barriers show normal diffusion for long times, but
anomalous diffusion at intermediate times. The effective exponents for square
distance v... | [
{
"created": "Tue, 5 Jun 2007 12:35:21 GMT",
"version": "v1"
}
] | 2007-06-06 | [
[
"Stauffer",
"Dietrich",
""
],
[
"Schulze",
"Christian",
""
],
[
"Heermann",
"Dieter W.",
""
]
] | We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous diffusion at intermediate times. The effective exponents for square distance ver... |
2201.07283 | Ushasi Roy | Ushasi Roy, Tyler Collins, Mohit K. Jolly, and Parag Katira | Biophysical and Biochemical mechanisms underlying Collective Cell
Migration in Cancer Metastasis | 27 pages, 2 figures, book chapter | null | null | null | q-bio.CB physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Multicellular collective migration is a ubiquitous strategy of cells to
translocate spatially in diverse tissue environments to accomplish a wide
variety of biological phenomena, viz. embryonic development, wound healing, and
tumor progression. Diverse cellular functions and behaviors, for instance, cell
protrusions,... | [
{
"created": "Tue, 18 Jan 2022 19:36:07 GMT",
"version": "v1"
}
] | 2022-01-20 | [
[
"Roy",
"Ushasi",
""
],
[
"Collins",
"Tyler",
""
],
[
"Jolly",
"Mohit K.",
""
],
[
"Katira",
"Parag",
""
]
] | Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor progression. Diverse cellular functions and behaviors, for instance, cell protrusions, a... |
1903.07231 | Nils Gehlenborg | Michael P Snyder, Shin Lin, Amanda Posgai, Mark Atkinson, Aviv Regev,
Jennifer Rood, Orit Rosen, Leslie Gaffney, Anna Hupalowska, Rahul Satija,
Nils Gehlenborg, Jay Shendure, Julia Laskin, Pehr Harbury, Nicholas A
Nystrom, Ziv Bar-Joseph, Kun Zhang, Katy B\"orner, Yiing Lin, Richard Conroy,
Dena Procaccini, Ana... | Mapping the Human Body at Cellular Resolution -- The NIH Common Fund
Human BioMolecular Atlas Program | 20 pages, 3 figures | null | 10.1038/s41586-019-1629-x | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Transformative technologies are enabling the construction of three
dimensional (3D) maps of tissues with unprecedented spatial and molecular
resolution. Over the next seven years, the NIH Common Fund Human Biomolecular
Atlas Program (HuBMAP) intends to develop a widely accessible framework for
comprehensively mapping... | [
{
"created": "Mon, 18 Mar 2019 02:18:13 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Jun 2019 15:06:19 GMT",
"version": "v2"
}
] | 2019-11-04 | [
[
"Snyder",
"Michael P",
"",
"for the HuBMAP Consortium"
],
[
"Lin",
"Shin",
"",
"for the HuBMAP Consortium"
],
[
"Posgai",
"Amanda",
"",
"for the HuBMAP Consortium"
],
[
"Atkinson",
"Mark",
"",
"for the HuBMAP Consortium"
],
[
"Reg... | Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping t... |
1511.06904 | Ralph Brinks | Ralph Brinks | An identifiability problem in a state model for partly undetected
chronic diseases | 5 pages, 1 figure | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, we proposed an state model (compartment model) to describe the
progression of a chronic disease with an pre-clinical (undiagnosed) state
before clinical diagnosis. It is an open question, if a sequence of
cross-sectional studies with mortality follow-up is sufficient to estimate the
true incidence rate of t... | [
{
"created": "Sat, 21 Nov 2015 17:30:22 GMT",
"version": "v1"
}
] | 2015-11-24 | [
[
"Brinks",
"Ralph",
""
]
] | Recently, we proposed an state model (compartment model) to describe the progression of a chronic disease with an pre-clinical (undiagnosed) state before clinical diagnosis. It is an open question, if a sequence of cross-sectional studies with mortality follow-up is sufficient to estimate the true incidence rate of the... |
1212.0356 | Christian Kuehn | Christian Kuehn | Warning signs for wave speed transitions of noisy Fisher-KPP invasion
fronts | 14 pages, 8 figures; preprint - comments and suggestions welcome | Theoretical Ecology, Vol. 6, No. 3, pp. 295-308, 2013 | 10.1007/s12080-013-0189-1 | null | q-bio.PE math.DS math.PR nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Invasion waves are a fundamental building block of theoretical ecology. In
this study we aim to take the first steps to link propagation failure and fast
acceleration of traveling waves to critical transitions (or tipping points).
The approach is based upon a detailed numerical study of various versions of
the Fisher... | [
{
"created": "Mon, 3 Dec 2012 11:43:03 GMT",
"version": "v1"
}
] | 2015-03-06 | [
[
"Kuehn",
"Christian",
""
]
] | Invasion waves are a fundamental building block of theoretical ecology. In this study we aim to take the first steps to link propagation failure and fast acceleration of traveling waves to critical transitions (or tipping points). The approach is based upon a detailed numerical study of various versions of the Fisher-K... |
0807.1898 | Marco Cosentino Lagomarsino | M. Cosentino Lagomarsino, A.L. Sellerio, P.D. Heijning, B. Bassetti | Universal Features in the Genome-level Evolution of Protein Domains | null | null | null | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein domains are found on genomes with notable statistical distributions,
which bear a high degree of similarity. Previous work has shown how these
distributions can be accounted for by simple models, where the main ingredients
are probabilities of duplication, innovation, and loss of domains. However, no
one so f... | [
{
"created": "Fri, 11 Jul 2008 17:36:26 GMT",
"version": "v1"
}
] | 2008-07-14 | [
[
"Lagomarsino",
"M. Cosentino",
""
],
[
"Sellerio",
"A. L.",
""
],
[
"Heijning",
"P. D.",
""
],
[
"Bassetti",
"B.",
""
]
] | Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far... |
1910.08352 | Michaela Hamm | Michaela Hamm and Barbara Drossel | The concerted emergence of well-known spatial and temporal ecological
patterns in an evolutionary food web model in space | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Ecological systems show a variety of characteristic patterns of biodiversity
in space and time. It is a challenge for theory to find models that can
reproduce and explain the observed patterns. Since the advent of island
biogeography these models revolve around speciation, dispersal, and extinction,
but they usually ... | [
{
"created": "Fri, 18 Oct 2019 11:50:16 GMT",
"version": "v1"
}
] | 2019-10-21 | [
[
"Hamm",
"Michaela",
""
],
[
"Drossel",
"Barbara",
""
]
] | Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these models revolve around speciation, dispersal, and extinction, but they usually ne... |
2211.06692 | Federico William Pasini | Federico W. Pasini, Alexandra N. Busch, J\'an Min\'a\v{c}, Krishnan
Padmanabhan, Lyle Muller | An algebraic approach to spike-time neural codes in the hippocampus | 11 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Although temporal coding through spike-time patterns has long been of
interest in neuroscience, the specific structures that could be useful for
spike-time codes remain highly unclear. Here, we introduce a new analytical
approach, using techniques from discrete mathematics, to study spike-time
codes. We focus on the ... | [
{
"created": "Sat, 12 Nov 2022 15:45:18 GMT",
"version": "v1"
}
] | 2022-11-15 | [
[
"Pasini",
"Federico W.",
""
],
[
"Busch",
"Alexandra N.",
""
],
[
"Mináč",
"Ján",
""
],
[
"Padmanabhan",
"Krishnan",
""
],
[
"Muller",
"Lyle",
""
]
] | Although temporal coding through spike-time patterns has long been of interest in neuroscience, the specific structures that could be useful for spike-time codes remain highly unclear. Here, we introduce a new analytical approach, using techniques from discrete mathematics, to study spike-time codes. We focus on the ph... |
2302.12714 | Maurice HT Ling | Zhu En Chay, Chin How Lee, Kun Cheng Lee, Jack SH Oon, Maurice HT Ling | Russel and Rao Coefficient is a Suitable Substitute for Dice Coefficient
in Studying Restriction Mapped Genetic Distances of Escherichia coli | null | iConcept Journal of Computational and Mathematical Biology 1:1
(2010) | null | null | q-bio.GN | http://creativecommons.org/licenses/by-sa/4.0/ | Escherichia coli is one of many bacterial inhabitants found in human
intestines and any adaptation as a result of mutations may affect its host. A
commonly used technique employed to study these mutations is Restriction
Fragment Length Polymorphism (RFLP) and is proceeded with a suitable distance
coefficient to quant... | [
{
"created": "Sun, 19 Feb 2023 02:39:00 GMT",
"version": "v1"
}
] | 2023-02-27 | [
[
"Chay",
"Zhu En",
""
],
[
"Lee",
"Chin How",
""
],
[
"Lee",
"Kun Cheng",
""
],
[
"Oon",
"Jack SH",
""
],
[
"Ling",
"Maurice HT",
""
]
] | Escherichia coli is one of many bacterial inhabitants found in human intestines and any adaptation as a result of mutations may affect its host. A commonly used technique employed to study these mutations is Restriction Fragment Length Polymorphism (RFLP) and is proceeded with a suitable distance coefficient to quantif... |
2307.02624 | James Brunner | James D. Brunner and Laverne A. Gallegos-Graves and Marie E. Kroeger | Inferring microbial interactions with their environment from genomic and
metagenomic data | 27 pages, 10 figure, 4 tables | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Microbial communities assemble through a complex set of interactions between
microbes and their environment, and the resulting metabolic impact on the host
ecosystem can be profound. Microbial activity is known to impact human health,
plant growth, water quality, and soil carbon storage which has lead to the
developm... | [
{
"created": "Wed, 5 Jul 2023 19:54:30 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Nov 2023 15:27:04 GMT",
"version": "v2"
}
] | 2023-11-09 | [
[
"Brunner",
"James D.",
""
],
[
"Gallegos-Graves",
"Laverne A.",
""
],
[
"Kroeger",
"Marie E.",
""
]
] | Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant growth, water quality, and soil carbon storage which has lead to the developmen... |
2403.15092 | Rub\'en Calvo Ib\'a\~nez | Rub\'en Calvo, Carles Martorell, Guillermo B. Morales, Serena Di Santo
and Miguel A. Mu\~noz | Frequency-dependent covariance reveals critical spatio-temporal patterns
of synchronized activity in the human brain | null | null | null | null | q-bio.NC cond-mat.dis-nn cond-mat.stat-mech physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Recent analyses combining advanced theoretical techniques and high-quality
data from thousands of simultaneously recorded neurons provide strong support
for the hypothesis that neural dynamics operate near the edge of instability
across regions in the brain. However, these analyses, as well as related
studies, often ... | [
{
"created": "Fri, 22 Mar 2024 10:21:28 GMT",
"version": "v1"
}
] | 2024-03-25 | [
[
"Calvo",
"Rubén",
""
],
[
"Martorell",
"Carles",
""
],
[
"Morales",
"Guillermo B.",
""
],
[
"Di Santo",
"Serena",
""
],
[
"Muñoz",
"Miguel A.",
""
]
] | Recent analyses combining advanced theoretical techniques and high-quality data from thousands of simultaneously recorded neurons provide strong support for the hypothesis that neural dynamics operate near the edge of instability across regions in the brain. However, these analyses, as well as related studies, often fa... |
2105.10344 | Muhammad Usman Sanwal | Usman Sanwal, Thai Son Hoang, Luigia Petre and Ion Petre | Towards Scalable Modeling of Biology in Event-B | null | null | null | null | q-bio.MN cs.CL | http://creativecommons.org/licenses/by/4.0/ | Biology offers many examples of large-scale, complex, concurrent systems:
many processes take place in parallel, compete on resources and influence each
other's behavior. The scalable modeling of biological systems continues to be a
very active field of research. In this paper we introduce a new approach based
on Eve... | [
{
"created": "Thu, 20 May 2021 13:37:06 GMT",
"version": "v1"
}
] | 2021-05-24 | [
[
"Sanwal",
"Usman",
""
],
[
"Hoang",
"Thai Son",
""
],
[
"Petre",
"Luigia",
""
],
[
"Petre",
"Ion",
""
]
] | Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very active field of research. In this paper we introduce a new approach based on Event... |
2309.03911 | Mamata Das | Mamata Das, Selvakumar K., P.J.A. Alphonse | Identifying Essential Hub Genes and Protein Complexes in Malaria GO Data
using Semantic Similarity Measures | 23 pages, 15 figures | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | Hub genes play an essential role in biological systems because of their
interaction with other genes. A vocabulary used in bioinformatics called Gene
Ontology (GO) describes how genes and proteins operate. This flexible ontology
illustrates the operation of molecular, biological, and cellular processes
(Pmol, Pbio, P... | [
{
"created": "Wed, 9 Aug 2023 05:10:41 GMT",
"version": "v1"
}
] | 2023-09-11 | [
[
"Das",
"Mamata",
""
],
[
"K.",
"Selvakumar",
""
],
[
"Alphonse",
"P. J. A.",
""
]
] | Hub genes play an essential role in biological systems because of their interaction with other genes. A vocabulary used in bioinformatics called Gene Ontology (GO) describes how genes and proteins operate. This flexible ontology illustrates the operation of molecular, biological, and cellular processes (Pmol, Pbio, Pce... |
2104.03558 | Govind Kaigala | Iago Pereiro, Anna Fomitcheva-Khartchenko, Govind V. Kaigala | Shake It or Shrink It: Mass Transport and Kinetics in Surface Bioassays
