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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1702.04515 | Ivo Siekmann | Ivo Siekmann and Michael Bengfort and Horst Malchow | Invasion patterns in competitive systems | 10 pages, 9 figures, 1 table, submitted to European Physical Journal
Special Topics (EPJST) | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Stochastic reaction-diffusion equations are a popular modelling approach for
studying interacting populations in a heterogeneous environment under the
influence of environmental fluctuations. Although the theoretical basis of
alternative models such as Fokker-Planck diffusion is not less convincing,
movement of popul... | [
{
"created": "Wed, 15 Feb 2017 09:30:14 GMT",
"version": "v1"
}
] | 2017-02-16 | [
[
"Siekmann",
"Ivo",
""
],
[
"Bengfort",
"Michael",
""
],
[
"Malchow",
"Horst",
""
]
] | Stochastic reaction-diffusion equations are a popular modelling approach for studying interacting populations in a heterogeneous environment under the influence of environmental fluctuations. Although the theoretical basis of alternative models such as Fokker-Planck diffusion is not less convincing, movement of populat... |
1804.09667 | Achim Schilling | Richard Gerum, Hinrich Rahlfs, Matthias Streb, Patrick Krauss, Claus
Metzner, Konstantin Tziridis, Michael G\"unther, Holger Schulze, Walter
Kellermann, Achim Schilling | Open(G)PIAS: An open source solution for the construction of a
high-precision Acoustic-Startle-Response (ASR) setup for tinnitus screening
and threshold estimation in rodents | null | null | 10.3389/fnbeh.2019.00140 | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The acoustic startle reflex (ASR) that can be induced by a loud sound
stimulus can be used as a versatile tool to, e.g., estimate hearing thresholds
or identify subjective tinnitus percepts in rodents. These techniques are based
on the fact that the ASR amplitude can be suppressed by a pre-stimulus of
lower, non-star... | [
{
"created": "Wed, 25 Apr 2018 16:31:53 GMT",
"version": "v1"
}
] | 2019-10-01 | [
[
"Gerum",
"Richard",
""
],
[
"Rahlfs",
"Hinrich",
""
],
[
"Streb",
"Matthias",
""
],
[
"Krauss",
"Patrick",
""
],
[
"Metzner",
"Claus",
""
],
[
"Tziridis",
"Konstantin",
""
],
[
"Günther",
"Michael",
""
],... | The acoustic startle reflex (ASR) that can be induced by a loud sound stimulus can be used as a versatile tool to, e.g., estimate hearing thresholds or identify subjective tinnitus percepts in rodents. These techniques are based on the fact that the ASR amplitude can be suppressed by a pre-stimulus of lower, non-startl... |
1507.02452 | Juergen Reingruber | J\'er\^ome Cartailler and J\"urgen Reingruber | Facilitated diffusion framework for transcription factor search with
conformational changes | Article+SI, 3 figures, 25 pages total. To appear in Physical Biology
2015 | null | 10.1088/1478-3975/12/4/046012 | null | q-bio.SC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cellular responses often require the fast activation or repression of
specific genes, which depends on Transcription Factors (TFs) that have to
quickly find the promoters of these genes within a large genome. Transcription
Factors (TFs) search for their DNA promoter target by alternating between bulk
diffusion and sl... | [
{
"created": "Thu, 9 Jul 2015 10:39:16 GMT",
"version": "v1"
}
] | 2015-09-02 | [
[
"Cartailler",
"Jérôme",
""
],
[
"Reingruber",
"Jürgen",
""
]
] | Cellular responses often require the fast activation or repression of specific genes, which depends on Transcription Factors (TFs) that have to quickly find the promoters of these genes within a large genome. Transcription Factors (TFs) search for their DNA promoter target by alternating between bulk diffusion and slid... |
1702.06538 | Caitlyn Parmelee | Caitlyn M. Parmelee | Applications of Discrete Mathematics for Understanding Dynamics of
Synapses and Networks in Neuroscience | PhD Thesis | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical modeling has broad applications in neuroscience whether modeling
the dynamics of a single synapse or an entire network of neurons. In Part I, we
model vesicle replenishment and release at the photoreceptor synapse to better
understand how visual information is processed. In Part II, we explore a simple
m... | [
{
"created": "Tue, 21 Feb 2017 18:38:58 GMT",
"version": "v1"
}
] | 2017-02-23 | [
[
"Parmelee",
"Caitlyn M.",
""
]
] | Mathematical modeling has broad applications in neuroscience whether modeling the dynamics of a single synapse or an entire network of neurons. In Part I, we model vesicle replenishment and release at the photoreceptor synapse to better understand how visual information is processed. In Part II, we explore a simple mod... |
1303.1302 | David Lukatsky | Ariel Afek and David B. Lukatsky | Genome-wide organization of eukaryotic pre-initiation complex is
influenced by nonconsensus protein-DNA binding | null | Biophysical Journal 104, 1107 (2013) | 10.1016/j.bpj.2013.01.038 | null | q-bio.BM q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Genome-wide binding preferences of the key components of eukaryotic
pre-initiation complex (PIC) have been recently measured with high resolution
in Saccharomyces cerevisiae by Rhee and Pugh (Nature (2012) 483:295-301). Yet
the rules determining the PIC binding specificity remain poorly understood. In
this study we s... | [
{
"created": "Wed, 6 Mar 2013 11:12:04 GMT",
"version": "v1"
}
] | 2013-03-07 | [
[
"Afek",
"Ariel",
""
],
[
"Lukatsky",
"David B.",
""
]
] | Genome-wide binding preferences of the key components of eukaryotic pre-initiation complex (PIC) have been recently measured with high resolution in Saccharomyces cerevisiae by Rhee and Pugh (Nature (2012) 483:295-301). Yet the rules determining the PIC binding specificity remain poorly understood. In this study we sho... |
1206.6490 | Bob Eisenberg | Bob Eisenberg | Living Devices | Typos Corrected in Second Version | null | null | null | q-bio.OT physics.hist-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The physiological tradition of biological research analyzes biological
systems using reduced descriptions much as an engineer uses a 'black box'
description of an amplifier. Simple models have been used by physiologists for
a very long time. Physiologists have successfully analyzed a broad range of
biological systems... | [
{
"created": "Wed, 27 Jun 2012 21:14:56 GMT",
"version": "v1"
},
{
"created": "Thu, 5 Jul 2012 12:26:37 GMT",
"version": "v2"
}
] | 2012-07-06 | [
[
"Eisenberg",
"Bob",
""
]
] | The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long time. Physiologists have successfully analyzed a broad range of biological systems u... |
1412.1579 | Musa Mammadov | Robin J. Evans and Musa Mammadov | Dynamics of Ebola epidemics in West Africa 2014 | null | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This paper investigates the dynamics of Ebola virus transmission in West
Africa during 2014. The reproduction numbers for the total period of epidemic
and for different consequent time intervals are estimated based on a newly
suggested linear model. It contains one major variable - the average time of
infectiousness ... | [
{
"created": "Thu, 4 Dec 2014 08:05:47 GMT",
"version": "v1"
},
{
"created": "Tue, 9 Dec 2014 04:13:47 GMT",
"version": "v2"
}
] | 2014-12-10 | [
[
"Evans",
"Robin J.",
""
],
[
"Mammadov",
"Musa",
""
]
] | This paper investigates the dynamics of Ebola virus transmission in West Africa during 2014. The reproduction numbers for the total period of epidemic and for different consequent time intervals are estimated based on a newly suggested linear model. It contains one major variable - the average time of infectiousness (t... |
1707.07247 | Baohua Zhou | Baohua Zhou, David Hofmann, Itai Pinkoviezky, Samuel J. Sober, and
Ilya Nemenman | Chance, long tails, and inference: a non-Gaussian, Bayesian theory of
vocal learning in songbirds | null | null | 10.1073/pnas.1713020115 | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Traditional theories of sensorimotor learning posit that animals use sensory
error signals to find the optimal motor command in the face of Gaussian sensory
and motor noise. However, most such theories cannot explain common behavioral
observations, for example that smaller sensory errors are more readily
corrected th... | [
{
"created": "Sun, 23 Jul 2017 04:43:54 GMT",
"version": "v1"
}
] | 2022-06-08 | [
[
"Zhou",
"Baohua",
""
],
[
"Hofmann",
"David",
""
],
[
"Pinkoviezky",
"Itai",
""
],
[
"Sober",
"Samuel J.",
""
],
[
"Nemenman",
"Ilya",
""
]
] | Traditional theories of sensorimotor learning posit that animals use sensory error signals to find the optimal motor command in the face of Gaussian sensory and motor noise. However, most such theories cannot explain common behavioral observations, for example that smaller sensory errors are more readily corrected than... |
1802.01996 | Donald Forsdyke Dr. | Donald R. Forsdyke | When acting as a reproductive barrier for sympatric speciation, hybrid
sterility can only be primary | 22 pages, 3 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by-nc-sa/4.0/ | In many animals parental gametes unite to form a zygote that develops into an
adult with gonads that, in turn, produce gametes. Interruption of this germinal
cycle by prezygotic or postzygotic reproductive barriers can result in two
independent cycles, each with the potential to evolve into a new species. When
the sp... | [
{
"created": "Tue, 6 Feb 2018 15:17:17 GMT",
"version": "v1"
},
{
"created": "Sun, 18 Feb 2018 19:43:03 GMT",
"version": "v2"
},
{
"created": "Mon, 24 Sep 2018 19:45:03 GMT",
"version": "v3"
},
{
"created": "Sat, 9 Mar 2019 18:59:29 GMT",
"version": "v4"
}
] | 2019-03-12 | [
[
"Forsdyke",
"Donald R.",
""
]
] | In many animals parental gametes unite to form a zygote that develops into an adult with gonads that, in turn, produce gametes. Interruption of this germinal cycle by prezygotic or postzygotic reproductive barriers can result in two independent cycles, each with the potential to evolve into a new species. When the spec... |
2404.03718 | Diogo L. Pires | Diogo L. Pires, Mark Broom | The rules of multiplayer cooperation in networks of communities | 28 pages, 6 figures, 4 tables | null | null | null | q-bio.PE physics.soc-ph | http://creativecommons.org/licenses/by/4.0/ | Community organization permeates both social and biological complex systems.
To study its interplay with behavior emergence, we model mobile structured
populations with multiplayer interactions. We derive general analytical methods
for evolutionary dynamics under high home fidelity when populations
self-organize into... | [
{
"created": "Thu, 4 Apr 2024 18:00:00 GMT",
"version": "v1"
}
] | 2024-04-08 | [
[
"Pires",
"Diogo L.",
""
],
[
"Broom",
"Mark",
""
]
] | Community organization permeates both social and biological complex systems. To study its interplay with behavior emergence, we model mobile structured populations with multiplayer interactions. We derive general analytical methods for evolutionary dynamics under high home fidelity when populations self-organize into n... |
2007.11968 | Justyna Signerska-Rynkowska | Jonathan Rubin, Justyna Signerska-Rynkowska, Jonathan D. Touboul | Type III Responses to Transient Inputs in Hybrid Nonlinear Neuron Models | null | null | null | null | q-bio.NC math.DS nlin.AO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Experimental characterization of neuronal dynamics involves recording both of
spontaneous activity patterns and of responses to transient and sustained
inputs. While much theoretical attention has been devoted to the spontaneous
activity of neurons, less is known about the dynamic mechanisms shaping their
responses t... | [
{
"created": "Thu, 23 Jul 2020 12:32:51 GMT",
"version": "v1"
}
] | 2020-07-24 | [
[
"Rubin",
"Jonathan",
""
],
[
"Signerska-Rynkowska",
"Justyna",
""
],
[
"Touboul",
"Jonathan D.",
""
]
] | Experimental characterization of neuronal dynamics involves recording both of spontaneous activity patterns and of responses to transient and sustained inputs. While much theoretical attention has been devoted to the spontaneous activity of neurons, less is known about the dynamic mechanisms shaping their responses to ... |
2304.01346 | Lautaro Estienne | Lautaro Estienne | Towards an Hybrid Hodgkin-Huxley Action Potential Generation Model | null | null | 10.1109/RPIC53795.2021.9648523 | null | q-bio.NC cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Mathematical models for the generation of the action potential can improve
the understanding of physiological mechanisms that are consequence of the
electrical activity in neurons. In such models, some equations involving
empirically obtained functions of the membrane potential are usually defined.
