Base datasets
Collection
Basic datasets from which other combined datasets are formed. • 6 items • Updated
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 sequencelengths 1 147 | abstract stringlengths 24 3.75k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0707.0026 | Maria A. Avi\~no-Diaz | Maria A. Avino-Diaz | Introducing a Probabilistic Structure on Sequential Dynamical Systems,
Simulation and Reduction of Probabilistic Sequential Networks | 14 pages | null | null | null | q-bio.GN math.PR q-bio.MN | null | A probabilistic structure on sequential dynamical systems is introduced here,
the new model will be called Probabilistic Sequential Network, PSN. The
morphisms of Probabilistic Sequential Networks are defined using two algebraic
conditions. It is proved here that two homomorphic Probabilistic Sequential
Networks have... | [
{
"created": "Fri, 29 Jun 2007 23:34:16 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Apr 2008 13:44:03 GMT",
"version": "v2"
}
] | 2008-04-30 | [
[
"Avino-Diaz",
"Maria A.",
""
]
] | A probabilistic structure on sequential dynamical systems is introduced here, the new model will be called Probabilistic Sequential Network, PSN. The morphisms of Probabilistic Sequential Networks are defined using two algebraic conditions. It is proved here that two homomorphic Probabilistic Sequential Networks have t... |
1810.12954 | Li Xiao | Li Xiao, Julia M. Stephen, Tony W. Wilson, Vince D. Calhoun, and
Yu-Ping Wang | Alternating Diffusion Map Based Fusion of Multimodal Brain Connectivity
Networks for IQ Prediction | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To explain individual differences in development, behavior, and cognition,
most previous studies focused on projecting resting-state functional MRI (fMRI)
based functional connectivity (FC) data into a low-dimensional space via linear
dimensionality reduction techniques, followed by executing analysis operations.
How... | [
{
"created": "Tue, 30 Oct 2018 18:29:50 GMT",
"version": "v1"
}
] | 2018-11-01 | [
[
"Xiao",
"Li",
""
],
[
"Stephen",
"Julia M.",
""
],
[
"Wilson",
"Tony W.",
""
],
[
"Calhoun",
"Vince D.",
""
],
[
"Wang",
"Yu-Ping",
""
]
] | To explain individual differences in development, behavior, and cognition, most previous studies focused on projecting resting-state functional MRI (fMRI) based functional connectivity (FC) data into a low-dimensional space via linear dimensionality reduction techniques, followed by executing analysis operations. Howev... |
2111.08507 | Akankshita Dash | Akankshita Dash | Machine Learning for Genomic Data | Number of pages: 53 | null | null | null | q-bio.GN cs.LG | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This report explores the application of machine learning techniques on short
timeseries gene expression data. Although standard machine learning algorithms
work well on longer time-series', they often fail to find meaningful insights
from fewer timepoints. In this report, we explore model-based clustering
techniques.... | [
{
"created": "Mon, 15 Nov 2021 14:34:20 GMT",
"version": "v1"
}
] | 2021-11-17 | [
[
"Dash",
"Akankshita",
""
]
] | This report explores the application of machine learning techniques on short timeseries gene expression data. Although standard machine learning algorithms work well on longer time-series', they often fail to find meaningful insights from fewer timepoints. In this report, we explore model-based clustering techniques. W... |
1401.8028 | Mercedes P\'erez Mill\'an | Mercedes P\'erez Mill\'an and Alicia Dickenstein | Implicit dose-response curves | The final publication is available at Springer via
http://dx.doi.org/10.1007/s00285-014-0809-4 | null | 10.1007/s00285-014-0809-4 | null | q-bio.QM math.AG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We develop tools from computational algebraic geometry for the study of
steady state features of autonomous polynomial dynamical systems via
elimination of variables. In particular, we obtain nontrivial bounds for the
steady state concentration of a given species in biochemical reaction networks
with mass-action kine... | [
{
"created": "Thu, 30 Jan 2014 23:25:46 GMT",
"version": "v1"
},
{
"created": "Fri, 11 Jul 2014 10:25:00 GMT",
"version": "v2"
}
] | 2014-07-14 | [
[
"Millán",
"Mercedes Pérez",
""
],
[
"Dickenstein",
"Alicia",
""
]
] | We develop tools from computational algebraic geometry for the study of steady state features of autonomous polynomial dynamical systems via elimination of variables. In particular, we obtain nontrivial bounds for the steady state concentration of a given species in biochemical reaction networks with mass-action kineti... |
2003.13932 | Samuel Willian Schwertner Costiche | Rodrigo A. Schulz, Carlos H. Coimbra-Ara\'ujo and Samuel W. S.
Costiche | COVID-19: A model for studying the evolution of contamination in Brazil | 18 pages, 4 figures; corrected references and parameters | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In the present article we introduce an epidemiological model for the
investigation of the spread of epidemics caused by viruses. The model is
applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus
(aka "novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model
is used as a basis ... | [
{
"created": "Tue, 31 Mar 2020 03:12:14 GMT",
"version": "v1"
},
{
"created": "Wed, 1 Apr 2020 05:00:47 GMT",
"version": "v2"
},
{
"created": "Thu, 2 Apr 2020 12:57:16 GMT",
"version": "v3"
},
{
"created": "Wed, 8 Apr 2020 23:07:57 GMT",
"version": "v4"
}
] | 2020-04-10 | [
[
"Schulz",
"Rodrigo A.",
""
],
[
"Coimbra-Araújo",
"Carlos H.",
""
],
[
"Costiche",
"Samuel W. S.",
""
]
] | In the present article we introduce an epidemiological model for the investigation of the spread of epidemics caused by viruses. The model is applied specifically to COVID-19, the disease caused by the SARS-Cov-2 virus (aka "novel coronavirus"). The SIR (Susceptible - Infectious - Recovered) model is used as a basis fo... |
2009.10378 | Jean-Sebastien Guez | Val\'erie Lecl\'ere, Max B\'echet, Akram Adam, Jean-Sebastien Guez
(IP), Bernard Wathelet, Marc Ongena, Philippe Thonart, Fr\'ed\'erique Gancel,
Marl\'ene Chollet-Imbert, Philippe Jacques | Mycosubtilin Overproduction by Bacillus subtilis BBG100 Enhances the
Organism's Antagonistic and Biocontrol Activities | null | Applied and Environmental Microbiology, American Society for
Microbiology, 2005, 71, pp.4577 - 4584 | 10.1128/AEM.71.8.4577-4584.2005 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A Bacillus subtilis derivative was obtained from strain ATCC 6633 by
replacement of the native promoter of the mycosubtilin operon by a constitutive
promoter originating from the replication gene repU of the Staphylococcus
aureus plasmid pUB110. The recombinant strain, designated BBG100, produced up
to 15-fold more m... | [
{
"created": "Tue, 22 Sep 2020 08:10:13 GMT",
"version": "v1"
}
] | 2020-09-23 | [
[
"Leclére",
"Valérie",
"",
"IP"
],
[
"Béchet",
"Max",
"",
"IP"
],
[
"Adam",
"Akram",
"",
"IP"
],
[
"Guez",
"Jean-Sebastien",
"",
"IP"
],
[
"Wathelet",
"Bernard",
""
],
[
"Ongena",
"Marc",
""
],
[
"Th... | A Bacillus subtilis derivative was obtained from strain ATCC 6633 by replacement of the native promoter of the mycosubtilin operon by a constitutive promoter originating from the replication gene repU of the Staphylococcus aureus plasmid pUB110. The recombinant strain, designated BBG100, produced up to 15-fold more myc... |
1503.07552 | Andrey Shilnikov L | D. Alacam and A.L. Shilnikov | Making a swim central pattern generator out of latent parabolic bursters | null | null | null | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the rhythmogenesis of oscillatory patterns emerging in network
motifs composed of inhibitory coupled tonic spiking neurons represented by the
Plant model of R15 nerve cells. Such motifs are argued to be used as building
blocks for a larger central pattern generator network controlling swim
locomotion of sea ... | [
{
"created": "Wed, 25 Mar 2015 20:54:56 GMT",
"version": "v1"
}
] | 2015-03-27 | [
[
"Alacam",
"D.",
""
],
[
"Shilnikov",
"A. L.",
""
]
] | We study the rhythmogenesis of oscillatory patterns emerging in network motifs composed of inhibitory coupled tonic spiking neurons represented by the Plant model of R15 nerve cells. Such motifs are argued to be used as building blocks for a larger central pattern generator network controlling swim locomotion of sea sl... |
0706.3195 | George Bass Ph.D. | George E. Bass | Genetic Transferability of Anomalous Irradiation Alterations of
Antibiotic Activity | 17 pages, 3 figures | null | null | null | q-bio.BM | null | It previously has been discovered that visible light irradiation of
crystalline substrates can lead to enhancement of subsequent enzymatic reaction
rates as sharply peaked oscillatory functions of irradiation time. The
particular activating irradiation times can vary with source of a given enzyme
and thus, presumably... | [
{
"created": "Thu, 21 Jun 2007 17:24:15 GMT",
"version": "v1"
}
] | 2007-06-22 | [
[
"Bass",
"George E.",
""
]
] | It previously has been discovered that visible light irradiation of crystalline substrates can lead to enhancement of subsequent enzymatic reaction rates as sharply peaked oscillatory functions of irradiation time. The particular activating irradiation times can vary with source of a given enzyme and thus, presumably, ... |
2106.10041 | Michael Inouye | Ewan Birney, Michael Inouye, Jennifer Raff, Adam Rutherford, Aylwyn
Scally | The language of race, ethnicity, and ancestry in human genetic research | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | The language commonly used in human genetics can inadvertently pose problems
for multiple reasons. Terms like "ancestry", "ethnicity", and other ways of
grouping people can have complex, often poorly understood, or multiple meanings
within the various fields of genetics, between different domains of biological
scienc... | [
{
"created": "Fri, 18 Jun 2021 10:24:15 GMT",
"version": "v1"
}
] | 2021-06-21 | [
[
"Birney",
"Ewan",
""
],
[
"Inouye",
"Michael",
""
],
[
"Raff",
"Jennifer",
""
],
[
"Rutherford",
"Adam",
""
],
[
"Scally",
"Aylwyn",
""
]
] | The language commonly used in human genetics can inadvertently pose problems for multiple reasons. Terms like "ancestry", "ethnicity", and other ways of grouping people can have complex, often poorly understood, or multiple meanings within the various fields of genetics, between different domains of biological sciences... |
1812.05780 | Silke Bergeler | Matthias Kober, Silke Bergeler, Erwin Frey | Can a flux-based mechanism explain positioning of protein clusters in a
three-dimensional cell geometry? | 9 pages, 4 figures, 10 pages of supplemental information (including 4
figures and 1 table) | null | 10.1016/j.bpj.2019.06.031 | null | q-bio.SC physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The plane of bacterial cell division must be precisely positioned. In the
bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster,
which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic,
but biased manner towards midcell, where it initiates cell division.
