id stringlengths 9 13 | submitter stringlengths 4 48 | authors stringlengths 4 9.62k | title stringlengths 4 343 | comments stringlengths 2 480 ⌀ | journal-ref stringlengths 9 309 ⌀ | doi stringlengths 12 138 ⌀ | report-no stringclasses 277
values | categories stringlengths 8 87 | license stringclasses 9
values | orig_abstract stringlengths 27 3.76k | versions listlengths 1 15 | update_date stringlengths 10 10 | authors_parsed listlengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1604.06089 | Richard Mann | Richard P. Mann | Towards a fully predictive model of flight paths in pigeons navigating
in the familiar area: prediction across differing individuals | 8 pages, 2 figures, Royal Institute of Navigation Conference on
Animal Navigation 2016 | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper will detail the basis of our previously developed predictive model
for pigeon flight paths based on observations of the specific individual being
predicted. We will then describe how this model can be adapted to predict the
flight of a new, unobserved bird, based on observations of other individuals
from t... | [
{
"created": "Wed, 20 Apr 2016 18:58:13 GMT",
"version": "v1"
}
] | 2016-04-22 | [
[
"Mann",
"Richard P.",
""
]
] | This paper will detail the basis of our previously developed predictive model for pigeon flight paths based on observations of the specific individual being predicted. We will then describe how this model can be adapted to predict the flight of a new, unobserved bird, based on observations of other individuals from the... |
1906.03314 | Jiawei Zhang | Jiawei Zhang | Secrets of the Brain: An Introduction to the Brain Anatomical Structure
and Biological Function | 34 pages, 19 figures | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we will provide an introduction to the brain structure and
function. Brain is an astonishing living organ inside our heads, weighing about
1.5kg, consisting of billions of tiny cells. The brain enables us to sense the
world around us (to touch, to smell, to see and to hear, etc.), to think and to
respo... | [
{
"created": "Fri, 31 May 2019 03:07:33 GMT",
"version": "v1"
}
] | 2019-06-11 | [
[
"Zhang",
"Jiawei",
""
]
] | In this paper, we will provide an introduction to the brain structure and function. Brain is an astonishing living organ inside our heads, weighing about 1.5kg, consisting of billions of tiny cells. The brain enables us to sense the world around us (to touch, to smell, to see and to hear, etc.), to think and to respond... |
1702.00329 | Hon-Cheong So | Hon-Cheong So | Epigenome-wide association study and integrative analysis with the
transcriptome based on GWAS summary statistics | null | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The past decade has seen a rapid growth in omics technologies. Genome-wide
association studies (GWAS) have uncovered susceptibility variants for a variety
of complex traits. However, the functional significance of most discovered
variants are still not fully understood. On the other hand, there is increasing
interest... | [
{
"created": "Wed, 1 Feb 2017 15:59:30 GMT",
"version": "v1"
},
{
"created": "Tue, 21 Feb 2017 07:13:30 GMT",
"version": "v2"
}
] | 2017-02-22 | [
[
"So",
"Hon-Cheong",
""
]
] | The past decade has seen a rapid growth in omics technologies. Genome-wide association studies (GWAS) have uncovered susceptibility variants for a variety of complex traits. However, the functional significance of most discovered variants are still not fully understood. On the other hand, there is increasing interest i... |
1601.00891 | Iddo Friedberg | Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel
D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M
Verspoor, Asa Ben-Hur, Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah
Youngs, Richard Bonneau, Alexandra Lin, Sayed ME Sahraeian, Pier Luigi
Martelli, Giuseppe Profi... | An expanded evaluation of protein function prediction methods shows an
improvement in accuracy | Submitted to Genome Biology | null | 10.1186/s13059-016-1037-6 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The increasing volume and variety of genotypic and phenotypic
data is a major defining characteristic of modern biomedical sciences. At the
same time, the limitations in technology for generating data and the inherently
stochastic nature of biomolecular events have led to the discrepancy between
the volum... | [
{
"created": "Sun, 3 Jan 2016 00:55:23 GMT",
"version": "v1"
}
] | 2016-12-07 | [
[
"Jiang",
"Yuxiang",
""
],
[
"Oron",
"Tal Ronnen",
""
],
[
"Clark",
"Wyatt T",
""
],
[
"Bankapur",
"Asma R",
""
],
[
"D'Andrea",
"Daniel",
""
],
[
"Lepore",
"Rosalba",
""
],
[
"Funk",
"Christopher S",
""
]... | Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations in technology for generating data and the inherently stochastic nature of biomolecular events have led to the discrepancy between the volume ... |
2304.08299 | Bingxin Zhou | Bingxin Zhou, Outongyi Lv, Kai Yi, Xinye Xiong, Pan Tan, Liang Hong,
Yu Guang Wang | Accurate and Definite Mutational Effect Prediction with Lightweight
Equivariant Graph Neural Networks | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Directed evolution as a widely-used engineering strategy faces obstacles in
finding desired mutants from the massive size of candidate modifications. While
deep learning methods learn protein contexts to establish feasible searching
space, many existing models are computationally demanding and fail to predict
how spe... | [
{
"created": "Thu, 13 Apr 2023 09:51:49 GMT",
"version": "v1"
}
] | 2023-04-18 | [
[
"Zhou",
"Bingxin",
""
],
[
"Lv",
"Outongyi",
""
],
[
"Yi",
"Kai",
""
],
[
"Xiong",
"Xinye",
""
],
[
"Tan",
"Pan",
""
],
[
"Hong",
"Liang",
""
],
[
"Wang",
"Yu Guang",
""
]
] | Directed evolution as a widely-used engineering strategy faces obstacles in finding desired mutants from the massive size of candidate modifications. While deep learning methods learn protein contexts to establish feasible searching space, many existing models are computationally demanding and fail to predict how speci... |
2207.12367 | Simona Vulpe | Cosima Rughinis, Mihai Dima, Simona-Nicoleta Vulpe, Razvan Rughinis,
Sorina Vasile | Patterns of protection, infection, and detection: Country-level
effectiveness of COVID 19 vaccination in reducing mortality worldwide | 43 pages, 4 figures, 3 tables, 2 supplementary materials | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | We investigated the negative relationship between mortality and COVID-19
vaccination at ecological level, which has been established through clinical
trials and other investigations at the individual level. We conducted an
exploratory, correlational, country-level analysis of open data centralized by
Our World in Dat... | [
{
"created": "Fri, 8 Jul 2022 11:41:42 GMT",
"version": "v1"
}
] | 2022-07-26 | [
[
"Rughinis",
"Cosima",
""
],
[
"Dima",
"Mihai",
""
],
[
"Vulpe",
"Simona-Nicoleta",
""
],
[
"Rughinis",
"Razvan",
""
],
[
"Vasile",
"Sorina",
""
]
] | We investigated the negative relationship between mortality and COVID-19 vaccination at ecological level, which has been established through clinical trials and other investigations at the individual level. We conducted an exploratory, correlational, country-level analysis of open data centralized by Our World in Data ... |
2405.05864 | Alireza Soleimani | Alireza Soleimani and Herre Jelger Risselada | SMARTINI3: Systematic Parametrization of Realistic Multi-Scale Membrane
Models via Unsupervised Learning and Multi-Objective Evolutionary Algorithms | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by/4.0/ | In this study, we utilize genetic algorithms to develop a realistic implicit
solvent ultra-coarse-grained (PC) membrane model comprising only three
interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3
is its compatibility with realistic membrane proteins, for example, modeled
within the Mart... | [
{
"created": "Thu, 9 May 2024 15:52:40 GMT",
"version": "v1"
}
] | 2024-05-10 | [
[
"Soleimani",
"Alireza",
""
],
[
"Risselada",
"Herre Jelger",
""
]
] | In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its compatibility with realistic membrane proteins, for example, modeled within the Martin... |
0904.3535 | Thierry Rabilloud | C\'ecile Lelong (BBSI), Mireille Chevallet (BBSI), Sylvie Luche
(BBSI), Thierry Rabilloud (BBSI) | Silver Staining of Proteins in 2DE Gels | null | Methods in molecular biology (Clifton, N.J.) 519 (2009) 339-350 | 10.1007/978-1-59745-281-6_21 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Silver staining detects proteins after electrophoretic separation on
polyacrylamide gels. Its main positive features are its excellent sensitivity
(in the low nanogram range) and the use of very simple and cheap equipment and
chemicals. The sequential phases of silver staining are protein fixation, then
sensitization... | [
{
"created": "Wed, 22 Apr 2009 19:27:23 GMT",
"version": "v1"
}
] | 2009-04-23 | [
[
"Lelong",
"Cécile",
"",
"BBSI"
],
[
"Chevallet",
"Mireille",
"",
"BBSI"
],
[
"Luche",
"Sylvie",
"",
"BBSI"
],
[
"Rabilloud",
"Thierry",
"",
"BBSI"
]
] | Silver staining detects proteins after electrophoretic separation on polyacrylamide gels. Its main positive features are its excellent sensitivity (in the low nanogram range) and the use of very simple and cheap equipment and chemicals. The sequential phases of silver staining are protein fixation, then sensitization, ... |
0709.4206 | Ney Lemke | Joao Paulo Muller da Silva, Marcio Luis Acencio, Jose Carlos Merino
Mombach, Renata Vieira, Jose Guliherme Camargo da Silva, Ney Lemke, Marialva
Sinigaglia | In silico network topology-based prediction of gene essentiality | null | null | null | null | q-bio.GN physics.bio-ph | null | The identification of genes essential for survival is important for the
understanding of the minimal requirements for cellular life and for drug
design. As experimental studies with the purpose of building a catalog of
essential genes for a given organism are time-consuming and laborious, a
computational approach whi... | [
{
"created": "Wed, 26 Sep 2007 16:35:32 GMT",
"version": "v1"
}
] | 2007-09-27 | [
[
"da Silva",
"Joao Paulo Muller",
""
],
[
"Acencio",
"Marcio Luis",
""
],
[
"Mombach",
"Jose Carlos Merino",
""
],
[
"Vieira",
"Renata",
""
],
[
"da Silva",
"Jose Guliherme Camargo",
""
],
[
"Lemke",
"Ney",
""
],
[
... | The identification of genes essential for survival is important for the understanding of the minimal requirements for cellular life and for drug design. As experimental studies with the purpose of building a catalog of essential genes for a given organism are time-consuming and laborious, a computational approach which... |
1112.5006 | Gilles Guillot | Gilles Guillot, Sabrina Renaud, Ronan Ledevin, Joahn Michaux, Julien
Claude | A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic
Data | null | null | null | null | q-bio.PE q-bio.QM stat.AP stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recognition of evolutionary units (species, populations) requires integrating
several kinds of data such as genetic or phenotypic markers or spatial
information, in order to get a comprehensive view concerning the
differentiation of the units. We propose a statistical model with a double
original advantage: (i) it in... | [
{
"created": "Wed, 21 Dec 2011 12:34:40 GMT",
"version": "v1"
}
] | 2011-12-22 | [
[
"Guillot",
"Gilles",
""
],
[
"Renaud",
"Sabrina",
""
],
[
"Ledevin",
"Ronan",
""
],
[
"Michaux",
"Joahn",
""
],
[
"Claude",
"Julien",
""
]
] | Recognition of evolutionary units (species, populations) requires integrating several kinds of data such as genetic or phenotypic markers or spatial information, in order to get a comprehensive view concerning the differentiation of the units. We propose a statistical model with a double original advantage: (i) it inco... |
2311.05668 | Philip Bourne | Terence R. Johnson and Philip E. Bourne | The Biological Data Sustainability Paradox | 12 pages 5852 words 1 figure | null | null | null | q-bio.OT cs.DB | http://creativecommons.org/licenses/by/4.0/ | Biological data in digital form has become a, if not the, driving force
behind innovations in biology, medicine, and the environment. No study and no
model would be complete without access to digital data (including text)
collected by others and available in public repositories. With this ascent in
the fundamental im... | [
{
"created": "Thu, 9 Nov 2023 14:56:27 GMT",
"version": "v1"
}
] | 2023-11-13 | [
[
"Johnson",
"Terence R.",
""
],
[
"Bourne",
"Philip E.",
""
]
] | Biological data in digital form has become a, if not the, driving force behind innovations in biology, medicine, and the environment. No study and no model would be complete without access to digital data (including text) collected by others and available in public repositories. With this ascent in the fundamental impo... |