The best known of ... | [
{
"created": "Wed, 15 Mar 2023 22:39:23 GMT",
"version": "v1"
}
] | 2023-04-05 | [
[
"Estienne",
"Lautaro",
""
]
] | Mathematical models for the generation of the action potential can improve the understanding of physiological mechanisms that are consequence of the electrical activity in neurons. In such models, some equations involving empirically obtained functions of the membrane potential are usually defined. The best known of th... |
2205.14945 | Pablo Cruz-Morales | Pablo Cruz-Morales | Functional and evolutionary genomics of the Streptomyces metabolism | 175 pages | PhD thesis, published by Cinvestav-LANGEBIO MEXICO 2013 | null | null | q-bio.GN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | This thesis is focused in the study of the evolution of the metabolic
repertoire of Streptomyces, which are renowned as proficient producers of
bioactive Natural Products (NPs). The main goal of my work was to contribute
into the understanding of the evolutionary mechanisms behind the evolution of
NP biosynthetic pat... | [
{
"created": "Mon, 30 May 2022 09:25:35 GMT",
"version": "v1"
}
] | 2022-05-31 | [
[
"Cruz-Morales",
"Pablo",
""
]
] | This thesis is focused in the study of the evolution of the metabolic repertoire of Streptomyces, which are renowned as proficient producers of bioactive Natural Products (NPs). The main goal of my work was to contribute into the understanding of the evolutionary mechanisms behind the evolution of NP biosynthetic pathw... |
2109.08261 | Alexander Kaiser | Alexander D. Kaiser, Rohan Shad, Nicole Schiavone, William Hiesinger,
Alison L. Marsden | Controlled Comparison of Simulated Hemodynamics across Tricuspid and
Bicuspid Aortic Valves | null | null | 10.1007/s10439-022-02983-4 | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Bicuspid aortic valve is the most common congenital heart defect, affecting
1-2% of the global population. Patients with bicuspid valves frequently develop
dilation and aneurysms of the ascending aorta. Both hemodynamic and genetic
factors are believed to contribute to dilation, yet the precise mechanism
underlying t... | [
{
"created": "Fri, 17 Sep 2021 00:45:25 GMT",
"version": "v1"
},
{
"created": "Wed, 13 Oct 2021 23:07:56 GMT",
"version": "v2"
},
{
"created": "Fri, 20 May 2022 20:33:02 GMT",
"version": "v3"
}
] | 2022-08-26 | [
[
"Kaiser",
"Alexander D.",
""
],
[
"Shad",
"Rohan",
""
],
[
"Schiavone",
"Nicole",
""
],
[
"Hiesinger",
"William",
""
],
[
"Marsden",
"Alison L.",
""
]
] | Bicuspid aortic valve is the most common congenital heart defect, affecting 1-2% of the global population. Patients with bicuspid valves frequently develop dilation and aneurysms of the ascending aorta. Both hemodynamic and genetic factors are believed to contribute to dilation, yet the precise mechanism underlying thi... |
1805.04975 | Brian Lee | Brian C. Lee, Meng Kuan Lin, Yan Fu, Junichi Hata, Michael I. Miller,
Partha P. Mitra | Multimodal Cross-registration and Quantification of Metric Distortions
in Whole Brain Histology of Marmoset using Diffeomorphic Mappings | null | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Whole brain neuroanatomy using tera-voxel light-microscopic data sets is of
much current interest. A fundamental problem in this field is the mapping of
individual brain data sets to a reference space. Previous work has not
rigorously quantified the distortions in brain geometry from in-vivo to ex-vivo
brains due to ... | [
{
"created": "Mon, 14 May 2018 00:36:28 GMT",
"version": "v1"
},
{
"created": "Wed, 17 Apr 2019 04:26:23 GMT",
"version": "v2"
}
] | 2019-04-18 | [
[
"Lee",
"Brian C.",
""
],
[
"Lin",
"Meng Kuan",
""
],
[
"Fu",
"Yan",
""
],
[
"Hata",
"Junichi",
""
],
[
"Miller",
"Michael I.",
""
],
[
"Mitra",
"Partha P.",
""
]
] | Whole brain neuroanatomy using tera-voxel light-microscopic data sets is of much current interest. A fundamental problem in this field is the mapping of individual brain data sets to a reference space. Previous work has not rigorously quantified the distortions in brain geometry from in-vivo to ex-vivo brains due to th... |
1902.10604 | Peter Zeidman | Peter Zeidman, Amirhossein Jafarian, Mohamed L. Seghier, Vladimir
Litvak, Hayriye Cagnan, Cathy J. Price, Karl J. Friston | A tutorial on group effective connectivity analysis, part 2: second
level analysis with PEB | null | null | 10.1016/j.neuroimage.2019.06.032 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This tutorial provides a worked example of using Dynamic Causal Modelling
(DCM) and Parametric Empirical Bayes (PEB) to characterise inter-subject
variability in neural circuitry (effective connectivity). This involves
specifying a hierarchical model with two or more levels. At the first level,
state space models (DC... | [
{
"created": "Wed, 27 Feb 2019 15:54:08 GMT",
"version": "v1"
}
] | 2019-07-15 | [
[
"Zeidman",
"Peter",
""
],
[
"Jafarian",
"Amirhossein",
""
],
[
"Seghier",
"Mohamed L.",
""
],
[
"Litvak",
"Vladimir",
""
],
[
"Cagnan",
"Hayriye",
""
],
[
"Price",
"Cathy J.",
""
],
[
"Friston",
"Karl J.",
... | This tutorial provides a worked example of using Dynamic Causal Modelling (DCM) and Parametric Empirical Bayes (PEB) to characterise inter-subject variability in neural circuitry (effective connectivity). This involves specifying a hierarchical model with two or more levels. At the first level, state space models (DCMs... |
1312.7283 | Nicholas Schafer | N.P. Schafer, B.L. Kim, W. Zheng, P.G. Wolynes | Learning to Fold Proteins Using Energy Landscape Theory | 95 pages, 22 figures | null | null | null | q-bio.BM cond-mat.soft cond-mat.stat-mech physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | This review is a tutorial for scientists interested in the problem of protein
structure prediction, particularly those interested in using coarse-grained
molecular dynamics models that are optimized using lessons learned from the
energy landscape theory of protein folding. We also present a review of the
results of t... | [
{
"created": "Tue, 24 Dec 2013 18:15:44 GMT",
"version": "v1"
}
] | 2014-01-06 | [
[
"Schafer",
"N. P.",
""
],
[
"Kim",
"B. L.",
""
],
[
"Zheng",
"W.",
""
],
[
"Wolynes",
"P. G.",
""
]
] | This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy landscape theory of protein folding. We also present a review of the results of the... |
1508.05226 | Mvogo Alain | Alain Mvogo, Antoine Tambue, Germain Hubert Ben-Bolie, Timoleon Crepin
Kofane | Localized modulated wave solutions in diffusive glucose-insulin systems | null | Phys. Lett. A (2016) | 10.1016/j.physleta.2016.04.039 | null | q-bio.TO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We investigate intercellular insulin dynamics in an array of diffusively
coupled pancreatic islet \b{eta}-cells. The cells are connected via gap
junction coupling, where nearest neighbor interactions are included. Through
the multiple scale expansion in the semi-discrete approximation, we show that
the insulin dynami... | [
{
"created": "Fri, 21 Aug 2015 09:47:24 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Aug 2015 08:57:50 GMT",
"version": "v2"
},
{
"created": "Thu, 27 Aug 2015 16:05:19 GMT",
"version": "v3"
},
{
"created": "Mon, 31 Aug 2015 11:59:45 GMT",
"version": "v4"
},
{
"c... | 2016-05-02 | [
[
"Mvogo",
"Alain",
""
],
[
"Tambue",
"Antoine",
""
],
[
"Ben-Bolie",
"Germain Hubert",
""
],
[
"Kofane",
"Timoleon Crepin",
""
]
] | We investigate intercellular insulin dynamics in an array of diffusively coupled pancreatic islet \b{eta}-cells. The cells are connected via gap junction coupling, where nearest neighbor interactions are included. Through the multiple scale expansion in the semi-discrete approximation, we show that the insulin dynamics... |
1904.08937 | Barak Brill | Barak Brill, Amnon Amir, Ruth Heller | Testing for differential abundance in compositional counts data, with
application to microbiome studies | null | null | null | null | q-bio.GN stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Identifying which taxa in our microbiota are associated with traits of
interest is important for advancing science and health. However, the
identification is challenging because the measured vector of taxa counts (by
amplicon sequencing) is compositional, so a change in the abundance of one
taxon in the microbiota in... | [
{
"created": "Thu, 18 Apr 2019 13:39:58 GMT",
"version": "v1"
},
{
"created": "Sun, 2 Jun 2019 11:44:29 GMT",
"version": "v2"
},
{
"created": "Thu, 1 Aug 2019 11:12:02 GMT",
"version": "v3"
},
{
"created": "Mon, 5 Aug 2019 12:56:08 GMT",
"version": "v4"
},
{
"crea... | 2020-03-31 | [
[
"Brill",
"Barak",
""
],
[
"Amir",
"Amnon",
""
],
[
"Heller",
"Ruth",
""
]
] | Identifying which taxa in our microbiota are associated with traits of interest is important for advancing science and health. However, the identification is challenging because the measured vector of taxa counts (by amplicon sequencing) is compositional, so a change in the abundance of one taxon in the microbiota indu... |
0812.1864 | Gerald Fournier | G\'erald Fournier (LEPS) | Paul Alsberg (1883-1965) et le transfert adaptatif du biologique au
technique : un pr\'ecurseur de la "cultural niche construction" ? | 16 pages | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose, in this paper, both a presentation and a discussion of Paul
Alsberg's thesis on the supposed specificity principle of human evolution. The
author maintains a difference of nature between Man and Animal relying on an
opposition between "body-adaptation" - that of the Animal - and
"extrabodily-adaptation" -... | [
{
"created": "Wed, 10 Dec 2008 08:38:18 GMT",
"version": "v1"
}
] | 2008-12-11 | [
[
"Fournier",
"Gérald",
"",
"LEPS"
]
] | We propose, in this paper, both a presentation and a discussion of Paul Alsberg's thesis on the supposed specificity principle of human evolution. The author maintains a difference of nature between Man and Animal relying on an opposition between "body-adaptation" - that of the Animal - and "extrabodily-adaptation" - t... |
2402.03410 | Daniel Schindler | Stijn T. de Vries, Laura Kley and Daniel Schindler | Use of a Golden Gate plasmid set enabling scarless MoClo-compatible
transcription unit assembly | 26 pages, 5 figures | null | null | null | q-bio.OT | http://creativecommons.org/licenses/by/4.0/ | Golden Gate cloning has become a powerful and widely used DNA assembly
method. Its modular nature and the reusability of standardized parts allow
rapid construction of transcription units and multi-gene constructs.