Previously, a po... | [
{
"created": "Fri, 14 Dec 2018 05:01:04 GMT",
"version": "v1"
}
] | 2019-09-04 | [
[
"Kober",
"Matthias",
""
],
[
"Bergeler",
"Silke",
""
],
[
"Frey",
"Erwin",
""
]
] | The plane of bacterial cell division must be precisely positioned. In the bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster, which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic, but biased manner towards midcell, where it initiates cell division. Previously, a posi... |
2206.07542 | Abdulah Fawaz | Abdulah Fawaz, Logan Z. Williams, A. David Edwards, Emma Robinson | A Deep Generative Model of Neonatal Cortical Surface Development | null | null | null | null | q-bio.NC cs.CV cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | The neonatal cortical surface is known to be affected by preterm birth, and
the subsequent changes to cortical organisation have been associated with
poorer neurodevelopmental outcomes. Deep Generative models have the potential
to lead to clinically interpretable models of disease, but developing these on
the cortica... | [
{
"created": "Wed, 15 Jun 2022 13:59:43 GMT",
"version": "v1"
},
{
"created": "Wed, 22 Jun 2022 12:16:33 GMT",
"version": "v2"
}
] | 2022-06-23 | [
[
"Fawaz",
"Abdulah",
""
],
[
"Williams",
"Logan Z.",
""
],
[
"Edwards",
"A. David",
""
],
[
"Robinson",
"Emma",
""
]
] | The neonatal cortical surface is known to be affected by preterm birth, and the subsequent changes to cortical organisation have been associated with poorer neurodevelopmental outcomes. Deep Generative models have the potential to lead to clinically interpretable models of disease, but developing these on the cortical ... |
1912.09929 | Benjamin M. Friedrich | Jens Karschau, Andre Scholich, Jonathan Wise, Hernan
Morales-Navarette, Yannis Kalaidzidis, Marino Zerial, Benjamin M Friedrich | Resilience of three-dimensional sinusoidal networks in liver tissue | 20 pages, 7 figures | null | 10.1371/journal.pcbi.1007965 | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Can three-dimensional, microvasculature networks still ensure blood supply if
individual links fail? We address this question in the sinusoidal network, a
plexus-like microvasculature network, which transports nutrient-rich blood to
every hepatocyte in liver tissue, by building on recent advances in
high-resolution i... | [
{
"created": "Fri, 20 Dec 2019 16:41:54 GMT",
"version": "v1"
}
] | 2020-09-09 | [
[
"Karschau",
"Jens",
""
],
[
"Scholich",
"Andre",
""
],
[
"Wise",
"Jonathan",
""
],
[
"Morales-Navarette",
"Hernan",
""
],
[
"Kalaidzidis",
"Yannis",
""
],
[
"Zerial",
"Marino",
""
],
[
"Friedrich",
"Benjamin M"... | Can three-dimensional, microvasculature networks still ensure blood supply if individual links fail? We address this question in the sinusoidal network, a plexus-like microvasculature network, which transports nutrient-rich blood to every hepatocyte in liver tissue, by building on recent advances in high-resolution ima... |
0809.1127 | Naoki Masuda Dr. | Yuko K. Takahashi, Hiroshi Kori, Naoki Masuda | Self-organization of feedforward structure and entrainment in excitatory
neural networks with spike-timing-dependent plasticity | 11 figures, 1 table | Physical Review E, 79, 051904 (2009) | 10.1103/PhysRevE.79.051904 | null | q-bio.NC cond-mat.dis-nn | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Spike-timing dependent plasticity (STDP) is an organizing principle of
biological neural networks. While synchronous firing of neurons is considered
to be an important functional block in the brain, how STDP shapes neural
networks possibly toward synchrony is not entirely clear. We examine relations
between STDP and ... | [
{
"created": "Sat, 6 Sep 2008 03:44:09 GMT",
"version": "v1"
},
{
"created": "Thu, 11 Sep 2008 11:41:50 GMT",
"version": "v2"
},
{
"created": "Wed, 20 May 2009 11:23:05 GMT",
"version": "v3"
}
] | 2009-05-20 | [
[
"Takahashi",
"Yuko K.",
""
],
[
"Kori",
"Hiroshi",
""
],
[
"Masuda",
"Naoki",
""
]
] | Spike-timing dependent plasticity (STDP) is an organizing principle of biological neural networks. While synchronous firing of neurons is considered to be an important functional block in the brain, how STDP shapes neural networks possibly toward synchrony is not entirely clear. We examine relations between STDP and sy... |
2305.14369 | Eloy Philip Theo Geenjaar | Eloy Geenjaar, Donghyun Kim, Riyasat Ohib, Marlena Duda, Amrit
Kashyap, Sergey Plis, Vince Calhoun | Learning low-dimensional dynamics from whole-brain data improves task
capture | 9 pages, 4 figures | null | null | null | q-bio.NC cs.CE cs.LG | http://creativecommons.org/licenses/by/4.0/ | The neural dynamics underlying brain activity are critical to understanding
cognitive processes and mental disorders. However, current voxel-based
whole-brain dimensionality reduction techniques fall short of capturing these
dynamics, producing latent timeseries that inadequately relate to behavioral
tasks. To addres... | [
{
"created": "Thu, 18 May 2023 18:43:13 GMT",
"version": "v1"
}
] | 2023-05-25 | [
[
"Geenjaar",
"Eloy",
""
],
[
"Kim",
"Donghyun",
""
],
[
"Ohib",
"Riyasat",
""
],
[
"Duda",
"Marlena",
""
],
[
"Kashyap",
"Amrit",
""
],
[
"Plis",
"Sergey",
""
],
[
"Calhoun",
"Vince",
""
]
] | The neural dynamics underlying brain activity are critical to understanding cognitive processes and mental disorders. However, current voxel-based whole-brain dimensionality reduction techniques fall short of capturing these dynamics, producing latent timeseries that inadequately relate to behavioral tasks. To address ... |
q-bio/0607028 | Garegin Papoian | Yueheng Lan, Garegin A. Papoian | The interplay between discrete noise and nonlinear chemical kinetics in
a signal amplification cascade | 16 pages, 9 figures | null | 10.1063/1.2358342 | null | q-bio.MN q-bio.QM | null | We used various analytical and numerical techniques to elucidate signal
propagation in a small enzymatic cascade which is subjected to external and
internal noise. The nonlinear character of catalytic reactions, which underlie
protein signal transduction cascades, renders stochastic signaling dynamics in
cytosol bioc... | [
{
"created": "Wed, 19 Jul 2006 06:41:28 GMT",
"version": "v1"
}
] | 2009-11-13 | [
[
"Lan",
"Yueheng",
""
],
[
"Papoian",
"Garegin A.",
""
]
] | We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein signal transduction cascades, renders stochastic signaling dynamics in cytosol bioche... |
1611.00285 | Till Frank | J.M. Gordon, S. Kim, T.D. Frank | Linear non-equilibrium thermodynamics of human voluntary behavior: a
canonical-dissipative Fokker-Planck equation approach involving potentials
beyond the harmonic oscillator case | 6 pages, 0 figure | Condens. Matter Phys., vol. 19, No. 3, 34001 (2016) | 10.5488/CMP.19.34001 | null | q-bio.NC cond-mat.soft cond-mat.stat-mech | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A novel experimental paradigm and a novel modelling approach are presented to
investigate oscillatory human motor performance by means of a key concept from
condensed matter physics, namely, thermodynamic state variables. To this end,
in the novel experimental paradigm participants performed pendulum swinging
movemen... | [
{
"created": "Thu, 15 Sep 2016 16:10:43 GMT",
"version": "v1"
}
] | 2017-02-13 | [
[
"Gordon",
"J. M.",
""
],
[
"Kim",
"S.",
""
],
[
"Frank",
"T. D.",
""
]