2307.00084 | Milind Kunchur | Milind N. Kunchur | The Human Auditory System and Audio | 32 pages, 22 figures, 19 equations, 218 cited references | Applied Acoustics (Elsevier), Volume 211, August 2023, 109507 | 10.1016/j.apacoust.2023.109507 | null | q-bio.NC cs.SD eess.AS | http://creativecommons.org/licenses/by/4.0/ | This work reviews the human auditory system, elucidating some of the
specialized mechanisms and non-linear pathways along the chain of events
between physical sound and its perception. Customary relationships between
frequency, time, and phase--such as the uncertainty principle--that hold for
linear systems, do not a... | [
{
"created": "Fri, 30 Jun 2023 18:41:49 GMT",
"version": "v1"
},
{
"created": "Fri, 28 Jul 2023 20:37:39 GMT",
"version": "v2"
}
] | 2023-08-01 | [
[
"Kunchur",
"Milind N.",
""
]
] | This work reviews the human auditory system, elucidating some of the specialized mechanisms and non-linear pathways along the chain of events between physical sound and its perception. Customary relationships between frequency, time, and phase--such as the uncertainty principle--that hold for linear systems, do not app... |
1209.5242 | Michael GB Blum | Nicolas Duforet-Frebourg, Michael G. B. Blum | Non-stationary patterns of isolation-by-distance: inferring measures of
local genetic differentiation with Bayesian kriging | In press, Evolution 2014 | null | 10.1111/evo.12342 | null | q-bio.PE stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Patterns of isolation-by-distance arise when population differentiation
increases with increasing geographic distances. Patterns of
isolation-by-distance are usually caused by local spatial dispersal, which
explains why differences of allele frequencies between populations accumulate
with distance. However, spatial v... | [
{
"created": "Mon, 24 Sep 2012 12:17:15 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Sep 2012 09:36:36 GMT",
"version": "v2"
},
{
"created": "Tue, 7 Jan 2014 08:44:31 GMT",
"version": "v3"
}
] | 2014-01-08 | [
[
"Duforet-Frebourg",
"Nicolas",
""
],
[
"Blum",
"Michael G. B.",
""
]
] | Patterns of isolation-by-distance arise when population differentiation increases with increasing geographic distances. Patterns of isolation-by-distance are usually caused by local spatial dispersal, which explains why differences of allele frequencies between populations accumulate with distance. However, spatial var... |
1012.3938 | Natalja Strelkowa | Natalja Strelkowa and Mauricio Barahona | Transient dynamics around unstable periodic orbits in the generalized
repressilator model | 24 pages, 8 figures | null | 10.1063/1.3574387 | null | q-bio.MN q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the spatio-temporal dynamics of the generalized repressilator, a
system of coupled repressing genes arranged in a directed ring topology, and
give analytical conditions for the emergence of a cascade of unstable periodic
orbits (UPOs) that lead to reachable long-lived oscillating transients. Such
transients ... | [
{
"created": "Fri, 17 Dec 2010 17:42:12 GMT",
"version": "v1"
}
] | 2015-05-20 | [
[
"Strelkowa",
"Natalja",
""
],
[
"Barahona",
"Mauricio",
""
]
] | We study the spatio-temporal dynamics of the generalized repressilator, a system of coupled repressing genes arranged in a directed ring topology, and give analytical conditions for the emergence of a cascade of unstable periodic orbits (UPOs) that lead to reachable long-lived oscillating transients. Such transients do... |
1109.2650 | Eder Zavala | Eder Zavala, Mois\'es Santill\'an | An analysis of overall network architecture reveals an infinite-period
bifurcation underlying oscillation arrest in the segmentation clock | 11 pages, 5 figures, added references, added figures, extended
supporting material, revised arguments in the discussion, corrected typos | null | null | null | q-bio.CB physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Unveiling the mechanisms through which the somitogenesis regulatory network
exerts spatiotemporal control of the somitic patterning has required a
combination of experimental and mathematical modeling strategies. Significant
progress has been made for the zebrafish clockwork. However, due to its
complexity, the clock... | [
{
"created": "Tue, 13 Sep 2011 00:03:19 GMT",
"version": "v1"
},
{
"created": "Fri, 23 Mar 2012 02:36:56 GMT",
"version": "v2"
}
] | 2015-03-13 | [
[
"Zavala",
"Eder",
""
],
[
"Santillán",
"Moisés",
""
]
] | Unveiling the mechanisms through which the somitogenesis regulatory network exerts spatiotemporal control of the somitic patterning has required a combination of experimental and mathematical modeling strategies. Significant progress has been made for the zebrafish clockwork. However, due to its complexity, the clockwo... |
2101.02947 | Michael Grinfeld | Michael Grinfeld | An enzymatic hormesis box | 7 pages, 2 figures | null | null | null | q-bio.BM q-bio.SC | http://creativecommons.org/licenses/by/4.0/ | We present a simple enzymatic system that is capable of a biphasic response
under competitive inhibition. This is arguably the simplest system that can be
said to be hormetic
| [
{
"created": "Fri, 8 Jan 2021 10:28:36 GMT",
"version": "v1"
}
] | 2021-01-11 | [
[
"Grinfeld",
"Michael",
""
]
] | We present a simple enzymatic system that is capable of a biphasic response under competitive inhibition. This is arguably the simplest system that can be said to be hormetic |
1803.08573 | Katherine Medina | Victor Flores and Katherine Medina | The effects of cyclical simulation on the axon hillock diameter of
murine intracortical neurons | 12 pages; submitted to PlosOne | null | null | null | q-bio.NC | http://creativecommons.org/publicdomain/zero/1.0/ | Changes to the axon hillock in frequently firing neurons are known to be
important predictors of early disease states. Studying this phenomenon is
critical to understanding the first insult implicated in multiple
neuro-degenerative disorders. To study these changes we used cyclical
stimulations using micro-electrodes... | [
{
"created": "Thu, 22 Mar 2018 20:18:15 GMT",
"version": "v1"
}
] | 2018-03-26 | [
[
"Flores",
"Victor",
""
],
[
"Medina",
"Katherine",
""
]
] | Changes to the axon hillock in frequently firing neurons are known to be important predictors of early disease states. Studying this phenomenon is critical to understanding the first insult implicated in multiple neuro-degenerative disorders. To study these changes we used cyclical stimulations using micro-electrodes t... |
1707.04885 | Min Xu | Chengqian Che, Ruogu Lin, Xiangrui Zeng, Karim Elmaaroufi, John
Galeotti, and Min Xu | Improved deep learning based macromolecules structure classification
from electron cryo tomograms | Preliminary working report | null | 10.1007/s00138-018-0949-4 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cellular processes are governed by macromolecular complexes inside the cell.
Study of the native structures of macromolecular complexes has been extremely
difficult due to lack of data. With recent breakthroughs in Cellular electron
cryo tomography (CECT) 3D imaging technology, it is now possible for
researchers to g... | [
{
"created": "Sun, 16 Jul 2017 14:25:31 GMT",
"version": "v1"
}
] | 2018-06-12 | [
[
"Che",
"Chengqian",
""
],
[
"Lin",
"Ruogu",
""
],
[
"Zeng",
"Xiangrui",
""
],
[
"Elmaaroufi",
"Karim",
""
],
[
"Galeotti",
"John",
""
],
[
"Xu",
"Min",
""
]
] | Cellular processes are governed by macromolecular complexes inside the cell. Study of the native structures of macromolecular complexes has been extremely difficult due to lack of data. With recent breakthroughs in Cellular electron cryo tomography (CECT) 3D imaging technology, it is now possible for researchers to gai... |
2406.01107 | Yujiang Wang | Bethany Little, Nida Alyas, Alexander Surtees, Gavin P Winston, John S
Duncan, David A Cousins, John-Paul Taylor, Peter Taylor, Karoline Leiberg,
Yujiang Wang | Brain Morphology Normative modelling platform for abnormality and
Centile estimation: Brain MoNoCle | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Normative models of brain structure estimate the effects of covariates such
as age and sex using large samples of healthy controls. These models can then
be applied to smaller clinical cohorts to distinguish disease effects from
other covariates. However, these advanced statistical modelling approaches can
be difficu... | [
{
"created": "Mon, 3 Jun 2024 08:41:53 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Jun 2024 20:10:43 GMT",
"version": "v2"
}
] | 2024-06-28 | [
[
"Little",
"Bethany",
""
],
[
"Alyas",
"Nida",
""
],
[
"Surtees",
"Alexander",
""
],
[
"Winston",
"Gavin P",
""
],
[
"Duncan",
"John S",
""
],
[
"Cousins",
"David A",
""
],
[
"Taylor",
"John-Paul",
""
],
... | Normative models of brain structure estimate the effects of covariates such as age and sex using large samples of healthy controls. These models can then be applied to smaller clinical cohorts to distinguish disease effects from other covariates. However, these advanced statistical modelling approaches can be difficult... |
2304.05700 | Enya Weidner | Enya M. Weidner, Stephan Moratti, Sebastian Schindler, Philip Grewe,
Christian G. Bien, Johanna Kissler | Amygdala and cortical gamma band responses to emotional faces depend on
the attended to valence | null | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | The amygdala is assumed to contribute to a bottom-up attentional bias during
visual processing of emotional faces. Still, how its response to emotion
interacts with top-down attention is not fully understood. It is also unclear
if amygdala activity and scalp EEG respond to emotion and attention in a
similar way. Ther... | [
{
"created": "Wed, 12 Apr 2023 08:42:32 GMT",
"version": "v1"
},
{
"created": "Tue, 16 May 2023 11:11:34 GMT",
"version": "v2"
}
] | 2023-05-17 | [
[
"Weidner",
"Enya M.",
""
],
[
"Moratti",
"Stephan",
""
],
[
"Schindler",
"Sebastian",
""
],
[
"Grewe",
"Philip",
""
],
[
"Bien",
"Christian G.",
""
],
[
"Kissler",
"Johanna",
""
]
] | The amygdala is assumed to contribute to a bottom-up attentional bias during visual processing of emotional faces. Still, how its response to emotion interacts with top-down attention is not fully understood. It is also unclear if amygdala activity and scalp EEG respond to emotion and attention in a similar way. Theref... |
2009.08023 | Shantanu Jain | Yisu Peng (1), Shantanu Jain (1), Yong Fuga Li (2), Michal Gregus (3
and 4), Alexander R. Ivanov (3 and 4), Olga Vitek (1 and 4) and Predrag
Radivojac (1) ((1) Khoury College of Computer Sciences, Northeastern
University, (2) Illumina Inc., (3) Department of Chemistry and Chemical
Biology, Northeastern Universi... | New mixture models for decoy-free false discovery rate estimation in
mass-spectrometry proteomics | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Accurate estimation of false discovery rate (FDR) of spectral
identification is a central problem in mass spectrometry-based proteomics. Over
the past two decades, target decoy approaches (TDAs) and decoy-free approaches
(DFAs), have been widely used to estimate FDR. TDAs use a database of decoy
species t... | [
{
"created": "Thu, 17 Sep 2020 02:22:15 GMT",
"version": "v1"
}
] | 2020-09-18 | [
[
"Peng",
"Yisu",
"",
"3\n and 4"
],
[
"Jain",
"Shantanu",
"",
"3\n and 4"
],
[
"Li",
"Yong Fuga",
"",
"3\n and 4"
],
[
"Gregus",
"Michal",
"",
"3\n and 4"
],
[
"Ivanov",
"Alexander R.",
"",
"3 and 4"
],
[
"V... | Motivation: Accurate estimation of false discovery rate (FDR) of spectral identification is a central problem in mass spectrometry-based proteomics. Over the past two decades, target decoy approaches (TDAs) and decoy-free approaches (DFAs), have been widely used to estimate FDR. TDAs use a database of decoy species to ... |
0805.0835 | Masaki Sasai | Kohei Eguchi, Mitsumasa Yoda, Tomoki P. Terada, and Masaki Sasai | Mechanism of robust circadian oscillation of KaiC phosphorylation in
vitro | null | null | 10.1529/biophysj.107.127555 | null | q-bio.MN cond-mat.dis-nn q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and
KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust
circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415
(2005)). This finding indicates that protein-protein interactions and the
associated hydro... | [
{
"created": "Wed, 7 May 2008 04:15:40 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Eguchi",
"Kohei",
""
],
[
"Yoda",
"Mitsumasa",
""
],
[
"Terada",
"Tomoki P.",
""
],
[
"Sasai",
"Masaki",
""
]
] | By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415 (2005)). This finding indicates that protein-protein interactions and the associated hydroly... |
1403.1562 | Krzysztof Bartoszek | Krzysztof Bartoszek | The Laplace Motion in Phylogenetic Comparative Methods | http://kkzmbm.mimuw.edu.pl/?pageId=4&sprawId=18 | Proceedings of the Eighteenth National Conference on Applications
of Mathematics in Biology and Medicine, 2012 | null | null | q-bio.PE math.PR stat.AP stat.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The majority of current phylogenetic comparative methods assume that the
stochastic evolutionary process is homogeneous over the phylogeny or offer
relaxations of this in rather limited and usually parameter expensive ways.