Using Agitation and Microfluidics | 12 pages | null | null | null | q-bio.CB q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Surface assays, such as ELISA and immunofluorescence, are nothing short of
ubiquitous in biotechnology and medical diagnostics today. The development and
optimization of these assays generally focuses on three aspects: immobilization
chemistry, ligand-receptor interaction and concentrations of ligands, buffers
and sa... | [
{
"created": "Thu, 8 Apr 2021 07:19:43 GMT",
"version": "v1"
}
] | 2021-04-09 | [
[
"Pereiro",
"Iago",
""
],
[
"Fomitcheva-Khartchenko",
"Anna",
""
],
[
"Kaigala",
"Govind V.",
""
]
] | Surface assays, such as ELISA and immunofluorescence, are nothing short of ubiquitous in biotechnology and medical diagnostics today. The development and optimization of these assays generally focuses on three aspects: immobilization chemistry, ligand-receptor interaction and concentrations of ligands, buffers and samp... |
1007.2070 | Indrani Bose | Sayantari Ghosh, Kamakshi Sureka, Bhaswar Ghosh, Indrani Bose, Joyoti
Basu and Manikuntala Kundu | Phenotypic Heterogeneity in Mycobacterial Stringent Response | 24 pages,8 figures, supplementary information and 5 supplementary
figures | BMC Systems Biology 2011, 5:18 | 10.1186/1752-0509-5-18 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A common survival strategy of microorganisms subjected to stress involves the
generation of phenotypic heterogeneity in the isogenic microbial population
enabling a subset of the population to survive under stress. In a recent study,
a mycobacterial population of M. smegmatis was shown to develop phenotypic
heterogen... | [
{
"created": "Tue, 13 Jul 2010 10:18:02 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Feb 2011 09:13:18 GMT",
"version": "v2"
}
] | 2011-02-04 | [
[
"Ghosh",
"Sayantari",
""
],
[
"Sureka",
"Kamakshi",
""
],
[
"Ghosh",
"Bhaswar",
""
],
[
"Bose",
"Indrani",
""
],
[
"Basu",
"Joyoti",
""
],
[
"Kundu",
"Manikuntala",
""
]
] | A common survival strategy of microorganisms subjected to stress involves the generation of phenotypic heterogeneity in the isogenic microbial population enabling a subset of the population to survive under stress. In a recent study, a mycobacterial population of M. smegmatis was shown to develop phenotypic heterogenei... |
1104.2532 | Sebastiano Stramaglia | Sebastiano Stramaglia, Daniele Marinazzo, Mario Pellicoro, and Marina
de Tommaso | Abnormal effective connectivity in migraine with aura under photic
stimulation | 4 pages, 6 figures | null | null | null | q-bio.NC cond-mat.dis-nn physics.med-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Migraine patients with aura show a peculiar pattern of visual reactivity
compared with those of migraine patients without aura: an increased effective
connectivity, connected to a reduced synchronization among EEG channels, for
frequencies in the beta band. The effective connectivity is evaluated in terms
of the Gran... | [
{
"created": "Wed, 13 Apr 2011 15:51:15 GMT",
"version": "v1"
},
{
"created": "Wed, 11 May 2011 18:19:53 GMT",
"version": "v2"
}
] | 2011-05-12 | [
[
"Stramaglia",
"Sebastiano",
""
],
[
"Marinazzo",
"Daniele",
""
],
[
"Pellicoro",
"Mario",
""
],
[
"de Tommaso",
"Marina",
""
]
] | Migraine patients with aura show a peculiar pattern of visual reactivity compared with those of migraine patients without aura: an increased effective connectivity, connected to a reduced synchronization among EEG channels, for frequencies in the beta band. The effective connectivity is evaluated in terms of the Grange... |
q-bio/0608037 | Yong Chen | Shao-Meng Qin, Yong Chen and Pan Zhang | Network growth approach to macroevolution | 16 pages, 7 figures, published version | New J. Phys. 9 (2007) 220 | 10.1088/1367-2630/9/7/220 | null | q-bio.PE | null | We propose a novel network growth model coupled with the competition
interaction to simulate macroevolution. Our work shows that the competition
plays an important role in macroevolution and it is more rational to describe
the interaction between species by network structures. Our model presents a
complete picture of... | [
{
"created": "Fri, 25 Aug 2006 08:40:47 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Nov 2006 10:32:10 GMT",
"version": "v2"
},
{
"created": "Sat, 10 Mar 2007 03:41:36 GMT",
"version": "v3"
},
{
"created": "Wed, 11 Jul 2007 05:42:07 GMT",
"version": "v4"
}
] | 2007-07-11 | [
[
"Qin",
"Shao-Meng",
""
],
[
"Chen",
"Yong",
""
],
[
"Zhang",
"Pan",
""
]
] | We propose a novel network growth model coupled with the competition interaction to simulate macroevolution. Our work shows that the competition plays an important role in macroevolution and it is more rational to describe the interaction between species by network structures. Our model presents a complete picture of t... |
1110.2727 | Irina Manina | I.V. Manina, N.M. Peretolchina, N.S. Saprikina, A.M. Kozlov, I.N.
Mikhaylova, K.I. Jordanya A.Y. Barishnikov | Prospects of using Antagonist Histamine H2-Receptor (Cimetidinum) as
Adjuvant for Melanoma Biotherapy Treatment | 14 pages, 5 figures; ISSN 0236-297X. International Journal of
Immunopathology, Allergology, Infectology. 2010, #4: P. 42-51 | International Journal of Immunopathology, Allergology, Infectology
2010, #4: P. 42-51 | null | null | q-bio.TO q-bio.CB | http://creativecommons.org/licenses/publicdomain/ | Improvement of anti-tumor biotherapy effectiveness by modification of immune
response with histamine H2 receptor Cimetidinum (CM) was studied using the
experimental murine model of B16 F10 melanoma in vivo. It is shown that skin
melanoma biotherapy by antitumor whole-cell GM-CSF-producing vaccine with the
addition of... | [
{
"created": "Wed, 12 Oct 2011 18:17:47 GMT",
"version": "v1"
}
] | 2011-10-13 | [
[
"Manina",
"I. V.",
""
],
[
"Peretolchina",
"N. M.",
""
],
[
"Saprikina",
"N. S.",
""
],
[
"Kozlov",
"A. M.",
""
],
[
"Mikhaylova",
"I. N.",
""
],
[
"Barishnikov",
"K. I. Jordanya A. Y.",
""
]
] | Improvement of anti-tumor biotherapy effectiveness by modification of immune response with histamine H2 receptor Cimetidinum (CM) was studied using the experimental murine model of B16 F10 melanoma in vivo. It is shown that skin melanoma biotherapy by antitumor whole-cell GM-CSF-producing vaccine with the addition of C... |
2001.11582 | Jeff Mohl | Jeff T. Mohl, Valeria C. Caruso, Surya T. Tokdar, Jennifer M. Groh | Sensitivity and specificity of a Bayesian single trial analysis for time
varying neural signals | Accepted for publication in Neurons, Behavior, Data analysis, and
Theory | Neurons, Behavior, Data Analysis, and Theory, 2020 | 10.1101/690958 | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | We recently reported the existence of fluctuations in neural signals that may
permit neurons to code multiple simultaneous stimuli sequentially across time.
This required deploying a novel statistical approach to permit investigation of
neural activity at the scale of individual trials. Here we present tests using
sy... | [
{
"created": "Thu, 30 Jan 2020 21:59:06 GMT",
"version": "v1"
}
] | 2020-02-03 | [
[
"Mohl",
"Jeff T.",
""
],
[
"Caruso",
"Valeria C.",
""
],
[
"Tokdar",
"Surya T.",
""
],
[
"Groh",
"Jennifer M.",
""
]
] | We recently reported the existence of fluctuations in neural signals that may permit neurons to code multiple simultaneous stimuli sequentially across time. This required deploying a novel statistical approach to permit investigation of neural activity at the scale of individual trials. Here we present tests using synt... |
2401.04155 | Jiajia Liu | Jiajia Liu, Mengyuan Yang, Yankai Yu, Haixia Xu, Kang Li and Xiaobo
Zhou | Large language models in bioinformatics: applications and perspectives | 7 figures | null | null | null | q-bio.QM cs.CL | http://creativecommons.org/licenses/by/4.0/ | Large language models (LLMs) are a class of artificial intelligence models
based on deep learning, which have great performance in various tasks,
especially in natural language processing (NLP). Large language models
typically consist of artificial neural networks with numerous parameters,
trained on large amounts of... | [
{
"created": "Mon, 8 Jan 2024 17:26:59 GMT",
"version": "v1"
}
] | 2024-01-10 | [
[
"Liu",
"Jiajia",
""
],
[
"Yang",
"Mengyuan",
""
],
[
"Yu",
"Yankai",
""
],
[
"Xu",
"Haixia",
""
],
[
"Li",
"Kang",
""
],
[
"Zhou",
"Xiaobo",
""
]
] | Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of artificial neural networks with numerous parameters, trained on large amounts of u... |
1110.3317 | David Albers | DJ Albers, George Hripcsak, and Michael Schmidt | Population physiology: leveraging population scale (EHR) data to
understand human endocrine dynamics | null | null | 10.1371/journal.pone.0048058 | null | q-bio.QM nlin.CG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Studying physiology over a broad population for long periods of time is
difficult primarily because collecting human physiologic data is intrusive,
dangerous, and expensive. Electronic health record (EHR) data promise to
support the development and testing of mechanistic physiologic models on
diverse population, but ... | [
{
"created": "Fri, 14 Oct 2011 17:52:50 GMT",
"version": "v1"
}
] | 2015-05-30 | [
[
"Albers",
"DJ",
""
],
[
"Hripcsak",
"George",
""
],
[
"Schmidt",
"Michael",
""
]
] | Studying physiology over a broad population for long periods of time is difficult primarily because collecting human physiologic data is intrusive, dangerous, and expensive. Electronic health record (EHR) data promise to support the development and testing of mechanistic physiologic models on diverse population, but li... |
2006.03735 | Caroline Uhler | Anastasiya Belyaeva, Louis Cammarata, Adityanarayanan Radhakrishnan,
Chandler Squires, Karren Dai Yang, G.V. Shivashankar, Caroline Uhler | Causal Network Models of SARS-CoV-2 Expression and Aging to Identify
Candidates for Drug Repurposing | null | null | 10.1038/s41467-021-21056-z | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Given the severity of the SARS-CoV-2 pandemic, a major challenge is to
rapidly repurpose existing approved drugs for clinical interventions. While a
number of data-driven and experimental approaches have been suggested in the
context of drug repurposing, a platform that systematically integrates
available transcripto... | [
{
"created": "Fri, 5 Jun 2020 23:16:44 GMT",
"version": "v1"
}
] | 2021-04-28 | [
[
"Belyaeva",
"Anastasiya",
""
],
[
"Cammarata",
"Louis",
""
],
[
"Radhakrishnan",
"Adityanarayanan",
""
],
[
"Squires",
"Chandler",
""
],
[
"Yang",
"Karren Dai",
""
],
[
"Shivashankar",
"G. V.",
""
],
[
"Uhler",
... | Given the severity of the SARS-CoV-2 pandemic, a major challenge is to rapidly repurpose existing approved drugs for clinical interventions. While a number of data-driven and experimental approaches have been suggested in the context of drug repurposing, a platform that systematically integrates available transcriptomi... |
2012.08580 | Yuan Luo | Yuan Luo, Chengsheng Mao | PANTHER: Pathway Augmented Nonnegative Tensor factorization for
HighER-order feature learning | Accepted by 35th AAAI Conference on Artificial Intelligence (AAAI
2021) | null | null | null | q-bio.QM cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genetic pathways usually encode molecular mechanisms that can inform targeted
interventions. It is often challenging for existing machine learning approaches
to jointly model genetic pathways (higher-order features) and variants (atomic
features), and present to clinicians interpretable models. In order to build
more... | [
{
"created": "Tue, 15 Dec 2020 19:39:55 GMT",
"version": "v1"
}
] | 2021-11-19 | [
[
"Luo",
"Yuan",
""
],
[
"Mao",
"Chengsheng",
""
]
] | Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more a... |
1307.7658 | Daniel Larremore | Daniel B. Larremore, Woodrow L. Shew, Edward Ott, Francesco
Sorrentino, Juan G. Restrepo | Inhibition causes ceaseless dynamics in networks of excitable nodes | 11 pages, 6 figures | Phys. Rev. Lett. 112, 138103 (2014) | 10.1103/PhysRevLett.112.138103 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The collective dynamics of a network of excitable nodes changes dramatically
when inhibitory nodes are introduced. We consider inhibitory nodes which may be
activated just like excitatory nodes but, upon activating, decrease the
probability of activation of network neighbors. We show that, although the
direct effect ... | [
{
"created": "Mon, 29 Jul 2013 17:36:18 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Dec 2013 20:49:45 GMT",
"version": "v2"
},
{
"created": "Fri, 21 Feb 2014 17:20:05 GMT",
"version": "v3"
}
] | 2014-04-03 | [
[
"Larremore",
"Daniel B.",
""
],
[
"Shew",
"Woodrow L.",
""
],
[
"Ott",
"Edward",
""
],
[
"Sorrentino",
"Francesco",
""
],
[
"Restrepo",
"Juan G.",
""
]
] | The collective dynamics of a network of excitable nodes changes dramatically when inhibitory nodes are introduced. We consider inhibitory nodes which may be activated just like excitatory nodes but, upon activating, decrease the probability of activation of network neighbors. We show that, although the direct effect of... |
2406.19041 | Manuel Morante | Manuel Morante, Kristian Fr{\o}lich and Naveed ur Rehman | Multiscale Functional Connectivity: Exploring the brain functional
connectivity at different timescales | 33 pages, 7 figures and 3 tables | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-sa/4.0/ | Human brains exhibit highly organized multiscale neurophysiological dynamics.