Importantly, its modular structure makes it compatible with laboratory
automation, allowing for systema... | [
{
"created": "Mon, 5 Feb 2024 16:04:54 GMT",
"version": "v1"
}
] | 2024-02-07 | [
[
"de Vries",
"Stijn T.",
""
],
[
"Kley",
"Laura",
""
],
[
"Schindler",
"Daniel",
""
]
] | Golden Gate cloning has become a powerful and widely used DNA assembly method. Its modular nature and the reusability of standardized parts allow rapid construction of transcription units and multi-gene constructs. Importantly, its modular structure makes it compatible with laboratory automation, allowing for systemati... |
1507.01962 | Andrea De Martino | Fabrizio Capuani, Daniele De Martino, Enzo Marinari, Andrea De Martino | Quantitative constraint-based computational model of tumor-to-stroma
coupling via lactate shuttle | 26 pages incl. supporting material | Scientific Reports 5, 11880 (2015) | 10.1038/srep11880 | null | q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Cancer cells utilize large amounts of ATP to sustain growth, relying
primarily on non-oxidative, fermentative pathways for its production. In many
types of cancers this leads, even in the presence of oxygen, to the secretion
of carbon equivalents (usually in the form of lactate) in the cell's
surroundings, a feature ... | [
{
"created": "Tue, 7 Jul 2015 20:31:24 GMT",
"version": "v1"
}
] | 2015-07-09 | [
[
"Capuani",
"Fabrizio",
""
],
[
"De Martino",
"Daniele",
""
],
[
"Marinari",
"Enzo",
""
],
[
"De Martino",
"Andrea",
""
]
] | Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even in the presence of oxygen, to the secretion of carbon equivalents (usually in the form of lactate) in the cell's surroundings, a feature kn... |
1406.2573 | Dagmar Iber | Britta Velten, Erkan Uenal and Dagmar Iber | Image-based Parameter Inference for Spatio-temporal models of
Organogenesis | NOLTA 2014: 2014 Int'l Symposium on Nonlinear Theory & its
Applications, to be held in Luzern, Switzerland from September 14-18, 2014 | null | null | null | q-bio.QM q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Advances in imaging technology now provide us with detailed 3D data on gene
expression patterns in developing embryos. This information can be used to
build predictive mathematical models of embryogenesis. Current modelling
approaches are, however, limited by lack of methods to automatically infer the
regulatory netw... | [
{
"created": "Tue, 10 Jun 2014 14:55:19 GMT",
"version": "v1"
}
] | 2014-06-11 | [
[
"Velten",
"Britta",
""
],
[
"Uenal",
"Erkan",
""
],
[
"Iber",
"Dagmar",
""
]
] | Advances in imaging technology now provide us with detailed 3D data on gene expression patterns in developing embryos. This information can be used to build predictive mathematical models of embryogenesis. Current modelling approaches are, however, limited by lack of methods to automatically infer the regulatory networ... |
1702.06463 | Aditya Gilra | Aditya Gilra, Wulfram Gerstner | Predicting non-linear dynamics by stable local learning in a recurrent
spiking neural network | null | eLife 2017;6:e28295 | 10.7554/eLife.28295 | null | q-bio.NC cs.LG cs.NE cs.SY | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Brains need to predict how the body reacts to motor commands. It is an open
question how networks of spiking neurons can learn to reproduce the non-linear
body dynamics caused by motor commands, using local, online and stable learning
rules. Here, we present a supervised learning scheme for the feedforward and
recurr... | [
{
"created": "Tue, 21 Feb 2017 16:15:34 GMT",
"version": "v1"
},
{
"created": "Wed, 26 Apr 2017 17:58:00 GMT",
"version": "v2"
}
] | 2017-11-30 | [
[
"Gilra",
"Aditya",
""
],
[
"Gerstner",
"Wulfram",
""
]
] | Brains need to predict how the body reacts to motor commands. It is an open question how networks of spiking neurons can learn to reproduce the non-linear body dynamics caused by motor commands, using local, online and stable learning rules. Here, we present a supervised learning scheme for the feedforward and recurren... |
1611.07677 | Claus Metzner | Patrick Krauss, Claus Metzner, Achim Schilling, Konstantin Tziridis,
Maximilian Traxdorf and Holger Schulze | A statistical method for analyzing and comparing spatiotemporal cortical
activation patterns | null | null | null | null | q-bio.QM q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We present a new statistical method to analyze multichannel steady-state
local field potentials (LFP) recorded within different sensory cortices of
different rodent species. Our spatiotemporal multi-dimensional cluster
statistics (MCS) method enables statistical analyzing and comparing clusters of
data points in n-di... | [
{
"created": "Wed, 23 Nov 2016 08:08:17 GMT",
"version": "v1"
}
] | 2016-11-24 | [
[
"Krauss",
"Patrick",
""
],
[
"Metzner",
"Claus",
""
],
[
"Schilling",
"Achim",
""
],
[
"Tziridis",
"Konstantin",
""
],
[
"Traxdorf",
"Maximilian",
""
],
[
"Schulze",
"Holger",
""
]
] | We present a new statistical method to analyze multichannel steady-state local field potentials (LFP) recorded within different sensory cortices of different rodent species. Our spatiotemporal multi-dimensional cluster statistics (MCS) method enables statistical analyzing and comparing clusters of data points in n-dime... |
2112.03259 | Mihir Rao | Mihir Rao | Novel Local Radiomic Bayesian Classifiers for Non-Invasive Prediction of
MGMT Methylation Status in Glioblastoma | null | null | null | null | q-bio.QM cs.CV eess.IV | http://creativecommons.org/licenses/by/4.0/ | Glioblastoma, an aggressive brain cancer, is amongst the most lethal of all
cancers. Expression of the O6-methylguanine-DNA-methyltransferase (MGMT) gene
in glioblastoma tumor tissue is of clinical importance as it has a significant
effect on the efficacy of Temozolomide, the primary chemotherapy treatment
administer... | [
{
"created": "Tue, 30 Nov 2021 04:53:23 GMT",
"version": "v1"
}
] | 2021-12-07 | [
[
"Rao",
"Mihir",
""
]
] | Glioblastoma, an aggressive brain cancer, is amongst the most lethal of all cancers. Expression of the O6-methylguanine-DNA-methyltransferase (MGMT) gene in glioblastoma tumor tissue is of clinical importance as it has a significant effect on the efficacy of Temozolomide, the primary chemotherapy treatment administered... |
1310.3518 | Mikl\'os Cs\H{u}r\"os | Mikl\'os Cs\H{u}r\"os | Non-identifiability of identity coefficients at biallelic loci | 18 pages, 3 figures, 2 tables | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Shared genealogies introduce allele dependencies in diploid genotypes, as
alleles within an individual or between different individuals will likely match
when they originate from a recent common ancestor. At a locus shared by a pair
of diploid individuals, there are nine combinatorially distinct modes of
identity-by-... | [
{
"created": "Sun, 13 Oct 2013 20:27:37 GMT",
"version": "v1"
}
] | 2013-10-15 | [
[
"Csűrös",
"Miklós",
""
]
] | Shared genealogies introduce allele dependencies in diploid genotypes, as alleles within an individual or between different individuals will likely match when they originate from a recent common ancestor. At a locus shared by a pair of diploid individuals, there are nine combinatorially distinct modes of identity-by-de... |
1012.5775 | Giangiacomo Bravo | Giangiacomo Bravo and Lucia Tamburino | Are two resources really better than one? Some unexpected results of the
availability of substitutes | 14 pages, 8 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The possibility of exploiting multiple resources is usually regarded as
positive from both the economic and the environmental point of view. However,
resource switching may also lead to unsustainable growth and, ultimately, to an
equilibrium condition which is worse than the one that could have been achieved
with a s... | [
{
"created": "Tue, 28 Dec 2010 15:10:11 GMT",
"version": "v1"
}
] | 2010-12-30 | [
[
"Bravo",
"Giangiacomo",
""
],
[
"Tamburino",
"Lucia",
""
]
] | The possibility of exploiting multiple resources is usually regarded as positive from both the economic and the environmental point of view. However, resource switching may also lead to unsustainable growth and, ultimately, to an equilibrium condition which is worse than the one that could have been achieved with a sin... |
2207.09250 | Matteo Aldeghi | Matteo Aldeghi, David E. Graff, Nathan Frey, Joseph A. Morrone, Edward
O. Pyzer-Knapp, Kirk E. Jordan, Connor W. Coley | Roughness of molecular property landscapes and its impact on
modellability | 17 pages, 6 figures, 2 tables (SI with 17 pages, 16 figures) | J. Chem. Inf. Model. 2022, 62, 19, 4660-4671 | 10.1021/acs.jcim.2c00903 | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In molecular discovery and drug design, structure-property relationships and
activity landscapes are often qualitatively or quantitatively analyzed to guide
the navigation of chemical space. The roughness (or smoothness) of these
molecular property landscapes is one of their most studied geometric
attributes, as it c... | [
{
"created": "Tue, 19 Jul 2022 13:05:59 GMT",
"version": "v1"
}
] | 2022-10-13 | [
[
"Aldeghi",
"Matteo",
""
],
[
"Graff",
"David E.",
""
],
[
"Frey",
"Nathan",
""
],
[
"Morrone",
"Joseph A.",
""
],
[
"Pyzer-Knapp",
"Edward O.",
""
],
[
"Jordan",
"Kirk E.",
""
],
[
"Coley",
"Connor W.",
""
... | In molecular discovery and drug design, structure-property relationships and activity landscapes are often qualitatively or quantitatively analyzed to guide the navigation of chemical space. The roughness (or smoothness) of these molecular property landscapes is one of their most studied geometric attributes, as it can... |
1504.00539 | R.K. Brojen Singh | G. Reenaroy Devi, R. K. Brojen Singh, Ram Ramaswamy | Synchronization efficiency in coupled stochastic oscillators: The role
of connection topology | null | null | null | null | q-bio.SC nlin.AO physics.bio-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study the efficiency of synchronization in ensembles of identical coupled
stochastic oscillator systems. By deriving a chemical Langevin equation, we
measure the rate at which the systems synchronize. The rate at which the
difference in the Hilbert phases of the systems evolve provides a suitable
order parameter, ... | [
{
"created": "Thu, 2 Apr 2015 13:12:59 GMT",
"version": "v1"
}
] | 2015-04-03 | [
[
"Devi",
"G. Reenaroy",
""
],
[
"Singh",
"R. K. Brojen",
""
],
[
"Ramaswamy",
"Ram",
""
]
] | We study the efficiency of synchronization in ensembles of identical coupled stochastic oscillator systems. By deriving a chemical Langevin equation, we measure the rate at which the systems synchronize. The rate at which the difference in the Hilbert phases of the systems evolve provides a suitable order parameter, an... |
1809.10389 | Piero Fariselli | Ludovica Montanucci, Pier Luigi Martelli, Nir Ben-Tal, Piero Fariselli | A natural upper bound to the accuracy of predicting protein stability
changes upon mutations | null | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Accurate prediction of protein stability changes upon single-site variations
(DDG) is important for protein design, as well as our understanding of the
mechanism of genetic diseases. The performance of high-throughput computational
methods to this end is evaluated mostly based on the Pearson correlation
coefficient b... | [
{
"created": "Thu, 27 Sep 2018 08:01:32 GMT",
"version": "v1"
}
] | 2018-09-28 | [
[
"Montanucci",
"Ludovica",
""
],
[
"Martelli",
"Pier Luigi",
""
],
[
"Ben-Tal",
"Nir",
""
],
[
"Fariselli",
"Piero",
""
]
] | Accurate prediction of protein stability changes upon single-site variations (DDG) is important for protein design, as well as our understanding of the mechanism of genetic diseases. The performance of high-throughput computational methods to this end is evaluated mostly based on the Pearson correlation coefficient bet... |
1606.03138 | Qinsi Wang | Qinsi Wang and Natasa Miskov-Zivanov and Bing Liu and James R. Faeder
and Michael Lotze and Edmund M. Clarke | Formal Modeling and Analysis of Pancreatic Cancer Microenvironment | null | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The focus of pancreatic cancer research has been shifted from pancreatic
cancer cells towards their microenvironment, involving pancreatic stellate
cells that interact with cancer cells and influence tumor progression. To
quantitatively understand the pancreatic cancer microenvironment, we construct
a computational m... | [
{
"created": "Thu, 9 Jun 2016 22:51:35 GMT",
"version": "v1"
}
] | 2016-06-13 | [
[
"Wang",
"Qinsi",
""
],
[
"Miskov-Zivanov",
"Natasa",
""
],
[
"Liu",
"Bing",
""
],
[
"Faeder",
"James R.",
""
],
[
"Lotze",
"Michael",
""
],
[
"Clarke",
"Edmund M.",
""
]
] | The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer cells and influence tumor progression. To quantitatively understand the pancreatic cancer microenvironment, we construct a computational mod... |
2206.05915 | Ulrich S. Schwarz | Oliver M. Drozdowski, Falko Ziebert and Ulrich S. Schwarz (Heidelberg
University, Germany) | Optogenetic switching of migration of contractile cells | 12 pages including supplement, 5 main and 4 supplemental figures | Communications Physics 6:158 (2023) | 10.1038/s42005-023-01275-0 | null | q-bio.SC cond-mat.soft | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Cell crawling on flat substrates is based on intracellular flows of the actin
cytoskeleton that are driven by both actin polymerization at the front and
myosin contractility at the back. The new experimental tool of optogenetics
makes it possible to spatially control contraction and thereby possibly also
cell migrati... | [
{
"created": "Mon, 13 Jun 2022 06:00:26 GMT",
"version": "v1"
}
] | 2023-07-04 | [
[
"Drozdowski",
"Oliver M.",
"",
"Heidelberg\n University, Germany"
],
[
"Ziebert",
"Falko",
"",
"Heidelberg\n University, Germany"
],
[
"Schwarz",
"Ulrich S.",
"",
"Heidelberg\n University, Germany"
]
] | Cell crawling on flat substrates is based on intracellular flows of the actin cytoskeleton that are driven by both actin polymerization at the front and myosin contractility at the back. The new experimental tool of optogenetics makes it possible to spatially control contraction and thereby possibly also cell migration... |
2009.06457 | Punam Bedi | Punam Bedi, Shivani, Pushkar Gole, Neha Gupta, Vinita Jindal | Projections for COVID-19 spread in India and its worst affected five
states using the Modified SEIRD and LSTM models | null | null | null | null | q-bio.PE cs.CY physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The last leg of the year 2019 gave rise to a virus named COVID-19 (Corona
Virus Disease 2019). Since the beginning of this infection in India, the
government implemented several policies and restrictions to curtail its spread
among the population. As the time passed, these restrictions were relaxed and
people were ad... | [
{
"created": "Mon, 7 Sep 2020 07:38:10 GMT",
"version": "v1"
}
] | 2020-09-15 | [
[
"Bedi",
"Punam",
""
],
[
"Shivani",
"",
""
],
[
"Gole",
"Pushkar",
""
],
[
"Gupta",
"Neha",
""
],
[
"Jindal",
"Vinita",
""
]
] | The last leg of the year 2019 gave rise to a virus named COVID-19 (Corona Virus Disease 2019). Since the beginning of this infection in India, the government implemented several policies and restrictions to curtail its spread among the population. As the time passed, these restrictions were relaxed and people were advi... |
0801.1885 | Takuma Tanaka | Takuma Tanaka, Takeshi Kaneko, Toshio Aoyagi | Recurrent infomax generates cell assemblies, avalanches, and simple
cell-like selectivity | 16 pages, 4 figures | null | null | null | q-bio.NC cond-mat.dis-nn | null | Through evolution, animals have acquired central nervous systems (CNSs),
which are extremely efficient information processing devices that improve an
animal's adaptability to various environments. It has been proposed that the
process of information maximization (infomax), which maximizes the information
transmission... | [
{
"created": "Sun, 13 Jan 2008 08:16:23 GMT",
"version": "v1"
}
] | 2008-01-15 | [
[
"Tanaka",
"Takuma",
""
],
[
"Kaneko",
"Takeshi",
""
],
[
"Aoyagi",
"Toshio",
""
]
] | Through evolution, animals have acquired central nervous systems (CNSs), which are extremely efficient information processing devices that improve an animal's adaptability to various environments. It has been proposed that the process of information maximization (infomax), which maximizes the information transmission f... |
1612.09474 | Eduardo Garc\'ia-Portugu\'es | Michael Golden, Eduardo Garc\'ia-Portugu\'es, Michael S{\o}rensen,
Kanti V. Mardia, Thomas Hamelryck, Jotun Hein | A generative angular model of protein structure evolution | 23 pages, 10 figures. Supplementary material: 5 pages, 4 figures | Molecular Biology and Evolution, 34(8):2085-2100, 2017 | 10.1093/molbev/msx137 | null | q-bio.PE stat.ME | http://creativecommons.org/licenses/by-sa/4.0/ | Recently described stochastic models of protein evolution have demonstrated
that the inclusion of structural information in addition to amino acid
sequences leads to a more reliable estimation of evolutionary parameters. We
present a generative, evolutionary model of protein structure and sequence that
is valid on a ... | [
{
"created": "Fri, 30 Dec 2016 12:25:05 GMT",
"version": "v1"
},
{
"created": "Mon, 8 May 2017 20:08:18 GMT",
"version": "v2"
},
{
"created": "Wed, 29 Apr 2020 12:45:09 GMT",
"version": "v3"
},
{
"created": "Mon, 21 Sep 2020 09:42:02 GMT",
"version": "v4"
}
] | 2020-09-22 | [
[
"Golden",
"Michael",
""
],
[
"García-Portugués",
"Eduardo",
""
],
[
"Sørensen",
"Michael",
""
],
[
"Mardia",
"Kanti V.",
""
],
[
"Hamelryck",
"Thomas",
""
],
[
"Hein",
"Jotun",
""
]
] | Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a lo... |
2211.02553 | Cristiano Capone | Cristiano Capone, Cosimo Lupo, Paolo Muratore, Pier Stanislao Paolucci | Beyond spiking networks: the computational advantages of dendritic
amplification and input segregation | arXiv admin note: substantial text overlap with arXiv:2201.11717 | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The brain can efficiently learn a wide range of tasks, motivating the search
for biologically inspired learning rules for improving current artificial
intelligence technology. Most biological models are composed of point neurons,
and cannot achieve the state-of-the-art performances in machine learning.