Here we make a preliminary investigation, by means of a numerical experiment,
whether the Lapl... | [
{
"created": "Thu, 6 Mar 2014 20:24:38 GMT",
"version": "v1"
}
] | 2014-03-07 | [
[
"Bartoszek",
"Krzysztof",
""
]
] | The majority of current phylogenetic comparative methods assume that the stochastic evolutionary process is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a preliminary investigation, by means of a numerical experiment, whether the Laplac... |
1505.01066 | Jayajit Das | Jayajit Das, Sayak Mukherjee, Susan E. Hodge | Maximum Entropy estimation of probability distribution of variables in
higher dimensions from lower dimensional data | in review | Entropy 2015, 17(7), 4986-4999 | 10.3390/e17074986 | null | q-bio.QM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A common statistical situation concerns inferring an unknown distribution
Q(x) from a known distribution P(y), where X (dimension n), and Y (dimension m)
have a known functional relationship. Most commonly, n<m, and the task is
relatively straightforward. For example, if Y1 and Y2 are independent random
variables, ea... | [
{
"created": "Tue, 5 May 2015 16:19:21 GMT",
"version": "v1"
}
] | 2016-02-01 | [
[
"Das",
"Jayajit",
""
],
[
"Mukherjee",
"Sayak",
""
],
[
"Hodge",
"Susan E.",
""
]
] | A common statistical situation concerns inferring an unknown distribution Q(x) from a known distribution P(y), where X (dimension n), and Y (dimension m) have a known functional relationship. Most commonly, n<m, and the task is relatively straightforward. For example, if Y1 and Y2 are independent random variables, each... |
2109.00123 | Pik-Yin Lai | Mao-Xiang Wang, Arthur Lander, and Pik-Yin Lai | Regulatory Feedback Effects on Tissue Growth Dynamics in a Two-Stage
Cell Lineage Model | to be published in Physical Review E | null | 10.1103/PhysRevE.104.034405 | null | q-bio.TO physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Identifying the mechanism of intercellular feedback regulation is critical
for the basic understanding of tissue growth control in organisms. In this
paper, we analyze a tissue growth model consisting of a single lineage of two
cell types regulated by negative feedback signalling molecules that undergo
spatial diffus... | [
{
"created": "Wed, 1 Sep 2021 00:14:31 GMT",
"version": "v1"
}
] | 2021-09-22 | [
[
"Wang",
"Mao-Xiang",
""
],
[
"Lander",
"Arthur",
""
],
[
"Lai",
"Pik-Yin",
""
]
] | Identifying the mechanism of intercellular feedback regulation is critical for the basic understanding of tissue growth control in organisms. In this paper, we analyze a tissue growth model consisting of a single lineage of two cell types regulated by negative feedback signalling molecules that undergo spatial diffusio... |
2211.02636 | Zibin Zhao | Zibin Zhao | Towards Alzheimer's Disease Progression Assessment: A Review of Machine
Learning Methods | 16 pages, 3 figures | null | null | null | q-bio.NC cs.LG q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Alzheimer's Disease (AD), as the most devastating neurodegenerative disease
worldwide, has reached nearly 10 million new cases annually. Current technology
provides unprecedented opportunities to study the progression and etiology of
this disease with the advanced in imaging techniques. With the recent emergence
of a... | [
{
"created": "Tue, 1 Nov 2022 07:50:06 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Nov 2022 06:35:45 GMT",
"version": "v2"
}
] | 2022-11-14 | [
[
"Zhao",
"Zibin",
""
]
] | Alzheimer's Disease (AD), as the most devastating neurodegenerative disease worldwide, has reached nearly 10 million new cases annually. Current technology provides unprecedented opportunities to study the progression and etiology of this disease with the advanced in imaging techniques. With the recent emergence of a s... |
2005.13074 | Cecilia Jarne Dr | Cecilia Jarne | Different eigenvalue distributions encode the same temporal tasks in
recurrent neural networks | 19 pages, 10 Figures | null | 10.1007/s11571-022-09802-5 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Different brain areas, such as the cortex and, more specifically, the
prefrontal cortex, show great recurrence in their connections, even in early
sensory areas. {Several approaches and methods based on trained networks have
been proposed to model and describe these regions. It is essential to
understand the dynamics... | [
{
"created": "Tue, 26 May 2020 22:41:32 GMT",
"version": "v1"
},
{
"created": "Tue, 23 Jun 2020 19:08:24 GMT",
"version": "v2"
},
{
"created": "Mon, 18 Oct 2021 14:39:01 GMT",
"version": "v3"
},
{
"created": "Mon, 24 Jan 2022 20:06:39 GMT",
"version": "v4"
},
{
"c... | 2022-04-25 | [
[
"Jarne",
"Cecilia",
""
]
] | Different brain areas, such as the cortex and, more specifically, the prefrontal cortex, show great recurrence in their connections, even in early sensory areas. {Several approaches and methods based on trained networks have been proposed to model and describe these regions. It is essential to understand the dynamics b... |
2007.09671 | Mariana Recamonde-Mendoza | Jo\~ao Schapke, Anderson Tavares, Mariana Recamonde-Mendoza | EPGAT: Gene Essentiality Prediction With Graph Attention Networks | Published in IEEE/ACM Transactions on Computational Biology and
Bioinformatics | null | 10.1109/TCBB.2021.3054738 | null | q-bio.MN cs.LG q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The identification of essential genes/proteins is a critical step towards a
better understanding of human biology and pathology. Computational approaches
helped to mitigate experimental constraints by exploring machine learning (ML)
methods and the correlation of essentiality with biological information,
especially p... | [
{
"created": "Sun, 19 Jul 2020 13:47:15 GMT",
"version": "v1"
}
] | 2021-08-02 | [
[
"Schapke",
"João",
""
],
[
"Tavares",
"Anderson",
""
],
[
"Recamonde-Mendoza",
"Mariana",
""
]
] | The identification of essential genes/proteins is a critical step towards a better understanding of human biology and pathology. Computational approaches helped to mitigate experimental constraints by exploring machine learning (ML) methods and the correlation of essentiality with biological information, especially pro... |
q-bio/0601013 | Gerhard Schmid | Gerhard Schmid, Igor Goychuk, Peter Hanggi | Effect of channel block on the spiking activity of excitable membranes
in a stochastic Hodgkin-Huxley model | 10 pages, 3 figures, published 2004 | PHYSICAL BIOLOGY 1, pp. 61-66 (2004) | 10.1088/1478-3967/1/2/002 | null | q-bio.SC | null | The influence of intrinsic channel noise on the spontaneous spiking activity
of poisoned excitable membrane patches is studied by use of a stochastic
generalization of the Hodgkin-Huxley model. Internal noise stemming from the
stochastic dynamics of individual ion channels is known to affect the
collective properties... | [
{
"created": "Wed, 11 Jan 2006 13:53:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Schmid",
"Gerhard",
""
],
[
"Goychuk",
"Igor",
""
],
[
"Hanggi",
"Peter",
""
]
] | The influence of intrinsic channel noise on the spontaneous spiking activity of poisoned excitable membrane patches is studied by use of a stochastic generalization of the Hodgkin-Huxley model. Internal noise stemming from the stochastic dynamics of individual ion channels is known to affect the collective properties o... |
2110.09017 | Thomas Bochynek | Thomas Bochynek, Florian Schiffers, Andr\'e Aichert, Oliver Cossairt,
Simon Garnier, Michael Rubenstein | Anatomy of a superorganism -- structure and growth dynamics of army ant
bivouacs | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Beyond unicellular and multicellular organisms, there is a third type of
structural complexity in living animals: that of the mechanical self-assembly
of groups of distinct multicellular organisms into dynamical, functional
structures. One of the most striking examples of such structures is the army
ant bivouac, a ne... | [
{
"created": "Mon, 18 Oct 2021 05:09:41 GMT",
"version": "v1"
}
] | 2021-10-19 | [
[
"Bochynek",
"Thomas",
""
],
[
"Schiffers",
"Florian",
""
],
[
"Aichert",
"André",
""
],
[
"Cossairt",
"Oliver",
""
],
[
"Garnier",
"Simon",
""
],
[
"Rubenstein",
"Michael",
""
]
] | Beyond unicellular and multicellular organisms, there is a third type of structural complexity in living animals: that of the mechanical self-assembly of groups of distinct multicellular organisms into dynamical, functional structures. One of the most striking examples of such structures is the army ant bivouac, a nest... |
2303.08822 | Val\'erie Voorsluijs | Val\'erie Voorsluijs, Francesco Avanzini, Gianmaria Falasco,
Massimiliano Esposito, Alexander Skupin | Nonequilibrium calcium dynamics optimizes the energetic efficiency of
mitochondrial metabolism | null | null | null | null | q-bio.MN cond-mat.other cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | Living organisms continuously harness energy to perform complex functions for
their adaptation and survival while part of that energy is dissipated in the
form of heat or chemical waste. Determining the energetic cost and the
efficiency of specific cellular processes remains a largely open problem. Here,
we analyze t... | [
{
"created": "Wed, 15 Mar 2023 13:24:39 GMT",
"version": "v1"
},
{
"created": "Wed, 29 Mar 2023 06:15:10 GMT",
"version": "v2"
},
{
"created": "Fri, 4 Aug 2023 16:28:23 GMT",
"version": "v3"
}
] | 2023-08-07 | [
[
"Voorsluijs",
"Valérie",
""
],
[
"Avanzini",
"Francesco",
""
],
[
"Falasco",
"Gianmaria",
""
],
[
"Esposito",
"Massimiliano",
""
],
[
"Skupin",
"Alexander",
""
]
] | Living organisms continuously harness energy to perform complex functions for their adaptation and survival while part of that energy is dissipated in the form of heat or chemical waste. Determining the energetic cost and the efficiency of specific cellular processes remains a largely open problem. Here, we analyze the... |
1703.04022 | Christian Temp Kerskens | Christian Kerskens | Comments on the arterial spin labelling quantification recommended by
the ISMRM perfusion study group and the European consortium for ASL in
dementia | not relevant anymore | null | null | null | q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A petition for more careful considerations towards the usage of a
quantification approach for ASL which has been recommended by the ISMRM
perfusion study group and the European consortium for ASL in dementia.
| [
{
"created": "Sat, 11 Mar 2017 19:47:45 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Jun 2017 18:12:29 GMT",
"version": "v2"
}
] | 2017-06-06 | [
[
"Kerskens",
"Christian",
""
]
] | A petition for more careful considerations towards the usage of a quantification approach for ASL which has been recommended by the ISMRM perfusion study group and the European consortium for ASL in dementia. |
2311.10443 | Matthew Hartley | Teresa Zulueta-Coarasa, Florian Jug, Aastha Mathur, Josh Moore, Arrate
Mu\~noz-Barrutia, Liviu Anita, Kola Babalola, Pete Bankhead, Perrine
Gilloteaux, Nodar Gogoberidze, Martin Jones, Gerard J. Kleywegt, Paul Korir,
Anna Kreshuk, Ayb\"uke K\"upc\"u Yolda\c{s}, Luca Marconato, Kedar Narayan,
Nils Norlin, Bugra ... | MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to
improve the reuse of AI datasets for bioimage analysis | 16 pages, 3 figures | null | null | null | q-bio.OT eess.IV | http://creativecommons.org/licenses/by/4.0/ | Artificial Intelligence methods are powerful tools for biological image
analysis and processing. High-quality annotated images are key to training and
developing new methods, but access to such data is often hindered by the lack
of standards for sharing datasets. We brought together community experts in a
workshop to... | [
{
"created": "Fri, 17 Nov 2023 10:49:58 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Nov 2023 09:31:32 GMT",
"version": "v2"
}
] | 2023-11-23 | [
[
"Zulueta-Coarasa",
"Teresa",
""
],
[
"Jug",
"Florian",
""
],
[
"Mathur",
"Aastha",
""
],
[
"Moore",
"Josh",
""
],
[
"Muñoz-Barrutia",
"Arrate",
""
],
[
"Anita",
"Liviu",
""
],
[
"Babalola",
"Kola",
""
],
... | Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to d... |
q-bio/0611058 | Tilo Beyer | Tilo Beyer and Michael Meyer-Hermann | Mechanisms of organogenesis of primary lymphoid follicles | 31 pages, 2 figures | null | null | null | q-bio.TO q-bio.CB | null | Primary lymphoid follicles in secondary lymphoid tissue of mammals are the
backbone for the formation of follicular dendritic cell networks. These are
important for germinal center reactions. In the context of organogenesis
molecular requirements for the formation of follicles have been identified. The
present study ... | [
{
"created": "Fri, 17 Nov 2006 16:05:03 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Beyer",
"Tilo",
""
],
[
"Meyer-Hermann",
"Michael",
""
]
] | Primary lymphoid follicles in secondary lymphoid tissue of mammals are the backbone for the formation of follicular dendritic cell networks. These are important for germinal center reactions. In the context of organogenesis molecular requirements for the formation of follicles have been identified. The present study co... |
2401.04862 | William Cannon | William R. Cannon, Ethan King, Katherine A. Huening and Justin A.
North | Redox Poise during Rhodospirillum rubrum Phototrophic Growth Drives
Large-scale Changes in Macromolecular Synthesis Pathways | null | null | null | null | q-bio.MN q-bio.CB q-bio.SC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | During photoheterotrophic growth on organic substrates, purple nonsulfur
photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by
multiple means, including oxidation of organic substrates, oxidation of
inorganic electron donors (e.g. H$_2$), and by reverse electron flow from the
photosynthetic elec... | [
{
"created": "Wed, 10 Jan 2024 00:40:22 GMT",
"version": "v1"
}
] | 2024-01-11 | [
[
"Cannon",
"William R.",
""
],
[
"King",
"Ethan",
""
],
[
"Huening",
"Katherine A.",
""
],
[
"North",
"Justin A.",
""
]
] | During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g. H$_2$), and by reverse electron flow from the photosynthetic electr... |
1808.08948 | Tom Chou | Song Xu and Tom Chou | Immigration-induced phase transition in a regulated multispecies
birth-death process | 22 pages, 8 figures, accepted to J. Phys. A | null | 10.1088/1751-8121/aadcb4 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Power-law-distributed species counts or clone counts arise in many biological
settings such as multispecies cell populations, population genetics, and
ecology. This empirical observation that the number of species $c_{k}$
represented by $k$ individuals scales as negative powers of $k$ is also
supported by a series of... | [
{
"created": "Mon, 27 Aug 2018 17:54:22 GMT",
"version": "v1"
}
] | 2018-09-26 | [
[
"Xu",
"Song",
""
],
[
"Chou",
"Tom",
""
]
] | Power-law-distributed species counts or clone counts arise in many biological settings such as multispecies cell populations, population genetics, and ecology. This empirical observation that the number of species $c_{k}$ represented by $k$ individuals scales as negative powers of $k$ is also supported by a series of t... |
2302.07820 | Walid Hachem | Imane Akjouj, Walid Hachem, Myl\`ene Ma\"ida, Jamal Najim | Equilibria of large random Lotka-Volterra systems with vanishing
species: a mathematical approach | null | null | null | null | q-bio.PE math.PR | http://creativecommons.org/licenses/by/4.0/ | Ecosystems with a large number of species are often modelled as
Lotka-Volterra dynamical systems built around a large random interaction
matrix. Under some known conditions, a global equilibrium exists and is unique.