] | A novel experimental paradigm and a novel modelling approach are presented to investigate oscillatory human motor performance by means of a key concept from condensed matter physics, namely, thermodynamic state variables. To this end, in the novel experimental paradigm participants performed pendulum swinging movements... |
1909.06442 | Devin Taylor | Devin Taylor, Simeon Spasov and Pietro Li\`o | Co-Attentive Cross-Modal Deep Learning for Medical Evidence Synthesis
and Decision Making | 7 pages, 2 figures, Machine Learning for Health (ML4H) at NeurIPS
2019 - Extended Abstract, clarified graph and math notation, typos corrected | null | null | null | q-bio.QM cs.LG stat.ML | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern medicine requires generalised approaches to the synthesis and
integration of multimodal data, often at different biological scales, that can
be applied to a variety of evidence structures, such as complex disease
analyses and epidemiological models. However, current methods are either slow
and expensive, or in... | [
{
"created": "Fri, 13 Sep 2019 20:49:55 GMT",
"version": "v1"
},
{
"created": "Fri, 8 Nov 2019 06:58:53 GMT",
"version": "v2"
}
] | 2019-11-11 | [
[
"Taylor",
"Devin",
""
],
[
"Spasov",
"Simeon",
""
],
[
"Liò",
"Pietro",
""
]
] | Modern medicine requires generalised approaches to the synthesis and integration of multimodal data, often at different biological scales, that can be applied to a variety of evidence structures, such as complex disease analyses and epidemiological models. However, current methods are either slow and expensive, or inef... |
1101.3570 | Lev Soyfer | Lev Isaakovich Soyfer | Processes of the correlation of space (lengths) and time (duration)in
human perception | The text of this work, which totals of 183 pages, consists of seven
chapters, references, and four appendices. Major part of the work includes 30
tables and 3 figures. Appendices consist of 37 tables and 4 figures | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by/3.0/ | To study the processes and mechanisms of the correlation between space and
time, particularly between lengths and durations in human perception, a special
method (device and procedure) to conduct this experiment was designed and
called LDR (Length Duration Relation) In the present study a pilot and three
series of th... | [
{
"created": "Mon, 17 Jan 2011 20:38:38 GMT",
"version": "v1"
}
] | 2011-01-20 | [
[
"Soyfer",
"Lev Isaakovich",
""
]
] | To study the processes and mechanisms of the correlation between space and time, particularly between lengths and durations in human perception, a special method (device and procedure) to conduct this experiment was designed and called LDR (Length Duration Relation) In the present study a pilot and three series of the ... |
1304.4274 | Natalia Denesyuk | Natalia A. Denesyuk and D. Thirumalai | Entropic stabilization of the folded states of RNA due to macromolecular
crowding | null | null | 10.1007/s12551-013-0119-x | null | q-bio.BM cond-mat.soft physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We review the effects of macromolecular crowding on the folding of RNA by
considering the simplest scenario when excluded volume interactions between
crowding particles and RNA dominate. Using human telomerase enzyme as an
example, we discuss how crowding can alter the equilibrium between pseudoknot
and hairpin state... | [
{
"created": "Mon, 15 Apr 2013 21:37:49 GMT",
"version": "v1"
}
] | 2013-04-17 | [
[
"Denesyuk",
"Natalia A.",
""
],
[
"Thirumalai",
"D.",
""
]
] | We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we discuss how crowding can alter the equilibrium between pseudoknot and hairpin states ... |
2402.03675 | Chenqing Hua | Chenqing Hua, Connor Coley, Guy Wolf, Doina Precup, Shuangjia Zheng | Effective Protein-Protein Interaction Exploration with PPIretrieval | null | null | null | null | q-bio.BM cs.AI cs.CE cs.LG | http://creativecommons.org/publicdomain/zero/1.0/ | Protein-protein interactions (PPIs) are crucial in regulating numerous
cellular functions, including signal transduction, transportation, and immune
defense. As the accuracy of multi-chain protein complex structure prediction
improves, the challenge has shifted towards effectively navigating the vast
complex universe... | [
{
"created": "Tue, 6 Feb 2024 03:57:06 GMT",
"version": "v1"
}
] | 2024-02-07 | [
[
"Hua",
"Chenqing",
""
],
[
"Coley",
"Connor",
""
],
[
"Wolf",
"Guy",
""
],
[
"Precup",
"Doina",
""
],
[
"Zheng",
"Shuangjia",
""
]
] | Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the challenge has shifted towards effectively navigating the vast complex universe t... |
1407.4854 | Kazuhiro Takemoto | Kazuhiro Takemoto | Metabolic networks are almost nonfractal: A comprehensive evaluation | 7 pages, 5 figures | Phys. Rev. E 90, 022802 (2014) | 10.1103/PhysRevE.90.022802 | null | q-bio.MN physics.data-an physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Network self-similarity or fractality are widely accepted as an important
topological property of metabolic networks; however, recent studies cast doubt
on the reality of self-similarity in the networks. Therefore, we perform a
comprehensive evaluation of metabolic network fractality using a box-covering
method with ... | [
{
"created": "Thu, 17 Jul 2014 22:39:23 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Jul 2014 03:18:32 GMT",
"version": "v2"
}
] | 2014-08-05 | [
[
"Takemoto",
"Kazuhiro",
""
]
] | Network self-similarity or fractality are widely accepted as an important topological property of metabolic networks; however, recent studies cast doubt on the reality of self-similarity in the networks. Therefore, we perform a comprehensive evaluation of metabolic network fractality using a box-covering method with an... |
2112.10230 | Johannes M\"uller | Johannes M\"uller and Aurelien Tellier and Michael Kurschilgen | A model of opinion dynamics with echo chambers explains the spatial
distribution of vaccine hesitancy | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Vaccination hesitancy is a major obstacle to achieving and maintaining herd
immunity. It is therefore of prime importance for public health authorities to
understand the dynamics of an anti-vaccine opinion in the population. We
introduce a novel mathematical model of opinion dynamics with spatial
reinforcement, which... | [
{
"created": "Sun, 19 Dec 2021 19:02:22 GMT",
"version": "v1"
}
] | 2021-12-21 | [
[
"Müller",
"Johannes",
""
],
[
"Tellier",
"Aurelien",
""
],
[
"Kurschilgen",
"Michael",
""
]
] | Vaccination hesitancy is a major obstacle to achieving and maintaining herd immunity. It is therefore of prime importance for public health authorities to understand the dynamics of an anti-vaccine opinion in the population. We introduce a novel mathematical model of opinion dynamics with spatial reinforcement, which c... |
2008.01781 | Wentian Li | Wentian Li, Yannis Almirantis, Astero Provata | Revisiting the Neutral Dynamics Derived Limiting Guanine-Cytosine
Content Using the Human De Novo Point Mutation Data | 4 figures | Meta Gene 31: 100994 (2022) | 10.1016/j.mgene.2021.100994 | null | q-bio.GN q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | We revisit the topic of human genome guanine-cytosine content under neutral
evolution. For this study, the de novo mutation data within human is used to
estimate mutational rate instead of using base substitution data between
related species. We then define a new measure of mutation bias which separate