Recent works h... | [
{
"created": "Fri, 4 Nov 2022 16:20:15 GMT",
"version": "v1"
}
] | 2022-11-07 | [
[
"Capone",
"Cristiano",
""
],
[
"Lupo",
"Cosimo",
""
],
[
"Muratore",
"Paolo",
""
],
[
"Paolucci",
"Pier Stanislao",
""
]
] | The brain can efficiently learn a wide range of tasks, motivating the search for biologically inspired learning rules for improving current artificial intelligence technology. Most biological models are composed of point neurons, and cannot achieve the state-of-the-art performances in machine learning. Recent works hav... |
1906.08548 | Patricia Faisca | Ana Nunes and Patr\'icia FN Fa\'isca | Knotted Proteins: Tie Etiquette in Structural Biology | 33 pages, 5 figures, accepted for publication | Contemporary Mathematics (AMS) 2019 | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | A small fraction of all protein structures characterized so far are
entangled. The challenge of understanding the properties of these knotted
proteins, and the why and the how of their natural folding process, has been
taken up in the past decade with different approaches, such as structural
characterization, in vitr... | [
{
"created": "Thu, 20 Jun 2019 10:48:27 GMT",
"version": "v1"
}
] | 2019-06-21 | [
[
"Nunes",
"Ana",
""
],
[
"Faísca",
"Patrícia FN",
""
]
] | A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past decade with different approaches, such as structural characterization, in vitro ... |
0809.2585 | Razvan Radulescu M.D. | Razvan Tudor Radulescu | Contagious obesity: from adenovirus 36 to RB dysfunction | 6 pages, 1 figure | null | null | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Significant overweight represents a major health problem in industrialized
countries. Besides its known metabolic origins, this condition may also have an
infectious cause, as recently postulated. Here, it is surmised that the
potentially causative adenovirus 36 contributes to such disorder by
inactivating the retino... | [
{
"created": "Mon, 15 Sep 2008 18:43:24 GMT",
"version": "v1"
}
] | 2008-09-16 | [
[
"Radulescu",
"Razvan Tudor",
""
]
] | Significant overweight represents a major health problem in industrialized countries. Besides its known metabolic origins, this condition may also have an infectious cause, as recently postulated. Here, it is surmised that the potentially causative adenovirus 36 contributes to such disorder by inactivating the retinobl... |
2110.04335 | Evan Yip | Evan Yip, Herbert Sauro | Computing Sensitivities in Reaction Networks using Finite Difference
Methods | null | null | null | null | q-bio.QM q-bio.MN | http://creativecommons.org/licenses/by/4.0/ | In this article, we investigate various numerical methods for computing
scaled or logarithmic sensitivities of the form $\partial \ln y/\partial \ln
x$. The methods tested include One Point, Two Point, Five Point, and the
Richardson Extrapolation. The different methods were applied to a variety of
mathematical functi... | [
{
"created": "Fri, 8 Oct 2021 18:55:52 GMT",
"version": "v1"
}
] | 2021-10-12 | [
[
"Yip",
"Evan",
""
],
[
"Sauro",
"Herbert",
""
]
] | In this article, we investigate various numerical methods for computing scaled or logarithmic sensitivities of the form $\partial \ln y/\partial \ln x$. The methods tested include One Point, Two Point, Five Point, and the Richardson Extrapolation. The different methods were applied to a variety of mathematical function... |
2107.01379 | Nicholas Senofsky | Nicholas Senofsky, Justin Faber, Dolores Bozovic | Vestibular Drop Attacks and Meniere's Disease as Results of Otolithic
Membrane Damage -- A Numerical Model | 12 Pages, 4 Figures | null | null | null | q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | BACKGROUND: Meniere's Disease (MD) is a condition of the inner ear with
symptoms affecting both vestibular and hearing functions. Some patients with MD
experience vestibular drop attacks (VDAs), which are violent falls caused by
spurious vestibular signals from the utricle and/or saccule. Recent surgical
work has sho... | [
{
"created": "Sat, 3 Jul 2021 08:34:18 GMT",
"version": "v1"
}
] | 2021-07-06 | [
[
"Senofsky",
"Nicholas",
""
],
[
"Faber",
"Justin",
""
],
[
"Bozovic",
"Dolores",
""
]
] | BACKGROUND: Meniere's Disease (MD) is a condition of the inner ear with symptoms affecting both vestibular and hearing functions. Some patients with MD experience vestibular drop attacks (VDAs), which are violent falls caused by spurious vestibular signals from the utricle and/or saccule. Recent surgical work has shown... |
0804.1202 | Jean-Charles Boisson | Jean-Charles Boisson (LIFL, INRIA Lille - Nord Europe), Laetitia
Jourdan (LIFL, INRIA Futurs), El-Ghazali Talbi (INRIA Futurs) | A Preliminary Work on Evolutionary Identification of Protein Variants
and New Proteins on Grids | null | Dans AINA 2006, HIPCOMB Workshop (2006) | null | null | q-bio.BM q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein identification is one of the major task of Proteomics researchers.
Protein identification could be resumed by searching the best match between an
experimental mass spectrum and proteins from a database. Nevertheless this
approach can not be used to identify new proteins or protein variants. In this
paper an e... | [
{
"created": "Tue, 8 Apr 2008 07:49:57 GMT",
"version": "v1"
}
] | 2008-12-18 | [
[
"Boisson",
"Jean-Charles",
"",
"LIFL, INRIA Lille - Nord Europe"
],
[
"Jourdan",
"Laetitia",
"",
"LIFL, INRIA Futurs"
],
[
"Talbi",
"El-Ghazali",
"",
"INRIA Futurs"
]
] | Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach can not be used to identify new proteins or protein variants. In this paper an evo... |
2209.13045 | Anne-Florence Bitbol | Nicola Dietler, Umberto Lupo and Anne-Florence Bitbol | Impact of phylogeny on structural contact inference from protein
sequence data | 31 pages, 19 figures, 3 tables | null | null | null | q-bio.BM physics.bio-ph q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Local and global inference methods have been developed to infer structural
contacts from multiple sequence alignments of homologous proteins. They rely on
correlations in amino-acid usage at contacting sites. Because homologous
proteins share a common ancestry, their sequences also feature phylogenetic
correlations, ... | [
{
"created": "Mon, 26 Sep 2022 21:57:46 GMT",
"version": "v1"
},
{
"created": "Fri, 2 Dec 2022 14:32:43 GMT",
"version": "v2"
},
{
"created": "Thu, 5 Jan 2023 22:46:39 GMT",
"version": "v3"
}
] | 2023-01-09 | [
[
"Dietler",
"Nicola",
""
],
[
"Lupo",
"Umberto",
""
],
[
"Bitbol",
"Anne-Florence",
""
]
] | Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino-acid usage at contacting sites. Because homologous proteins share a common ancestry, their sequences also feature phylogenetic correlations, wh... |
2407.01649 | Ruidong Wu | Ruidong Wu, Ruihan Guo, Rui Wang, Shitong Luo, Yue Xu, Jiahan Li,
Jianzhu Ma, Qiang Liu, Yunan Luo, Jian Peng | FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group
Frames | null | null | null | null | q-bio.QM cs.LG | http://creativecommons.org/licenses/by/4.0/ | Despite the striking success of general protein folding models such as
AlphaFold2(AF2, Jumper et al. (2021)), the accurate computational modeling of
antibody-antigen complexes remains a challenging task. In this paper, we first
analyze AF2's primary loss function, known as the Frame Aligned Point Error
(FAPE), and ra... | [
{
"created": "Mon, 1 Jul 2024 06:47:21 GMT",
"version": "v1"
}
] | 2024-07-03 | [
[
"Wu",
"Ruidong",
""
],
[
"Guo",
"Ruihan",
""
],
[
"Wang",
"Rui",
""
],
[
"Luo",
"Shitong",
""
],
[
"Xu",
"Yue",
""
],
[
"Li",
"Jiahan",
""
],
[
"Ma",
"Jianzhu",
""
],
[
"Liu",
"Qiang",
""
... | Despite the striking success of general protein folding models such as AlphaFold2(AF2, Jumper et al. (2021)), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and rais... |
2102.11071 | Fernando Saldana PhD | Hugo Flores-Arguedas, Jos\'e Ariel Camacho-Guti\'errez, Fernando
Salda\~na | Estimating the impact of non-pharmaceutical interventions and
vaccination on the progress of the COVID-19 epidemic in Mexico: a
mathematical approach | 19 pages, 6 figures | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Non-pharmaceutical interventions have been critical in the fight against the
COVID-19 pandemic. However, these sanitary measures have been partially lifted
due to socioeconomic factors causing a worrisome rebound of the epidemic in
several countries. In this work, we assess the effectiveness of the mitigation
impleme... | [
{
"created": "Fri, 19 Feb 2021 15:26:28 GMT",
"version": "v1"
}
] | 2021-02-23 | [
[
"Flores-Arguedas",
"Hugo",
""
],
[
"Camacho-Gutiérrez",
"José Ariel",
""
],
[
"Saldaña",
"Fernando",
""
]
] | Non-pharmaceutical interventions have been critical in the fight against the COVID-19 pandemic. However, these sanitary measures have been partially lifted due to socioeconomic factors causing a worrisome rebound of the epidemic in several countries. In this work, we assess the effectiveness of the mitigation implement... |
1611.00110 | Susan Khor | Susan Khor | Folding with a protein's native shortcut network | Major modifications and additions | null | null | null | q-bio.MN q-bio.BM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | A complex network approach to protein folding is proposed. The graph object
is the network of shortcut edges present in a native-state protein (SCN0).
Although SCN0s are found via an intuitive message passing algorithm (S.