In this article, we rigorously study its statistical properties in the large
dimensional regime. Such... | [
{
"created": "Wed, 15 Feb 2023 18:01:48 GMT",
"version": "v1"
},
{
"created": "Mon, 31 Jul 2023 12:45:41 GMT",
"version": "v2"
}
] | 2023-08-01 | [
[
"Akjouj",
"Imane",
""
],
[
"Hachem",
"Walid",
""
],
[
"Maïda",
"Mylène",
""
],
[
"Najim",
"Jamal",
""
]
] | Ecosystems with a large number of species are often modelled as Lotka-Volterra dynamical systems built around a large random interaction matrix. Under some known conditions, a global equilibrium exists and is unique. In this article, we rigorously study its statistical properties in the large dimensional regime. Such a... |
1908.02316 | Matthias Fischer | Matthias M. Fischer | A mechanistic model of disjunctive metabolic symbioses in microbes | 19 pages, 4 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Lately, experimental research on microbial symbioses based on nutrient
exchange and interdependence has yielded a number of interesting findings,
however an in-depth mathematical description of the exact underlying dynamics
of such symbiotic associations is still missing. Here, we derive and analyse a
mechanistic mat... | [
{
"created": "Tue, 6 Aug 2019 18:32:49 GMT",
"version": "v1"
}
] | 2019-08-08 | [
[
"Fischer",
"Matthias M.",
""
]
] | Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such symbiotic associations is still missing. Here, we derive and analyse a mechanistic mathe... |
1601.01788 | Taoyang Wu | Katharina T. Huber and Vincent Moulton and Taoyang Wu | Transforming phylogenetic networks: Moving beyond tree space | 27 pages, 13 figures | null | null | null | q-bio.PE math.CO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Phylogenetic networks are a generalization of phylogenetic trees that are
used to represent reticulate evolution. Unrooted phylogenetic networks form a
special class of such networks, which naturally generalize unrooted
phylogenetic trees. In this paper we define two operations on unrooted
phylogenetic networks, one ... | [
{
"created": "Fri, 8 Jan 2016 08:10:24 GMT",
"version": "v1"
}
] | 2016-01-11 | [
[
"Huber",
"Katharina T.",
""
],
[
"Moulton",
"Vincent",
""
],
[
"Wu",
"Taoyang",
""
]
] | Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of... |
2102.12374 | Kasey Laurent | Kasey M. Laurent, Bob Fogg, Tobias Ginsburg, Casey Halverson, Michael
Lanzone, Tricia A. Miller, David W. Winkler, Gregory P. Bewley | Turbulence explains the accelerations of an eagle in natural flight | 21 pages, 4 figures | null | 10.1073/pnas.2102588118 | null | q-bio.QM physics.bio-ph physics.flu-dyn | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Turbulent winds and gusts fluctuate on a wide range of timescales from
milliseconds to minutes and longer, a range that overlaps the timescales of
avian flight behavior, yet the importance of turbulence to avian behavior is
unclear. By combining wind speed data with the measured accelerations of a
golden eagle (Aquil... | [
{
"created": "Fri, 19 Feb 2021 15:56:34 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Mar 2021 17:13:17 GMT",
"version": "v2"
},
{
"created": "Tue, 4 May 2021 13:51:03 GMT",
"version": "v3"
},
{
"created": "Wed, 19 May 2021 16:46:15 GMT",
"version": "v4"
}
] | 2021-07-07 | [
[
"Laurent",
"Kasey M.",
""
],
[
"Fogg",
"Bob",
""
],
[
"Ginsburg",
"Tobias",
""
],
[
"Halverson",
"Casey",
""
],
[
"Lanzone",
"Michael",
""
],
[
"Miller",
"Tricia A.",
""
],
[
"Winkler",
"David W.",
""
],
... | Turbulent winds and gusts fluctuate on a wide range of timescales from milliseconds to minutes and longer, a range that overlaps the timescales of avian flight behavior, yet the importance of turbulence to avian behavior is unclear. By combining wind speed data with the measured accelerations of a golden eagle (Aquila ... |
2310.13866 | Grzegorz A Rempala | Grzegorz A. Rempala | Equivalence of Mass Action and Poisson Network SIR Epidemic Models | 2 figures | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This brief note highlights a largely overlooked similarity between the SIR
ordinary differential equations used for epidemics on the configuration model
of a Poisson network and the classical mass-action SIR equations introduced
nearly a century ago by Kermack and McKendrick. We demonstrate that the decline
pattern i... | [
{
"created": "Sat, 21 Oct 2023 00:07:48 GMT",
"version": "v1"
}
] | 2023-10-24 | [
[
"Rempala",
"Grzegorz A.",
""
]
] | This brief note highlights a largely overlooked similarity between the SIR ordinary differential equations used for epidemics on the configuration model of a Poisson network and the classical mass-action SIR equations introduced nearly a century ago by Kermack and McKendrick. We demonstrate that the decline pattern in ... |
2003.08684 | Silvia Licciardi | Giuseppe Dattoli, Emanuele Di Palma, Silvia Licciardi, Elio Sabia | A Note on the Evolution of Covid-19 in Italy | 10 pages, 11 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We employ methods largely exploited in Physics, in the analysis of the
evolution of dynamical systems, to study the pattern of the Covid-19 infection
in Italy. The techniques we employ are based on the use of logistic function
and of its derivative, namely the Hubbert function. The latter is exploited to
give a predi... | [
{
"created": "Thu, 19 Mar 2020 11:05:07 GMT",
"version": "v1"
}
] | 2020-03-20 | [
[
"Dattoli",
"Giuseppe",
""
],
[
"Di Palma",
"Emanuele",
""
],
[
"Licciardi",
"Silvia",
""
],
[
"Sabia",
"Elio",
""
]
] | We employ methods largely exploited in Physics, in the analysis of the evolution of dynamical systems, to study the pattern of the Covid-19 infection in Italy. The techniques we employ are based on the use of logistic function and of its derivative, namely the Hubbert function. The latter is exploited to give a predict... |
1003.4756 | Douady Stephane | Etienne Couturier, Sylvain Courrech du Pont, St\'ephane Douady | The filling law: a general framework for leaf shape diversity and its
consequences on folded leaves | 27 p., 28 fig., article | null | null | null | q-bio.TO nlin.AO | http://creativecommons.org/licenses/by-nc-sa/3.0/ | Leaves are packed in a bud in different ways, being flat, enrolled, or
folded, but always filling the whole bud volume. This {\guillemotleft} filling
law {\guillemotright} has many consequences, in particular on the shape of
growing folded leaves. This is shown here for different types of folding and
packing. The fol... | [
{
"created": "Wed, 24 Mar 2010 21:26:25 GMT",
"version": "v1"
},
{
"created": "Thu, 7 Oct 2010 20:06:13 GMT",
"version": "v2"
}
] | 2010-10-11 | [
[
"Couturier",
"Etienne",
""
],
[
"Pont",
"Sylvain Courrech du",
""
],
[
"Douady",
"Stéphane",
""
]
] | Leaves are packed in a bud in different ways, being flat, enrolled, or folded, but always filling the whole bud volume. This {\guillemotleft} filling law {\guillemotright} has many consequences, in particular on the shape of growing folded leaves. This is shown here for different types of folding and packing. The folde... |
q-bio/0701038 | Vittoria Colizza | Vittoria Colizza, Alain Barrat, Marc Barthelemy, Alain-Jacques
Valleron, Alessandro Vespignani | Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and
Containment Interventions | 16 pages | PLoS Med 4(1): e13. (2007) | 10.1371/journal.pmed.0040013 | null | q-bio.OT cond-mat.stat-mech physics.soc-ph | null | We present a study of the worldwide spread of a pandemic influenza and its
possible containment at a global level taking into account all available
information on air travel. We studied a metapopulation stochastic epidemic
model on a global scale that considers airline travel flow data among urban
areas. We provided ... | [
{
"created": "Wed, 24 Jan 2007 18:32:50 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Colizza",
"Vittoria",
""
],
[
"Barrat",
"Alain",
""
],
[
"Barthelemy",
"Marc",
""
],
[
"Valleron",
"Alain-Jacques",
""
],
[
"Vespignani",
"Alessandro",
""
]
] | We present a study of the worldwide spread of a pandemic influenza and its possible containment at a global level taking into account all available information on air travel. We studied a metapopulation stochastic epidemic model on a global scale that considers airline travel flow data among urban areas. We provided a ... |
1810.10894 | Panteleimon Vafeidis | Panteleimon Vafeidis, Vasilios K. Kimiskidis, Dimitris Kugiumtzis | Evaluation of algorithms for correction of transcranial magnetic
stimulation induced artifacts in electroencephalograms | 18 pages, 7 figures, 2 tables. Med Biol Eng Comput (2019) | null | 10.1007/s11517-019-02053-3 | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transcranial magnetic stimulation combined with electroencephalography
(TMS-EEG) is widely used to study the reactivity and connectivity of brain
regions for clinical or research purposes. The electromagnetic pulse of the TMS
device generates at the instant of administration an artifact of large
amplitude and a durat... | [
{
"created": "Thu, 25 Oct 2018 14:27:26 GMT",
"version": "v1"
}
] | 2019-10-30 | [
[
"Vafeidis",
"Panteleimon",
""
],
[
"Kimiskidis",
"Vasilios K.",
""
],
[
"Kugiumtzis",
"Dimitris",
""
]
] | Transcranial magnetic stimulation combined with electroencephalography (TMS-EEG) is widely used to study the reactivity and connectivity of brain regions for clinical or research purposes. The electromagnetic pulse of the TMS device generates at the instant of administration an artifact of large amplitude and a duratio... |
2405.00838 | Jayoung Ryu | Jayoung Ryu, Romain Lopez, Charlotte Bunne, Aviv Regev | Cross-modality Matching and Prediction of Perturbation Responses with
Labeled Gromov-Wasserstein Optimal Transport | 16 pages, 4 figures, correspondence to Aviv Regev and Romain Lopez | null | null | null | q-bio.GN math.OC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | It is now possible to conduct large scale perturbation screens with complex
readout modalities, such as different molecular profiles or high content cell
images. While these open the way for systematic dissection of causal cell
circuits, integrated such data across screens to maximize our ability to
predict circuits ... | [
{
"created": "Wed, 1 May 2024 19:59:45 GMT",
"version": "v1"
}
] | 2024-05-03 | [
[
"Ryu",
"Jayoung",
""
],
[
"Lopez",
"Romain",
""
],
[
"Bunne",
"Charlotte",
""
],
[
"Regev",
"Aviv",
""
]
] | It is now possible to conduct large scale perturbation screens with complex readout modalities, such as different molecular profiles or high content cell images. While these open the way for systematic dissection of causal cell circuits, integrated such data across screens to maximize our ability to predict circuits po... |
1807.11654 | Akram Yazdani PhD | Akram Yazdani, Raul Mendez Giraldez, Ahmad Samiei | Insights into Complex Brain Functions Related to Schizophrenia Disorder
through Causal Network Analysis | null | null | null | null | q-bio.GN q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Gene expression represents a fundamental interface between genes and
environment in the development and ongoing plasticity of the human organism.
Individual differences in gene expression are likely to underpin much of human
diversity, including psychiatric illness. Gene expression shows a distinct
regulatory pattern... | [
{
"created": "Tue, 31 Jul 2018 04:18:22 GMT",
"version": "v1"
},
{
"created": "Tue, 28 May 2019 14:02:50 GMT",
"version": "v2"
}
] | 2019-05-31 | [
[
"Yazdani",
"Akram",
""
],
[
"Giraldez",
"Raul Mendez",
""
],
[
"Samiei",
"Ahmad",
""
]
] | Gene expression represents a fundamental interface between genes and environment in the development and ongoing plasticity of the human organism. Individual differences in gene expression are likely to underpin much of human diversity, including psychiatric illness. Gene expression shows a distinct regulatory pattern i... |
2405.01664 | Dilawar Ahmad Mir | Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers | Stress-induced Eukaryotic Translational Regulatory Mechanisms | 37 Pages, Figures 7, Review Article | null | null | null | q-bio.MN | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The eukaryotic protein synthesis process entails intricate stages governed by
diverse mechanisms to tightly regulate translation. Translational regulation
during stress is pivotal for maintaining cellular homeostasis, ensuring the
accurate expression of essential proteins crucial for survival. This selective
translat... | [
{
"created": "Thu, 2 May 2024 18:34:53 GMT",
"version": "v1"
}
] | 2024-05-06 | [
[
"Mir",
"Dilawar Ahmad",
""
],
[
"Ma",
"Zhengxin",
""
],
[
"Horrocks",
"Jordan",
""
],
[
"Rogers",
"Aric N",
""
]
] | The eukaryotic protein synthesis process entails intricate stages governed by diverse mechanisms to tightly regulate translation. Translational regulation during stress is pivotal for maintaining cellular homeostasis, ensuring the accurate expression of essential proteins crucial for survival. This selective translatio... |
2202.13282 | Vijay Rajagopal | Vijay Rajagopal, Senthil Arumugam, Peter Hunter, Afshin Khadangi,
Joshua Chung, Michael Pan | The Cell Physiome: What do we need in a computational physiology
framework for predicting single cell biology? | Minor text edits to fix minor grammatical errors and figure reference | null | null | null | q-bio.CB physics.bio-ph q-bio.QM q-bio.SC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Modern biology and biomedicine are undergoing a big-data explosion needing
advanced computational algorithms to extract mechanistic insights on the
physiological state of living cells. We present the motivation for the Cell
Physiome: a framework and approach for creating, sharing, and using
biophysics-based computati... | [
{
"created": "Sun, 27 Feb 2022 03:36:45 GMT",
"version": "v1"
},
{
"created": "Sat, 5 Mar 2022 05:02:27 GMT",
"version": "v2"
}
] | 2022-03-08 | [
[
"Rajagopal",
"Vijay",
""
],
[
"Arumugam",
"Senthil",
""
],
[
"Hunter",
"Peter",
""
],
[
"Khadangi",
"Afshin",
""
],
[
"Chung",
"Joshua",
""
],
[
"Pan",
"Michael",
""
]
] | Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a framework and approach for creating, sharing, and using biophysics-based computation... |
2005.02188 | Guo-Wei Wei | Rui Wang, Yuta Hozumi, Changchuan Yin and Guo-Wei Wei | Mutations on COVID-19 diagnostic targets | 3 tables and 6 pages, and 48 tables in the Supporting Material | null | null | null | q-bio.GN q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Effective, sensitive, and reliable diagnostic reagents are of paramount
importance for combating the ongoing coronavirus disease 2019 (COVID-19)
pandemic at a time there is no preventive vaccine nor specific drug available
for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It would be
an absolute trage... | [
{
"created": "Tue, 5 May 2020 13:57:25 GMT",
"version": "v1"
}
] | 2020-05-06 | [
[
"Wang",