Understanding those dynamic changes and the neuronal networks involved is
critical for understanding how the brain functions in health and disease.
Functional Magnetic Resonance Imaging (fMRI) is a prevalent neuroimaging
technique for study... | [
{
"created": "Thu, 27 Jun 2024 09:48:05 GMT",
"version": "v1"
}
] | 2024-06-28 | [
[
"Morante",
"Manuel",
""
],
[
"Frølich",
"Kristian",
""
],
[
"Rehman",
"Naveed ur",
""
]
] | Human brains exhibit highly organized multiscale neurophysiological dynamics. Understanding those dynamic changes and the neuronal networks involved is critical for understanding how the brain functions in health and disease. Functional Magnetic Resonance Imaging (fMRI) is a prevalent neuroimaging technique for studyin... |
1304.1262 | Conrad Sanderson | Arnold Wiliem, Yongkang Wong, Conrad Sanderson, Peter Hobson, Shaokang
Chen, Brian C. Lovell | Classification of Human Epithelial Type 2 Cell Indirect
Immunofluoresence Images via Codebook Based Descriptors | null | IEEE Workshop on Applications of Computer Vision (WACV), pp.
95-102, 2013 | 10.1109/WACV.2013.6475005 | null | q-bio.CB cs.CV q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Anti-Nuclear Antibody (ANA) clinical pathology test is commonly used to
identify the existence of various diseases. A hallmark method for identifying
the presence of ANAs is the Indirect Immunofluorescence method on Human
Epithelial (HEp-2) cells, due to its high sensitivity and the large range of
antigens that c... | [
{
"created": "Thu, 4 Apr 2013 07:51:32 GMT",
"version": "v1"
}
] | 2013-04-05 | [
[
"Wiliem",
"Arnold",
""
],
[
"Wong",
"Yongkang",
""
],
[
"Sanderson",
"Conrad",
""
],
[
"Hobson",
"Peter",
""
],
[
"Chen",
"Shaokang",
""
],
[
"Lovell",
"Brian C.",
""
]
] | The Anti-Nuclear Antibody (ANA) clinical pathology test is commonly used to identify the existence of various diseases. A hallmark method for identifying the presence of ANAs is the Indirect Immunofluorescence method on Human Epithelial (HEp-2) cells, due to its high sensitivity and the large range of antigens that can... |
1704.02577 | Myrl Marmarelis | Myrl G. Marmarelis | Efficient and Robust Polylinear Analysis of Noisy Time Series | 6 pages, 9 figures | null | null | null | q-bio.QM stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A method is proposed to generate an optimal fit of a number of connected
linear trend segments onto time-series data. To be able to efficiently handle
many lines, the method employs a stochastic search procedure to determine
optimal transition point locations. Traditional methods use exhaustive grid
searches, which s... | [
{
"created": "Sun, 9 Apr 2017 09:15:15 GMT",
"version": "v1"
}
] | 2017-04-11 | [
[
"Marmarelis",
"Myrl G.",
""
]
] | A method is proposed to generate an optimal fit of a number of connected linear trend segments onto time-series data. To be able to efficiently handle many lines, the method employs a stochastic search procedure to determine optimal transition point locations. Traditional methods use exhaustive grid searches, which sev... |
1906.07794 | Milad Mostavi | Milad Mostavi, Yu-Chiao Chiu, Yufei Huang, Yidong Chen | Convolutional neural network models for cancer type prediction based on
gene expression | 34 pages, 5 figures, This paper was presented at ICIBM June, 2019 at
Ohio Columbus, and will be published in BMC Genomics journal. Keywords: Deep
Learning; Convolutional Neural Networks, The Cancer Genome Atlas; Cancer type
prediction; Cancer gene markers; Breast cancer subtype prediction | null | null | null | q-bio.GN cs.LG q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Background Precise prediction of cancer types is vital for cancer diagnosis
and therapy. Important cancer marker genes can be inferred through predictive
model. Several studies have attempted to build machine learning models for this
task however none has taken into consideration the effects of tissue of origin
that ... | [
{
"created": "Tue, 18 Jun 2019 20:27:35 GMT",
"version": "v1"
}
] | 2019-06-20 | [
[
"Mostavi",
"Milad",
""
],
[
"Chiu",
"Yu-Chiao",
""
],
[
"Huang",
"Yufei",
""
],
[
"Chen",
"Yidong",
""
]
] | Background Precise prediction of cancer types is vital for cancer diagnosis and therapy. Important cancer marker genes can be inferred through predictive model. Several studies have attempted to build machine learning models for this task however none has taken into consideration the effects of tissue of origin that ca... |
1501.02278 | Jose H H Grisi-Filho Prof Dr | Jos\'e Henrique Hildebrand Grisi-Filho, Marcos Amaku | Caracteriza\c{c}\~ao de circuitos pecu\'arios com base em redes de
movimenta\c{c}\~ao de animais | 46 pages, PhD Thesis, Portuguese | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/3.0/ | A network is a set of nodes that are linked together by a set of edges.
Networks can represent any set of objects that have relations among themselves.
Communities are sets of nodes that are related in an important way, probably
sharing common properties and/or playing similar roles within a network. When
network ana... | [
{
"created": "Fri, 9 Jan 2015 21:24:48 GMT",
"version": "v1"
}
] | 2015-01-13 | [
[
"Grisi-Filho",
"José Henrique Hildebrand",
""
],
[
"Amaku",
"Marcos",
""
]
] | A network is a set of nodes that are linked together by a set of edges. Networks can represent any set of objects that have relations among themselves. Communities are sets of nodes that are related in an important way, probably sharing common properties and/or playing similar roles within a network. When network analy... |
0909.4158 | Thierry Rabilloud | Thierry Rabilloud (BBSI), Ali R Vaezzadeh, Noelle Potier, C\'ecile
Lelong (BBSI), Emmanuelle Leize-Wagner, Mireille Chevallet (BBSI) | Power and limitations of electrophoretic separations in proteomics
strategies | null | Mass Spectrometry Reviews 28, 5 (2009) 816-43 | 10.1002/mas.20204 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteomics can be defined as the large-scale analysis of proteins. Due to the
complexity of biological systems, it is required to concatenate various
separation techniques prior to mass spectrometry. These techniques, dealing
with proteins or peptides, can rely on chromatography or electrophoresis. In
this review, th... | [
{
"created": "Wed, 23 Sep 2009 09:29:36 GMT",
"version": "v1"
}
] | 2009-09-24 | [
[
"Rabilloud",
"Thierry",
"",
"BBSI"
],
[
"Vaezzadeh",
"Ali R",
"",
"BBSI"
],
[
"Potier",
"Noelle",
"",
"BBSI"
],
[
"Lelong",
"Cécile",
"",
"BBSI"
],
[
"Leize-Wagner",
"Emmanuelle",
"",
"BBSI"
],
[
"Chevallet",
... | Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the ... |
1605.03076 | Bernhard Mehlig | M. Rafajlovic, A. Emanuelsson, K. Johannesson, R. K. Butlin, B. Mehlig | A universal mechanism generating clusters of differentiated loci during
divergence-with-migration | 32 pages, 4 figures, 1 table, supplementary material | Evolution 70 (2016) 1609 | 10.1111/evo.12957 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-wide patterns of genetic divergence reveal mechanisms of adaptation
under gene flow. Empirical data show that divergence is mostly concentrated in
narrow genomic regions. This pattern may arise because differentiated loci
protect nearby mutations from gene flow, but recent theory suggests this
mechanism is ins... | [
{
"created": "Tue, 10 May 2016 16:01:59 GMT",
"version": "v1"
}
] | 2017-02-21 | [
[
"Rafajlovic",
"M.",
""
],
[
"Emanuelsson",
"A.",
""
],
[
"Johannesson",
"K.",
""
],
[
"Butlin",
"R. K.",
""
],
[
"Mehlig",
"B.",
""
]
] | Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect nearby mutations from gene flow, but recent theory suggests this mechanism is insuf... |
1807.00061 | Elisenda Feliu | Meritxell S\'aez, Carsten Wiuf, Elisenda Feliu | Nonnegative linear elimination for chemical reaction networks | null | null | null | null | q-bio.MN math.DS physics.chem-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider linear elimination of variables in steady state equations of a
chemical reaction network. Particular subsets of variables corresponding to
sets of so-called reactant-noninteracting species, are introduced. The steady
state equations for the variables in such a set, taken together with potential
linear con... | [
{
"created": "Fri, 29 Jun 2018 20:34:59 GMT",
"version": "v1"
}
] | 2018-07-03 | [
[
"Sáez",
"Meritxell",
""
],
[
"Wiuf",
"Carsten",
""
],
[
"Feliu",
"Elisenda",
""
]
] | We consider linear elimination of variables in steady state equations of a chemical reaction network. Particular subsets of variables corresponding to sets of so-called reactant-noninteracting species, are introduced. The steady state equations for the variables in such a set, taken together with potential linear conse... |
1612.03760 | Daniele Marinazzo | Javier Rasero, Mario Pellicoro, Leonardo Angelini, Jesus M. Cortes,
Daniele Marinazzo, and Sebastiano Stramaglia | Consensus clustering approach to group brain connectivity matrices | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A novel approach rooted on the notion of consensus clustering, a strategy
developed for community detection in complex networks, is proposed to cope with
the heterogeneity that characterizes connectivity matrices in health and
disease. The method can be summarized as follows:
(i) define, for each node, a distance m... | [
{
"created": "Mon, 12 Dec 2016 16:10:05 GMT",
"version": "v1"
},
{
"created": "Mon, 8 May 2017 12:56:16 GMT",
"version": "v2"
}
] | 2017-05-09 | [
[
"Rasero",
"Javier",
""
],
[
"Pellicoro",
"Mario",
""
],
[
"Angelini",
"Leonardo",
""
],
[
"Cortes",
"Jesus M.",
""
],
[
"Marinazzo",
"Daniele",
""
],
[
"Stramaglia",
"Sebastiano",
""
]
] | A novel approach rooted on the notion of consensus clustering, a strategy developed for community detection in complex networks, is proposed to cope with the heterogeneity that characterizes connectivity matrices in health and disease. The method can be summarized as follows: (i) define, for each node, a distance matri... |
2209.03324 | Casey Barkan | Casey O. Barkan and Robijn F. Bruinsma | Geometric Signatures of Switching Behavior in Mechanobiology | 6 pages, 3 figures | null | 10.1016/j.bpj.2022.11.1173 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The proteins involved in cells' mechanobiological processes have evolved
specialized and surprising responses to applied forces. Biochemical
transformations that show catch-to-slip switching and force-induced pathway
switching serve important functions in cell adhesion, mechano-sensing and
signaling, and protein fold... | [
{
"created": "Wed, 7 Sep 2022 17:33:04 GMT",
"version": "v1"
},
{
"created": "Mon, 26 Sep 2022 09:53:23 GMT",
"version": "v2"
},
{
"created": "Sun, 26 Feb 2023 18:48:01 GMT",
"version": "v3"
}
] | 2023-07-19 | [
[
"Barkan",
"Casey O.",
""
],
[
"Bruinsma",
"Robijn F.",
""
]
] | The proteins involved in cells' mechanobiological processes have evolved specialized and surprising responses to applied forces. Biochemical transformations that show catch-to-slip switching and force-induced pathway switching serve important functions in cell adhesion, mechano-sensing and signaling, and protein foldin... |
0909.2985 | Jerome Vanclay | Jerome K. Vanclay, Peter J. Sands | Calibrating the self-thinning frontier | Typos corrected, missing reference added | Forest Ecology and Management 259 (2009) 81-85 | 10.1016/j.foreco.2009.09.045 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calibration of the self-thinning frontier in even-aged monocultures is
hampered by scarce data and by subjective decisions about the proximity of data
to the frontier. We present a simple model that applies to observations of the
full trajectory of stand mean diameter across a range of densities not close to
the fron... | [
{
"created": "Wed, 16 Sep 2009 11:33:42 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Oct 2009 10:19:54 GMT",
"version": "v2"
}
] | 2009-11-17 | [
[
"Vanclay",
"Jerome K.",
""
],
[
"Sands",
"Peter J.",
""
]
] | Calibration of the self-thinning frontier in even-aged monocultures is hampered by scarce data and by subjective decisions about the proximity of data to the frontier. We present a simple model that applies to observations of the full trajectory of stand mean diameter across a range of densities not close to the fronti... |
1702.07649 | Quinton Skilling | Quinton M Skilling, Daniel Maruyama, Nicolette Ognjanovski, Sara J
Aton, and Michal Zochowski | Criticality, stability, competition, and consolidation of new
representations in brain networks | 6 Figures | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain forms and stores distributed representations from sparse external
input that compete for neuronal resources with already stored memory traces. It
is unclear what dynamical properties of neural systems allow formation and
subsequent consolidation of new, distributed memory representations under these
conditi... | [
{
"created": "Fri, 24 Feb 2017 16:30:54 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Feb 2018 17:47:23 GMT",
"version": "v2"
}
] | 2018-02-08 | [
[
"Skilling",
"Quinton M",
""
],
[
"Maruyama",
"Daniel",
""
],
[
"Ognjanovski",
"Nicolette",
""
],
[
"Aton",
"Sara J",
""
],
[
"Zochowski",
"Michal",
""
]
] | The brain forms and stores distributed representations from sparse external input that compete for neuronal resources with already stored memory traces. It is unclear what dynamical properties of neural systems allow formation and subsequent consolidation of new, distributed memory representations under these condition... |
1008.5166 | Saket Navlakha | Saket Navlakha and Carl Kingsford | Network Archaeology: Uncovering Ancient Networks from Present-day