the de novo mu... | [
{
"created": "Tue, 4 Aug 2020 19:31:21 GMT",
"version": "v1"
}
] | 2022-03-15 | [
[
"Li",
"Wentian",
""
],
[
"Almirantis",
"Yannis",
""
],
[
"Provata",
"Astero",
""
]
] | We revisit the topic of human genome guanine-cytosine content under neutral evolution. For this study, the de novo mutation data within human is used to estimate mutational rate instead of using base substitution data between related species. We then define a new measure of mutation bias which separate the de novo muta... |
0810.4547 | Bradly Alicea | Bradly Alicea | Hierarchies of Biocomplexity: modeling lifes energetic complexity | 11 pages, 9 figures, 1 table | null | null | null | q-bio.PE q-bio.OT | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, a model for understanding the effects of selection using
systems- level computational approaches is introduced. A number of concepts and
principles essential for understanding the motivation for constructing the
model will be introduced first. This will be followed by a description of
parameters, measu... | [
{
"created": "Fri, 24 Oct 2008 20:32:11 GMT",
"version": "v1"
},
{
"created": "Fri, 7 Nov 2008 19:19:15 GMT",
"version": "v2"
},
{
"created": "Wed, 4 Mar 2009 15:53:36 GMT",
"version": "v3"
}
] | 2009-03-04 | [
[
"Alicea",
"Bradly",
""
]
] | In this paper, a model for understanding the effects of selection using systems- level computational approaches is introduced. A number of concepts and principles essential for understanding the motivation for constructing the model will be introduced first. This will be followed by a description of parameters, measure... |
1410.6763 | Denis Semenov A. | Denis A. Semenov | Epigenetic effects of cytosine derivatives are caused by their tautomers
in Hoogsteen base pairs | 6 pages, 5 figures | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Deoxycitidine in solution exists as two tautomers one of which is an
uncanonical imino one. The latter can dominate with such derivatives as
5-methyl, 5-hydroxymethyl- and 5-formylcytosine. The imino tautomer potentially
is able to form a hoosteen GC base pair. To detect such pair, it is suggested
to use 1H15N NMR. F... | [
{
"created": "Sat, 30 Aug 2014 18:15:05 GMT",
"version": "v1"
}
] | 2014-10-27 | [
[
"Semenov",
"Denis A.",
""
]
] | Deoxycitidine in solution exists as two tautomers one of which is an uncanonical imino one. The latter can dominate with such derivatives as 5-methyl, 5-hydroxymethyl- and 5-formylcytosine. The imino tautomer potentially is able to form a hoosteen GC base pair. To detect such pair, it is suggested to use 1H15N NMR. For... |
1606.03630 | Cameron Mura | Cameron Mura | The Structures, Functions, and Evolution of Sm-like Archaeal Proteins
(SmAPs) | 215 pages, distributed across an Abstract, Synopsis, five Chapters
(the main body) and an Appendix; the work in this dissertation was performed
in the Eisenberg lab at UCLA from ca. 1999 to 2002 | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Sm proteins were discovered nearly 20 years ago as a group of small antigenic
proteins ($\approx$ 90-120 residues). Since then, an extensive amount of
biochemical and genetic data have illuminated the crucial roles of these
proteins in forming ribonucleoprotein (RNP) complexes that are used in RNA
processing, e.g., s... | [
{
"created": "Sat, 11 Jun 2016 21:20:30 GMT",
"version": "v1"
}
] | 2016-06-14 | [
[
"Mura",
"Cameron",
""
]
] | Sm proteins were discovered nearly 20 years ago as a group of small antigenic proteins ($\approx$ 90-120 residues). Since then, an extensive amount of biochemical and genetic data have illuminated the crucial roles of these proteins in forming ribonucleoprotein (RNP) complexes that are used in RNA processing, e.g., spl... |
1905.00555 | Abhishek Deshpande | Abhishek Deshpande, Thomas E. Ouldridge | Optimizing enzymatic catalysts for rapid turnover of substrates with low
enzyme sequestration | 16 pages, 9 figures | Biological Cybernetics 2020 | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse the mechanism of enzyme-substrate catalysis from the perspective
of minimizing the load on the enzymes through sequestration, whilst maintaining
at least a minimum reaction flux. In particular, we ask: which binding free
energies of the enzyme-substrate and enzyme-product reaction intermediates
minimize th... | [
{
"created": "Thu, 2 May 2019 02:41:46 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Sep 2020 19:31:15 GMT",
"version": "v2"
}
] | 2020-09-21 | [
[
"Deshpande",
"Abhishek",
""
],
[
"Ouldridge",
"Thomas E.",
""
]
] | We analyse the mechanism of enzyme-substrate catalysis from the perspective of minimizing the load on the enzymes through sequestration, whilst maintaining at least a minimum reaction flux. In particular, we ask: which binding free energies of the enzyme-substrate and enzyme-product reaction intermediates minimize the ... |
1502.07793 | James Herbert-Read | James E. Herbert-Read, Ashley J.W. Ward, David J.T. Sumpter, Richard
P. Mann | Escape path complexity and its context dependency in Pacific blue-eyes
(Pseudomugil signifer) | 9 pages | null | 10.1242/jeb.154534 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The escape trajectories animals take following a predatory attack appear to
show high degrees of apparent 'randomness' - a property that has been described
as 'protean behaviour'. Here we present a method of quantifying the escape
trajectories of individual animals using a path complexity approach. When fish
(Pseudom... | [
{
"created": "Thu, 26 Feb 2015 23:47:14 GMT",
"version": "v1"
}
] | 2022-09-13 | [
[
"Herbert-Read",
"James E.",
""
],
[
"Ward",
"Ashley J. W.",
""
],
[
"Sumpter",
"David J. T.",
""
],
[
"Mann",
"Richard P.",
""
]
] | The escape trajectories animals take following a predatory attack appear to show high degrees of apparent 'randomness' - a property that has been described as 'protean behaviour'. Here we present a method of quantifying the escape trajectories of individual animals using a path complexity approach. When fish (Pseudomug... |
1607.02642 | Wayne Hayes | Nil Mamano and Wayne Hayes | SANA: Simulated Annealing Network Alignment Applied to Biological
Networks | null | null | null | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The alignment of biological networks has the potential to teach us as much
about biology and disease as has sequence alignment. Sequence alignment can be
optimally solved in polynomial time. In contrast, network alignment is
$NP$-hard, meaning optimal solutions are impossible to find, and the quality of
found alignme... | [
{
"created": "Sat, 9 Jul 2016 18:13:30 GMT",
"version": "v1"
}
] | 2016-07-12 | [
[
"Mamano",
"Nil",
""
],
[
"Hayes",
"Wayne",
""
]
] | The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard, meaning optimal solutions are impossible to find, and the quality of found alignment... |
2310.10598 | Jenna Fromer | Jenna C. Fromer, David E. Graff, Connor W. Coley | Pareto Optimization to Accelerate Multi-Objective Virtual Screening | null | null | null | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The discovery of therapeutic molecules is fundamentally a multi-objective
optimization problem. One formulation of the problem is to identify molecules
that simultaneously exhibit strong binding affinity for a target protein,
minimal off-target interactions, and suitable pharmacokinetic properties.