Milgram, Psychology Today, May 1967 pp. 61-67), they are meaningful enough that
the logarithm f... | [
{
"created": "Tue, 1 Nov 2016 02:43:28 GMT",
"version": "v1"
},
{
"created": "Wed, 25 Jan 2017 05:30:59 GMT",
"version": "v2"
},
{
"created": "Tue, 2 May 2017 17:38:18 GMT",
"version": "v3"
},
{
"created": "Wed, 13 Dec 2017 22:25:31 GMT",
"version": "v4"
}
] | 2017-12-15 | [
[
"Khor",
"Susan",
""
]
] | A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram, Psychology Today, May 1967 pp. 61-67), they are meaningful enough that the logarithm for... |
q-bio/0407022 | Bari\c{s} \"Oztop | B. \"Oztop, M. R. Ejtehadi, S. S. Plotkin | Protein folding rates correlate with heterogeneity of folding mechanism | 11 pages, 3 figures, 1 table | null | 10.1103/PhysRevLett.93.208105 | null | q-bio.QM q-bio.BM | null | By observing trends in the folding kinetics of experimental 2-state proteins
at their transition midpoints, and by observing trends in the barrier heights
of numerous simulations of coarse grained, C-alpha model, Go proteins, we show
that folding rates correlate with the degree of heterogeneity in the formation
of na... | [
{
"created": "Wed, 14 Jul 2004 22:33:59 GMT",
"version": "v1"
}
] | 2009-11-10 | [
[
"Öztop",
"B.",
""
],
[
"Ejtehadi",
"M. R.",
""
],
[
"Plotkin",
"S. S.",
""
]
] | By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that folding rates correlate with the degree of heterogeneity in the formation of nati... |
1911.05316 | Ziqi Ke | Ziqi Ke, Haris Vikalo | A Graph Auto-Encoder for Haplotype Assembly and Viral Quasispecies
Reconstruction | null | null | null | null | q-bio.GN cs.AI cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Reconstructing components of a genomic mixture from data obtained by means of
DNA sequencing is a challenging problem encountered in a variety of
applications including single individual haplotyping and studies of viral
communities. High-throughput DNA sequencing platforms oversample mixture
components to provide mas... | [
{
"created": "Wed, 13 Nov 2019 06:32:48 GMT",
"version": "v1"
}
] | 2019-11-14 | [
[
"Ke",
"Ziqi",
""
],
[
"Vikalo",
"Haris",
""
]
] | Reconstructing components of a genomic mixture from data obtained by means of DNA sequencing is a challenging problem encountered in a variety of applications including single individual haplotyping and studies of viral communities. High-throughput DNA sequencing platforms oversample mixture components to provide massi... |
1306.5262 | Fabrizio De Vico Fallani | Fabrizio De Vico Fallani, Floriana Pichiorri, Giovanni Morone, Marco
Molinari, Fabio Babiloni, Febo Cincotti, Donatella Mattia | Multiscale Topological Properties Of Functional Brain Networks During
Motor Imagery After Stroke | Neuroimage, accepted manuscript (unedited version) available online
19-June-2013 | null | 10.1016/j.neuroimage.2013.06.039 | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In recent years, network analyses have been used to evaluate brain
reorganization following stroke. However, many studies have often focused on
single topological scales, leading to an incomplete model of how focal brain
lesions affect multiple network properties simultaneously and how changes on
smaller scales influ... | [
{
"created": "Fri, 21 Jun 2013 22:02:49 GMT",
"version": "v1"
}
] | 2014-09-10 | [
[
"Fallani",
"Fabrizio De Vico",
""
],
[
"Pichiorri",
"Floriana",
""
],
[
"Morone",
"Giovanni",
""
],
[
"Molinari",
"Marco",
""
],
[
"Babiloni",
"Fabio",
""
],
[
"Cincotti",
"Febo",
""
],
[
"Mattia",
"Donatella",... | In recent years, network analyses have been used to evaluate brain reorganization following stroke. However, many studies have often focused on single topological scales, leading to an incomplete model of how focal brain lesions affect multiple network properties simultaneously and how changes on smaller scales influen... |
1312.1876 | Vince Grolmusz | Balazs Szalkai, Vince K. Grolmusz, Vince I. Grolmusz, Coalition
Against Major Diseases | Identifying Combinatorial Biomarkers by Association Rule Mining in the
CAMD Alzheimer's Database | null | null | null | null | q-bio.NC stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Background: The concept of combinatorial biomarkers was conceived around
2010: it was noticed that simple biomarkers are often inadequate for
recognizing and characterizing complex diseases.
Methods: Here we present an algorithmic search method for complex biomarkers
which may predict or indicate Alzheimer's diseas... | [
{
"created": "Fri, 6 Dec 2013 14:55:53 GMT",
"version": "v1"
}
] | 2013-12-09 | [
[
"Szalkai",
"Balazs",
""
],
[
"Grolmusz",
"Vince K.",
""
],
[
"Grolmusz",
"Vince I.",
""
],
[
"Diseases",
"Coalition Against Major",
""
]
] | Background: The concept of combinatorial biomarkers was conceived around 2010: it was noticed that simple biomarkers are often inadequate for recognizing and characterizing complex diseases. Methods: Here we present an algorithmic search method for complex biomarkers which may predict or indicate Alzheimer's disease (A... |
2109.09801 | Rebekah Rogers | Brandon A. Turner, Theresa R. Miorin, Nicholas B. Stewart, Robert W.
Reid, Cathy C. Moore, Rebekah L. Rogers | Chromosomal rearrangements as a source of local adaptation in island
Drosophila | 53 pages; 3 tables, 6 figures main; 1 table, 20 figures supplement | null | null | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Chromosomal rearrangements act as a source of genetic novelty by shuffling
DNA throughout the genome. These mutations can produce chimeric genes, induce
de novo gene formation, or alter gene expression changes for existing genes.
Here, we explore how these mutations may serve as agents of evolutionary change
as popul... | [
{
"created": "Mon, 20 Sep 2021 19:19:16 GMT",
"version": "v1"
}
] | 2021-09-22 | [
[
"Turner",
"Brandon A.",
""
],
[
"Miorin",
"Theresa R.",
""
],
[
"Stewart",
"Nicholas B.",
""
],
[
"Reid",
"Robert W.",
""
],
[
"Moore",
"Cathy C.",
""
],
[
"Rogers",
"Rebekah L.",
""
]
] | Chromosomal rearrangements act as a source of genetic novelty by shuffling DNA throughout the genome. These mutations can produce chimeric genes, induce de novo gene formation, or alter gene expression changes for existing genes. Here, we explore how these mutations may serve as agents of evolutionary change as populat... |
1304.4856 | Ulrike Ober | Ulrike Ober, Alexander Malinowski, Martin Schlather, Henner Simianer | The Expected Linkage Disequilibrium in Finite Populations Revisited | 32 pages, 11 Figures, formatting edits compared to v1 (pdf-links) | null | null | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The expected level of linkage disequilibrium (LD) in a finite ideal
population at equilibrium is of relevance for many applications in population
and quantitative genetics. Several recursion formulae have been proposed during
the last decades, whose derivations mostly contain heuristic parts and
therefore remain math... | [
{
"created": "Wed, 17 Apr 2013 15:15:38 GMT",
"version": "v1"
},
{
"created": "Thu, 18 Apr 2013 11:15:17 GMT",
"version": "v2"
}
] | 2013-04-19 | [
[
"Ober",
"Ulrike",
""
],
[
"Malinowski",
"Alexander",
""
],
[
"Schlather",
"Martin",
""
],
[
"Simianer",
"Henner",
""
]
] | The expected level of linkage disequilibrium (LD) in a finite ideal population at equilibrium is of relevance for many applications in population and quantitative genetics. Several recursion formulae have been proposed during the last decades, whose derivations mostly contain heuristic parts and therefore remain mathem... |
2308.15264 | Sangita Swapnasrita | Charlotte A Veser, Aur\'elie MF Carlier, Silvia M Mih\u{a}il\u{a},
Sangita Swapnasrita | Embracing Sex-specific Differences in Engineered Kidney Models for
Enhanced Biological Understanding | 44 pages, 6 figures | null | null | null | q-bio.TO | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In vitro models play a crucial role in advancing our understanding of
biological processes, disease mechanisms, and developing screening platforms
for drug discovery. Kidneys play an instrumental role in transport and
elimination of drugs and toxins. However, despite the well-established
patient-to-patient difference... | [
{
"created": "Tue, 29 Aug 2023 12:48:20 GMT",
"version": "v1"
}
] | 2023-08-30 | [
[
"Veser",
"Charlotte A",
""
],
[
"Carlier",
"Aurélie MF",
""
],
[
"Mihăilă",
"Silvia M",
""
],
[
"Swapnasrita",
"Sangita",
""
]
] | In vitro models play a crucial role in advancing our understanding of biological processes, disease mechanisms, and developing screening platforms for drug discovery. Kidneys play an instrumental role in transport and elimination of drugs and toxins. However, despite the well-established patient-to-patient differences ... |
1507.02119 | Louxin Zhang | Andreas D.M. Gunawan, Bhaskar DasGupta, Louxin Zhang | Locating a Tree in a Reticulation-Visible Network in Cubic Time | 25 pages, 3 figures | null | null | null | q-bio.PE cs.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this work, we answer an open problem in the study of phylogenetic
networks. Phylogenetic trees are rooted binary trees in which all edges are
directed away from the root, whereas phylogenetic networks are rooted acyclic
digraphs. For the purpose of evolutionary model validation, biologists often
want to know wheth... | [
{
"created": "Wed, 8 Jul 2015 12:18:03 GMT",
"version": "v1"
},
{
"created": "Wed, 11 Nov 2015 04:29:05 GMT",
"version": "v2"
}
] | 2015-11-12 | [
[
"Gunawan",
"Andreas D. M.",
""
],
[
"DasGupta",
"Bhaskar",
""
],
[
"Zhang",
"Louxin",
""
]
] | In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the purpose of evolutionary model validation, biologists often want to know whether... |
q-bio/0410022 | Supratim Sengupta | Supratim Sengupta and Paul G. Higgs | A Unified Model of Codon Reassignment in Alternative Genetic Codes | Latex file, 11 pages including 5 ps figures; revised version; to
appear in 'Genetics' | Genetics 170 (2005) 831-840 | null | null | q-bio.PE | null | Many modified genetic codes are found in specific genomes in which one or
more codons have been reassigned to a different amino acid from that in the
canonical code. We present a model that unifies four possible mechanisms for
reassignment, based on the observation that reassignment involves a gain and a
loss. The lo... | [
{
"created": "Tue, 19 Oct 2004 22:12:54 GMT",
"version": "v1"
},
{
"created": "Sun, 24 Oct 2004 21:26:18 GMT",
"version": "v2"
},
{
"created": "Wed, 2 Feb 2005 19:26:39 GMT",
"version": "v3"
}
] | 2007-07-17 | [
[
"Sengupta",
"Supratim",
""
],
[
"Higgs",
"Paul G.",
""
]
] | Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment, based on the observation that reassignment involves a gain and a loss. The loss... |
1804.11081 | Michael B\"orsch | Ilka Starke, Gary D. Glick, Michael B\"orsch | Visualizing mitochondrial FoF1-ATP synthase as the target of the
immunomodulatory drug Bz-423 | 10 pages, 2 figures | null | null | null | q-bio.SC q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Targeting the mitochondrial enzyme FoF1-ATP synthase and modulating its
catalytic activities with small molecules is a promising new approach for
treatment of autoimmune diseases. The immuno-modulatory compound Bz-423 is such
a drug that binds to subunit OSCP of the mitochondrial FoF1-ATP synthase and
induces apoptos... | [
{
"created": "Mon, 30 Apr 2018 08:36:05 GMT",
"version": "v1"
}
] | 2018-05-01 | [
[
"Starke",
"Ilka",
""
],
[
"Glick",
"Gary D.",
""
],
[
"Börsch",
"Michael",
""
]
] | Targeting the mitochondrial enzyme FoF1-ATP synthase and modulating its catalytic activities with small molecules is a promising new approach for treatment of autoimmune diseases. The immuno-modulatory compound Bz-423 is such a drug that binds to subunit OSCP of the mitochondrial FoF1-ATP synthase and induces apoptosis... |
q-bio/0611037 | Tatyana Sharpee | Tatyana O. Sharpee, Hiroki Sugihara, Andrei V. Kurgansky, Sergei P.