"Rui",
""
],
[
"Hozumi",
"Yuta",
""
],
[
"Yin",
"Changchuan",
""
],
[
"Wei",
"Guo-Wei",
""
]
] | Effective, sensitive, and reliable diagnostic reagents are of paramount importance for combating the ongoing coronavirus disease 2019 (COVID-19) pandemic at a time there is no preventive vaccine nor specific drug available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It would be an absolute tragedy... |
1911.04638 | David Abramov | David Abramov, Jasmine Otto, Mahika Dubey, Cassia Artanegara, Pierre
Boutillier, Walter Fontana, Angus G. Forbes | RuleVis: Constructing Patterns and Rules for Rule-Based Models | 4 pages, 6 figures, presented at IEEE VIS 2019 | null | null | null | q-bio.QM cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce RuleVis, a web-based application for defining and editing
"correct-by-construction" executable rules that model biochemical
functionality, which can be used to simulate the behavior of protein-protein
interaction networks and other complex systems. Rule-based models involve
emergent effects based on the ... | [
{
"created": "Tue, 12 Nov 2019 02:24:58 GMT",
"version": "v1"
}
] | 2019-11-13 | [
[
"Abramov",
"David",
""
],
[
"Otto",
"Jasmine",
""
],
[
"Dubey",
"Mahika",
""
],
[
"Artanegara",
"Cassia",
""
],
[
"Boutillier",
"Pierre",
""
],
[
"Fontana",
"Walter",
""
],
[
"Forbes",
"Angus G.",
""
]
] | We introduce RuleVis, a web-based application for defining and editing "correct-by-construction" executable rules that model biochemical functionality, which can be used to simulate the behavior of protein-protein interaction networks and other complex systems. Rule-based models involve emergent effects based on the in... |
1907.12045 | Lisa Buchauer | Lisa Buchauer, Hedda Wardemann | Calculating Germinal Centre Reactions | null | Current Opinion in Systems Biology 18:1-8 (2019) | 10.1016/j.coisb.2019.10.004 | null | q-bio.QM q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Germinal centres are anatomically defined lymphoid organ structures that
mediate B cell affinity maturation and affect the quality of humoral immune
responses. Mathematical models based on differential equations or agent-based
simulations have been widely used to deepen our understanding of the cellular
and molecular... | [
{
"created": "Sun, 28 Jul 2019 08:49:33 GMT",
"version": "v1"
}
] | 2019-11-22 | [
[
"Buchauer",
"Lisa",
""
],
[
"Wardemann",
"Hedda",
""
]
] | Germinal centres are anatomically defined lymphoid organ structures that mediate B cell affinity maturation and affect the quality of humoral immune responses. Mathematical models based on differential equations or agent-based simulations have been widely used to deepen our understanding of the cellular and molecular p... |
1407.4137 | Eric Jonas | Eric Jonas and Konrad Kording | Automatic discovery of cell types and microcircuitry from neural
connectomics | null | null | null | null | q-bio.NC stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neural connectomics has begun producing massive amounts of data,
necessitating new analysis methods to discover the biological and computational
structure. It has long been assumed that discovering neuron types and their
relation to microcircuitry is crucial to understanding neural function. Here we
developed a nonpa... | [
{
"created": "Tue, 15 Jul 2014 20:14:05 GMT",
"version": "v1"
}
] | 2014-07-17 | [
[
"Jonas",
"Eric",
""
],
[
"Kording",
"Konrad",
""
]
] | Neural connectomics has begun producing massive amounts of data, necessitating new analysis methods to discover the biological and computational structure. It has long been assumed that discovering neuron types and their relation to microcircuitry is crucial to understanding neural function. Here we developed a nonpara... |
2002.08294 | Anders Ledberg | Anders Ledberg | Exponential increase in mortality with age is a generic property of a
simple model system of damage accumulation and death | null | null | 10.1371/journal.pone.0233384 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The risk of dying increases exponentially with age, in humans as well as in
many other species. This increase is often attributed to the "accumulation of
damage" known to occur in many biological structures and systems. The aim of
this paper is to describe a generic model of damage accumulation and death in
which mor... | [
{
"created": "Wed, 19 Feb 2020 17:11:10 GMT",
"version": "v1"
}
] | 2020-07-01 | [
[
"Ledberg",
"Anders",
""
]
] | The risk of dying increases exponentially with age, in humans as well as in many other species. This increase is often attributed to the "accumulation of damage" known to occur in many biological structures and systems. The aim of this paper is to describe a generic model of damage accumulation and death in which morta... |
1708.04025 | Etienne Thevenot | Alexis Delabri\`ere (CEA), Ulli Hohenester, Benoit Colsch, Christophe
Junot, Fran\c{c}ois Fenaille, Etienne Th\'evenot (CEA) | proFIA: A data preprocessing workflow for Flow Injection Analysis
coupled to High-Resolution Mass Spectrometry | Bioinformatics, Oxford University Press (OUP), 2017 | null | 10.1093/bioinformatics/btx458 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Flow Injection Analysis coupled to High-Resolution Mass
Spectrometry (FIA-HRMS) is a promising approach for high-throughput
metabolomics. FIA-HRMS data, however, cannot be preprocessed with current
software tools which rely on liquid chromatography separation, or handle low
resolution data only. Results: ... | [
{
"created": "Mon, 14 Aug 2017 07:37:18 GMT",
"version": "v1"
}
] | 2017-08-15 | [
[
"Delabrière",
"Alexis",
"",
"CEA"
],
[
"Hohenester",
"Ulli",
"",
"CEA"
],
[
"Colsch",
"Benoit",
"",
"CEA"
],
[
"Junot",
"Christophe",
"",
"CEA"
],
[
"Fenaille",
"François",
"",
"CEA"
],
[
"Thévenot",
"Etien... | Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Results: We... |
2206.10370 | In\^es Guerreiro | In\^es C. Guerreiro, Matteo di Volo, Boris Gutkin | A new generation of reduction methods for networks of neurons with
complex dynamic phenotypes | reduction method for bursting neurons added | null | null | null | q-bio.NC cond-mat.stat-mech | http://creativecommons.org/licenses/by/4.0/ | Collective dynamics of spiking networks of neurons has been of central
interest to both computation neuroscience and network science. Over the past
years a new generation of neural population models based on exact reductions
(ER) of spiking networks have been developed. However, most of these efforts
have been limite... | [
{
"created": "Tue, 21 Jun 2022 13:20:02 GMT",
"version": "v1"
},
{
"created": "Mon, 23 Oct 2023 11:55:09 GMT",
"version": "v2"
}
] | 2023-10-24 | [
[
"Guerreiro",
"Inês C.",
""
],
[
"di Volo",
"Matteo",
""
],
[
"Gutkin",
"Boris",
""
]
] | Collective dynamics of spiking networks of neurons has been of central interest to both computation neuroscience and network science. Over the past years a new generation of neural population models based on exact reductions (ER) of spiking networks have been developed. However, most of these efforts have been limited ... |
2107.11458 | Sanna Gudmundsson | Sanna Gudmundsson, Moriel Singer-Berk, Nicholas A. Watts, William Phu,
Julia K. Goodrich, Matthew Solomonson, Genome Aggregation Database
Consortium, Heidi L. Rehm, Daniel G. MacArthur, Anne ODonnell-Luria | Variant interpretation using population databases: lessons from gnomAD | Version 3: Includes updates to mirror the latest features and layouts
available on the gnomAD browser and general improvements to text and figures
(clarifications, typos, additional references etc.) as well as the addition
of Table S1, S2, Figure S1, S2 and S5 | null | 10.1002/humu.24309 | null | q-bio.GN | http://creativecommons.org/licenses/by/4.0/ | Reference population databases are an essential tool in variant and gene
interpretation. Their use guides the identification of pathogenic variants
amidst the sea of benign variation present in every human genome, and supports
the discovery of new disease-gene relationships. The Genome Aggregation
Database (gnomAD) i... | [
{
"created": "Fri, 23 Jul 2021 20:56:50 GMT",
"version": "v1"
},
{
"created": "Thu, 4 Nov 2021 15:01:14 GMT",
"version": "v2"
},
{
"created": "Sun, 16 Jan 2022 18:36:52 GMT",
"version": "v3"
}
] | 2022-01-19 | [
[
"Gudmundsson",
"Sanna",
""
],
[
"Singer-Berk",
"Moriel",
""
],
[
"Watts",
"Nicholas A.",
""
],
[
"Phu",
"William",
""
],
[
"Goodrich",
"Julia K.",
""
],
[
"Solomonson",
"Matthew",
""
],
[
"Consortium",
"Genome ... | Reference population databases are an essential tool in variant and gene interpretation. Their use guides the identification of pathogenic variants amidst the sea of benign variation present in every human genome, and supports the discovery of new disease-gene relationships. The Genome Aggregation Database (gnomAD) is ... |
1505.03827 | Daniel Korytowski | Daniel A. Korytowski and Hal L. Smith | Persistence in Phage-Bacteria Communities with Nested and One-to-One
Infection Networks | 15 pages. arXiv admin note: substantial text overlap with
arXiv:1406.5461 | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We show that a bacteria and bacteriophage system with either a perfectly
nested or a one-to-one infection network is permanent, a.k.a uniformly
persistent, provided that bacteria that are superior competitors for nutrient
devote the least to defence against infection and the virus that are the most
efficient at infec... | [
{
"created": "Thu, 14 May 2015 18:32:28 GMT",
"version": "v1"
},
{
"created": "Thu, 28 May 2015 04:10:37 GMT",
"version": "v2"
}
] | 2015-05-29 | [
[
"Korytowski",
"Daniel A.",
""
],
[
"Smith",
"Hal L.",
""
]
] | We show that a bacteria and bacteriophage system with either a perfectly nested or a one-to-one infection network is permanent, a.k.a uniformly persistent, provided that bacteria that are superior competitors for nutrient devote the least to defence against infection and the virus that are the most efficient at infecti... |
1807.02985 | Bartlomiej Waclaw Dr | Craig Watson, Paul Hush, Joshua Williams, Angela Dawson, Nikola Ojkic,
Simon Titmuss, and Bartlomiej Waclaw | Reduced adhesion between cells and substrate confers selective advantage
in bacterial colonies | 7 pages, 7 figures, submitted to the EPL Special Issue "Evolutionary
modeling and experimental evolution" | null | 10.1209/0295-5075/123/68001 | null | q-bio.PE physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Microbial colonies cultured on agar Petri dishes have become a model system
to study biological evolution in populations expanding in space. Processes such
as clonal segregation and gene surfing have been shown to be affected by
interactions between microbial cells and their environment. In this work we
investigate t... | [
{
"created": "Mon, 9 Jul 2018 08:18:06 GMT",
"version": "v1"
}
] | 2018-10-17 | [
[
"Watson",
"Craig",
""
],
[
"Hush",
"Paul",
""
],
[
"Williams",
"Joshua",
""
],
[
"Dawson",
"Angela",
""
],
[
"Ojkic",
"Nikola",
""
],
[
"Titmuss",
"Simon",
""
],
[
"Waclaw",
"Bartlomiej",
""
]
] | Microbial colonies cultured on agar Petri dishes have become a model system to study biological evolution in populations expanding in space. Processes such as clonal segregation and gene surfing have been shown to be affected by interactions between microbial cells and their environment. In this work we investigate the... |
1409.0761 | Tom Nye | Tom M. W. Nye | An algorithm for constructing principal geodesics in phylogenetic
treespace | 6 figures, IEEE/ACM Transactions on Computational Biology and
Bioinformatics, Vol. 11, No. 2, 2014 | null | 10.1109/TCBB.2014.2309599 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Most phylogenetic analyses result in a sample of trees, but summarizing and
visualizing these samples can be challenging. Consensus trees often provide
limited information about a sample, and so methods such as consensus networks,
clustering and multidimensional scaling have been developed and applied to tree
samples... | [
{
"created": "Tue, 2 Sep 2014 15:41:13 GMT",
"version": "v1"
}
] | 2014-09-03 | [
[
"Nye",
"Tom M. W.",
""
]
] | Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks, clustering and multidimensional scaling have been developed and applied to tree samples. ... |
0910.1916 | Iain Johnston | Iain G. Johnston, Ard A. Louis, Jonathan P. K. Doye | Modelling the Self-Assembly of Virus Capsids | 16 pages, 11 figures | J. Phys.: Condens. Matter 22 104101 (2010) | 10.1088/0953-8984/22/10/104101 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We use computer simulations to study a model, first proposed by Wales [1],
for the reversible and monodisperse self-assembly of simple icosahedral virus
capsid structures. The success and efficiency of assembly as a function of
thermodynamic and geometric factors can be qualitatively related to the
potential energy l... | [
{
"created": "Sat, 10 Oct 2009 12:15:06 GMT",
"version": "v1"
}
] | 2010-02-24 | [
[
"Johnston",
"Iain G.",
""
],
[
"Louis",
"Ard A.",
""
],
[
"Doye",
"Jonathan P. K.",
""
]
] | We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy lan... |
q-bio/0506021 | Eli Eisenberg | Moshe Havilio, Erez Y. Levanon, Galia Lerman, Martin Kupiec and Eli
Eisenberg | Evidence for abundant transcription of non-coding regions in the
Saccharomyces cerevisiae genome | Journal version available at
http://www.biomedcentral.com/1471-2164/6/93/abstract | BMC Genomics 6:93 (2005) | 10.1186/1471-2164-6-93 | null | q-bio.GN | null | Background: Recent studies in a growing number of organisms have yielded
accumulating evidence that a significant portion of the non-coding region in
the genome is transcribed. We address this issue in the yeast Saccharomyces
cerevisiae.
Results: Taking into account the absence of a significantly large yeast EST
da... | [
{
"created": "Thu, 16 Jun 2005 13:28:40 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Havilio",
"Moshe",
""
],
[
"Levanon",
"Erez Y.",
""
],
[
"Lerman",
"Galia",
""
],
[
"Kupiec",
"Martin",
""
],
[
"Eisenberg",
"Eli",
""
]
] | Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae. Results: Taking into account the absence of a significantly large yeast EST databa... |
1912.12762 | Andrey Kuznetsov | I. A. Kuznetsov and A. V. Kuznetsov | How old are dense core vesicles residing in en passant boutons:
Simulation of the mean age of dense core vesicles in axonal arbors accounting
for resident and transiting vesicle populations | Final, accepted manuscript version | Proc. R. Soc. A, vol. 476: 20200454, 2020 | 10.1098/rspa.2020.0454 | null | q-bio.SC q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In neurons, neuropeptides are synthesized in the soma and are then
transported along the axon in dense core vesicles (DCVs). DCVs are captured in
varicosities located along the axon terminal called en passant boutons, which
are active terminal sites that accumulate and release neurotransmitters.