Inspired by prior ... | [
{
"created": "Mon, 16 Oct 2023 17:19:46 GMT",
"version": "v1"
}
] | 2023-10-17 | [
[
"Fromer",
"Jenna C.",
""
],
[
"Graff",
"David E.",
""
],
[
"Coley",
"Connor W.",
""
]
] | The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal off-target interactions, and suitable pharmacokinetic properties. Inspired by prior wo... |
1611.05918 | Sujoy Ganguly | Sujoy Ganguly and Olivier Trottier and Xin Liang and Hugo
Bowne-Anderson and Jonathon Howard | Morphology of Fly Larval Class IV Dendrites Accords with a Random
Branching and Contact Based Branch Deletion Model | 12 pages, 4 figures. Supplementary Information: 3 Figures | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Dendrites are branched neuronal processes that receive input signals from
other neurons or the outside world [1]. To maintain connectivity as the
organism grows, dendrites must also continue to grow. For example, the
dendrites in the peripheral nervous system continue to grow and branch to
maintain proper coverage of... | [
{
"created": "Thu, 17 Nov 2016 22:08:20 GMT",
"version": "v1"
}
] | 2016-11-21 | [
[
"Ganguly",
"Sujoy",
""
],
[
"Trottier",
"Olivier",
""
],
[
"Liang",
"Xin",
""
],
[
"Bowne-Anderson",
"Hugo",
""
],
[
"Howard",
"Jonathon",
""
]
] | Dendrites are branched neuronal processes that receive input signals from other neurons or the outside world [1]. To maintain connectivity as the organism grows, dendrites must also continue to grow. For example, the dendrites in the peripheral nervous system continue to grow and branch to maintain proper coverage of t... |
1708.02603 | Tae Seung Kang | Tae Seung Kang and Arunava Banerjee | Learning Feedforward and Recurrent Deterministic Spiking Neuron Network
Feedback Controllers | null | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We address the problem of learning feedback control where the controller is a
network constructed solely of deterministic spiking neurons. In contrast to
previous investigations that were based on a spike rate model of the neuron,
the control signal here is determined by the precise temporal positions of
spikes gener... | [
{
"created": "Tue, 8 Aug 2017 18:42:17 GMT",
"version": "v1"
},
{
"created": "Tue, 25 Sep 2018 22:54:29 GMT",
"version": "v2"
}
] | 2018-09-27 | [
[
"Kang",
"Tae Seung",
""
],
[
"Banerjee",
"Arunava",
""
]
] | We address the problem of learning feedback control where the controller is a network constructed solely of deterministic spiking neurons. In contrast to previous investigations that were based on a spike rate model of the neuron, the control signal here is determined by the precise temporal positions of spikes generat... |
1307.5468 | Changbong Hyeon | Jeseong Yoon, D. Thirumalai, Changbong Hyeon | Urea-induced denaturation of PreQ1-riboswitch | 41 pages, 18 figures | J. Am. Chem. Soc. 2013 | 10.1016/j.bpj.2012.11.1853 | null | q-bio.BM cond-mat.soft | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Urea, a polar molecule with a large dipole moment, not only destabilizes the
folded RNA structures, but can also enhance the folding rates of large
ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is
well understood, the action of urea on RNA has barely been explored. We
performed extensiv... | [
{
"created": "Sat, 20 Jul 2013 22:02:38 GMT",
"version": "v1"
}
] | 2017-08-23 | [
[
"Yoon",
"Jeseong",
""
],
[
"Thirumalai",
"D.",
""
],
[
"Hyeon",
"Changbong",
""
]
] | Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive ... |
2010.12127 | Dongqi Han | Dongqi Han, Erik De Schutter, Sungho Hong | Lamina-specific neuronal properties promote robust, stable signal
propagation in feedforward networks | NeurIPS 2020 | null | null | null | q-bio.NC cs.NE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Feedforward networks (FFN) are ubiquitous structures in neural systems and
have been studied to understand mechanisms of reliable signal and information
transmission. In many FFNs, neurons in one layer have intrinsic properties that
are distinct from those in their pre-/postsynaptic layers, but how this affects
netwo... | [
{
"created": "Fri, 23 Oct 2020 01:57:46 GMT",
"version": "v1"
}
] | 2020-10-26 | [
[
"Han",
"Dongqi",
""
],
[
"De Schutter",
"Erik",
""
],
[
"Hong",
"Sungho",
""
]
] | Feedforward networks (FFN) are ubiquitous structures in neural systems and have been studied to understand mechanisms of reliable signal and information transmission. In many FFNs, neurons in one layer have intrinsic properties that are distinct from those in their pre-/postsynaptic layers, but how this affects network... |
2201.07338 | Noelia Ferruz | Noelia Ferruz and Birte H\"ocker | Controllable Protein Design with Language Models | This is a version before peer-review. A view-only, peer-reviewed,
published version can be found here: https://rdcu.be/cQbmH. The peer-reviewed
version is under embargo at Nat Mach Intell until 12/2022 | Controllable protein design with language models. Nat Mach Intell
4, 521-532, 2022 | 10.1038/s42256-022-00499-z | null | q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | The 21st century is presenting humankind with unprecedented environmental and
medical challenges. The ability to design novel proteins tailored for specific
purposes could transform our ability to respond timely to these issues. Recent
advances in the field of artificial intelligence are now setting the stage to
make... | [
{
"created": "Tue, 18 Jan 2022 22:23:03 GMT",
"version": "v1"
},
{
"created": "Mon, 22 Aug 2022 18:44:27 GMT",
"version": "v2"
}
] | 2022-08-24 | [
[
"Ferruz",
"Noelia",
""
],
[
"Höcker",
"Birte",
""
]
] | The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent advances in the field of artificial intelligence are now setting the stage to make t... |
1602.08314 | Pramod Shinde | Pramod Shinde and Sarika Jalan | A multilayer PPI network analysis of different life stages in C. elegans | null | EPL (Europhysics Letters). 2015 Dec 17;112(5):58001 | 10.1209/0295-5075/112/58001 | null | q-bio.MN q-bio.PE q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular networks act as the backbone of cellular activities, providing an
{excellent} opportunity to understand the developmental changes in an organism.
While network data usually constitute only stationary network graphs,
constructing multilayer PPI network may provide clues to the particular
developmental role a... | [
{
"created": "Fri, 26 Feb 2016 13:26:52 GMT",
"version": "v1"
}
] | 2016-02-29 | [
[
"Shinde",
"Pramod",
""
],
[
"Jalan",
"Sarika",
""
]
] | Molecular networks act as the backbone of cellular activities, providing an {excellent} opportunity to understand the developmental changes in an organism. While network data usually constitute only stationary network graphs, constructing multilayer PPI network may provide clues to the particular developmental role at ... |
q-bio/0501013 | Anthonie Muller | Anthonie W. J. Muller | Thermosynthesis as energy source for the RNA World: a new model for the
origin of life | 12 pages, 6 figures; changes in text (minor) and 2 figures | null | null | null | q-bio.PE | null | The thermosynthesis concept, biological free energy gain from thermal
cycling, is combined with the concept of the RNA World. The resulting overall
origin of life model gives new explanations for the emergence of the genetic
code and the ribosome. The first protein named pF1 obtains the energy to
support the RNA worl... | [
{
"created": "Tue, 11 Jan 2005 19:06:12 GMT",
"version": "v1"
},
{
"created": "Wed, 30 Mar 2005 21:48:04 GMT",
"version": "v2"
}
] | 2007-05-23 | [
[
"Muller",
"Anthonie W. J.",
""
]
] | The thermosynthesis concept, biological free energy gain from thermal cycling, is combined with the concept of the RNA World. The resulting overall origin of life model gives new explanations for the emergence of the genetic code and the ribosome. The first protein named pF1 obtains the energy to support the RNA world ... |
1702.02510 | Juan Abdon Miranda Correa | Juan Abdon Miranda-Correa and Mojtaba Khomami Abadi and Nicu Sebe and
Ioannis Patras | AMIGOS: A Dataset for Affect, Personality and Mood Research on
Individuals and Groups | 14 pages, Transaction on Affective Computing | null | null | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present AMIGOS-- A dataset for Multimodal research of affect, personality
traits and mood on Individuals and GrOupS. Different to other databases, we
elicited affect using both short and long videos in two social contexts, one
with individual viewers and one with groups of viewers. The database allows the
multimod... | [
{
"created": "Thu, 2 Feb 2017 08:04:47 GMT",
"version": "v1"
},
{
"created": "Tue, 28 Mar 2017 14:27:10 GMT",
"version": "v2"
},
{
"created": "Thu, 13 Apr 2017 16:10:00 GMT",
"version": "v3"
}
] | 2017-04-14 | [
[
"Miranda-Correa",
"Juan Abdon",
""
],
[
"Abadi",
"Mojtaba Khomami",
""
],
[
"Sebe",
"Nicu",
""
],
[
"Patras",
"Ioannis",
""
]
] | We present AMIGOS-- A dataset for Multimodal research of affect, personality traits and mood on Individuals and GrOupS. Different to other databases, we elicited affect using both short and long videos in two social contexts, one with individual viewers and one with groups of viewers. The database allows the multimodal... |
2008.08758 | Affan Affan | Affan Affan and Tamer Inanc | Semi-Blind and l1 Robust System Identification for Anemia Management | Under-review at The Fifth IEEE/ACM conference on Connected Health:
Applications, Systems and Engineering Technologies (CHASE) 2020 | null | null | null | q-bio.QM cs.SY eess.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chronic diseases such as cancer, diabetes, heart diseases, chronic kidney
disease (CKD) require a drug management system that ensures a stable and robust
output of the patient's condition in response to drug dosage. In the case of
CKD, the patients suffer from the deficiency of red blood cell count and
external human... | [
{
"created": "Thu, 20 Aug 2020 03:50:10 GMT",
"version": "v1"
}
] | 2020-08-21 | [
[
"Affan",
"Affan",
""
],
[
"Inanc",
"Tamer",
""
]
] | Chronic diseases such as cancer, diabetes, heart diseases, chronic kidney disease (CKD) require a drug management system that ensures a stable and robust output of the patient's condition in response to drug dosage. In the case of CKD, the patients suffer from the deficiency of red blood cell count and external human r... |
1111.6916 | Nilima Nigam | Marc Ryser, Svetlana V. Komarova, Nilima Nigam | The cellular dynamics of bone remodeling: a mathematical model | null | SIAM J. Appl. Math. 70, pp. 1899-1921 | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mechanical properties of vertebrate bone are largely determined by a
process which involves the complex interplay of three different cell types.
This process is called {\it bone remodeling}, and occurs asynchronously at
multiple sites in the mature skeleton. The cells involved are bone resorbing
osteoclasts, bone... | [
{
"created": "Sun, 27 Nov 2011 21:43:03 GMT",
"version": "v1"
}
] | 2011-11-30 | [
[
"Ryser",
"Marc",
""
],
[
"Komarova",
"Svetlana V.",
""
],
[
"Nigam",
"Nilima",
""
]
] | The mechanical properties of vertebrate bone are largely determined by a process which involves the complex interplay of three different cell types. This process is called {\it bone remodeling}, and occurs asynchronously at multiple sites in the mature skeleton. The cells involved are bone resorbing osteoclasts, bone m... |
1111.6631 | Arash Sangari Mr. | Arash Sangari, Adel Ardalan, Larry Lambe, Hamid Eghbalnia and Amir H.