Interactions | 16 pages, 10 figures | null | 10.1371/journal.pcbi.1001119 | null | q-bio.MN cs.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Often questions arise about old or extinct networks. What proteins interacted
in a long-extinct ancestor species of yeast? Who were the central players in
the Last.fm social network 3 years ago? Our ability to answer such questions
has been limited by the unavailability of past versions of networks. To
overcome these... | [
{
"created": "Mon, 30 Aug 2010 21:00:27 GMT",
"version": "v1"
}
] | 2015-05-19 | [
[
"Navlakha",
"Saket",
""
],
[
"Kingsford",
"Carl",
""
]
] | Often questions arise about old or extinct networks. What proteins interacted in a long-extinct ancestor species of yeast? Who were the central players in the Last.fm social network 3 years ago? Our ability to answer such questions has been limited by the unavailability of past versions of networks. To overcome these l... |
1403.2352 | Benoit Gauzens | Benoit Gauzens, Elisa Th\'ebault, G\'erard Lacroix, St\'ephane
Legendre | Trophic groups and modules: two levels of group detection in food webs | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Within food webs, species can be partitioned into groups according to various
criteria. Two notions have received particular attention: trophic groups, which
have been used for decades in the ecological literature, and more recently,
modules. The relationship between these two group definitions remains unknown
in emp... | [
{
"created": "Fri, 21 Feb 2014 09:59:31 GMT",
"version": "v1"
},
{
"created": "Mon, 13 Apr 2015 12:51:37 GMT",
"version": "v2"
}
] | 2015-04-14 | [
[
"Gauzens",
"Benoit",
""
],
[
"Thébault",
"Elisa",
""
],
[
"Lacroix",
"Gérard",
""
],
[
"Legendre",
"Stéphane",
""
]
] | Within food webs, species can be partitioned into groups according to various criteria. Two notions have received particular attention: trophic groups, which have been used for decades in the ecological literature, and more recently, modules. The relationship between these two group definitions remains unknown in empir... |
2309.14523 | Christian Klos | Christian Klos, Raoul-Martin Memmesheimer | Smooth Exact Gradient Descent Learning in Spiking Neural Networks | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Artificial neural networks are highly successfully trained with
backpropagation. For spiking neural networks, however, a similar gradient
descent scheme seems prohibitive due to the sudden, disruptive (dis-)appearance
of spikes. Here, we demonstrate exact gradient descent learning based on
spiking dynamics that chang... | [
{
"created": "Mon, 25 Sep 2023 20:51:00 GMT",
"version": "v1"
}
] | 2023-09-27 | [
[
"Klos",
"Christian",
""
],
[
"Memmesheimer",
"Raoul-Martin",
""
]
] | Artificial neural networks are highly successfully trained with backpropagation. For spiking neural networks, however, a similar gradient descent scheme seems prohibitive due to the sudden, disruptive (dis-)appearance of spikes. Here, we demonstrate exact gradient descent learning based on spiking dynamics that change ... |
2006.08356 | Luigi Brugnano | Luigi Brugnano, Felice Iavernaro, Paolo Zanzottera | The hidden side of COVID-19 spread in Italy | 21 pages, 10 figures | Math Meth Appl Sci. (2020) 1-14 | 10.1002/mma.7039 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background. The paper concerns the SARS-CoV2 (COVID-19) pandemic that,
starting from the end of February 2020, began spreading along the Italian
peninsula, by first attacking small communities in north regions, and then
extending to the center and south of Italy, including the two main islands.
Objective. The creat... | [
{
"created": "Thu, 11 Jun 2020 18:26:15 GMT",
"version": "v1"
}
] | 2020-11-25 | [
[
"Brugnano",
"Luigi",
""
],
[
"Iavernaro",
"Felice",
""
],
[
"Zanzottera",
"Paolo",
""
]
] | Background. The paper concerns the SARS-CoV2 (COVID-19) pandemic that, starting from the end of February 2020, began spreading along the Italian peninsula, by first attacking small communities in north regions, and then extending to the center and south of Italy, including the two main islands. Objective. The creation ... |
2304.01348 | James Stone Dr | James V Stone | Methods for Estimating Neural Information | 7 pages, 2 figures | null | null | null | q-bio.NC cs.IT math.IT | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Estimating the Shannon information associated with individual neurons is a
non-trivial problem. Three key methods used to estimate the mutual information
between neuron inputs and outputs are described, and a list of further readings
is provided.
| [
{
"created": "Tue, 20 Dec 2022 12:13:48 GMT",
"version": "v1"
}
] | 2023-04-05 | [
[
"Stone",
"James V",
""
]
] | Estimating the Shannon information associated with individual neurons is a non-trivial problem. Three key methods used to estimate the mutual information between neuron inputs and outputs are described, and a list of further readings is provided. |
q-bio/0611074 | Pitman Damien | Janko Gravner (1), Damien Pitman (1), Sergey Gavrilets (2), ((1)
Mathematics Department, University of California, Davis, (2) Department of
Ecology and Evolutionary Biology and Mathematics, University of Tennessee,
Knoxville) | Percolation on fitness landscapes: effects of correlation, phenotype,
and incompatibilities | 31 pages, 4 figures, 1 table | null | null | null | q-bio.PE | null | We study how correlations in the random fitness assignment may affect the
structure of fitness landscapes. We consider three classes of fitness models.
The first is a continuous phenotype space in which individuals are
characterized by a large number of continuously varying traits such as size,
weight, color, or conc... | [
{
"created": "Thu, 23 Nov 2006 04:16:41 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Gravner",
"Janko",
""
],
[
"Pitman",
"Damien",
""
],
[
"Gavrilets",
"Sergey",
""
]
] | We study how correlations in the random fitness assignment may affect the structure of fitness landscapes. We consider three classes of fitness models. The first is a continuous phenotype space in which individuals are characterized by a large number of continuously varying traits such as size, weight, color, or concen... |
0912.1637 | Joshua Vogelstein | Joshua T. Vogelstein, Adam M. Packer, Tim A. Machado, Tanya Sippy,
Baktash Babadi, Rafael Yuste, Liam Paninski | Fast non-negative deconvolution for spike train inference from
population calcium imaging | 22 pages, 10 figures | null | 10.1152/jn.01073.2009 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Calcium imaging for observing spiking activity from large populations of
neurons are quickly gaining popularity. While the raw data are fluorescence
movies, the underlying spike trains are of interest. This work presents a fast
non-negative deconvolution filter to infer the approximately most likely spike
train for e... | [
{
"created": "Wed, 9 Dec 2009 19:19:19 GMT",
"version": "v1"
}
] | 2011-02-21 | [
[
"Vogelstein",
"Joshua T.",
""
],
[
"Packer",
"Adam M.",
""
],
[
"Machado",
"Tim A.",
""
],
[
"Sippy",
"Tanya",
""
],
[
"Babadi",
"Baktash",
""
],
[
"Yuste",
"Rafael",
""
],
[
"Paninski",
"Liam",
""
]
] | Calcium imaging for observing spiking activity from large populations of neurons are quickly gaining popularity. While the raw data are fluorescence movies, the underlying spike trains are of interest. This work presents a fast non-negative deconvolution filter to infer the approximately most likely spike train for eac... |
0810.2946 | Aleksandra Walczak | Aleksandra M. Walczak and Peter G. Wolynes | Gene-gene cooperativity in small networks | 22 pages, 10 figures | null | 10.1016/j.bpj.2009.03.005 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show how to construct a reduced description of interacting genes in noisy,
small regulatory networks using coupled binary "spin" variables. Treating both
the protein number and gene expression state variables stochastically and on
equal footing we propose a mapping which connects the molecular level
description of... | [
{
"created": "Thu, 16 Oct 2008 15:28:58 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Walczak",
"Aleksandra M.",
""
],
[
"Wolynes",
"Peter G.",
""
]
] | We show how to construct a reduced description of interacting genes in noisy, small regulatory networks using coupled binary "spin" variables. Treating both the protein number and gene expression state variables stochastically and on equal footing we propose a mapping which connects the molecular level description of n... |
2201.04927 | Alain Destexhe | Davide Forcella, Alberto Romagnoni, Alain Destexhe | Neuronal cable equations derived from the hydrodynamic motion of charged
particles | null | null | 10.1007/s00033-023-01986-y | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Neuronal cable theory is usually derived from an electric analogue of the
membrane, which contrasts with the slow movement of ions in aqueous media. We
show here that it is possible to derive neuronal cable equations from a
different perspective, based on the laws of hydrodynamic motion of charged
particles (Navier-S... | [
{
"created": "Thu, 13 Jan 2022 12:52:09 GMT",
"version": "v1"
}
] | 2023-04-26 | [
[
"Forcella",
"Davide",
""
],
[
"Romagnoni",
"Alberto",
""
],
[
"Destexhe",
"Alain",
""
]
] | Neuronal cable theory is usually derived from an electric analogue of the membrane, which contrasts with the slow movement of ions in aqueous media. We show here that it is possible to derive neuronal cable equations from a different perspective, based on the laws of hydrodynamic motion of charged particles (Navier-Sto... |
2406.02659 | Andrew Luo | Jacob Yeung, Andrew F. Luo, Gabriel Sarch, Margaret M. Henderson, Deva
Ramanan, Michael J. Tarr | Neural Representations of Dynamic Visual Stimuli | null | null | null | null | q-bio.NC cs.AI cs.CV | http://creativecommons.org/licenses/by/4.0/ | Humans experience the world through constantly changing visual stimuli, where
scenes can shift and move, change in appearance, and vary in distance. The
dynamic nature of visual perception is a fundamental aspect of our daily lives,
yet the large majority of research on object and scene processing, particularly
using... | [
{
"created": "Tue, 4 Jun 2024 17:59:49 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Yeung",
"Jacob",
""
],
[
"Luo",
"Andrew F.",
""
],
[
"Sarch",
"Gabriel",
""
],
[
"Henderson",
"Margaret M.",
""
],
[
"Ramanan",
"Deva",
""
],
[
"Tarr",
"Michael J.",
""
]
] | Humans experience the world through constantly changing visual stimuli, where scenes can shift and move, change in appearance, and vary in distance. The dynamic nature of visual perception is a fundamental aspect of our daily lives, yet the large majority of research on object and scene processing, particularly using f... |
2210.10901 | Alberto Coccarelli Coccarelli | Albertoo Coccarelli, Michael D. Nelson | Modeling Reactive Hyperemia to better understand and assess
Microvascular Function: a review of techniques | n/a | Annals of Biomedical Engineering 2023 | 10.1007/s10439-022-03134-5 | null | q-bio.TO | http://creativecommons.org/licenses/by/4.0/ | Reactive hyperemia is a well-established technique for the non-invasive
evaluation of the peripheral microcirculatory function, measured as the
magnitude of limb re-perfusion after a brief period of ischemia. Despite
widespread adoption by researchers and clinicians alike, many uncertainties
remain surrounding interp... | [
{
"created": "Wed, 19 Oct 2022 21:42:27 GMT",
"version": "v1"
}
] | 2023-02-03 | [
[
"Coccarelli",
"Albertoo",
""
],
[
"Nelson",
"Michael D.",
""
]
] | Reactive hyperemia is a well-established technique for the non-invasive evaluation of the peripheral microcirculatory function, measured as the magnitude of limb re-perfusion after a brief period of ischemia. Despite widespread adoption by researchers and clinicians alike, many uncertainties remain surrounding interpre... |
2005.10517 | Marco Storace PhD | Valentina Baruzzi, Matteo Lodi, Marco Storace, Andrey Shilnikov | Generalized half-center oscillators with short-term synaptic plasticity | null | Phys. Rev. E 102, 032406 (2020) | 10.1103/PhysRevE.102.032406 | null | q-bio.NC math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | How can we develop simple yet realistic models of the small neural circuits
known as central pattern generators (CPGs), which contribute to generate
complex multi-phase locomotion in living animals? In this paper we introduce a
new model (with design criteria) of a generalized half-center oscillator
(gHCO), (pools of... | [
{
"created": "Thu, 21 May 2020 08:43:16 GMT",
"version": "v1"
}
] | 2020-09-16 | [
[
"Baruzzi",
"Valentina",
""
],
[
"Lodi",
"Matteo",
""
],
[
"Storace",
"Marco",
""
],
[
"Shilnikov",
"Andrey",
""
]
] | How can we develop simple yet realistic models of the small neural circuits known as central pattern generators (CPGs), which contribute to generate complex multi-phase locomotion in living animals? In this paper we introduce a new model (with design criteria) of a generalized half-center oscillator (gHCO), (pools of) ... |
1910.06965 | Samaneh Jozashoori | Samaneh Jozashoori, Amir Jozashoori, Heiko Schoof | AFDP: An Automated Function Description Prediction Approach to Improve
Accuracy of Protein Function Predictions | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | With the rapid growth in high-throughput biological sequencing technologies
and subsequently the amount of produced omics data, it is essential to develop
automated methods to annotate the functionality of unknown genes and proteins.