Recently developed ex... | [
{
"created": "Mon, 30 Dec 2019 00:07:33 GMT",
"version": "v1"
},
{
"created": "Sat, 1 Feb 2020 16:39:11 GMT",
"version": "v2"
},
{
"created": "Wed, 6 May 2020 17:00:06 GMT",
"version": "v3"
},
{
"created": "Fri, 16 Oct 2020 18:25:00 GMT",
"version": "v4"
}
] | 2020-10-20 | [
[
"Kuznetsov",
"I. A.",
""
],
[
"Kuznetsov",
"A. V.",
""
]
] | In neurons, neuropeptides are synthesized in the soma and are then transported along the axon in dense core vesicles (DCVs). DCVs are captured in varicosities located along the axon terminal called en passant boutons, which are active terminal sites that accumulate and release neurotransmitters. Recently developed expe... |
0712.3383 | Thibault Lagache | Thibault Lagache and David Holcman | Effective Motion of a Virus Trafficking Inside a Biological Cell | 22 pages, 6 figures, accepted in SIAM Journal of Applied Mathematics | null | null | null | q-bio.QM q-bio.SC | null | Virus trafficking is fundamental for infection success and plasmid cytosolic
trafficking is a key step of gene delivery. Based on the main physical
properties of the cellular transport machinery such as microtubules, motor
proteins, our goal here is to derive a mathematical model to study cytoplasmic
trafficking. Bec... | [
{
"created": "Thu, 20 Dec 2007 12:05:35 GMT",
"version": "v1"
}
] | 2007-12-21 | [
[
"Lagache",
"Thibault",
""
],
[
"Holcman",
"David",
""
]
] | Virus trafficking is fundamental for infection success and plasmid cytosolic trafficking is a key step of gene delivery. Based on the main physical properties of the cellular transport machinery such as microtubules, motor proteins, our goal here is to derive a mathematical model to study cytoplasmic trafficking. Becau... |
2305.19654 | Polina Turishcheva | Polina Turishcheva, Paul G. Fahey, Laura Hansel, Rachel Froebe, Kayla
Ponder, Michaela Vystr\v{c}ilov\'a, Konstantin F. Willeke, Mohammad Bashiri,
Eric Wang, Zhiwei Ding, Andreas S. Tolias, Fabian H. Sinz, Alexander S. Ecker | The Dynamic Sensorium competition for predicting large-scale mouse
visual cortex activity from videos | arXiv admin note: substantial text overlap with arXiv:2206.08666 | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Understanding how biological visual systems process information is
challenging due to the complex nonlinear relationship between neuronal
responses and high-dimensional visual input. Artificial neural networks have
already improved our understanding of this system by allowing computational
neuroscientists to create p... | [
{
"created": "Wed, 31 May 2023 08:40:12 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Jul 2024 08:53:07 GMT",
"version": "v2"
}
] | 2024-07-15 | [
[
"Turishcheva",
"Polina",
""
],
[
"Fahey",
"Paul G.",
""
],
[
"Hansel",
"Laura",
""
],
[
"Froebe",
"Rachel",
""
],
[
"Ponder",
"Kayla",
""
],
[
"Vystrčilová",
"Michaela",
""
],
[
"Willeke",
"Konstantin F.",
... | Understanding how biological visual systems process information is challenging due to the complex nonlinear relationship between neuronal responses and high-dimensional visual input. Artificial neural networks have already improved our understanding of this system by allowing computational neuroscientists to create pre... |
1508.05317 | David Murrugarra | David Murrugarra and Alan Veliz-Cuba and Boris Aguilar and Reinhard
Laubenbacher | Identification of control targets in Boolean molecular network models
via computational algebra | 12 pages, 4 figures, 2 tables | BMC Systems Biology, 10:94, 2016 | 10.1186/s12918-016-0332-x | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Many problems in biomedicine and other areas of the life sciences
can be characterized as control problems, with the goal of finding strategies
to change a disease or otherwise undesirable state of a biological system into
another, more desirable, state through an intervention, such as a drug or other
the... | [
{
"created": "Fri, 21 Aug 2015 15:46:34 GMT",
"version": "v1"
},
{
"created": "Thu, 3 Sep 2015 21:38:12 GMT",
"version": "v2"
},
{
"created": "Mon, 1 Aug 2016 17:49:21 GMT",
"version": "v3"
},
{
"created": "Mon, 3 Oct 2016 17:54:39 GMT",
"version": "v4"
}
] | 2016-10-04 | [
[
"Murrugarra",
"David",
""
],
[
"Veliz-Cuba",
"Alan",
""
],
[
"Aguilar",
"Boris",
""
],
[
"Laubenbacher",
"Reinhard",
""
]
] | Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into another, more desirable, state through an intervention, such as a drug or other thera... |
1909.05215 | Ellen Zhong | Ellen D. Zhong, Tristan Bepler, Joseph H. Davis, Bonnie Berger | Reconstructing continuous distributions of 3D protein structure from
cryo-EM images | null | International Conference on Learning Representations (ICLR), 2020 | null | null | q-bio.QM cs.CV cs.LG eess.IV stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cryo-electron microscopy (cryo-EM) is a powerful technique for determining
the structure of proteins and other macromolecular complexes at near-atomic
resolution. In single particle cryo-EM, the central problem is to reconstruct
the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and
randomly ori... | [
{
"created": "Wed, 11 Sep 2019 17:13:06 GMT",
"version": "v1"
},
{
"created": "Thu, 12 Dec 2019 23:45:23 GMT",
"version": "v2"
},
{
"created": "Sat, 15 Feb 2020 04:31:46 GMT",
"version": "v3"
}
] | 2020-02-18 | [
[
"Zhong",
"Ellen D.",
""
],
[
"Bepler",
"Tristan",
""
],
[
"Davis",
"Joseph H.",
""
],
[
"Berger",
"Bonnie",
""
]
] | Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly orien... |
1406.1028 | Rui Vilela-Mendes | Hugo C. Mendes, Alberto Murta and R. Vilela Mendes | Long range dependence and the dynamics of exploited fish populations | 14 pages, 6 figures | Advances in Complex Systems 18 (2015) 1550017 | 10.1142/S0219525915500174 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Long range dependence or long memory is a feature of many processes in the
natural world, which provides important insights on the underlying mechanisms
that generate the observed data. The usual tools available to characterize the
phenomenon are mostly based on second order correlations. However, the long
memory eff... | [
{
"created": "Wed, 4 Jun 2014 12:50:52 GMT",
"version": "v1"
}
] | 2016-05-11 | [
[
"Mendes",
"Hugo C.",
""
],
[
"Murta",
"Alberto",
""
],
[
"Mendes",
"R. Vilela",
""
]
] | Long range dependence or long memory is a feature of many processes in the natural world, which provides important insights on the underlying mechanisms that generate the observed data. The usual tools available to characterize the phenomenon are mostly based on second order correlations. However, the long memory effec... |
0901.3233 | Bernhard Mehlig | A. Eriksson, B. Mehlig, M. Panova, C. Andre, and K. Johannesson | Multiple paternity: determining the minimum number of sires of a large
brood | 16 pages, 5 figures, 3 tables | Molecular Ecology Resources 10, 282 (2010) | 10.1111/j.1755-0998.2009.02753.x | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We describe an efficient algorithm for determining exactly the minimum number
of sires consistent with the multi-locus genotypes of a mother and her progeny.
We consider cases where a simple exhaustive search through all possible sets of
sires is impossible in practice (because it would take too long to complete).
Ou... | [
{
"created": "Wed, 21 Jan 2009 10:58:14 GMT",
"version": "v1"
}
] | 2012-06-13 | [
[
"Eriksson",
"A.",
""
],
[
"Mehlig",
"B.",
""
],
[
"Panova",
"M.",
""
],
[
"Andre",
"C.",
""
],
[
"Johannesson",
"K.",
""
]
] | We describe an efficient algorithm for determining exactly the minimum number of sires consistent with the multi-locus genotypes of a mother and her progeny. We consider cases where a simple exhaustive search through all possible sets of sires is impossible in practice (because it would take too long to complete). Our ... |
2105.03961 | Thomas Schmidt | Thomas Schmidt | Is response priming based on surface color? Response to Skrzypulec
(2021) | 7 pages, 1 figure | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/4.0/ | Skrzypulec (2021) raises the question whether motor activation by masked
color primes is based on the same type of color representation as conscious
vision. He postulates that the literature on color processing without awareness
makes an implicit assumption that "conscious" and "unconscious" color
representations hav... | [
{
"created": "Sun, 9 May 2021 15:36:57 GMT",
"version": "v1"
},
{
"created": "Tue, 11 May 2021 09:13:21 GMT",
"version": "v2"
}
] | 2021-05-12 | [
[
"Schmidt",
"Thomas",
""
]
] | Skrzypulec (2021) raises the question whether motor activation by masked color primes is based on the same type of color representation as conscious vision. He postulates that the literature on color processing without awareness makes an implicit assumption that "conscious" and "unconscious" color representations have ... |
1010.4459 | Marco Zamparo | Marco Zamparo, Antonio Trovato and Amos Maritan | A simplified exactly solvable model for beta-amyloid aggregation | 4 pages, 2 figures | Phys. Rev. Lett. 105, 108102 (2010) | 10.1103/PhysRevLett.105.108102 | null | q-bio.BM cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose an exactly solvable simplified statistical mechanical model for
the thermodynamics of beta-amyloid aggregation, generalizing a well-studied
model for protein folding. The monomer concentration is explicitly taken into
account as well as a non trivial dependence on the microscopic degrees of
freedom of the ... | [
{
"created": "Thu, 21 Oct 2010 12:54:31 GMT",
"version": "v1"
}
] | 2010-10-22 | [
[
"Zamparo",
"Marco",
""
],
[
"Trovato",
"Antonio",
""
],
[
"Maritan",
"Amos",
""
]
] | We propose an exactly solvable simplified statistical mechanical model for the thermodynamics of beta-amyloid aggregation, generalizing a well-studied model for protein folding. The monomer concentration is explicitly taken into account as well as a non trivial dependence on the microscopic degrees of freedom of the si... |
q-bio/0606017 | Wentian Li | Wen Fury, Franak Batliwalla, Peter K. Gregersen, and Wentian Li | Overlapping Probabilities of Top Ranking Gene Lists, Hypergeometric
Distribution, and Stringency of Gene Selection Criterion | submitted to IEEE/EMBS Conference'06 | Proceedings of 28th Annual International Conference of the
Engineering in Medicine and Biology Society, IEEE (2006), pages 5531-5534 | 10.1109/IEMBS.2006.260828 | q-bio.QM/0606017 | q-bio.QM | null | When the same set of genes appear in two top ranking gene lists in two
different studies, it is often of interest to estimate the probability for this
being a chance event. This overlapping probability is well known to follow the
hypergeometric distribution. Usually, the lengths of top-ranking gene lists are
assumed ... | [
{
"created": "Wed, 14 Jun 2006 20:40:14 GMT",
"version": "v1"
}
] | 2009-11-09 | [
[
"Fury",
"Wen",
""
],
[
"Batliwalla",
"Franak",
""
],
[
"Gregersen",
"Peter K.",
""
],
[
"Li",
"Wentian",
""
]
] | When the same set of genes appear in two top ranking gene lists in two different studies, it is often of interest to estimate the probability for this being a chance event. This overlapping probability is well known to follow the hypergeometric distribution. Usually, the lengths of top-ranking gene lists are assumed to... |
1903.04347 | Ionut Barnoaiea | Ionut Barnoaiea | Using satellite image classification and digital terrain modelling to
assess forest species distribution on mountain slopes.A case study in Varatec
Forest District | null | Proceedings of the 4 th International Conference Integrated
Management of Environmental Resources, 2017 | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The relation between ecological conditions and geomorphological factors is
considered the basis for species distribution in Romania. In this context, the
location of each species within parts of the mountain slopes is difficult on a
medium to brad scale level. The paper presents methodology to combine
vegetation data... | [
{
"created": "Mon, 11 Mar 2019 15:02:14 GMT",
"version": "v1"
}
] | 2019-03-12 | [
[
"Barnoaiea",
"Ionut",
""
]
] | The relation between ecological conditions and geomorphological factors is considered the basis for species distribution in Romania. In this context, the location of each species within parts of the mountain slopes is difficult on a medium to brad scale level. The paper presents methodology to combine vegetation data, ... |
2402.09330 | Carlos Oliver Dr. | Carlos Oliver, Vincent Mallet, J\'er\^ome Waldisp\"uhl | 3D-based RNA function prediction tools in rnaglib | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Understanding the connection between complex structural features of RNA and
biological function is a fundamental challenge in evolutionary studies and in
RNA design. However, building datasets of RNA 3D structures and making
appropriate modeling choices remains time-consuming and lacks standardization.