Assadi | Mathematical Analysis and Computational Integration of Massive
Heterogeneous Data from the Human Retina | 9 pages, 3 figures, submitted and accepted in Damor2012 conference:
http://www.uninova.pt/damor2012/index.php?page=authors | null | null | null | q-bio.QM cs.IR math.SP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Modern epidemiology integrates knowledge from heterogeneous collections of
data consisting of numerical, descriptive and imaging. Large-scale
epidemiological studies use sophisticated statistical analysis, mathematical
models using differential equations and versatile analytic tools that handle
numerical data. In con... | [
{
"created": "Mon, 28 Nov 2011 22:01:19 GMT",
"version": "v1"
},
{
"created": "Wed, 10 Oct 2012 19:52:29 GMT",
"version": "v2"
}
] | 2012-10-11 | [
[
"Sangari",
"Arash",
""
],
[
"Ardalan",
"Adel",
""
],
[
"Lambe",
"Larry",
""
],
[
"Eghbalnia",
"Hamid",
""
],
[
"Assadi",
"Amir H.",
""
]
] | Modern epidemiology integrates knowledge from heterogeneous collections of data consisting of numerical, descriptive and imaging. Large-scale epidemiological studies use sophisticated statistical analysis, mathematical models using differential equations and versatile analytic tools that handle numerical data. In contr... |
1411.2103 | Michael Schaub | Yazan N. Billeh, Michael T. Schaub, Costas A. Anastassiou, Mauricio
Barahona, Christof Koch | Revealing cell assemblies at multiple levels of granularity | 18 pages; 13 Figures; published as open access in J Neuro Methods | Journal of Neuroscience Methods, Volume 236, 30 October 2014,
Pages 92-106, ISSN 0165-0270 | 10.1016/j.jneumeth.2014.08.011 | null | q-bio.NC physics.data-an | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: Current neuronal monitoring techniques, such as calcium imaging
and multi-electrode arrays, enable recordings of spiking activity from hundreds
of neurons simultaneously. Of primary importance in systems neuroscience is the
identification of cell assemblies: groups of neurons that cooperate in some
form w... | [
{
"created": "Sat, 8 Nov 2014 10:02:33 GMT",
"version": "v1"
}
] | 2014-11-11 | [
[
"Billeh",
"Yazan N.",
""
],
[
"Schaub",
"Michael T.",
""
],
[
"Anastassiou",
"Costas A.",
""
],
[
"Barahona",
"Mauricio",
""
],
[
"Koch",
"Christof",
""
]
] | Background: Current neuronal monitoring techniques, such as calcium imaging and multi-electrode arrays, enable recordings of spiking activity from hundreds of neurons simultaneously. Of primary importance in systems neuroscience is the identification of cell assemblies: groups of neurons that cooperate in some form wit... |
1510.05917 | Gestionnaire Hal-Upmc | Genevi\'eve Rodier (IGMM, IRCM), Olivier Kirsh (IGMM), Mart\'in
Baraibar (B2A), Thibault Houl\'es (IGMM, IPBS, IRCM), Matthieu Lacroix (UTA,
IRCM), H\'el\'ene Delpech (IGMM, IRCM), Elodie Hatchi (IGMM), St\'ephanie
Arnould (IGMM, IRCM), Dany Severac, Emeric Dubois, Julie Caramel (IGMM), Eric
Julien (IGMM, IRCM)... | The Transcription Factor E4F1 Coordinates CHK1-Dependent Checkpoint and
Mitochondrial Functions | null | Cell Reports, Elsevier, 2015, 11 (2), pp.220-233.
\<10.1016/j.celrep.2015.03.024\> | 10.1016/j.celrep.2015.03.024 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recent data support the notion that a group of key transcriptional regulators
involved in tumorigenesis, including MYC, p53, E2F1, and BMI1, share an
intriguing capacity to simultaneously regulate metabolism and cell cycle. Here,
we show that another factor, the multifunctional protein E4F1, directly
controls genes i... | [
{
"created": "Wed, 14 Oct 2015 13:28:27 GMT",
"version": "v1"
}
] | 2015-10-21 | [
[
"Rodier",
"Geneviéve",
"",
"IGMM, IRCM"
],
[
"Kirsh",
"Olivier",
"",
"IGMM"
],
[
"Baraibar",
"Martín",
"",
"B2A"
],
[
"Houlés",
"Thibault",
"",
"IGMM, IPBS, IRCM"
],
[
"Lacroix",
"Matthieu",
"",
"UTA,\n IRCM"
],
[... | Recent data support the notion that a group of key transcriptional regulators involved in tumorigenesis, including MYC, p53, E2F1, and BMI1, share an intriguing capacity to simultaneously regulate metabolism and cell cycle. Here, we show that another factor, the multifunctional protein E4F1, directly controls genes inv... |
2310.09529 | Katherine Ge | Katherine Ge, Dayna Olson, and Michel F. Sanner | Docking Peptides into HIV/FIV Protease with Deep Learning and Focused
Peptide Docking Methods | 9 Pages, 5 Figures, 2 Tables | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Molecular docking is a structure-based computational drug design technique
for predicting the interaction between a small molecule (ligand) and a
macromolecule (receptor). Over the past three decades various docking software
programs have been developed, mostly for drug-like molecules. With the recent
interest in pep... | [
{
"created": "Sat, 14 Oct 2023 08:14:54 GMT",
"version": "v1"
}
] | 2023-10-18 | [
[
"Ge",
"Katherine",
""
],
[
"Olson",
"Dayna",
""
],
[
"Sanner",
"Michel F.",
""
]
] | Molecular docking is a structure-based computational drug design technique for predicting the interaction between a small molecule (ligand) and a macromolecule (receptor). Over the past three decades various docking software programs have been developed, mostly for drug-like molecules. With the recent interest in pepti... |
2311.09261 | Yongqi Zhang | Yongqi Zhang, Quanming Yao, Ling Yue, Xian Wu, Ziheng Zhang, Zhenxi
Lin, Yefeng Zheng | Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural
Network with Biomedical Network | Accepted by Nature Computational Science | null | null | null | q-bio.QM cs.AI cs.CE cs.LG | http://creativecommons.org/licenses/by/4.0/ | Accurately predicting drug-drug interactions (DDI) for emerging drugs, which
offer possibilities for treating and alleviating diseases, with computational
methods can improve patient care and contribute to efficient drug development.