There are developed tools such as AHRD applying known proteins characterization
to a... | [
{
"created": "Tue, 15 Oct 2019 12:19:34 GMT",
"version": "v1"
}
] | 2019-10-17 | [
[
"Jozashoori",
"Samaneh",
""
],
[
"Jozashoori",
"Amir",
""
],
[
"Schoof",
"Heiko",
""
]
] | With the rapid growth in high-throughput biological sequencing technologies and subsequently the amount of produced omics data, it is essential to develop automated methods to annotate the functionality of unknown genes and proteins. There are developed tools such as AHRD applying known proteins characterization to ann... |
2210.01691 | Kevin McKee | Kevin McKee, Ian Crandell, Rishidev Chaudhuri, Randall O'Reilly | Adaptive Synaptic Failure Enables Sampling from Posterior Predictive
Distributions in the Brain | 23 pages, 5 figures. arXiv admin note: text overlap with
arXiv:2111.09780 | null | null | null | q-bio.NC stat.ML | http://creativecommons.org/licenses/by/4.0/ | Bayesian interpretations of neural processing require that biological
mechanisms represent and operate upon probability distributions in accordance
with Bayes' theorem. Many have speculated that synaptic failure constitutes a
mechanism of variational, i.e., approximate, Bayesian inference in the brain.
Whereas models... | [
{
"created": "Tue, 4 Oct 2022 15:41:44 GMT",
"version": "v1"
}
] | 2022-10-05 | [
[
"McKee",
"Kevin",
""
],
[
"Crandell",
"Ian",
""
],
[
"Chaudhuri",
"Rishidev",
""
],
[
"O'Reilly",
"Randall",
""
]
] | Bayesian interpretations of neural processing require that biological mechanisms represent and operate upon probability distributions in accordance with Bayes' theorem. Many have speculated that synaptic failure constitutes a mechanism of variational, i.e., approximate, Bayesian inference in the brain. Whereas models h... |
2405.18402 | Athulya Ram | Leonid Bunimovich and Athulya Ram | Antigenic Cooperation in Viral Populations: Redistribution of Loads
Among Altruistic Viruses and Maximal Load per Altruist | 37 pages, 9 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The paper continues the study of the phenomenon of local immunodeficiency
(LI) in viral cross-immunoreactivity networks, with a focus on the roles and
interactions between altruistic and persistent viral variants. As always, only
the state of stable (i.e. observable) LI is analysed. First, we show that a
single altru... | [
{
"created": "Tue, 28 May 2024 17:44:02 GMT",
"version": "v1"
}
] | 2024-05-29 | [
[
"Bunimovich",
"Leonid",
""
],
[
"Ram",
"Athulya",
""
]
] | The paper continues the study of the phenomenon of local immunodeficiency (LI) in viral cross-immunoreactivity networks, with a focus on the roles and interactions between altruistic and persistent viral variants. As always, only the state of stable (i.e. observable) LI is analysed. First, we show that a single altruis... |
1404.6448 | Markus Pagitz Dr | Markus Pagitz, Manuel Pagitz and C. H\"uhne | A modular approach to adaptive structures | 15 pages, 9 figures | null | 10.1088/1748-3182/9/4/046005 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A remarkable property of nastic, shape changing plants is their complete
fusion between actuators and structure. This is achieved by combining a large
number of cells whose geometry, internal pressures and material properties are
optimized for a given set of target shapes and stiffness requirements. An
advantage of s... | [
{
"created": "Fri, 25 Apr 2014 15:03:15 GMT",
"version": "v1"
},
{
"created": "Fri, 17 Jul 2015 18:56:58 GMT",
"version": "v2"
}
] | 2015-07-20 | [
[
"Pagitz",
"Markus",
""
],
[
"Pagitz",
"Manuel",
""
],
[
"Hühne",
"C.",
""
]
] | A remarkable property of nastic, shape changing plants is their complete fusion between actuators and structure. This is achieved by combining a large number of cells whose geometry, internal pressures and material properties are optimized for a given set of target shapes and stiffness requirements. An advantage of suc... |
1505.01642 | Thomas Risler | Pedro Campinho, Martin Behrndt, Jonas Ranft, Thomas Risler, Nicolas
Minc and Carl-Philipp Heisenberg | Tension-oriented cell divisions limit anisotropic tissue tension in
epithelial spreading during zebrafish epiboly | Methods, supplementary information and associated references are
available in the published online version of the paper at
http://www.nature.com/doifinder/10.1038/ncb2869 | Nature Cell Biology 15 (12), 1405-1414 (2013) | 10.1038/ncb2869 | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Epithelial spreading is a common and fundamental aspect of various
developmental and disease-related processes such as epithelial closure and
wound healing. A key challenge for epithelial tissues undergoing spreading is
to increase their surface area without disrupting epithelial integrity. Here we
show that orientin... | [
{
"created": "Thu, 7 May 2015 09:55:08 GMT",
"version": "v1"
}
] | 2015-05-08 | [
[
"Campinho",
"Pedro",
""
],
[
"Behrndt",
"Martin",
""
],
[
"Ranft",
"Jonas",
""
],
[
"Risler",
"Thomas",
""
],
[
"Minc",
"Nicolas",
""
],
[
"Heisenberg",
"Carl-Philipp",
""
]
] | Epithelial spreading is a common and fundamental aspect of various developmental and disease-related processes such as epithelial closure and wound healing. A key challenge for epithelial tissues undergoing spreading is to increase their surface area without disrupting epithelial integrity. Here we show that orienting ... |
1804.09256 | Giuseppe Tronci | Giuseppe Tronci | The application of collagen in advanced wound dressings | 37 pages, 6 figures, 1 table (to appear in "Advanced Textiles for
Wound Care, 2nd ed") | Advanced Textiles for Wound Care (2nd ed), 2018 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic wounds fail to proceed through an orderly and timely self healing
process, resulting in cutaneous damage with full thickness in depth and leading
to a major healthcare and economic burden worldwide. In the UK alone, 200,000
patients suffer from a chronic wound, whilst the global advanced wound care
market is ... | [
{
"created": "Tue, 24 Apr 2018 20:54:36 GMT",
"version": "v1"
},
{
"created": "Fri, 27 Apr 2018 11:39:08 GMT",
"version": "v2"
}
] | 2018-04-30 | [
[
"Tronci",
"Giuseppe",
""
]
] | Chronic wounds fail to proceed through an orderly and timely self healing process, resulting in cutaneous damage with full thickness in depth and leading to a major healthcare and economic burden worldwide. In the UK alone, 200,000 patients suffer from a chronic wound, whilst the global advanced wound care market is ex... |
1903.05288 | Sang-Yoon Kim | Sang-Yoon Kim and Woochang Lim | Effect of Interpopulation Spike-Timing-Dependent Plasticity on
Synchronized Rhythms in Neuronal Networks with Inhibitory and Excitatory
Populations | null | null | null | null | q-bio.NC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider clustered small-world networks with both inhibitory (I) and
excitatory (E) populations. This I-E neuronal network has adaptive dynamic I to
E and E to I interpopulation synaptic strengths, governed by interpopulation
spike-timing-dependent plasticity (STDP). In previous works without STDPs, fast
sparsely ... | [
{
"created": "Wed, 13 Mar 2019 01:55:15 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Aug 2019 01:02:38 GMT",
"version": "v2"
},
{
"created": "Mon, 10 Feb 2020 08:26:23 GMT",
"version": "v3"
},
{
"created": "Tue, 11 Feb 2020 05:43:03 GMT",
"version": "v4"
}
] | 2020-02-12 | [
[
"Kim",
"Sang-Yoon",
""
],
[
"Lim",
"Woochang",
""
]
] | We consider clustered small-world networks with both inhibitory (I) and excitatory (E) populations. This I-E neuronal network has adaptive dynamic I to E and E to I interpopulation synaptic strengths, governed by interpopulation spike-timing-dependent plasticity (STDP). In previous works without STDPs, fast sparsely sy... |
1308.4187 | Tahir Yusufaly | Tahir I. Yusufaly, Yun Li and Wilma K. Olson | 5-Methylation of Cytosine in CG:CG Base-Pair Steps: A Physicochemical
Mechanism for the Epigenetic Control of DNA Nanomechanics | Accepted to J. Phys. Chem. B. Supplemental Information available upon
request | null | 10.1021/jp409887t | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Van der Waals density functional theory is integrated with analysis of a
non-redundant set of protein-DNA crystal structures from the Nucleic Acid
Database to study the stacking energetics of CG:CG base-pair steps,
specifically the role of cytosine 5-methylation. Principal component analysis
of the steps reveals the ... | [
{
"created": "Mon, 19 Aug 2013 22:59:08 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2013 21:39:31 GMT",
"version": "v2"
},
{
"created": "Sun, 8 Dec 2013 19:41:44 GMT",
"version": "v3"
}
] | 2013-12-10 | [
[
"Yusufaly",
"Tahir I.",
""
],
[
"Li",
"Yun",
""
],
[
"Olson",
"Wilma K.",
""
]
] | Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the steps reveals the do... |
1312.3382 | Xiaobei Zhou | Xiaobei Zhou and Helen Lindsay and Mark D. Robinson | Robustly detecting differential expression in RNA sequencing data using
observation weights | 18 pages, 6 figures (v2) | null | null | null | q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A popular approach for comparing gene expression levels between (replicated)
conditions of RNA sequencing data relies on counting reads that map to features
of interest. Within such count-based methods, many flexible and advanced
statistical approaches now exist and offer the ability to adjust for covariates
(e.g., b... | [
{
"created": "Thu, 12 Dec 2013 02:01:15 GMT",
"version": "v1"
},
{
"created": "Fri, 14 Mar 2014 16:15:39 GMT",
"version": "v2"
}
] | 2014-03-17 | [
[
"Zhou",
"Xiaobei",
""
],
[
"Lindsay",
"Helen",
""
],
[
"Robinson",
"Mark D.",
""
]
] | A popular approach for comparing gene expression levels between (replicated) conditions of RNA sequencing data relies on counting reads that map to features of interest. Within such count-based methods, many flexible and advanced statistical approaches now exist and offer the ability to adjust for covariates (e.g., bat... |
2311.16126 | Fang Wu | Fang Wu, Stan Z. Li | A Hierarchical Training Paradigm for Antibody Structure-sequence
Co-design | null | null | null | null | q-bio.BM cs.CE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Therapeutic antibodies are an essential and rapidly expanding drug modality.