In this chapte... | [
{
"created": "Wed, 14 Feb 2024 17:22:03 GMT",
"version": "v1"
},
{
"created": "Fri, 3 May 2024 09:01:17 GMT",
"version": "v2"
}
] | 2024-05-06 | [
[
"Oliver",
"Carlos",
""
],
[
"Mallet",
"Vincent",
""
],
[
"Waldispühl",
"Jérôme",
""
]
] | Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate modeling choices remains time-consuming and lacks standardization. In this chapter,... |
1711.07162 | Matthew Simpson | Wang Jin, Kai-Yin Lo, Shih-En Chou, Scott W McCue, Matthew J Simpson | The role of initial geometry in experimental models of wound closing | null | Chemical Engineering Science 2018 | 10.1016/j.ces.2018.01.004 | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Wound healing assays are commonly used to study how populations of cells,
initialised on a two-dimensional surface, act to close an artificial wound
space. While real wounds have different shapes, standard wound healing assays
often deal with just one simple wound shape, and it is unclear whether varying
the wound sh... | [
{
"created": "Mon, 20 Nov 2017 05:58:39 GMT",
"version": "v1"
}
] | 2018-05-18 | [
[
"Jin",
"Wang",
""
],
[
"Lo",
"Kai-Yin",
""
],
[
"Chou",
"Shih-En",
""
],
[
"McCue",
"Scott W",
""
],
[
"Simpson",
"Matthew J",
""
]
] | Wound healing assays are commonly used to study how populations of cells, initialised on a two-dimensional surface, act to close an artificial wound space. While real wounds have different shapes, standard wound healing assays often deal with just one simple wound shape, and it is unclear whether varying the wound shap... |
2206.04206 | Ruriko Yoshida | Ruriko Yoshida and David Barnhill and Keiji Miura and Daniel Howe | Tropical Density Estimation of Phylogenetic Trees | 18 pages | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Much evidence from biological theory and empirical data indicates that, gene
tree, phylogenetic trees reconstructed from different genes (loci), do not have
to have exactly the same tree topologies. Such incongruence between gene trees
might be caused by some ``unusual'' evolutionary events, such as meiotic sexual
re... | [
{
"created": "Thu, 9 Jun 2022 01:06:27 GMT",
"version": "v1"
},
{
"created": "Fri, 12 Aug 2022 01:12:04 GMT",
"version": "v2"
},
{
"created": "Tue, 11 Jul 2023 13:22:00 GMT",
"version": "v3"
}
] | 2023-07-13 | [
[
"Yoshida",
"Ruriko",
""
],
[
"Barnhill",
"David",
""
],
[
"Miura",
"Keiji",
""
],
[
"Howe",
"Daniel",
""
]
] | Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees might be caused by some ``unusual'' evolutionary events, such as meiotic sexual reco... |
2103.03679 | Lu Liu | Xiaohan Zhang, Lu Liu, Guodong Long, Jing Jiang, Shenquan Liu | Episodic memory governs choices: An RNN-based reinforcement learning
model for decision-making task | Accepted to Neural Networks, Volume 134, February 2021, Pages 1-10 | null | 10.1016/j.neunet.2020.11.003 | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Typical methods to study cognitive function are to record the electrical
activities of animal neurons during the training of animals performing
behavioral tasks. A key problem is that they fail to record all the relevant
neurons in the animal brain. To alleviate this problem, we develop an RNN-based
Actor-Critic fram... | [
{
"created": "Sun, 24 Jan 2021 04:33:07 GMT",
"version": "v1"
}
] | 2021-03-08 | [
[
"Zhang",
"Xiaohan",
""
],
[
"Liu",
"Lu",
""
],
[
"Long",
"Guodong",
""
],
[
"Jiang",
"Jing",
""
],
[
"Liu",
"Shenquan",
""
]
] | Typical methods to study cognitive function are to record the electrical activities of animal neurons during the training of animals performing behavioral tasks. A key problem is that they fail to record all the relevant neurons in the animal brain. To alleviate this problem, we develop an RNN-based Actor-Critic framew... |
2310.11791 | Shanjun Mao | Shanjun Mao, Xiao Huang, Runjiu Chen, Chenyang Zhang, Yizhu Diao,
Zongjin Li, Qingzhe Wang, Shan Tang, and Shuixia Guo | STW-MD: A Novel Spatio-Temporal Weighting and Multi-Step Decision Tree
Method for Considering Spatial Heterogeneity in Brain Gene Expression Data | 11 pages, 6 figures | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Motivation: Gene expression during brain development or abnormal development
is a biological process that is highly dynamic in spatio and temporal. Due to
the lack of comprehensive integration of spatial and temporal dimensions of
brain gene expression data, previous studies have mainly focused on individual
brain re... | [
{
"created": "Wed, 18 Oct 2023 08:32:22 GMT",
"version": "v1"
}
] | 2023-10-19 | [
[
"Mao",
"Shanjun",
""
],
[
"Huang",
"Xiao",
""
],
[
"Chen",
"Runjiu",
""
],
[
"Zhang",
"Chenyang",
""
],
[
"Diao",
"Yizhu",
""
],
[
"Li",
"Zongjin",
""
],
[
"Wang",
"Qingzhe",
""
],
[
"Tang",
"Sh... | Motivation: Gene expression during brain development or abnormal development is a biological process that is highly dynamic in spatio and temporal. Due to the lack of comprehensive integration of spatial and temporal dimensions of brain gene expression data, previous studies have mainly focused on individual brain regi... |
q-bio/0410033 | Alexander Gorban | A.N. Gorban, T.G. Popova, A.Yu. Zinovyev | Four basic symmetry types in the universal 7-cluster structure of 143
complete bacterial genomic sequences | 13 pages, 4 figures | In Silico Biol. 5, 0025 (2005)
http://www.bioinfo.de/isb/2005/05/0025/ | null | null | q-bio.GN math.ST stat.TH | null | Coding information is the main source of heterogeneity (non-randomness) in
the sequences of bacterial genomes. This information can be naturally modeled
by analysing cluster structures in the "in-phase" triplet distributions of
relatively short genomic fragments (200-400bp). We found a universal 7-cluster
structure i... | [
{
"created": "Wed, 27 Oct 2004 20:31:06 GMT",
"version": "v1"
}
] | 2011-11-09 | [
[
"Gorban",
"A. N.",
""
],
[
"Popova",
"T. G.",
""
],
[
"Zinovyev",
"A. Yu.",
""
]
] | Coding information is the main source of heterogeneity (non-randomness) in the sequences of bacterial genomes. This information can be naturally modeled by analysing cluster structures in the "in-phase" triplet distributions of relatively short genomic fragments (200-400bp). We found a universal 7-cluster structure in ... |
1703.05099 | Christophe Guyeux | Huda Al-Nayyef and Christophe Guyeux and Jacques M. Bahi | Taenia Biomolecular Phylogeny and the Impact of Mitochondrial Genes on
this Latter | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Variations in mitochondrial genes are usually considered to infer
phylogenies. However some of these genes are lesser constraint than other ones,
and thus may blur the phylogenetic signals shared by the majority of the
mitochondrial DNA sequences. To investigate such effects, in this research
work, the molecular phyl... | [
{
"created": "Wed, 15 Mar 2017 12:01:24 GMT",
"version": "v1"
}
] | 2017-03-16 | [
[
"Al-Nayyef",
"Huda",
""
],
[
"Guyeux",
"Christophe",
""
],
[
"Bahi",
"Jacques M.",
""
]
] | Variations in mitochondrial genes are usually considered to infer phylogenies. However some of these genes are lesser constraint than other ones, and thus may blur the phylogenetic signals shared by the majority of the mitochondrial DNA sequences. To investigate such effects, in this research work, the molecular phylog... |
1612.09595 | Peter Waddell | Peter J. Waddell | Complimentary Phylogenetic Signals for Morphological Characters and
Quantitative 3D Shape Data within genus Homo | 12 pages, 6 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Estimating the phylogeny of the genus Homo is entering a new phase of vastly
improved data and methodology. There is increasing evidence of 6 to 10
competing species/lineages at any point in the last half million years, making
the elucidation of the relationships of individual specimens particularly
important. Recent... | [
{
"created": "Fri, 30 Dec 2016 20:51:22 GMT",
"version": "v1"
}
] | 2017-01-02 | [
[
"Waddell",
"Peter J.",
""
]
] | Estimating the phylogeny of the genus Homo is entering a new phase of vastly improved data and methodology. There is increasing evidence of 6 to 10 competing species/lineages at any point in the last half million years, making the elucidation of the relationships of individual specimens particularly important. Recent e... |
1606.09048 | Daniele De Martino | Daniele De Martino and Davide Masoero | Asymptotic analysis of noisy fitness maximization, applied to metabolism
and growth | 24 pages, 6 figures | JSTAT (2016), n 12 | 10.1088/1742-5468/aa4e8f | null | q-bio.PE cond-mat.stat-mech math-ph math.MP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We consider a population dynamics model coupling cell growth to a diffusion
in the space of metabolic phenotypes as it can be obtained from realistic
constraints-based modelling. In the asymptotic regime of slow diffusion, that
coincides with the relevant experimental range, the resulting non-linear
Fokker-Planck equ... | [
{
"created": "Wed, 29 Jun 2016 11:19:15 GMT",
"version": "v1"
},
{
"created": "Thu, 27 Oct 2016 08:08:30 GMT",
"version": "v2"
}
] | 2017-02-17 | [
[
"De Martino",
"Daniele",
""
],
[
"Masoero",
"Davide",
""
]
] | We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. In the asymptotic regime of slow diffusion, that coincides with the relevant experimental range, the resulting non-linear Fokker-Planck equat... |
2405.07238 | Vasileios Alevizos | Vasileios Alevizos, Clark Xu, Sabrina Edralin, Akebu Simasiku, Dimitra
Malliarou, Zongliang Yue, Antonis Messinis | Handwriting Anomalies and Learning Disabilities through Recurrent Neural
Networks and Geometric Pattern Analysis | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Dyslexia and dysgraphia are learning disabilities that significantly impact
reading, writing, and language processing capabilities. Dyslexia primarily
affects reading, manifesting as difficulties in word recognition and
phonological processing, where individuals struggle to connect sounds with
corresponding letters. ... | [
{
"created": "Sun, 12 May 2024 10:10:13 GMT",
"version": "v1"
}
] | 2024-05-14 | [
[
"Alevizos",
"Vasileios",
""
],
[
"Xu",
"Clark",
""
],
[
"Edralin",
"Sabrina",
""
],
[
"Simasiku",
"Akebu",
""
],
[
"Malliarou",
"Dimitra",
""
],
[
"Yue",
"Zongliang",
""
],
[
"Messinis",
"Antonis",
""
]
] | Dyslexia and dysgraphia are learning disabilities that significantly impact reading, writing, and language processing capabilities. Dyslexia primarily affects reading, manifesting as difficulties in word recognition and phonological processing, where individuals struggle to connect sounds with corresponding letters. Dy... |
1704.07184 | Yana Safonova | Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Maria A.
Turchaninova, Yana Safonova and Pavel A. Pevzner | Reconstructing antibody repertoires from error-prone immunosequencing
datasets | Short version was accepted to RECOMB 2017 | null | null | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Transforming error-prone immunosequencing datasets into antibody repertoires
is a fundamental problem in immunogenomics, and a prerequisite for studies of
immune responses. Although various repertoire reconstruction algorithms were
released in the last three years, it remains unclear how to benchmark them and
how to ... | [
{
"created": "Mon, 24 Apr 2017 12:46:40 GMT",
"version": "v1"
}
] | 2017-04-25 | [
[
"Shlemov",
"Alexander",
""
],
[
"Bankevich",
"Sergey",
""
],
[
"Bzikadze",
"Andrey",
""
],
[
"Turchaninova",
"Maria A.",
""
],
[
"Safonova",
"Yana",
""
],
[
"Pevzner",
"Pavel A.",
""
]
] | Transforming error-prone immunosequencing datasets into antibody repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last three years, it remains unclear how to benchmark them and how to as... |
1509.01194 | Andy Lewis-Pye | Andrew Lewis-Pye, Antonio Montalban | A mathematical analysis of the evolutionary benefits of sexual
reproduction | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The question as to why most higher organisms reproduce sexually has remained
open despite extensive research, and has been called "the queen of problems in
evolutionary biology". Theories dating back to Weismann have suggested that the
key must lie in the creation of increased variability in offspring, causing
enhanc... | [
{
"created": "Wed, 2 Sep 2015 05:17:15 GMT",
"version": "v1"
}
] | 2015-09-04 | [
[
"Lewis-Pye",
"Andrew",
""
],
[
"Montalban",
"Antonio",
""
]
] | The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key must lie in the creation of increased variability in offspring, causing enhanced... |
1510.00660 | Paolo Masulli | Paolo Masulli and Alessandro E. P. Villa | The topology of the directed clique complex as a network invariant | 13 pages, 3 figures. Figures and captions improved, typographical
changes | SpringerPlus (2016) 5(1), 1-12 | 10.1186/s40064-016-2022-y | null | q-bio.NC math.AT nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We introduce new algebro-topological invariants of directed networks, based
on the topological construction of the directed clique complex. The shape of
the underlying directed graph is encoded in a way that can be studied
mathematically to obtain network invariants such as the Euler characteristic
and the Betti numb... | [
{
"created": "Fri, 2 Oct 2015 17:49:02 GMT",
"version": "v1"
},
{
"created": "Wed, 4 Nov 2015 11:26:30 GMT",
"version": "v2"
},
{
"created": "Tue, 5 Apr 2016 15:07:31 GMT",
"version": "v3"
}
] | 2016-04-06 | [
[
"Masulli",
"Paolo",
""
],
[
"Villa",
"Alessandro E. P.",
""
]
] | We introduce new algebro-topological invariants of directed networks, based on the topological construction of the directed clique complex. The shape of the underlying directed graph is encoded in a way that can be studied mathematically to obtain network invariants such as the Euler characteristic and the Betti number... |
2301.04849 | Chen Shen | Chen Shen, Zhao Song, Lei Shi, Jun Tanimoto, and Zhen Wang | Exit options sustain altruistic punishment and decrease the second-order
free-riders, but it is not a panacea | 15 pages, 8 figures | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Altruistic punishment, where individuals incur personal costs to punish
others who have harmed third parties, presents an evolutionary conundrum as it
undermines individual fitness. Resolving this puzzle is crucial for
understanding the emergence and maintenance of human cooperation. This study
investigates the role ... | [
{
"created": "Thu, 12 Jan 2023 07:24:05 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Jul 2023 04:20:59 GMT",
"version": "v2"
}
] | 2023-07-27 | [
[
"Shen",
"Chen",
""
],
[
"Song",
"Zhao",
""
],
[
"Shi",
"Lei",
""
],
[
"Tanimoto",
"Jun",
""
],
[
"Wang",
"Zhen",
""
]
] | Altruistic punishment, where individuals incur personal costs to punish others who have harmed third parties, presents an evolutionary conundrum as it undermines individual fitness. Resolving this puzzle is crucial for understanding the emergence and maintenance of human cooperation. This study investigates the role of... |