However, many existing computational methods require large amounts of known DDI
info... | [
{
"created": "Wed, 15 Nov 2023 06:34:00 GMT",
"version": "v1"
}
] | 2023-11-17 | [
[
"Zhang",
"Yongqi",
""
],
[
"Yao",
"Quanming",
""
],
[
"Yue",
"Ling",
""
],
[
"Wu",
"Xian",
""
],
[
"Zhang",
"Ziheng",
""
],
[
"Lin",
"Zhenxi",
""
],
[
"Zheng",
"Yefeng",
""
]
] | Accurately predicting drug-drug interactions (DDI) for emerging drugs, which offer possibilities for treating and alleviating diseases, with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI inform... |
1403.2160 | Tiberiu Harko | Tiberiu Harko, Francisco S. N. Lobo, M. K. Mak | Exact analytical solutions of the Susceptible-Infected-Recovered (SIR)
epidemic model and of the SIR model with equal death and birth rates | 13 pages, 4 figures, accepted for publication in Applied Mathematics
and Computation | Applied Mathematics and Computation, 236, 2014, 184-194 | 10.1016/j.amc.2014.03.030 | null | q-bio.PE nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, the exact analytical solution of the
Susceptible-Infected-Recovered (SIR) epidemic model is obtained in a parametric
form. By using the exact solution we investigate some explicit models
corresponding to fixed values of the parameters, and show that the numerical
solution reproduces exactly the analyti... | [
{
"created": "Mon, 10 Mar 2014 08:21:07 GMT",
"version": "v1"
}
] | 2014-04-24 | [
[
"Harko",
"Tiberiu",
""
],
[
"Lobo",
"Francisco S. N.",
""
],
[
"Mak",
"M. K.",
""
]
] | In this paper, the exact analytical solution of the Susceptible-Infected-Recovered (SIR) epidemic model is obtained in a parametric form. By using the exact solution we investigate some explicit models corresponding to fixed values of the parameters, and show that the numerical solution reproduces exactly the analytica... |
1703.00226 | Thierry Mora | Jonathan Desponds, Andreas Mayer, Thierry Mora, Aleksandra M. Walczak | Population dynamics of immune repertoires | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The evolution of the adaptive immune system is characterized by changes in
the relative abundances of the B- and T-cell clones that make up its
repertoires. To fully capture this evolution, we need to describe the complex
dynamics of the response to pathogenic and self-antigenic stimulations, as well
as the statistic... | [
{
"created": "Wed, 1 Mar 2017 10:54:59 GMT",
"version": "v1"
}
] | 2017-03-02 | [
[
"Desponds",
"Jonathan",
""
],
[
"Mayer",
"Andreas",
""
],
[
"Mora",
"Thierry",
""
],
[
"Walczak",
"Aleksandra M.",
""
]
] | The evolution of the adaptive immune system is characterized by changes in the relative abundances of the B- and T-cell clones that make up its repertoires. To fully capture this evolution, we need to describe the complex dynamics of the response to pathogenic and self-antigenic stimulations, as well as the statistics ... |
2006.13752 | Paulo Zingano | Paulo R. Zingano, Janaina P. Zingano, Alessandra M. Silva and Carolina
P. Zingano | A matlab code to compute reproduction numbers with applications to the
Covid-19 outbreak | A complete matlab program (with about 500 lines) implementing the
algorithm described in this work can be downloaded for free at the following
URL address:
https://drive.google.com/drive/folders/16kLxlZyqH-QATOLQI6QWTx7qZnL3IoCP | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We discuss the generation of various reproduction ratios or numbers that are
very useful to monitor an ongoing epidemic like Covid-19 and examine the
effects of intervention measures. A detailed SEIR algorithm is described for
their computation, with applications given to the current Covid-19 outbreaks in
a number of... | [
{
"created": "Tue, 23 Jun 2020 17:57:28 GMT",
"version": "v1"
}
] | 2020-06-25 | [
[
"Zingano",
"Paulo R.",
""
],
[
"Zingano",
"Janaina P.",
""
],
[
"Silva",
"Alessandra M.",
""
],
[
"Zingano",
"Carolina P.",
""
]
] | We discuss the generation of various reproduction ratios or numbers that are very useful to monitor an ongoing epidemic like Covid-19 and examine the effects of intervention measures. A detailed SEIR algorithm is described for their computation, with applications given to the current Covid-19 outbreaks in a number of c... |
1902.01574 | Tzvetomir Tzvetanov | Tzvetomir Tzvetanov | Suppression and facilitation of motion perception in humans: a reply to
Schallmo & Murray (2018) | 9 pages | null | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In a recent publication (Tzvetanov (2018), bioRxiv 465807), I made an
extensive analysis with computational modelling and psychophysics of the simple
experimental design of Dr. D.Tadin (Tadin, Lappin, Gilroy and Blake (2003),
Nature, 424:312-315) about motion perception changes in humans due to size and
contrast of t... | [
{
"created": "Tue, 5 Feb 2019 07:34:35 GMT",
"version": "v1"
}
] | 2019-02-06 | [
[
"Tzvetanov",
"Tzvetomir",
""
]
] | In a recent publication (Tzvetanov (2018), bioRxiv 465807), I made an extensive analysis with computational modelling and psychophysics of the simple experimental design of Dr. D.Tadin (Tadin, Lappin, Gilroy and Blake (2003), Nature, 424:312-315) about motion perception changes in humans due to size and contrast of the... |
2103.06256 | Perrine Paul-Gilloteaux | Guillaume Potier, Fr\'ed\'eric Lavancier, Stephan Kunne and Perrine
Paul-Gilloteaux | A registration error estimation framework for correlative imaging | 10 pages 2 figures (made of 10 panels in total) | null | 10.1109/ICIP42928.2021.9506474 | null | q-bio.QM cs.CV | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Correlative imaging workflows are now widely used in bioimaging and aims to
image the same sample using at least two different and complementary imaging
modalities. Part of the workflow relies on finding the transformation linking a
source image to a target image. We are specifically interested in the
estimation of r... | [
{
"created": "Wed, 10 Mar 2021 18:43:18 GMT",
"version": "v1"
}
] | 2021-08-30 | [
[
"Potier",
"Guillaume",
""
],
[
"Lavancier",
"Frédéric",
""
],
[
"Kunne",
"Stephan",
""
],
[
"Paul-Gilloteaux",
"Perrine",
""
]
] | Correlative imaging workflows are now widely used in bioimaging and aims to image the same sample using at least two different and complementary imaging modalities. Part of the workflow relies on finding the transformation linking a source image to a target image. We are specifically interested in the estimation of reg... |
2012.05045 | Anindita Bhadra | Debottam Bhattacharjee and Anindita Bhadra | Response to sudden surge in human movement by an urban-adapted animal | 1 figure | Behav Ecol Sociobiol 75, 111 (2021) | 10.1007/s00265-021-03052-x | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Interaction with its immediate environment determines the ecology of an
organism. Species present in any habitat, wild or urban, may face extreme
pressure due to sudden perturbations. When such disturbances are unpredictable,
it becomes more challenging to tackle. Implementation of specific strategies is
therefore es... | [
{
"created": "Mon, 7 Dec 2020 12:27:34 GMT",
"version": "v1"
}
] | 2022-08-12 | [
[
"Bhattacharjee",
"Debottam",
""
],
[
"Bhadra",
"Anindita",
""
]
] | Interaction with its immediate environment determines the ecology of an organism. Species present in any habitat, wild or urban, may face extreme pressure due to sudden perturbations. When such disturbances are unpredictable, it becomes more challenging to tackle. Implementation of specific strategies is therefore esse... |
2407.07114 | Josh Morgan | Josh L. Morgan | Alternatives to the statistical mass confusion of testing for no-effect | 13 pages, 1 figure | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Statisticians and researchers have argued about the merits of effect size
estimation relative to hypothesis testing for decades. Cell biology has largely
avoided this debate and is now in a quantitation crisis. In experimental cell
biology, statistical analysis has grown to mean testing the null hypothesis
that there... | [
{
"created": "Fri, 28 Jun 2024 00:08:38 GMT",
"version": "v1"
}
] | 2024-07-11 | [
[
"Morgan",
"Josh L.",
""
]
] | Statisticians and researchers have argued about the merits of effect size estimation relative to hypothesis testing for decades. Cell biology has largely avoided this debate and is now in a quantitation crisis. In experimental cell biology, statistical analysis has grown to mean testing the null hypothesis that there w... |
2009.12023 | Alessandro Sanzeni | Alessandro Sanzeni and Mark H Histed and Nicolas Brunel | Emergence of irregular activity in networks of strongly coupled
conductance-based neurons | null | null | null | null | q-bio.NC physics.bio-ph | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Cortical neurons are characterized by irregular firing and a broad
distribution of rates. The balanced state model explains these observations
with a cancellation of mean excitatory and inhibitory currents, which makes
fluctuations drive firing. In networks of neurons with current-based synapses,
the balanced state e... | [
{
"created": "Fri, 25 Sep 2020 04:05:22 GMT",
"version": "v1"
},
{
"created": "Tue, 13 Oct 2020 22:02:23 GMT",
"version": "v2"
}
] | 2020-10-15 | [
[
"Sanzeni",
"Alessandro",
""
],
[
"Histed",
"Mark H",
""
],
[
"Brunel",
"Nicolas",
""
]
] | Cortical neurons are characterized by irregular firing and a broad distribution of rates. The balanced state model explains these observations with a cancellation of mean excitatory and inhibitory currents, which makes fluctuations drive firing. In networks of neurons with current-based synapses, the balanced state eme... |
2003.09796 | Jun Chen | Jun Chen, Komi Messan, Marisabel Rodriguez Messan, Gloria
DeGrandi-Hoffman, Dingyong Bai, Yun Kang | How to model honeybee population dynamics: stage structure and