The binding specificity between antibodies and antigens is decided by
complementarity-determining regions (CDRs) at the tips of these Y-shaped
proteins. In this paper, we propose a hierarchical training paradigm (HTP) for
the antibody sequen... | [
{
"created": "Mon, 30 Oct 2023 02:39:15 GMT",
"version": "v1"
}
] | 2023-11-29 | [
[
"Wu",
"Fang",
""
],
[
"Li",
"Stan Z.",
""
]
] | Therapeutic antibodies are an essential and rapidly expanding drug modality. The binding specificity between antibodies and antigens is decided by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this paper, we propose a hierarchical training paradigm (HTP) for the antibody sequence... |
1309.4441 | Astero Provata | A. Provata, C. Nicolis and G. Nicolis | DNA viewed as an out-of-equilibrium structure | null | null | 10.1103/PhysRevE.89.052105 | null | q-bio.GN cond-mat.stat-mech nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The complexity of the primary structure of human DNA is explored using
methods from nonequilibrium statistical mechanics, dynamical systems theory and
information theory. The use of chi-square tests shows that DNA cannot be
described as a low order Markov chain of order up to $r=6$. Although detailed
balance seems to... | [
{
"created": "Tue, 17 Sep 2013 08:01:24 GMT",
"version": "v1"
}
] | 2015-06-17 | [
[
"Provata",
"A.",
""
],
[
"Nicolis",
"C.",
""
],
[
"Nicolis",
"G.",
""
]
] | The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to $r=6$. Although detailed balance seems to h... |
2306.15912 | Yufan Liu | Yufan Liu and Boxue Tian | Protein-DNA binding sites prediction based on pre-trained protein
language model and contrastive learning | null | null | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein-DNA interaction is critical for life activities such as replication,
transcription, and splicing. Identifying protein-DNA binding residues is
essential for modeling their interaction and downstream studies. However,
developing accurate and efficient computational methods for this task remains
challenging. Imp... | [
{
"created": "Wed, 28 Jun 2023 04:27:27 GMT",
"version": "v1"
}
] | 2023-06-29 | [
[
"Liu",
"Yufan",
""
],
[
"Tian",
"Boxue",
""
]
] | Protein-DNA interaction is critical for life activities such as replication, transcription, and splicing. Identifying protein-DNA binding residues is essential for modeling their interaction and downstream studies. However, developing accurate and efficient computational methods for this task remains challenging. Impro... |
2408.05695 | Zhaoyu Liu | Zhaoyu Liu, Jingxun Chen, Mingkun Xu, David H. Gracias, Ken-Tye Yong,
Yuanyuan Wei, Ho-Pui Ho | Advancements in Programmable Lipid Nanoparticles: A Comprehensive Review
of the Four-Domain Model for Precision Drug Delivery | 53 pages, 9 figures | null | null | null | q-bio.BM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Programmable lipid nanoparticles (LNPs) represent a critical advancement in
drug delivery. It offers precise spatiotemporal control over drug distribution
and release, which is essential for treating complex diseases such as cancer
and genetic disorders. However, the design and understanding of these
sophisticated sy... | [
{
"created": "Sun, 11 Aug 2024 04:50:35 GMT",
"version": "v1"
},
{
"created": "Wed, 14 Aug 2024 02:11:49 GMT",
"version": "v2"
}
] | 2024-08-15 | [
[
"Liu",
"Zhaoyu",
""
],
[
"Chen",
"Jingxun",
""
],
[
"Xu",
"Mingkun",
""
],
[
"Gracias",
"David H.",
""
],
[
"Yong",
"Ken-Tye",
""
],
[
"Wei",
"Yuanyuan",
""
],
[
"Ho",
"Ho-Pui",
""
]
] | Programmable lipid nanoparticles (LNPs) represent a critical advancement in drug delivery. It offers precise spatiotemporal control over drug distribution and release, which is essential for treating complex diseases such as cancer and genetic disorders. However, the design and understanding of these sophisticated syst... |
0707.3224 | Rudolf A. Roemer | G. Cuniberti, E. Macia, A. Rodriguez, R. A. R\"omer | Tight-binding modeling of charge migration in DNA devices | 24 PDF pages of Springer SVMult LaTeX (included), ISBN-10:
3540724931, ISBN-13: 978-3540724933 | in "Charge Migration in DNA: Perspectives from Physics, Chemistry
and Biology" (T. Chakraborty, Ed.), Springer Verlag, Berlin, pp. 1-21 (2007),
ISBN: 978-3-540-72493-3 | 10.1007/978-3-540-72494-0_1 | null | q-bio.GN cond-mat.soft q-bio.OT | null | Long range charge transfer experiments in DNA oligomers and the subsequently
measured -- and very diverse -- transport response of DNA wires in solid state
experiments exemplifies the need for a thorough theoretical understanding of
charge migration in DNA-based natural and artificial materials. Here we present
a rev... | [
{
"created": "Sat, 21 Jul 2007 19:53:08 GMT",
"version": "v1"
}
] | 2015-05-13 | [
[
"Cuniberti",
"G.",
""
],
[
"Macia",
"E.",
""
],
[
"Rodriguez",
"A.",
""
],
[
"Römer",
"R. A.",
""
]
] | Long range charge transfer experiments in DNA oligomers and the subsequently measured -- and very diverse -- transport response of DNA wires in solid state experiments exemplifies the need for a thorough theoretical understanding of charge migration in DNA-based natural and artificial materials. Here we present a revie... |
q-bio/0310015 | Jan Karbowski | Jan Karbowski | How does connectivity between cortical areas depend on brain size?
Implications for efficient computation | brain, theoretical neuroanatomy, computational neuroanatomy, cortical
areas, scaling, connectivity | Journal of Computational Neuroscience 15, 347-356 (2003) | null | null | q-bio.NC q-bio.QM | null | A formula for an average connectivity between cortical areas in mammals is
derived. Based on comparative neuroanatomical data, it is found, surprisingly,
that this connectivity is either only weakly dependent or independent of brain
size. It is discussed how this formula can be used to estimate the average
length of ... | [
{
"created": "Tue, 14 Oct 2003 01:58:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Karbowski",
"Jan",
""
]
] | A formula for an average connectivity between cortical areas in mammals is derived. Based on comparative neuroanatomical data, it is found, surprisingly, that this connectivity is either only weakly dependent or independent of brain size. It is discussed how this formula can be used to estimate the average length of ax... |
1307.3358 | Andrea Riba Mr | Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino and Michele
Caselle | A combination of transcriptional and microRNA regulation improves the
stability of the relative concentrations of target genes | 23 pages, 10 figures | null | 10.1371/journal.pcbi.1003490 | null | q-bio.MN q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is well known that, under suitable conditions, microRNAs are able to fine
tune the relative concentration of their targets to any desired value. We show
that this function is particularly effective when one of the targets is a
Transcription Factor (TF) which regulates the other targets. This combination
defines a ... | [
{
"created": "Fri, 12 Jul 2013 07:57:17 GMT",
"version": "v1"
}
] | 2015-06-16 | [
[
"Riba",
"Andrea",
""
],
[
"Bosia",
"Carla",
""
],
[
"Baroudi",
"Mariama El",
""
],
[
"Ollino",
"Laura",
""
],
[
"Caselle",
"Michele",
""
]
] | It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a Transcription Factor (TF) which regulates the other targets. This combination defines a ne... |
1302.3261 | Dominique Vuillaume | O. Bichler, W. Zhao, F. Alibart, S. Pleutin, S. Lenfant, D. Vuillaume,
C. Gamrat | Pavlov's dog associative learning demonstrated on synaptic-like organic
transistors | null | Neural Computation 25(2), 549-566 (2013) | 10.1162/NECO_a_00377 | null | q-bio.NC cond-mat.dis-nn cs.ET cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this letter, we present an original demonstration of an associative
learning neural network inspired by the famous Pavlov's dogs experiment. A
single nanoparticle organic memory field effect transistor (NOMFET) is used to
implement each synapse. We show how the physical properties of this dynamic
memristive device... | [
{
"created": "Wed, 13 Feb 2013 22:18:49 GMT",
"version": "v1"
}
] | 2013-02-19 | [
[
"Bichler",
"O.",
""
],
[
"Zhao",
"W.",
""
],
[
"Alibart",
"F.",
""
],
[
"Pleutin",
"S.",
""
],
[
"Lenfant",
"S.",
""
],
[
"Vuillaume",
"D.",
""
],
[
"Gamrat",
"C.",
""
]
] | In this letter, we present an original demonstration of an associative learning neural network inspired by the famous Pavlov's dogs experiment. A single nanoparticle organic memory field effect transistor (NOMFET) is used to implement each synapse. We show how the physical properties of this dynamic memristive device c... |
q-bio/0610002 | Sergey Gavrilets | Sergey Gavrilets and Aaron Vose | The dynamics of Machiavellian intelligence | A revised version has been published by PNAS | null | 10.1073/pnas.0601428103 | null | q-bio.PE nlin.AO | null | The "Machiavellian intelligence" hypothesis (or the "social brain"
hypothesis) posits that large brains and distinctive cognitive abilities of
humans have evolved via intense social competition in which social competitors
developed increasingly sophisticated "Machiavellian" strategies as a means to
achieve higher soc... | [
{
"created": "Sun, 1 Oct 2006 12:11:24 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Oct 2006 12:27:32 GMT",
"version": "v2"
},
{
"created": "Mon, 30 Oct 2006 23:59:50 GMT",
"version": "v3"
}
] | 2009-11-13 | [
[
"Gavrilets",
"Sergey",
""
],
[
"Vose",
"Aaron",
""
]
] | The "Machiavellian intelligence" hypothesis (or the "social brain" hypothesis) posits that large brains and distinctive cognitive abilities of humans have evolved via intense social competition in which social competitors developed increasingly sophisticated "Machiavellian" strategies as a means to achieve higher socia... |
2112.06140 | Yashar Zeighami | Yashar Zeighami, Mahsa Dadar, Justine Daoust, Melissa Pelletier,
Laurent Biertho, Leonie Bouvet-Bouchard, Stephanie Fulton, Andre Tchernof,
Alain Dagher, Denis Richard, Alan Evans, Andreanne Michaud | Impact of Weight Loss on Brain Age: Improved Brain Health Following
Bariatric Surgery | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Overweight and obese individuals tend to have increased brain age, reflecting
poorer brain health likely due to grey and white matter atrophy related to
obesity. However, it is unclear if older brain age associated with obesity can
be reversed following weight loss and cardiometabolic health improvement. The
aim of t... | [
{
"created": "Sun, 12 Dec 2021 03:46:18 GMT",
"version": "v1"
}
] | 2021-12-14 | [
[
"Zeighami",
"Yashar",
""
],
[
"Dadar",
"Mahsa",
""
],
[
"Daoust",
"Justine",
""
],
[
"Pelletier",
"Melissa",
""
],
[
"Biertho",
"Laurent",
""
],
[
"Bouvet-Bouchard",
"Leonie",
""
],
[
"Fulton",
"Stephanie",
... | Overweight and obese individuals tend to have increased brain age, reflecting poorer brain health likely due to grey and white matter atrophy related to obesity. However, it is unclear if older brain age associated with obesity can be reversed following weight loss and cardiometabolic health improvement. The aim of thi... |
0806.3130 | Alfredo Iorio | Alfredo Iorio, Samik Sen, Siddhartha Sen | Do quantum effects hold together DNA condensates? | 8 pages, 6 figures | null | null | null | q-bio.QM cond-mat.soft q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The classical electrostatic interaction between DNA molecules in water in the
presence of counterions is reconsidered and we propose it is governed by a
modified Poisson-Boltzmann equation. Quantum fluctuations are then studied and
shown to lead to a vacuum interaction that is numerically computed for several
configu... | [
{
"created": "Thu, 19 Jun 2008 06:34:27 GMT",
"version": "v1"
}
] | 2008-06-20 | [
[
"Iorio",
"Alfredo",
""
],
[
"Sen",
"Samik",
""
],
[
"Sen",
"Siddhartha",
""
]
] | The classical electrostatic interaction between DNA molecules in water in the presence of counterions is reconsidered and we propose it is governed by a modified Poisson-Boltzmann equation. Quantum fluctuations are then studied and shown to lead to a vacuum interaction that is numerically computed for several configura... |
1912.12796 | Liang Zhang | Liang Zhang, He Zhang, David H. Mathews, Liang Huang | ThreshKnot: Thresholded ProbKnot for Improved RNA Secondary Structure
Prediction | null | null | null | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | RNA structure prediction is a challenging problem, especially with
pseudoknots. Recently, there has been a shift from the classical minimum free
energy-based methods (MFE) to partition function-based ones that assemble
structures using base-pairing probabilities. Two examples of the latter group
are the popular maxim... | [
{
"created": "Mon, 30 Dec 2019 03:13:07 GMT",
"version": "v1"
},
{