2106.06029 | Pedro F da Costa | Pedro F. da Costa, Rianne Haartsen, Elena Throm, Luke Mason, Anna Gui,
Robert Leech, Emily J.H. Jones | Neuroadaptive electroencephalography: a proof-of-principle study in
infants | 25 pages, 4 figures | null | null | null | q-bio.NC q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | A core goal of functional neuroimaging is to study how the environment is
processed in the brain. The mainstream paradigm involves concurrently measuring
a broad spectrum of brain responses to a small set of environmental features
preselected with reference to previous studies or a theoretical framework. As a
complem... | [
{
"created": "Thu, 10 Jun 2021 20:13:04 GMT",
"version": "v1"
}
] | 2021-06-14 | [
[
"da Costa",
"Pedro F.",
""
],
[
"Haartsen",
"Rianne",
""
],
[
"Throm",
"Elena",
""
],
[
"Mason",
"Luke",
""
],
[
"Gui",
"Anna",
""
],
[
"Leech",
"Robert",
""
],
[
"Jones",
"Emily J. H.",
""
]
] | A core goal of functional neuroimaging is to study how the environment is processed in the brain. The mainstream paradigm involves concurrently measuring a broad spectrum of brain responses to a small set of environmental features preselected with reference to previous studies or a theoretical framework. As a complemen... |
0807.1869 | Antonio Deiana | Antonio Deiana, Andrea Giansanti | Number of natively unfolded proteins scales with genome size | Submitted to Biophysics and Bioengineering Letters
http://padis2.uniroma1.it:81/ojs/index.php/CISB-BBL | null | null | null | q-bio.GN q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Natively unfolded proteins exist as an ensemble of flexible conformations
lacking a well defined tertiary structure along a large portion of their
polypeptide chain. Despite the absence of a stable configuration, they are
involved in important cellular processes. In this work we used from three
indicators of folding ... | [
{
"created": "Fri, 11 Jul 2008 15:22:48 GMT",
"version": "v1"
}
] | 2008-07-14 | [
[
"Deiana",
"Antonio",
""
],
[
"Giansanti",
"Andrea",
""
]
] | Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in important cellular processes. In this work we used from three indicators of folding st... |
2108.00371 | Eduardo Cocca Padovani | Eduardo C. Padovani | Macaque's Cortical Functional Connectivity Dynamics at the Onset of
Propofol-Induced Anesthesia | 20 pages, 5 figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Propofol, when administered for general anesthesia, induces oscillatory
dynamic brain states that are thought to underlie the drug's pharmacological
effects. Despite the elucidation of propofol's mechanisms of action at the
molecular level, its effects on neural circuits and overall cortical
functioning, which eventu... | [
{
"created": "Sun, 1 Aug 2021 06:08:26 GMT",
"version": "v1"
},
{
"created": "Tue, 5 Sep 2023 12:34:25 GMT",
"version": "v2"
}
] | 2023-09-06 | [
[
"Padovani",
"Eduardo C.",
""
]
] | Propofol, when administered for general anesthesia, induces oscillatory dynamic brain states that are thought to underlie the drug's pharmacological effects. Despite the elucidation of propofol's mechanisms of action at the molecular level, its effects on neural circuits and overall cortical functioning, which eventual... |
q-bio/0612035 | Andras Czirok | Andras Szabo, Erica D. Perryn, Andras Czirok | Network formation of tissue cells via preferential attraction to
elongated structures | null | null | 10.1103/PhysRevLett.98.038102 | null | q-bio.CB | null | Vascular and non-vascular cells often form an interconnected network in
vitro, similar to the early vascular bed of warm blooded embryos. Our
time-lapse recordings show that the network forms by extending sprouts, i.e.,
multicellular linear segments. To explain the emergence of such structures, we
propose a simple mo... | [
{
"created": "Mon, 18 Dec 2006 12:38:52 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Szabo",
"Andras",
""
],
[
"Perryn",
"Erica D.",
""
],
[
"Czirok",
"Andras",
""
]
] | Vascular and non-vascular cells often form an interconnected network in vitro, similar to the early vascular bed of warm blooded embryos. Our time-lapse recordings show that the network forms by extending sprouts, i.e., multicellular linear segments. To explain the emergence of such structures, we propose a simple mode... |
2405.11010 | Diego Bonatto | Ana Paula Wives, Isabelli Seiler de Medeiros Mendes, Sofia Turatti dos
Santos, and Diego Bonatto | Molecular techniques employed in CTG(Ser1) and CTG(Ala) D-xylose
metabolizing yeast clades for strain design and industrial applications | 32 pages, 4 tables | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | D-xylose is the second most abundant monosaccharide found in lignocellulose
and is of biotechnological importance for producing second-generation ethanol
and other high-value chemical compounds. D-xylose conversion to ethanol is
promoted by microbial fermentation, mainly by bacteria, yeasts, or filamentous
fungi. Con... | [
{
"created": "Fri, 17 May 2024 15:06:50 GMT",
"version": "v1"
},
{
"created": "Tue, 21 May 2024 16:32:50 GMT",
"version": "v2"
}
] | 2024-05-22 | [
[
"Wives",
"Ana Paula",
""
],
[
"Mendes",
"Isabelli Seiler de Medeiros",
""
],
[
"Santos",
"Sofia Turatti dos",
""
],
[
"Bonatto",
"Diego",
""
]
] | D-xylose is the second most abundant monosaccharide found in lignocellulose and is of biotechnological importance for producing second-generation ethanol and other high-value chemical compounds. D-xylose conversion to ethanol is promoted by microbial fermentation, mainly by bacteria, yeasts, or filamentous fungi. Consi... |
2005.11615 | Vahe Galstyan Mr. | Vahe Galstyan, Kabir Husain, Fangzhou Xiao, Arvind Murugan, Rob
Phillips | Proofreading through spatial gradients | null | null | null | null | q-bio.MN physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | Key enzymatic processes in biology use the nonequilibrium error correction
mechanism called kinetic proofreading to enhance their specificity. Kinetic
proofreading typically requires several dedicated structural features in the
enzyme, such as a nucleotide hydrolysis site and multiple enzyme-substrate
conformations t... | [
{
"created": "Sat, 23 May 2020 22:41:40 GMT",
"version": "v1"
}
] | 2020-05-26 | [
[
"Galstyan",
"Vahe",
""
],
[
"Husain",
"Kabir",
""
],
[
"Xiao",
"Fangzhou",
""
],
[
"Murugan",
"Arvind",
""
],
[
"Phillips",
"Rob",
""
]
] | Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such as a nucleotide hydrolysis site and multiple enzyme-substrate conformations tha... |
1902.07303 | Su-Chan Park | Alexander Klug, Su-Chan Park, Joachim Krug | Recombination and mutational robustness in neutral fitness landscapes | 15 figures, Supplementary appendix, supplementary figures | PLoS Comput Biol 15(8): e1006884 (2019) | 10.1371/journal.pcbi.1006884 | null | q-bio.PE cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mutational robustness quantifies the effect of random mutations on fitness.
When mutational robustness is high, most mutations do not change fitness or
have only a minor effect on it. From the point of view of fitness landscapes,
robust genotypes form neutral networks of almost equal fitness. Using
deterministic popu... | [
{
"created": "Tue, 19 Feb 2019 21:57:41 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Oct 2019 00:56:09 GMT",
"version": "v2"
}
] | 2019-10-22 | [
[
"Klug",
"Alexander",
""
],
[
"Park",
"Su-Chan",
""
],
[
"Krug",
"Joachim",
""
]
] | Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust genotypes form neutral networks of almost equal fitness. Using deterministic popula... |
1809.00449 | Peter Gawthrop | Peter J. Gawthrop and Edmund J. Crampin | Bond Graph Representation of Chemical Reaction Networks | null | IEEE Transactions on NanoBioscience ( Volume: 17 , Issue: 4 , Oct.
2018 ) | 10.1109/TNB.2018.2876391 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Bond Graph approach and the Chemical Reaction Network approach to
modelling biomolecular systems developed independently. This paper brings
together the two approaches by providing a bond graph interpretation of the
chemical reaction network concept of complexes. Both closed and open systems
are discussed.
The ... | [
{
"created": "Mon, 3 Sep 2018 04:21:43 GMT",
"version": "v1"
},
{
"created": "Sun, 14 Oct 2018 00:28:29 GMT",
"version": "v2"
}
] | 2019-07-04 | [
[
"Gawthrop",
"Peter J.",
""
],
[
"Crampin",
"Edmund J.",
""
]
] | The Bond Graph approach and the Chemical Reaction Network approach to modelling biomolecular systems developed independently. This paper brings together the two approaches by providing a bond graph interpretation of the chemical reaction network concept of complexes. Both closed and open systems are discussed. The meth... |
1709.01072 | Daniel Ruiz-Reyn\'es | Daniel Ruiz-Reyn\'es, Dami\`a Gomila, Tom\`as Sintes, Emilio
Hern\'andez-Garc\'ia, N\'uria Marb\`a, Carlos M. Duarte | Fairy circle landscapes under the sea | null | Science Advances, 2017, vol. 3, no 8, p. e1603262 | 10.1126/sciadv.1603262 | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Short-scale interactions yield large-scale vegetation patterns that, in turn,
shape ecosystem function across landscapes. Fairy circles, which are circular
patches bare of vegetation within otherwise continuous landscapes, are
characteristic features of semiarid grasslands. We report the occurrence of
submarine fairy... | [
{
"created": "Mon, 4 Sep 2017 11:55:36 GMT",
"version": "v1"
}
] | 2017-09-06 | [
[
"Ruiz-Reynés",
"Daniel",
""
],
[
"Gomila",
"Damià",
""
],
[
"Sintes",
"Tomàs",
""
],
[
"Hernández-García",
"Emilio",
""
],
[
"Marbà",
"Núria",
""
],
[
"Duarte",
"Carlos M.",
""
]
] | Short-scale interactions yield large-scale vegetation patterns that, in turn, shape ecosystem function across landscapes. Fairy circles, which are circular patches bare of vegetation within otherwise continuous landscapes, are characteristic features of semiarid grasslands. We report the occurrence of submarine fairy c... |
1602.08568 | Pavol Bokes | Pavol Bokes and Abhyudai Singh | Gene expression noise is affected differentially by feedback in burst
frequency and burst size | 27 pages, 11 figures | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Inside individual cells, expression of genes is stochastic across organisms
ranging from bacterial to human cells. A ubiquitous feature of stochastic
expression is burst-like synthesis of gene products, which drives considerable
intercellular variability in protein levels across an isogenic cell population.
One commo... | [
{
"created": "Sat, 27 Feb 2016 08:16:11 GMT",
"version": "v1"
},
{
"created": "Sun, 11 Sep 2016 14:35:39 GMT",
"version": "v2"
}
] | 2016-09-13 | [
[
"Bokes",
"Pavol",
""
],
[
"Singh",
"Abhyudai",
""
]
] | Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable intercellular variability in protein levels across an isogenic cell population. One common ... |
1401.1798 | Juli\'an Candia | Juli\'an Candia, Srujana Cherukuri, Yin Guo, Kshama A. Doshi, Jayanth
R. Banavar, Curt I. Civin, Wolfgang Losert | Uncovering low-dimensional, miR-based signatures of acute myeloid and
lymphoblastic leukemias with a machine-learning-driven network approach | 34 pages, 12 figures (contains Supporting Information). To appear in
Convergent Science Physical Oncology | Converg. Sci. Phys. Oncol. 1 (2015) 025002 | 10.1088/2057-1739/1/2/025002 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Complex phenotypic differences among different acute leukemias cannot be
fully captured by analyzing the expression levels of one single molecule, such
as a miR, at a time, but requires systematic analysis of large sets of miRs.
While a popular approach for analysis of such datasets is principal component
analysis (P... | [
{
"created": "Wed, 8 Jan 2014 20:07:43 GMT",
"version": "v1"
},
{
"created": "Fri, 22 Aug 2014 03:44:35 GMT",
"version": "v2"
},
{
"created": "Sat, 21 Nov 2015 00:21:27 GMT",
"version": "v3"
}
] | 2015-12-23 | [
[
"Candia",
"Julián",
""
],
[
"Cherukuri",
"Srujana",
""
],
[
"Guo",
"Yin",
""
],
[
"Doshi",
"Kshama A.",
""
],
[
"Banavar",
"Jayanth R.",
""
],
[
"Civin",
"Curt I.",
""
],
[
"Losert",
"Wolfgang",
""
]
] | Complex phenotypic differences among different acute leukemias cannot be fully captured by analyzing the expression levels of one single molecule, such as a miR, at a time, but requires systematic analysis of large sets of miRs. While a popular approach for analysis of such datasets is principal component analysis (PCA... |
2005.07706 | Carla Goldman | Alexandre Y. C. Cho, Victor R. C. M. Roque, Carla Goldman | The fast and the slow axonal transport: a unified approach based on
cargo and molecular motors coupled dynamics | null | Phys. Rev. E 102, 032410 (2020) | 10.1103/PhysRevE.102.032410 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The origins of the large differences observed to the rates with which the
diverse particles are conveyed along axonal microtubules are still a matter of
debate in the literature. There is evidence that certain neurodegenerative
diseases may be triggered by disturbances to the related transport processes.
Motivated by... | [
{
"created": "Fri, 15 May 2020 17:10:42 GMT",
"version": "v1"
}
] | 2020-09-30 | [
[
"Cho",
"Alexandre Y. C.",
""
],
[
"Roque",
"Victor R. C. M.",
""
],
[
"Goldman",
"Carla",
""
]
] | The origins of the large differences observed to the rates with which the diverse particles are conveyed along axonal microtubules are still a matter of debate in the literature. There is evidence that certain neurodegenerative diseases may be triggered by disturbances to the related transport processes. Motivated by t... |
1210.4938 | Thierry Rabilloud | C\'ecile Lelong (LCBM), Mireille Chevallet (LCBM), H\'el\`ene Diemer
(IPHC-DSA), Sylvie Luche (LCBM), Alain Van Dorsselaer (IPHC-DSA), Thierry
Rabilloud (LCBM) | Improved proteomic analysis of nuclear proteins, as exemplified by the
comparison of two myelo\"id cell lines nuclear proteomes | null | Journal of Proteomics (2012) epub ahead of print | 10.1016/j.jprot.2012.09.034 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | One of the challenges of the proteomic analysis by 2D-gel is to visualize the
low abundance proteins, particularly those localized in organelles. An
additional problem with nuclear proteins lies in their strong interaction with
nuclear acids. Several experimental procedures have been tested to increase, in
the nuclea... | [
{
"created": "Wed, 17 Oct 2012 20:02:51 GMT",
"version": "v1"
}
] | 2012-10-19 | [
[
"Lelong",
"Cécile",
"",
"LCBM"
],
[
"Chevallet",
"Mireille",
"",
"LCBM"
],
[
"Diemer",
"Hélène",
"",
"IPHC-DSA"
],
[
"Luche",
"Sylvie",
"",
"LCBM"
],
[
"Van Dorsselaer",
"Alain",
"",
"IPHC-DSA"
],
[
"Rabilloud"... | One of the challenges of the proteomic analysis by 2D-gel is to visualize the low abundance proteins, particularly those localized in organelles. An additional problem with nuclear proteins lies in their strong interaction with nuclear acids. Several experimental procedures have been tested to increase, in the nuclear ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.