Rebrik, Michael P. Stryker, and Kenneth D. Miller | Adaptive Filtering Enhances Information Transmission in Visual Cortex | 20 pages, 11 figures, includes supplementary information | Nature, vol. 439, pp. 936- 942 (02/23/2006) | 10.1038/nature04519 | null | q-bio.NC | null | Sensory neuroscience seeks to understand how the brain encodes natural
environments. However, neural coding has largely been studied using simplified
stimuli. In order to assess whether the brain's coding strategy depend on the
stimulus ensemble, we apply a new information-theoretic method that allows
unbiased calcul... | [
{
"created": "Thu, 9 Nov 2006 19:15:12 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Sharpee",
"Tatyana O.",
""
],
[
"Sugihara",
"Hiroki",
""
],
[
"Kurgansky",
"Andrei V.",
""
],
[
"Rebrik",
"Sergei P.",
""
],
[
"Stryker",
"Michael P.",
""
],
[
"Miller",
"Kenneth D.",
""
]
] | Sensory neuroscience seeks to understand how the brain encodes natural environments. However, neural coding has largely been studied using simplified stimuli. In order to assess whether the brain's coding strategy depend on the stimulus ensemble, we apply a new information-theoretic method that allows unbiased calculat... |
2002.02530 | Kevin McCloskey | Kevin McCloskey, Eric A. Sigel, Steven Kearnes, Ling Xue, Xia Tian,
Dennis Moccia, Diana Gikunju, Sana Bazzaz, Betty Chan, Matthew A. Clark, John
W. Cuozzo, Marie-Aude Gui\'e, John P. Guilinger, Christelle Huguet,
Christopher D. Hupp, Anthony D. Keefe, Christopher J. Mulhern, Ying Zhang,
and Patrick Riley | Machine learning on DNA-encoded libraries: A new paradigm for
hit-finding | null | null | 10.1021/acs.jmedchem.0c00452 | null | q-bio.QM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | DNA-encoded small molecule libraries (DELs) have enabled discovery of novel
inhibitors for many distinct protein targets of therapeutic value through
screening of libraries with up to billions of unique small molecules. We
demonstrate a new approach applying machine learning to DEL selection data by
identifying activ... | [
{
"created": "Fri, 31 Jan 2020 19:31:23 GMT",
"version": "v1"
}
] | 2020-06-15 | [
[
"McCloskey",
"Kevin",
""
],
[
"Sigel",
"Eric A.",
""
],
[
"Kearnes",
"Steven",
""
],
[
"Xue",
"Ling",
""
],
[
"Tian",
"Xia",
""
],
[
"Moccia",
"Dennis",
""
],
[
"Gikunju",
"Diana",
""
],
[
"Bazzaz",... | DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value through screening of libraries with up to billions of unique small molecules. We demonstrate a new approach applying machine learning to DEL selection data by identifying active ... |
1902.04614 | Melinda Liu Perkins | Melinda Liu Perkins, Murat Arcak | A Spatial Filtering Approach to Biological Patterning | null | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Interactions between neighboring cells are essential for generating or
refining patterns in a number of biological systems. We propose a discrete
filtering approach to predict how networks of cells modulate spatially varying
input signals to produce more complicated or precise output signals. The
interconnections bet... | [
{
"created": "Fri, 8 Feb 2019 23:32:13 GMT",
"version": "v1"
}
] | 2019-02-14 | [
[
"Perkins",
"Melinda Liu",
""
],
[
"Arcak",
"Murat",
""
]
] | Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals to produce more complicated or precise output signals. The interconnections betwe... |
1809.03835 | Mohammad Sultan Alam | Mohammad Sultan Alam | Analysis of Sequence Polymorphism of LINEs and SINEs in Entamoeba
histolytica | M.Tech Dissertation (2010-2012) under the guidance of Prof. Alok
Bhattacharya and Prof. Ram Ramaswamy in JNU. 59 pages, 28 figures, 8 tables | null | null | null | q-bio.PE cs.CE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The goal of this dissertation is to study the sequence polymorphism in
retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a
concept of equilibrium (stationary), has been used to understand the behaviour
of these elements. Two datasets of retrotransposons of Entamoeba histolytica
have been u... | [
{
"created": "Mon, 10 Sep 2018 10:33:39 GMT",
"version": "v1"
}
] | 2018-09-12 | [
[
"Alam",
"Mohammad Sultan",
""
]
] | The goal of this dissertation is to study the sequence polymorphism in retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a concept of equilibrium (stationary), has been used to understand the behaviour of these elements. Two datasets of retrotransposons of Entamoeba histolytica have been use... |
1407.4440 | Jack Heal | J. W. Heal, S. A. Wells, R. B. Freedman and R. A. R\"omer | Characterizing the folding core of the cyclophilin A - cyclosporin A
complex II: improving folding core predictions by including mobility | 9 pages, 6 figures | Biophys J. 108, 1739-1746 (2015) | 10.1016/j.bpj.2015.02.017 | null | q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Determining the folding core of a protein yields information about its
folding process and dynamics. The experimental procedures for identifying the
amino acids which make up the folding core include hydrogen-deuterium exchange
and $\Phi$-value analysis and can be expensive and time consuming. As such
there is a desi... | [
{
"created": "Wed, 16 Jul 2014 19:37:16 GMT",
"version": "v1"
}
] | 2015-04-09 | [
[
"Heal",
"J. W.",
""
],
[
"Wells",
"S. A.",
""
],
[
"Freedman",
"R. B.",
""
],
[
"Römer",
"R. A.",
""
]
] | Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids which make up the folding core include hydrogen-deuterium exchange and $\Phi$-value analysis and can be expensive and time consuming. As such there is a desire... |
1705.10647 | Jing Tu | Junji Li, Na Lu, Xulian Shi, Yi Qiao, Liang Chen, Mengqin Duan, Yong
Hou, Qinyu Ge, Yuhan Tao, Jing Tu, Zuhong Lu | MDA in Capillary for Whole Genome Amplification | null | Anal. Chem. 2017, 89, 10147-10152 | 10.1021/acs.analchem.7b02183 | null | q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Whole genome amplification (WGA) plays an important role in sample
preparation of low-input templates for high-throughput sequencing. Multiple
displacement amplification (MDA), a popular isothermal WGA method, suffers a
major hurdle of highly uneven amplification. Optimizations have been made in
the past by separatin... | [
{
"created": "Tue, 30 May 2017 13:53:25 GMT",
"version": "v1"
}
] | 2019-02-12 | [
[
"Li",
"Junji",
""
],
[
"Lu",
"Na",
""
],
[
"Shi",
"Xulian",
""
],
[
"Qiao",
"Yi",
""
],
[
"Chen",
"Liang",
""
],
[
"Duan",
"Mengqin",
""
],
[
"Hou",
"Yong",
""
],
[
"Ge",
"Qinyu",
""
],
... | Whole genome amplification (WGA) plays an important role in sample preparation of low-input templates for high-throughput sequencing. Multiple displacement amplification (MDA), a popular isothermal WGA method, suffers a major hurdle of highly uneven amplification. Optimizations have been made in the past by separating ... |
1109.2209 | Wilfred Ndifon | Wilfred Ndifon | Supporting information for: New methods for analyzing serological data
with applications to influenza surveillance | null | Influenza and Other Respiratory Viruses 5:206--212, 2011 | 10.1111/j.1750-2659.2010.00192.x | null | q-bio.PE q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | For decades, the hemagglutination-inhibition (HI) assay has been used in
epidemiological and basic biological studies of influenza viruses. The
mechanistic basis of the assay results (called titers) is not well understood.
The first part of this document describes a biophysical model of HI that
illuminates the mechan... | [
{
"created": "Sat, 10 Sep 2011 10:32:11 GMT",
"version": "v1"
}
] | 2011-09-13 | [
[
"Ndifon",
"Wilfred",
""
]
] | For decades, the hemagglutination-inhibition (HI) assay has been used in epidemiological and basic biological studies of influenza viruses. The mechanistic basis of the assay results (called titers) is not well understood. The first part of this document describes a biophysical model of HI that illuminates the mechanis... |
2204.11954 | Takeshi Yasui | Shogo Miyamura, Ryo Oe, Takuya Nakahara, Shota Okada, Shuji Taue, Yu
Tokizane, Takeo Minamikawa, Taka-aki Yano, Kunihiro Otsuka, Ayuko Sakane,
Takuya Sasaki, Koji Yasutomo, Taira Kajisa, and Takeshi Yasui | Rapid, high-sensitivity detection of biomolecules using dual-comb
biosensing: application to the SARS-CoV-2 nucleocapsid protein | 42 pages, 6 figures, 2 tables | Scientific Reports, volume 13, Article number: 14541 (2023) | 10.1038/s41598-023-41436-3 | null | q-bio.QM physics.optics | http://creativecommons.org/licenses/by/4.0/ | Rapid, sensitive detection of biomolecules is important for improved testing
methods for viruses as well as biomarkers and environmental hormones. For
example, testing for SARS-CoV-2 is essential in the fight against the COVID-19
pandemic. Reverse-transcription polymerase chain reaction (RT-PCR) is the
current standa... | [
{
"created": "Mon, 25 Apr 2022 20:30:34 GMT",
"version": "v1"
},
{
"created": "Tue, 26 Jul 2022 21:18:36 GMT",
"version": "v2"
}
] | 2023-10-24 | [
[
"Miyamura",
"Shogo",
""
],
[
"Oe",
"Ryo",
""
],
[
"Nakahara",
"Takuya",
""
],
[
"Okada",
"Shota",
""
],
[
"Taue",
"Shuji",
""
],
[
"Tokizane",
"Yu",
""
],
[
"Minamikawa",
"Takeo",
""
],
[
"Yano",
... | Rapid, sensitive detection of biomolecules is important for improved testing methods for viruses as well as biomarkers and environmental hormones. For example, testing for SARS-CoV-2 is essential in the fight against the COVID-19 pandemic. Reverse-transcription polymerase chain reaction (RT-PCR) is the current standard... |
q-bio/0309020 | Eli Eisenberg | Eli Eisenberg and Erez Y. Levanon | Human housekeeping genes are compact | null | Trends in Genetics, vol. 19, 362-365 (2003) | null | null | q-bio.GN | null | We identify a set of 575 human genes that are expressed in all conditions
tested in a publicly available database of microarray results. Based on this
common occurrence, the set is expected to be rich in "housekeeping" genes,
showing constitutive expression in all tissues. We compare selected aspects of
their genomic... | [
{
"created": "Tue, 30 Sep 2003 11:26:28 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Eisenberg",
"Eli",
""
],
[
"Levanon",
"Erez Y.",
""
]
] | We identify a set of 575 human genes that are expressed in all conditions tested in a publicly available database of microarray results. Based on this common occurrence, the set is expected to be rich in "housekeeping" genes, showing constitutive expression in all tissues. We compare selected aspects of their genomic s... |
1406.1793 | Jerome Vanclay | Jerome K. Vanclay | Planning horizons and end conditions for sustained yield studies in
continuous cover forests | 8 pages, 1 figure, 54 references, Ecological Indicators (2014) | Ecological Indicators 48 (2015) 436-439 | 10.1016/j.ecolind.2014.09.012 | null | q-bio.QM q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The contemporary forestry preoccupation with non-declining even-flow during
yield simulations detracts from more important questions about the constraints
that should bind the end of a simulation. Whilst long simulations help to
convey a sense of sustainability, they are inferior to stronger indicators such
as the op... | [
{
"created": "Sat, 7 Jun 2014 09:50:01 GMT",
"version": "v1"
},
{
"created": "Tue, 2 Sep 2014 14:25:37 GMT",
"version": "v2"
},
{
"created": "Thu, 11 Sep 2014 03:00:05 GMT",
"version": "v3"
}
] | 2014-10-07 | [
[
"Vanclay",
"Jerome K.",
""
]
] | The contemporary forestry preoccupation with non-declining even-flow during yield simulations detracts from more important questions about the constraints that should bind the end of a simulation. Whilst long simulations help to convey a sense of sustainability, they are inferior to stronger indicators such as the opti... |
0905.0701 | Ernest Montbrio | Alex Roxin, Ernest Montbrio | How effective delays shape oscillatory dynamics in neuronal networks | 59 pages, 25 figures | Physica D 240, (2011) 323-345 | 10.1016/j.physd.2010.09.009 | null | q-bio.NC nlin.PS q-bio.QM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Synaptic, dendritic and single-cell kinetics generate significant time delays
that shape the dynamics of large networks of spiking neurons. Previous work has
shown that such effective delays can be taken into account with a rate model
through the addition of an explicit, fixed delay [Roxin et al. PRL 238103
(2005)]. ... | [
{
"created": "Wed, 6 May 2009 16:15:10 GMT",
"version": "v1"
},
{
"created": "Thu, 13 Aug 2009 21:49:46 GMT",
"version": "v2"
},
{
"created": "Tue, 17 May 2011 14:56:45 GMT",
"version": "v3"
}
] | 2014-01-31 | [
[
"Roxin",
"Alex",
""
],
[
"Montbrio",
"Ernest",
""
]
] | Synaptic, dendritic and single-cell kinetics generate significant time delays that shape the dynamics of large networks of spiking neurons. Previous work has shown that such effective delays can be taken into account with a rate model through the addition of an explicit, fixed delay [Roxin et al. PRL 238103 (2005)]. He... |
2101.11400 | Jose Marie Antonio Minoza | Jose Marie Antonio Minoza, Vena Pearl Bongolan and Joshua Frankie Rayo | COVID-19 Agent-Based Model with Multi-objective Optimization for Vaccine
Distribution | null | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | Now that SARS-CoV-2 (COVID-19) vaccines are developed, it is very important
to plan its distribution strategy. In this paper, we formulated a
multi-objective linear programming model to optimize vaccine distribution and
applied it to the agent-based version of our age-stratified and
quarantine-modified SEIR with non-... | [
{
"created": "Wed, 27 Jan 2021 18:07:10 GMT",
"version": "v1"
}
] | 2021-01-28 | [
[
"Minoza",
"Jose Marie Antonio",
""
],
[
"Bongolan",
"Vena Pearl",
""
],
[
"Rayo",
"Joshua Frankie",
""
]
] | Now that SARS-CoV-2 (COVID-19) vaccines are developed, it is very important to plan its distribution strategy. In this paper, we formulated a multi-objective linear programming model to optimize vaccine distribution and applied it to the agent-based version of our age-stratified and quarantine-modified SEIR with non-li... |
1601.05388 | Steven N. Evans | Joshua G. Schraiber and Steven N. Evans and Montgomery Slatkin | Bayesian inference of natural selection from allele frequency time
series | 27 pages | null | null | null | q-bio.PE math.ST stat.TH | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The advent of accessible ancient DNA technology now allows the direct
ascertainment of allele frequencies in ancestral populations, thereby enabling
the use of allele frequency time series to detect and estimate natural
selection. Such direct observations of allele frequency dynamics are expected
to be more powerful ... | [
{
"created": "Wed, 20 Jan 2016 19:48:24 GMT",
"version": "v1"
}
] | 2016-01-21 | [
[
"Schraiber",
"Joshua G.",
""
],
[
"Evans",
"Steven N.",
""
],
[
"Slatkin",
"Montgomery",
""
]
] | The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such direct observations of allele frequency dynamics are expected to be more powerful th... |
2105.13705 | Arthur Prat-Carrabin | Arthur Prat-Carrabin and Michael Woodford | Bias and variance of the Bayesian-mean decoder | Accepted at NeurIPS 2021. 12 pages, 2 figures. Supplementary
Materials: 7 pages, 1 figure | Advances in Neural Information Processing Systems 34 (NeurIPS
2021) | null | null | q-bio.NC | http://creativecommons.org/licenses/by-nc-nd/4.0/ | Perception, in theoretical neuroscience, has been modeled as the encoding of
external stimuli into internal signals, which are then decoded. The Bayesian
mean is an important decoder, as it is optimal for purposes of both estimation
and discrimination. We present widely-applicable approximations to the bias and
to th... | [
{
"created": "Fri, 28 May 2021 09:59:37 GMT",
"version": "v1"
},
{
"created": "Mon, 6 Dec 2021 15:41:28 GMT",
"version": "v2"
}
] | 2022-03-03 | [
[
"Prat-Carrabin",
"Arthur",
""
],
[
"Woodford",
"Michael",
""
]
] | Perception, in theoretical neuroscience, has been modeled as the encoding of external stimuli into internal signals, which are then decoded. The Bayesian mean is an important decoder, as it is optimal for purposes of both estimation and discrimination. We present widely-applicable approximations to the bias and to the ... |
1309.1108 | Nicholas Glykos | Panagiotis I. Koukos and Nicholas M. Glykos | On the application of Good-Turing statistics to quantify convergence of
biomolecular simulations | null | null | 10.1021/ci4005817 | null | q-bio.QM q-bio.BM | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Quantifying convergence and sufficient sampling of macromolecular molecular
dynamics simulations is more often than not a source of controversy (and of
various ad hoc solutions) in the field. Clearly, the only reasonable,
consistent and satisfying way to infer convergence (or otherwise) of a
molecular dynamics trajec... | [
{
"created": "Wed, 4 Sep 2013 17:13:25 GMT",
"version": "v1"
},
{
"created": "Sat, 7 Sep 2013 09:19:41 GMT",
"version": "v2"
}
] | 2013-12-23 | [
[
"Koukos",
"Panagiotis I.",
""
],
[
"Glykos",
"Nicholas M.",
""
]
] | Quantifying convergence and sufficient sampling of macromolecular molecular dynamics simulations is more often than not a source of controversy (and of various ad hoc solutions) in the field. Clearly, the only reasonable, consistent and satisfying way to infer convergence (or otherwise) of a molecular dynamics trajecto... |
2306.16520 | Jean Pierre G\'omez Matos | Jean Pierre Gomez | Nonparametric causal discovery with applications to cancer
bioinformatics | Diploma Thesis in Computer Science. In spanish. Supervised by Drs
Gabriel Gil and Augusto Gonzalez. 74 pages, 11 figures, 12 tables | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by/4.0/ | Many natural phenomena are intrinsically causal. The discovery of the
cause-effect relationships implicit in these processes can help us to
understand and describe them more effectively, which boils down to causal
discovery about the data and variables that describe them. However, causal
discovery is not an easy task... | [
{
"created": "Wed, 28 Jun 2023 19:26:19 GMT",
"version": "v1"
},
{
"created": "Mon, 8 Jan 2024 05:11:44 GMT",
"version": "v2"
}
] | 2024-01-09 | [
[
"Gomez",
"Jean Pierre",
""
]
] | Many natural phenomena are intrinsically causal. The discovery of the cause-effect relationships implicit in these processes can help us to understand and describe them more effectively, which boils down to causal discovery about the data and variables that describe them. However, causal discovery is not an easy task. ... |
1805.04072 | Jamie Oaks | Jamie R. Oaks, Kerry A. Cobb, Vladimir N. Minin, Adam D. Leach\'e | Marginal likelihoods in phylogenetics: a review of methods and
applications | 33 pages, 3 figures | null | null | null | q-bio.PE | http://creativecommons.org/licenses/by/4.0/ | By providing a framework of accounting for the shared ancestry inherent to
all life, phylogenetics is becoming the statistical foundation of biology. The
importance of model choice continues to grow as phylogenetic models continue to
increase in complexity to better capture micro and macroevolutionary processes.