"created": "Thu, 9 Jan 2020 01:36:04 GMT",
"version": "v2"
}
] | 2020-01-10 | [
[
"Zhang",
"Liang",
""
],
[
"Zhang",
"He",
""
],
[
"Mathews",
"David H.",
""
],
[
"Huang",
"Liang",
""
]
] | RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using base-pairing probabilities. Two examples of the latter group are the popular maximum... |
q-bio/0611080 | Maksim Kouza M | Mai Suan Li, Maksim Kouza, Chin-Kun Hu | Refolding upon force quench and pathways of mechanical and thermal
unfolding of ubiquitin | 35 pages, 15 figures, 1 table | Biophysical Journal, 92, 547-561 (2007) | 10.1529/biophysj.106.087684 | null | q-bio.BM | null | The refolding from stretched initial conformations of ubiquitin (PDB ID:
1ubq) under the quenched force is studied using the Go model and the Langevin
dynamics. It is shown that the refolding decouples the collapse and folding
kinetics. The force quench refolding times scale as tau_F ~ exp(f_q*x_F/k_B*T),
where f_q i... | [
{
"created": "Fri, 24 Nov 2006 07:33:19 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Li",
"Mai Suan",
""
],
[
"Kouza",
"Maksim",
""
],
[
"Hu",
"Chin-Kun",
""
]
] | The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force quench refolding times scale as tau_F ~ exp(f_q*x_F/k_B*T), where f_q is ... |
1502.07075 | Bartosz Rozycki | Bartosz Rozycki and Marek Cieplak | Citrate synthase proteins in extremophilic organisms: Studies within a
structure-based model | published in J. Chem. Phys | Journal of Chemical Physics 141, 235102 (2014) | 10.1063/1.4903747 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study four citrate synthase homodimeric proteins within a structure-based
coarse-grained model. Two of these proteins come from thermophilic bacteria,
one from a cryophilic bacterium and one from a mesophilic organism; three are
in the closed and two in the open conformations. Even though the proteins
belong to th... | [
{
"created": "Wed, 25 Feb 2015 07:54:59 GMT",
"version": "v1"
}
] | 2015-02-26 | [
[
"Rozycki",
"Bartosz",
""
],
[
"Cieplak",
"Marek",
""
]
] | We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the ... |
2111.00194 | Yusuke Maeda | Yusuke T. Maeda | Negative autoregulation controls size scaling in confined gene
expression reactions | 7 pages, 5 figures | Scientific Reports 12, 10516 (2022) | 10.1038/s41598-022-14719-4 | null | q-bio.MN physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression via transcription-translation is the most fundamental
reaction to sustain biological systems, and complex reactions such as this one
occur in a small compartment of living cells. There is increasing evidence that
t physical effects, such as molecular crowding or excluded volume effects of
transcriptio... | [
{
"created": "Sat, 30 Oct 2021 07:05:40 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Apr 2022 15:57:28 GMT",
"version": "v2"
}
] | 2022-08-04 | [
[
"Maeda",
"Yusuke T.",
""
]
] | Gene expression via transcription-translation is the most fundamental reaction to sustain biological systems, and complex reactions such as this one occur in a small compartment of living cells. There is increasing evidence that t physical effects, such as molecular crowding or excluded volume effects of transcriptiona... |
1011.1109 | David Kleinhans | David Kleinhans, Per R. Jonsson | On the impact of dispersal asymmetry on metapopulation persistence | 19 pages, 5 figures | Journal of Theoretical Biology, 290, pages 37-45 (2011) | 10.1016/j.jtbi.2011.09.002 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Metapopulation theory for a long time has assumed dispersal to be symmetric,
i.e. patches are connected through migrants dispersing bi-directionally without
a preferred direction. However, for natural populations symmetry is often
broken, e.g. for species in the marine environment dispersing through the
transport of ... | [
{
"created": "Thu, 4 Nov 2010 10:52:13 GMT",
"version": "v1"
},
{
"created": "Wed, 8 Jun 2011 09:51:35 GMT",
"version": "v2"
},
{
"created": "Thu, 1 Sep 2011 09:53:04 GMT",
"version": "v3"
}
] | 2011-10-07 | [
[
"Kleinhans",
"David",
""
],
[
"Jonsson",
"Per R.",
""
]
] | Metapopulation theory for a long time has assumed dispersal to be symmetric, i.e. patches are connected through migrants dispersing bi-directionally without a preferred direction. However, for natural populations symmetry is often broken, e.g. for species in the marine environment dispersing through the transport of pe... |
1412.0780 | Zahra Aminzare | Jana L. Gevertz, Zahra Aminzare, Kerri-Ann Norton, Judith
Perez-Velazquez, Alexandria Volkening, Katarzyna A. Rejniak | Emergence of Anti-Cancer Drug Resistance: Exploring the Importance of
the Microenvironmental Niche via a Spatial Model | null | null | null | null | q-bio.PE q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Practically, all chemotherapeutic agents lead to drug resistance. Clinically,
it is a challenge to determine whether resistance arises prior to, or as a
result of, cancer therapy. Further, a number of different intracellular and
microenvironmental factors have been correlated with the emergence of drug
resistance. Wi... | [
{
"created": "Tue, 2 Dec 2014 04:17:38 GMT",
"version": "v1"
}
] | 2014-12-03 | [
[
"Gevertz",
"Jana L.",
""
],
[
"Aminzare",
"Zahra",
""
],
[
"Norton",
"Kerri-Ann",
""
],
[
"Perez-Velazquez",
"Judith",
""
],
[
"Volkening",
"Alexandria",
""
],
[
"Rejniak",
"Katarzyna A.",
""
]
] | Practically, all chemotherapeutic agents lead to drug resistance. Clinically, it is a challenge to determine whether resistance arises prior to, or as a result of, cancer therapy. Further, a number of different intracellular and microenvironmental factors have been correlated with the emergence of drug resistance. With... |
1409.4303 | Arnab Ganguly | Arnab Ganguly, Derya Altintan, Heinz Koeppl | Jump-Diffusion Approximation of Stochastic Reaction Dynamics: Error
bounds and Algorithms | 32 pages, 7 figures | null | null | null | q-bio.QM math.PR q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Biochemical reactions can happen on different time scales and also the
abundance of species in these reactions can be very different from each other.
Classical approaches, such as deterministic or stochastic approach, fail to
account for or to exploit this multi-scale nature, respectively. In this paper,
we propose a... | [
{
"created": "Mon, 15 Sep 2014 15:52:55 GMT",
"version": "v1"
}
] | 2014-09-16 | [
[
"Ganguly",
"Arnab",
""
],
[
"Altintan",
"Derya",
""
],
[
"Koeppl",
"Heinz",
""
]
] | Biochemical reactions can happen on different time scales and also the abundance of species in these reactions can be very different from each other. Classical approaches, such as deterministic or stochastic approach, fail to account for or to exploit this multi-scale nature, respectively. In this paper, we propose a j... |
2001.03761 | Marinho Lopes | Marinho A. Lopes, Jiaxiang Zhang, Dominik Krzemi\'nski, Khalid
Hamandi, Qi Chen, Lorenzo Livi, and Naoki Masuda | Recurrence Quantification Analysis of Dynamic Brain Networks | 77 pages, 11 figures; note: the acknowledgments section is the most
complete in this arxiv version (compared to the published version in EJN) | null | 10.1111/ejn.14960 | null | q-bio.NC cond-mat.dis-nn | http://creativecommons.org/licenses/by/4.0/ | Evidence suggests that brain network dynamics is a key determinant of brain
function and dysfunction. Here we propose a new framework to assess the
dynamics of brain networks based on recurrence analysis. Our framework uses
recurrence plots and recurrence quantification analysis to characterize dynamic
networks. For ... | [
{
"created": "Sat, 11 Jan 2020 14:41:34 GMT",
"version": "v1"
},
{
"created": "Wed, 16 Sep 2020 11:04:57 GMT",
"version": "v2"
}
] | 2020-09-17 | [
[
"Lopes",
"Marinho A.",
""
],
[
"Zhang",
"Jiaxiang",
""
],
[
"Krzemiński",
"Dominik",
""
],
[
"Hamandi",
"Khalid",
""
],
[
"Chen",
"Qi",
""
],
[
"Livi",
"Lorenzo",
""
],
[
"Masuda",
"Naoki",
""
]
] | Evidence suggests that brain network dynamics is a key determinant of brain function and dysfunction. Here we propose a new framework to assess the dynamics of brain networks based on recurrence analysis. Our framework uses recurrence plots and recurrence quantification analysis to characterize dynamic networks. For re... |
2003.12089 | Jun Chen | Komi Messan, Marisabel Rodriguez Messan, Jun Chen, Gloria
DeGrandi-Hoffman, Yun Kang | Population dynamics of Varroa mite and honeybee: Effects of parasitism
with age structure and seasonality | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Honeybees play an important role in the production of many agricultural crops
and in sustaining plant diversity in undisturbed ecosystems. The rapid decline
of honeybee populations have sparked great concern worldwide. Previous studies
have shown that the parasitic Varroa mite could be the main reason for colony
loss... | [
{
"created": "Thu, 26 Mar 2020 18:13:14 GMT",
"version": "v1"
},
{
"created": "Tue, 11 Aug 2020 00:04:48 GMT",
"version": "v2"
}
] | 2020-08-12 | [
[
"Messan",
"Komi",
""
],
[
"Messan",
"Marisabel Rodriguez",
""
],
[
"Chen",
"Jun",
""
],
[
"DeGrandi-Hoffman",
"Gloria",
""
],
[
"Kang",
"Yun",
""
]
] | Honeybees play an important role in the production of many agricultural crops and in sustaining plant diversity in undisturbed ecosystems. The rapid decline of honeybee populations have sparked great concern worldwide. Previous studies have shown that the parasitic Varroa mite could be the main reason for colony losses... |
1804.06984 | Seung Ki Baek | Yohsuke Murase and Seung Ki Baek | Seven rules to avoid the tragedy of the commons | 11 pages, 4 figures | null | 10.1016/j.jtbi.2018.04.027 | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cooperation among self-interested players in a social dilemma is fragile and
easily interrupted by mistakes. In this work, we study the repeated $n$-person
public-goods game and search for a strategy that forms a cooperative Nash
equilibrium in the presence of implementation error with a guarantee that the
resulting ... | [
{
"created": "Thu, 19 Apr 2018 02:55:03 GMT",
"version": "v1"
}
] | 2018-04-20 | [
[
"Murase",
"Yohsuke",
""
],
[
"Baek",
"Seung Ki",
""
]
] | Cooperation among self-interested players in a social dilemma is fragile and easily interrupted by mistakes. In this work, we study the repeated $n$-person public-goods game and search for a strategy that forms a cooperative Nash equilibrium in the presence of implementation error with a guarantee that the resulting pa... |
2103.07107 | Maxime Lenormand | Nicolas Dubos, Cl\'ementine Pr\'eau, Maxime Lenormand, Guillaume
Papuga, Sophie Montsarrat, Pierre Denelle, Marine Le Louarn, Stien Heremans,
May Roel, Philip Roche and Sandra Luque | Assessing the effect of sample bias correction in species distribution
models | 16 pages, 6 figures + Appendix | Ecological Indicators 145, 109487 (2022) | 10.1016/j.ecolind.2022.109487 | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Open-source biodiversity databases contain a large amount of species
occurrence records, but these are often spatially biased, which affects the
reliability of species distribution models based on these records. Sample bias
correction techniques include data filtering at the cost of record numbers or
require consider... | [
{
"created": "Fri, 12 Mar 2021 07:02:04 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Nov 2021 10:12:06 GMT",
"version": "v2"
},
{
"created": "Thu, 27 Oct 2022 06:50:50 GMT",
"version": "v3"
}
] | 2022-10-28 | [
[
"Dubos",
"Nicolas",
""
],
[
"Préau",
"Clémentine",
""
],
[
"Lenormand",
"Maxime",
""
],
[
"Papuga",
"Guillaume",
""
],
[
"Montsarrat",
"Sophie",
""
],
[
"Denelle",
"Pierre",
""
],
[
"Louarn",
"Marine Le",
"... | Open-source biodiversity databases contain a large amount of species occurrence records, but these are often spatially biased, which affects the reliability of species distribution models based on these records. Sample bias correction techniques include data filtering at the cost of record numbers or require considerab... |
1909.13667 | Matus Medo | Matus Medo, Daniel M. Aebersold, Michaela Medova | ProtRank: Bypassing the imputation of missing values in differential
expression analysis of proteomic data | 18 pages, 7 figures | null | null | null | q-bio.QM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Data from discovery proteomic and phosphoproteomic experiments typically
include missing values that correspond to proteins that have not been
identified in the analyzed sample. Replacing the missing values with random
numbers, a process known as "imputation", avoids apparent infinite fold-change
values. However, the... | [
{
"created": "Mon, 30 Sep 2019 13:05:31 GMT",
"version": "v1"
}
] | 2019-10-01 | [
[
"Medo",
"Matus",
""
],
[
"Aebersold",
"Daniel M.",
""
],
[
"Medova",
"Michaela",
""
]
] | Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values with random numbers, a process known as "imputation", avoids apparent infinite fold-change values. However, the p... |
2007.06623 | Joe Greener | Joe G Greener, Nikita Desai, Shaun M Kandathil, David T Jones | Near-complete protein structural modelling of the minimal genome | JGG and ND contributed equally to the work | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein tertiary structure prediction has improved dramatically in recent
years. A considerable fraction of various proteomes can be modelled in the
absence of structural templates. We ask whether our DMPfold method can model
all the proteins without templates in the JCVI-syn3.0 minimal genome, which
contains 438 pro... | [
{
"created": "Mon, 13 Jul 2020 18:53:03 GMT",
"version": "v1"
}
] | 2020-07-15 | [
[
"Greener",
"Joe G",
""
],
[
"Desai",
"Nikita",
""
],
[
"Kandathil",
"Shaun M",
""
],
[
"Jones",
"David T",
""
]
] | Protein tertiary structure prediction has improved dramatically in recent years. A considerable fraction of various proteomes can be modelled in the absence of structural templates. We ask whether our DMPfold method can model all the proteins without templates in the JCVI-syn3.0 minimal genome, which contains 438 prote... |
2005.13438 | Hyeoncheol Cho | Hyeoncheol Cho, Eok Kyun Lee, Insung S. Choi | InteractionNet: Modeling and Explaining of Noncovalent Protein-Ligand
Interactions with Noncovalent Graph Neural Network and Layer-Wise Relevance
Propagation | null | null | null | null | q-bio.BM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Expanding the scope of graph-based, deep-learning models to noncovalent
protein-ligand interactions has earned increasing attention in structure-based
drug design. Modeling the protein-ligand interactions with graph neural
networks (GNNs) has experienced difficulties in the conversion of
protein-ligand complex struct... | [
{
"created": "Tue, 12 May 2020 12:46:44 GMT",
"version": "v1"
}
] | 2020-05-28 | [
[
"Cho",
"Hyeoncheol",
""
],
[
"Lee",
"Eok Kyun",
""
],
[
"Choi",
"Insung S.",
""
]
] | Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the protein-ligand interactions with graph neural networks (GNNs) has experienced difficulties in the conversion of protein-ligand complex structur... |
0901.0287 | Aleksandar Stojmirovi\'c | Aleksandar Stojmirovi\'c and Yi-Kuo Yu | Information flow in interaction networks II: channels, path lengths and
potentials | Minor changes from v3. 30 pages, 7 figures. Plain LaTeX format. This
version contains some additional material compared to the journal submission:
two figures, one appendix and a few paragraphs | J Comput Biol. 19(4):379-403, 2012 | 10.1089/cmb.2010.0228 | null | q-bio.MN | http://creativecommons.org/licenses/publicdomain/ | In our previous publication, a framework for information flow in interaction
networks based on random walks with damping was formulated with two fundamental
modes: emitting and absorbing. While many other network analysis methods based
on random walks or equivalent notions have been developed before and after our
ear... | [
{
"created": "Fri, 2 Jan 2009 21:45:34 GMT",
"version": "v1"
},
{
"created": "Wed, 6 Oct 2010 00:11:10 GMT",
"version": "v2"
},
{
"created": "Wed, 14 Dec 2011 23:04:35 GMT",
"version": "v3"
},
{
"created": "Thu, 19 Apr 2012 16:15:19 GMT",
"version": "v4"
}
] | 2012-04-20 | [
[
"Stojmirović",
"Aleksandar",
""
],
[
"Yu",
"Yi-Kuo",
""
]
] | In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on random walks or equivalent notions have been developed before and after our earli... |
1111.6489 | Taiki Takahashi | Taiki Takahashi (1), Mizuho Shinada (1), Keigo Inukai (1,2), Shigehito
Tanida (1), Chisato Takahashi (1), Nobuhiro Mifune (1,2), Haruto Takagishi
(1,2), Yutaka Horita (1,2), Hirofumi Hashimoto (1,2), Kunihiro Yokota (1),
Tatsuya Kameda (1), Toshio Yamagishi (1) ((1) Department of Behavioral
Science, Hokkaido Un... | Stress hormones predict hyperbolic time-discount rates six months later
in adults | null | Neuro Endocrinol Lett. 2010;31(5):616-621 | null | null | q-bio.NC q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Objectives: Stress hormones have been associated with temporal discounting.
Although time-discount rate is shown to be stable over a long term, no study to
date examines whether individual differences in stress hormones could predict
individuals' time-discount rates in the relatively distant future (e.g., six
month l... | [
{
"created": "Tue, 22 Nov 2011 15:01:14 GMT",
"version": "v1"
}
] | 2012-12-04 | [
[
"Takahashi",
"Taiki",
""
],
[
"Shinada",
"Mizuho",
""
],
[
"Inukai",
"Keigo",
""
],
[
"Tanida",
"Shigehito",
""
],
[
"Takahashi",
"Chisato",
""
],
[
"Mifune",
"Nobuhiro",
""
],
[
"Takagishi",
"Haruto",
""
... | Objectives: Stress hormones have been associated with temporal discounting. Although time-discount rate is shown to be stable over a long term, no study to date examines whether individual differences in stress hormones could predict individuals' time-discount rates in the relatively distant future (e.g., six month lat... |
1901.01059 | Jochen Einbeck | Daniel Bonetti, Alexandre Delbem, Dorival Le\~ao, Jochen Einbeck | Estimation of Distribution Algorithm for Protein Structure Prediction | 45 pages, 13 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Proteins are essential for maintaining life. For example, knowing the
structure of a protein, cell regulatory mechanisms of organisms can be modeled,
supporting the development of disease treatments or the understanding of
relationships between protein structures and food attributes. However,
discovering the structur... | [
{
"created": "Fri, 4 Jan 2019 11:26:42 GMT",
"version": "v1"
}
] | 2019-01-07 | [
[
"Bonetti",
"Daniel",
""
],
[
"Delbem",
"Alexandre",
""
],
[
"Leão",
"Dorival",
""
],
[
"Einbeck",
"Jochen",
""
]
] | Proteins are essential for maintaining life. For example, knowing the structure of a protein, cell regulatory mechanisms of organisms can be modeled, supporting the development of disease treatments or the understanding of relationships between protein structures and food attributes. However, discovering the structure ... |
1312.5231 | Xiaofeng Liu | Xiaofeng Liu, Ning Xu and Aimin Jiang | Tortuosity Entropy: a measure of spatial complexity of behavioral
changes in animal movement data | 12 pages, 6 figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The goal of animal movement analysis is to understand how organisms explore
and exploit the complex and varying environment. Animals usually exhibit varied
and complicated movements, from apparently deterministic behaviors to highly
random ones. This is critical for assessing movement efficiency and strategies
that a... | [
{
"created": "Wed, 18 Dec 2013 17:27:10 GMT",
"version": "v1"
},
{
"created": "Thu, 16 Jan 2014 12:24:51 GMT",
"version": "v2"
}
] | 2014-01-17 | [
[
"Liu",
"Xiaofeng",
""
],
[
"Xu",
"Ning",
""
],
[
"Jiang",
"Aimin",
""
]
] | The goal of animal movement analysis is to understand how organisms explore and exploit the complex and varying environment. Animals usually exhibit varied and complicated movements, from apparently deterministic behaviors to highly random ones. This is critical for assessing movement efficiency and strategies that are... |
2106.14362 | Nan Zheng | Nan Zheng, Vincent Fitzpatrick, Ran Cheng, Linli Shi, David L. Kaplan,
Chen Yang | Photoacoustic Silk Scaffolds for Neural stimulation and Regeneration | null | null | null | null | q-bio.NC q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural interfaces using biocompatible scaffolds provide crucial properties
for the functional repair of nerve injuries and neurodegenerative diseases,
including cell adhesion, structural support, and mass transport. Neural
stimulation has also been found to be effective in promoting neural
regeneration. This work pro... | [
{
"created": "Mon, 28 Jun 2021 01:38:39 GMT",
"version": "v1"
}
] | 2021-06-29 | [
[
"Zheng",
"Nan",
""
],
[
"Fitzpatrick",
"Vincent",
""
],
[
"Cheng",
"Ran",
""
],
[
"Shi",
"Linli",
""
],
[
"Kaplan",
"David L.",
""
],
[
"Yang",
"Chen",
""
]
] | Neural interfaces using biocompatible scaffolds provide crucial properties for the functional repair of nerve injuries and neurodegenerative diseases, including cell adhesion, structural support, and mass transport. Neural stimulation has also been found to be effective in promoting neural regeneration. This work provi... |
2403.12987 | Bowen Gao | Bowen Gao, Minsi Ren, Yuyan Ni, Yanwen Huang, Bo Qiang, Zhi-Ming Ma,
Wei-Ying Ma, Yanyan Lan | Rethinking Specificity in SBDD: Leveraging Delta Score and Energy-Guided
Diffusion | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the field of Structure-based Drug Design (SBDD), deep learning-based
generative models have achieved outstanding performance in terms of docking
score. However, further study shows that the existing molecular generative
methods and docking scores both have lacked consideration in terms of
specificity, which means ... | [
{
"created": "Mon, 4 Mar 2024 07:40:25 GMT",
"version": "v1"
}
] | 2024-03-21 | [
[
"Gao",
"Bowen",
""
],
[
"Ren",
"Minsi",
""
],
[
"Ni",
"Yuyan",
""
],
[
"Huang",
"Yanwen",
""
],
[
"Qiang",
"Bo",
""
],
[
"Ma",
"Zhi-Ming",
""
],
[
"Ma",
"Wei-Ying",
""
],
[
"Lan",
"Yanyan",
... | In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and docking scores both have lacked consideration in terms of specificity, which means th... |
2312.14489 | Yann Sakref | Yann Sakref, Olivier Rivoire | On the exclusion of exponential autocatalysts by sub-exponential
autocatalysts | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Selection among autocatalytic species fundamentally depends on their growth
law: exponential species, whose number of copies grows exponentially, are
mutually exclusive, while sub-exponential ones, whose number of copies grows
polynomially, can coexist. Here we consider competitions between autocatalytic
species with... | [
{
"created": "Fri, 22 Dec 2023 07:35:41 GMT",
"version": "v1"
}
] | 2023-12-25 | [
[
"Sakref",
"Yann",
""
],
[
"Rivoire",
"Olivier",
""
]
] | Selection among autocatalytic species fundamentally depends on their growth law: exponential species, whose number of copies grows exponentially, are mutually exclusive, while sub-exponential ones, whose number of copies grows polynomially, can coexist. Here we consider competitions between autocatalytic species with d... |
1705.03398 | Anvar Shukurov | Anvar Shukurov and Mykhailo Videiko | The evolving system of Trypillian settlements | 36 pages, 14 figures, submitted to Journal of Archaeological Science | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Archaeological settlement systems are usually analysed in terms of the
relation between the rank of a settlement and its size (Zipf's law). We argue
that this approach is unreliable, and can be misleading, in application to
archaeological data where the recovery rate of settlements can be low and their
size estimates... | [
{
"created": "Tue, 9 May 2017 15:47:54 GMT",
"version": "v1"
}
] | 2017-05-10 | [
[
"Shukurov",
"Anvar",
""
],
[
"Videiko",
"Mykhailo",
""
]
] | Archaeological settlement systems are usually analysed in terms of the relation between the rank of a settlement and its size (Zipf's law). We argue that this approach is unreliable, and can be misleading, in application to archaeological data where the recovery rate of settlements can be low and their size estimates a... |
0910.4253 | Andrea Angelini | A. Angelini, A. Amato, G. Bianconi, B. Bassetti, M. Cosentino
Lagomarsino | Mean-field methods in evolutionary duplication-innovation-loss models
for the genome-level repertoire of protein domains | 10 Figures, 2 Tables | null | 10.1103/PhysRevE.81.021919 | null | q-bio.GN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a combined mean-field and simulation approach to different models
describing the dynamics of classes formed by elements that can appear,
disappear or copy themselves. These models, related to a paradigm
duplication-innovation model known as Chinese Restaurant Process, are devised
to reproduce the scaling b... | [
{
"created": "Thu, 22 Oct 2009 17:18:15 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Jan 2010 14:47:46 GMT",
"version": "v2"
}
] | 2015-05-14 | [
[
"Angelini",
"A.",
""
],
[
"Amato",
"A.",
""
],
[
"Bianconi",
"G.",
""
],
[
"Bassetti",
"B.",
""
],
[
"Lagomarsino",
"M. Cosentino",
""
]
] | We present a combined mean-field and simulation approach to different models describing the dynamics of classes formed by elements that can appear, disappear or copy themselves. These models, related to a paradigm duplication-innovation model known as Chinese Restaurant Process, are devised to reproduce the scaling beh... |
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