seasonality | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Western honeybees (Apis Mellifera) serve extremely important roles in our
ecosystem and economics as they are responsible for pollinating $ 215 billion
dollars annually over the world. Unfortunately, honeybee population and their
colonies have been declined dramatically. The purpose of this article is to
explore how ... | [
{
"created": "Sun, 22 Mar 2020 03:34:49 GMT",
"version": "v1"
}
] | 2020-03-24 | [
[
"Chen",
"Jun",
""
],
[
"Messan",
"Komi",
""
],
[
"Messan",
"Marisabel Rodriguez",
""
],
[
"DeGrandi-Hoffman",
"Gloria",
""
],
[
"Bai",
"Dingyong",
""
],
[
"Kang",
"Yun",
""
]
] | Western honeybees (Apis Mellifera) serve extremely important roles in our ecosystem and economics as they are responsible for pollinating $ 215 billion dollars annually over the world. Unfortunately, honeybee population and their colonies have been declined dramatically. The purpose of this article is to explore how we... |
1301.6561 | Alexey Mikaberidze | Alexey Mikaberidze, Bruce A. McDonald, Sebastian Bonhoeffer | Can high risk fungicides be used in mixtures without selecting for
fungicide resistance? | 51 pages, 6 figures, accepted for publication in Phytopathology | null | 10.1094/PHYTO-07-13-0204-R | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Fungicide mixtures produced by the agrochemical industry often contain
low-risk fungicides, to which fungal pathogens are fully sensitive, together
with high-risk fungicides known to be prone to fungicide resistance. Can these
mixtures provide adequate disease control while minimizing the risk for the
development of ... | [
{
"created": "Mon, 28 Jan 2013 14:42:46 GMT",
"version": "v1"
},
{
"created": "Fri, 20 Sep 2013 08:59:21 GMT",
"version": "v2"
}
] | 2013-09-23 | [
[
"Mikaberidze",
"Alexey",
""
],
[
"McDonald",
"Bruce A.",
""
],
[
"Bonhoeffer",
"Sebastian",
""
]
] | Fungicide mixtures produced by the agrochemical industry often contain low-risk fungicides, to which fungal pathogens are fully sensitive, together with high-risk fungicides known to be prone to fungicide resistance. Can these mixtures provide adequate disease control while minimizing the risk for the development of re... |
2009.03629 | Jozef Skakala | Jozef Skakala and Paolo Lazzari | Low complexity model to study scale dependence of phytoplankton dynamics
in the tropical Pacific | 21 pages, 12 figures | Phys. Rev. E 103, 012401 (2021) | 10.1103/PhysRevE.103.012401 | null | q-bio.PE physics.ao-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We demonstrate that a simple model based on reaction-diffusion-advection
(RDA) equation forced by realistic surface velocities and nutrients is skilled
in reproducing the distributions of the surface phytoplankton chlorophyll in
the tropical Pacific. We use the low-complexity RDA model to investigate the
scale-relati... | [
{
"created": "Tue, 8 Sep 2020 10:21:50 GMT",
"version": "v1"
},
{
"created": "Mon, 11 Jan 2021 22:02:03 GMT",
"version": "v2"
}
] | 2021-01-13 | [
[
"Skakala",
"Jozef",
""
],
[
"Lazzari",
"Paolo",
""
]
] | We demonstrate that a simple model based on reaction-diffusion-advection (RDA) equation forced by realistic surface velocities and nutrients is skilled in reproducing the distributions of the surface phytoplankton chlorophyll in the tropical Pacific. We use the low-complexity RDA model to investigate the scale-relation... |
2010.00504 | Sarah Marzen | Alexander Hsu and Sarah Marzen | Time cells might be optimized for predictive capacity, not redundancy
reduction or memory capacity | null | null | 10.1103/PhysRevE.102.062404 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Recently, researchers have found time cells in the hippocampus that appear to
contain information about the timing of past events. Some researchers have
argued that time cells are taking a Laplace transform of their input in order
to reconstruct the past stimulus. We argue that stimulus prediction, not
stimulus recon... | [
{
"created": "Thu, 1 Oct 2020 15:53:43 GMT",
"version": "v1"
}
] | 2020-12-30 | [
[
"Hsu",
"Alexander",
""
],
[
"Marzen",
"Sarah",
""
]
] | Recently, researchers have found time cells in the hippocampus that appear to contain information about the timing of past events. Some researchers have argued that time cells are taking a Laplace transform of their input in order to reconstruct the past stimulus. We argue that stimulus prediction, not stimulus reconst... |
2311.09354 | Kylie Trettner | Kylie J. Trettner, Jeremy Hsieh, Weikun Xiao, Jerry S.H. Lee, Andrea
M. Armani | Nondestructive, quantitative viability analysis of 3D tissue cultures
using machine learning image segmentation | 52 total pages, Main text and SI included, 35 figures (5 main text,
30 supplemental), 9 tables, 6 datasets (provided on linked GitHub), linked
image files on Zenodo | null | 10.1063/5.0189222 | null | q-bio.QM cs.LG eess.IV | http://creativecommons.org/licenses/by/4.0/ | Ascertaining the collective viability of cells in different cell culture
conditions has typically relied on averaging colorimetric indicators and is
often reported out in simple binary readouts. Recent research has combined
viability assessment techniques with image-based deep-learning models to
automate the characte... | [
{
"created": "Wed, 15 Nov 2023 20:28:31 GMT",
"version": "v1"
},
{
"created": "Mon, 4 Mar 2024 21:43:02 GMT",
"version": "v2"
},
{
"created": "Mon, 11 Mar 2024 22:12:25 GMT",
"version": "v3"
}
] | 2024-04-03 | [
[
"Trettner",
"Kylie J.",
""
],
[
"Hsieh",
"Jeremy",
""
],
[
"Xiao",
"Weikun",
""
],
[
"Lee",
"Jerry S. H.",
""
],
[
"Armani",
"Andrea M.",
""
]
] | Ascertaining the collective viability of cells in different cell culture conditions has typically relied on averaging colorimetric indicators and is often reported out in simple binary readouts. Recent research has combined viability assessment techniques with image-based deep-learning models to automate the characteri... |
1310.1593 | Tomasz Rutkowski | Shota Kono, Daiki Aminaka, Shoji Makino, and Tomasz M. Rutkowski | EEG Signal Processing and Classification for the Novel Tactile-Force
Brain-Computer Interface Paradigm | 6 pages (in conference proceedings original version); 6 figures,
submitted to The 9th International Conference on Signal Image Technology &
Internet Based Systems, December 2-5, 2013, Kyoto, Japan; to be available at
IEEE Xplore; IEEE Copyright 2013 | Proceedings of the 9th International Conference on Signal Image
Technology and Internet Based Systems, (Kyoto, Japan), pp. 812-817, IEEE
Computer Society, December 3-5, 2013 | 10.1109/SITIS.2013.132 | null | q-bio.NC cs.HC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The presented study explores the extent to which tactile-force stimulus
delivered to a hand holding a joystick can serve as a platform for a brain
computer interface (BCI). The four pressure directions are used to evoke
tactile brain potential responses, thus defining a tactile-force brain computer
interface (tfBCI).... | [
{
"created": "Sun, 6 Oct 2013 15:18:34 GMT",
"version": "v1"
},
{
"created": "Thu, 17 Oct 2013 07:52:01 GMT",
"version": "v2"
}
] | 2013-12-17 | [
[
"Kono",
"Shota",
""
],
[
"Aminaka",
"Daiki",
""
],
[
"Makino",
"Shoji",
""
],
[
"Rutkowski",
"Tomasz M.",
""
]
] | The presented study explores the extent to which tactile-force stimulus delivered to a hand holding a joystick can serve as a platform for a brain computer interface (BCI). The four pressure directions are used to evoke tactile brain potential responses, thus defining a tactile-force brain computer interface (tfBCI). W... |
1608.06146 | Sophie Kay | Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan,
Trevor Dale, James M. Osborne, David J. Gavaghan and Helen M. Byrne | The Role of the Hes1 Crosstalk Hub in Notch-Wnt Interactions of the
Intestinal Crypt | null | null | 10.1371/journal.pcbi.1005400 | null | q-bio.SC q-bio.CB q-bio.MN q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The Notch pathway plays a vital role in determining whether cells in the
intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate
specification is coordinated via Notch's interaction with the canonical Wnt
pathway. Here, we propose a new mathematical model of the Notch and Wnt
pathways, in which ... | [
{
"created": "Mon, 22 Aug 2016 12:32:08 GMT",
"version": "v1"
}
] | 2017-04-12 | [
[
"Kay",
"Sophie K.",
""
],
[
"Harrington",
"Heather A.",
""
],
[
"Shepherd",
"Sarah",
""
],
[
"Brennan",
"Keith",
""
],
[
"Dale",
"Trevor",
""
],
[
"Osborne",
"James M.",
""
],
[
"Gavaghan",
"David J.",
""
... | The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway. Here, we propose a new mathematical model of the Notch and Wnt pathways, in which th... |
1310.2968 | Tracy Heath | Tracy A. Heath, John P. Huelsenbeck, Tanja Stadler | The Fossilized Birth-Death Process: A Coherent Model of Fossil
Calibration for Divergence Time Estimation | 42 total pages including: 29 text pages, 5 tables, and 12 figures.
Work presented at Evolution 2013
(http://www.slideshare.net/trayc7/heath-evolution-2013) | null | 10.1073/pnas.1319091111 | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Time-calibrated species phylogenies are critical for addressing a wide range
of questions in evolutionary biology, such as those that elucidate historical
biogeography or uncover patterns of coevolution and diversification. Because
molecular sequence data are not informative on absolute time, external data,
most comm... | [
{
"created": "Thu, 10 Oct 2013 22:04:03 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Oct 2013 20:48:23 GMT",
"version": "v2"
}
] | 2014-07-11 | [
[
"Heath",
"Tracy A.",
""
],
[
"Huelsenbeck",
"John P.",
""
],
[
"Stadler",
"Tanja",
""
]
] | Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data, most common... |
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