In a... | [
{
"created": "Thu, 10 May 2018 17:26:09 GMT",
"version": "v1"
},
{
"created": "Mon, 21 Jan 2019 20:47:57 GMT",
"version": "v2"
},
{
"created": "Fri, 1 Feb 2019 20:03:10 GMT",
"version": "v3"
}
] | 2019-02-05 | [
[
"Oaks",
"Jamie R.",
""
],
[
"Cobb",
"Kerry A.",
""
],
[
"Minin",
"Vladimir N.",
""
],
[
"Leaché",
"Adam D.",
""
]
] | By providing a framework of accounting for the shared ancestry inherent to all life, phylogenetics is becoming the statistical foundation of biology. The importance of model choice continues to grow as phylogenetic models continue to increase in complexity to better capture micro and macroevolutionary processes. In a B... |
1504.04756 | James P. Crutchfield | Sarah E. Marzen and Michael R. DeWeese and James P. Crutchfield | Time Resolution Dependence of Information Measures for Spiking Neurons:
Atoms, Scaling, and Universality | 20 pages, 6 figures;
http://csc.ucdavis.edu/~cmg/compmech/pubs/trdctim.htm | null | null | null | q-bio.NC cond-mat.dis-nn cs.NE math.PR nlin.CD | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mutual information between stimulus and spike-train response is commonly
used to monitor neural coding efficiency, but neuronal computation broadly
conceived requires more refined and targeted information measures of
input-output joint processes. A first step towards that larger goal is to
develop information mea... | [
{
"created": "Sat, 18 Apr 2015 20:14:19 GMT",
"version": "v1"
}
] | 2015-04-21 | [
[
"Marzen",
"Sarah E.",
""
],
[
"DeWeese",
"Michael R.",
""
],
[
"Crutchfield",
"James P.",
""
]
] | The mutual information between stimulus and spike-train response is commonly used to monitor neural coding efficiency, but neuronal computation broadly conceived requires more refined and targeted information measures of input-output joint processes. A first step towards that larger goal is to develop information measu... |
1704.07280 | Joseba Dalmau | Joseba Dalmau | Asymptotic behavior of Eigen's quasispecies model | null | null | null | null | q-bio.PE math.DS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We study Eigen's quasispecies model in the asymptotic regime where the length
of the genotypes goes to infinity and the mutation probability goes to 0. A
limiting infinite system of differential equations is obtained. We prove the
convergence of the trajectories, as well as the convergence of the equilibrium
solution... | [
{
"created": "Mon, 24 Apr 2017 15:21:45 GMT",
"version": "v1"
}
] | 2017-04-25 | [
[
"Dalmau",
"Joseba",
""
]
] | We study Eigen's quasispecies model in the asymptotic regime where the length of the genotypes goes to infinity and the mutation probability goes to 0. A limiting infinite system of differential equations is obtained. We prove the convergence of the trajectories, as well as the convergence of the equilibrium solutions.... |
2106.07292 | Andreas Ott | Michael Bleher, Lukas Hahn, Maximilian Neumann, Juan Angel
Patino-Galindo, Mathieu Carriere, Ulrich Bauer, Raul Rabadan, Andreas Ott | Topological data analysis identifies emerging adaptive mutations in
SARS-CoV-2 | Major revisions; new analyses added | null | null | null | q-bio.PE cs.CG q-bio.GN q-bio.QM | http://creativecommons.org/licenses/by-nc-nd/4.0/ | The COVID-19 pandemic has initiated an unprecedented worldwide effort to
characterize its evolution through the mapping of mutations of the coronavirus
SARS-CoV-2. The early identification of mutations that could confer adaptive
advantages to the virus, such as higher infectivity or immune evasion, is of
paramount im... | [
{
"created": "Mon, 14 Jun 2021 10:38:40 GMT",
"version": "v1"
},
{
"created": "Mon, 14 Feb 2022 16:45:27 GMT",
"version": "v2"
},
{
"created": "Fri, 25 Aug 2023 22:38:26 GMT",
"version": "v3"
}
] | 2023-08-29 | [
[
"Bleher",
"Michael",
""
],
[
"Hahn",
"Lukas",
""
],
[
"Neumann",
"Maximilian",
""
],
[
"Patino-Galindo",
"Juan Angel",
""
],
[
"Carriere",
"Mathieu",
""
],
[
"Bauer",
"Ulrich",
""
],
[
"Rabadan",
"Raul",
""... | The COVID-19 pandemic has initiated an unprecedented worldwide effort to characterize its evolution through the mapping of mutations of the coronavirus SARS-CoV-2. The early identification of mutations that could confer adaptive advantages to the virus, such as higher infectivity or immune evasion, is of paramount impo... |
1512.08309 | Rakesh Malladi | Rakesh Malladi, Giridhar Kalamangalam, Nitin Tandon and Behnaam
Aazhang | Identifying Seizure Onset Zone from the Causal Connectivity Inferred
Using Directed Information | This paper is accepted for publication in IEEE Journal of Selected
Topics in Signal Processing, special issue on Advanced Signal Processing in
Brain Networks, October 2016. 16 pages, 11 figures and 2 tables | null | 10.1109/JSTSP.2016.2601485 | null | q-bio.NC cs.IT math.IT stat.ME | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In this paper, we developed a model-based and a data-driven estimator for
directed information (DI) to infer the causal connectivity graph between
electrocorticographic (ECoG) signals recorded from brain and to identify the
seizure onset zone (SOZ) in epileptic patients. Directed information, an
information theoretic... | [
{
"created": "Mon, 28 Dec 2015 02:53:24 GMT",
"version": "v1"
},
{
"created": "Tue, 16 Aug 2016 19:21:32 GMT",
"version": "v2"
}
] | 2016-11-03 | [
[
"Malladi",
"Rakesh",
""
],
[
"Kalamangalam",
"Giridhar",
""
],
[
"Tandon",
"Nitin",
""
],
[
"Aazhang",
"Behnaam",
""
]
] | In this paper, we developed a model-based and a data-driven estimator for directed information (DI) to infer the causal connectivity graph between electrocorticographic (ECoG) signals recorded from brain and to identify the seizure onset zone (SOZ) in epileptic patients. Directed information, an information theoretic q... |
2301.10203 | Sandra Nestler | Sandra Nestler, Moritz Helias and Matthieu Gilson | Neuronal architecture extracts statistical temporal patterns | null | null | 10.1103/PhysRevResearch.5.033177 | null | q-bio.NC cond-mat.dis-nn cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuronal systems need to process temporal signals. We here show how
higher-order temporal (co-)fluctuations can be employed to represent and
process information. Concretely, we demonstrate that a simple biologically
inspired feedforward neuronal model is able to extract information from up to
the third order cumulant... | [
{
"created": "Tue, 24 Jan 2023 18:21:33 GMT",
"version": "v1"
}
] | 2023-09-13 | [
[
"Nestler",
"Sandra",
""
],
[
"Helias",
"Moritz",
""
],
[
"Gilson",
"Matthieu",
""
]
] | Neuronal systems need to process temporal signals. We here show how higher-order temporal (co-)fluctuations can be employed to represent and process information. Concretely, we demonstrate that a simple biologically inspired feedforward neuronal model is able to extract information from up to the third order cumulant t... |
1909.08421 | Anindya Ghose Choudhury | Anindya Ghose-Choudhury and Partha Guha | Reduction and Hamiltonian aspects of a model for virus-tumour
interaction in oncolytic virotherapy | null | null | null | null | q-bio.PE math-ph math.MP nlin.SI | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyse the Hamiltonian structure of a system of first-order ordinary
differential equations used for modeling the interaction of an oncolytic virus
with a tumour cell population. The analysis is based on the existence of a
Jacobi Last Multiplier for the system and a time dependent first integral. For
suitable con... | [
{
"created": "Tue, 17 Sep 2019 04:56:32 GMT",
"version": "v1"
}
] | 2019-09-19 | [
[
"Ghose-Choudhury",
"Anindya",
""
],
[
"Guha",
"Partha",
""
]
] | We analyse the Hamiltonian structure of a system of first-order ordinary differential equations used for modeling the interaction of an oncolytic virus with a tumour cell population. The analysis is based on the existence of a Jacobi Last Multiplier for the system and a time dependent first integral. For suitable condi... |
1503.03445 | H. G. Solari | M. L. Fern\'andez, M. Otero, N. Schweigmann, H. G. Solari | A mathematically assisted reconstruction of the initial focus of the
yellow fever outbreak in Buenos Aires (1871) | 25 pages, 12 figures | Papers in Physics 5, 050002 (2013) | 10.4279/PIP.050002 | null | q-bio.PE | http://creativecommons.org/licenses/by/3.0/ | We discuss the historic mortality record corresponding to the initial focus
of the yellow fever epidemic outbreak registered in Buenos Aires during the
year 1871 as compared to simulations of a stochastic population dynamics model.
This model incorporates the biology of the urban vector of yellow fever, the
mosquito ... | [
{
"created": "Thu, 18 Dec 2014 10:35:53 GMT",
"version": "v1"
}
] | 2015-03-12 | [
[
"Fernández",
"M. L.",
""
],
[
"Otero",
"M.",
""
],
[
"Schweigmann",
"N.",
""
],
[
"Solari",
"H. G.",
""
]
] | We discuss the historic mortality record corresponding to the initial focus of the yellow fever epidemic outbreak registered in Buenos Aires during the year 1871 as compared to simulations of a stochastic population dynamics model. This model incorporates the biology of the urban vector of yellow fever, the mosquito Ae... |
2004.10118 | Alexei Vasetsky | E.M. Koltsova, E.S. Kurkina, A.M. Vasetsky | Mathematical Modeling of the Spread of COVID-19 in Moscow and Russian
Regions | null | null | null | null | q-bio.PE physics.soc-ph | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | To model the spread of COVID-19 coronavirus in Russian regions and in Moscow,
a discrete logistic equation describing the increase in the number of cases is
used. To check the adequacy of the mathematical model, the simulation results
were compared with the spread of coronavirus in China, in a number of European
and ... | [
{
"created": "Tue, 21 Apr 2020 15:55:38 GMT",
"version": "v1"
}
] | 2020-04-22 | [
[
"Koltsova",
"E. M.",
""
],
[
"Kurkina",
"E. S.",
""
],
[
"Vasetsky",
"A. M.",
""
]
] | To model the spread of COVID-19 coronavirus in Russian regions and in Moscow, a discrete logistic equation describing the increase in the number of cases is used. To check the adequacy of the mathematical model, the simulation results were compared with the spread of coronavirus in China, in a number of European and As... |
2212.11485 | An Mo | An Mo, Viktoriia Kamska, Fernanda Bribiesca-Contreras, Janet
Hauptmann, Monica Daley, Alexander Badri-Spr\"owitz | Biophysical Simulation Reveals the Mechanics of the Avian Lumbosacral
Organ | For supplementary materials, see https://doi.org/10.17617/3.VTHO81 | null | null | null | q-bio.TO | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The lumbosacral organ (LSO) is a lumbosacral spinal canal morphology that is
universally and uniquely found in birds. Recent studies suggested an
intraspinal mechanosensor function that relies on the compliant motion of soft
tissue in the spinal cord fluid. It has not yet been possible to observe LSO
soft tissue moti... | [
{
"created": "Thu, 22 Dec 2022 05:00:20 GMT",
"version": "v1"
},
{
"created": "Wed, 17 May 2023 08:16:32 GMT",
"version": "v2"
}
] | 2023-05-18 | [
[
"Mo",
"An",
""
],
[
"Kamska",
"Viktoriia",
""
],
[
"Bribiesca-Contreras",
"Fernanda",
""
],
[
"Hauptmann",
"Janet",
""
],
[
"Daley",
"Monica",
""
],
[
"Badri-Spröwitz",
"Alexander",
""
]
] | The lumbosacral organ (LSO) is a lumbosacral spinal canal morphology that is universally and uniquely found in birds. Recent studies suggested an intraspinal mechanosensor function that relies on the compliant motion of soft tissue in the spinal cord fluid. It has not yet been possible to observe LSO soft tissue motion... |
1410.8091 | Luca Canzian | Luca Canzian, Kun Zhao, Gerard C. L. Wong, Mihaela van der Schaar | A Dynamic Network Formation Model for Understanding Bacterial
Self-Organization into Micro-Colonies | null | null | null | null | q-bio.PE cs.GT q-bio.MN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We propose a general parametrizable model to capture the dynamic interaction
among bacteria in the formation of micro-colonies. micro-colonies represent the
first social step towards the formation of structured multicellular communities
known as bacterial biofilms, which protect the bacteria against antimicrobials.
I... | [
{
"created": "Thu, 23 Oct 2014 19:20:43 GMT",
"version": "v1"
}
] | 2014-10-30 | [
[
"Canzian",
"Luca",
""
],
[
"Zhao",
"Kun",
""
],
[
"Wong",
"Gerard C. L.",
""
],
[
"van der Schaar",
"Mihaela",
""
]
] | We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities known as bacterial biofilms, which protect the bacteria against antimicrobials. In ... |
2007.00577 | Wasiur R. KhudaBukhsh | Wasiur R. KhudaBukhsh and Hye-Won Kang and Eben Kenah and Grzegorz A.
Rempala | Incorporating age and delay into models for biophysical systems | 21 pages, 4 figures. Under review for publication | null | null | null | q-bio.PE | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | In many biological systems, chemical reactions or changes in a physical state
are assumed to occur instantaneously. For describing the dynamics of those
systems, Markov models that require exponentially distributed inter-event times
have been used widely. However, some biophysical processes such as gene
transcription... | [
{
"created": "Wed, 1 Jul 2020 16:03:50 GMT",
"version": "v1"
},
{
"created": "Fri, 3 Jul 2020 01:26:22 GMT",
"version": "v2"
}
] | 2020-07-06 | [
[
"KhudaBukhsh",
"Wasiur R.",
""
],
[
"Kang",
"Hye-Won",
""
],
[
"Kenah",
"Eben",
""
],
[
"Rempala",
"Grzegorz A.",
""
]
] | In many biological systems, chemical reactions or changes in a physical state are assumed to occur instantaneously. For describing the dynamics of those systems, Markov models that require exponentially distributed inter-event times have been used widely. However, some biophysical processes such as gene transcription a... |
1110.3742 | Heather Harrington | Heather A. Harrington, Micha{\l} Komorowski, Mariano Beguerisse
D\'iaz, Gian Michele Ratto, and Michael P.H. Stumpf | Dependence of MAPK mediated signaling on Erk isoforms and differences in
nuclear shuttling | 19 pages, 7 figures | null | null | null | q-bio.CB | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | The mitogen activated protein kinase (MAPK) family of proteins is involved in
regulating cellular fate activities such as proliferation, differentiation and
apoptosis. Their fundamental importance has attracted considerable attention on
different aspects of the MAPK signaling dynamics; this is particularly true for
t... | [
{
"created": "Mon, 17 Oct 2011 17:53:11 GMT",
"version": "v1"
},
{
"created": "Fri, 18 Nov 2011 17:42:56 GMT",
"version": "v2"
}
] | 2015-03-19 | [
[
"Harrington",
"Heather A.",
""
],
[
"Komorowski",
"Michał",
""
],
[
"Díaz",
"Mariano Beguerisse",
""
],
[
"Ratto",
"Gian Michele",
""
],
[
"Stumpf",
"Michael P. H.",
""
]
] | The mitogen activated protein kinase (MAPK) family of proteins is involved in regulating cellular fate activities such as proliferation, differentiation and apoptosis. Their fundamental importance has attracted considerable attention on different aspects of the MAPK signaling dynamics; this is particularly true for the... |
2208.12552 | Lucas Daniel Wittwer | Lucas Daniel Wittwer, Felix Reichel, Paul M\"uller, Jochen Guck,
Sebastian Aland | A New Hyperelastic Lookup Table for RT-DC | null | null | null | null | q-bio.QM | http://creativecommons.org/licenses/by-nc-sa/4.0/ | Real-time deformability cytometry (RT-DC) is an established method that
quantifies features like size, shape, and stiffness for whole cell populations
on a single-cell level in real time. To extract the cell stiffness, a lookup
table (LUT) disentangles the experimentally derived steady state cell
deformation and the ... | [
{
"created": "Fri, 26 Aug 2022 10:07:16 GMT",
"version": "v1"
}
] | 2022-08-29 | [
[
"Wittwer",
"Lucas Daniel",
""
],
[
"Reichel",
"Felix",
""
],
[
"Müller",
"Paul",
""
],
[
"Guck",
"Jochen",
""
],
[
"Aland",
"Sebastian",
""
]
] | Real-time deformability cytometry (RT-DC) is an established method that quantifies features like size, shape, and stiffness for whole cell populations on a single-cell level in real time. To extract the cell stiffness, a lookup table (LUT) disentangles the experimentally derived steady state cell deformation and the pr... |
q-bio/0309002 | Eduardo D. Sontag | David Angeli and Eduardo D. Sontag | Multi-Stability in Monotone Input/Output Systems | See http://www.math.rutgers.edu/~sontag for related work; to appear
in Systems and Control Letters | null | null | null | q-bio.QM q-bio.MN | null | This paper studies the emergence of multi-stability and hysteresis in those
systems that arise, under positive feedback, starting from monotone systems
with well-defined steady-state responses. Such feedback configurations appear
routinely in several fields of application, and especially in biology.
Characterizations... | [
{
"created": "Tue, 16 Sep 2003 14:08:09 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Angeli",
"David",
""
],
[
"Sontag",
"Eduardo D.",
""
]
] | This paper studies the emergence of multi-stability and hysteresis in those systems that arise, under positive feedback, starting from monotone systems with well-defined steady-state responses. Such feedback configurations appear routinely in several fields of application, and especially in biology. Characterizations o... |
2403.15284 | Andrea Arnold | Sara Amato, Andrea Arnold | A data-informed mathematical model of microglial cell dynamics during
ischemic stroke in the middle cerebral artery | 25 pages, 8 figures | null | null | null | q-bio.CB q-bio.QM stat.AP | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Neuroinflammation immediately follows the onset of ischemic stroke in the
middle cerebral artery. During this process, microglial cells are activated in
and recruited to the penumbra. Microglial cells can be activated into two
different phenotypes: M1, which can worsen brain injury; or M2, which can aid
in long-term ... | [
{
"created": "Fri, 22 Mar 2024 15:31:07 GMT",
"version": "v1"
}
] | 2024-03-25 | [
[
"Amato",
"Sara",
""
],
[
"Arnold",
"Andrea",
""
]
] | Neuroinflammation immediately follows the onset of ischemic stroke in the middle cerebral artery. During this process, microglial cells are activated in and recruited to the penumbra. Microglial cells can be activated into two different phenotypes: M1, which can worsen brain injury; or M2, which can aid in long-term re... |
1903.07394 | Keith Willison | Keith R Willison | An intracellular calcium frequency code model extended to the Riemann
zeta function | 11 pages, 5 figures,1 table, 1 appendix | null | null | null | q-bio.NC | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We have used the Nernst chemical potential treatment to couple the time
domains of sodium and calcium ion channel opening and closing rates to the
spatial domain of the diffusing waves of the travelling calcium ions inside
single cells. The model is plausibly evolvable with respect to the origins of
the molecular com... | [
{
"created": "Thu, 7 Feb 2019 12:04:20 GMT",
"version": "v1"
}
] | 2019-03-19 | [
[
"Willison",
"Keith R",
""
]
] | We have used the Nernst chemical potential treatment to couple the time domains of sodium and calcium ion channel opening and closing rates to the spatial domain of the diffusing waves of the travelling calcium ions inside single cells. The model is plausibly evolvable with respect to the origins of the molecular compo... |
2206.01685 | Charlotte Caucheteux | Juliette Millet, Charlotte Caucheteux, Pierre Orhan, Yves Boubenec,
Alexandre Gramfort, Ewan Dunbar, Christophe Pallier, Jean-Remi King | Toward a realistic model of speech processing in the brain with
self-supervised learning | Accepted to NeurIPS 2022 | Neural Information Processing Systems (NeurIPS), 2022 | null | null | q-bio.NC cs.AI cs.CL | http://creativecommons.org/licenses/by/4.0/ | Several deep neural networks have recently been shown to generate activations
similar to those of the brain in response to the same input. These algorithms,
however, remain largely implausible: they require (1) extraordinarily large
amounts of data, (2) unobtainable supervised labels, (3) textual rather than
raw sens... | [
{
"created": "Fri, 3 Jun 2022 17:01:46 GMT",
"version": "v1"
},
{
"created": "Mon, 20 Mar 2023 10:11:41 GMT",
"version": "v2"
}
] | 2023-03-21 | [
[
"Millet",
"Juliette",
""
],
[
"Caucheteux",
"Charlotte",
""
],
[
"Orhan",
"Pierre",
""
],
[
"Boubenec",
"Yves",
""
],
[
"Gramfort",
"Alexandre",
""
],
[
"Dunbar",
"Ewan",
""
],
[
"Pallier",
"Christophe",
""... | Several deep neural networks have recently been shown to generate activations similar to those of the brain in response to the same input. These algorithms, however, remain largely implausible: they require (1) extraordinarily large amounts of data, (2) unobtainable supervised labels, (3) textual rather than raw sensor... |
2108.01514 | Kai Wu | Kai Wu, Vinit Kumar Chugh, Venkatramana D. Krishna, Arturo di
Girolamo, Yongqiang Andrew Wang, Renata Saha, Shuang Liang, Maxim C-J
Cheeran, and Jian-Ping Wang | One-step, Wash-free, Nanoparticle Clustering-based Magnetic Particle
Spectroscopy (MPS) Bioassay Method for Detection of SARS-CoV-2 Spike and
Nucleocapsid Proteins in Liquid Phase | 35 pages, 14 figures | null | null | null | q-bio.QM physics.bio-ph | http://creativecommons.org/licenses/by/4.0/ | With the ongoing global pandemic of coronavirus disease 2019 (COVID-19),
there is an increasing quest for more accessible, easy-to-use, rapid,
inexpensive, and high accuracy diagnostic tools. Traditional disease diagnostic
methods such as qRT-PCR (quantitative reverse transcription-PCR) and ELISA
(enzyme-linked immun... | [
{
"created": "Sun, 1 Aug 2021 15:59:17 GMT",
"version": "v1"
}
] | 2021-08-04 | [
[
"Wu",
"Kai",
""
],
[
"Chugh",
"Vinit Kumar",
""
],
[
"Krishna",
"Venkatramana D.",
""
],
[
"di Girolamo",
"Arturo",
""
],
[
"Wang",
"Yongqiang Andrew",
""
],
[
"Saha",
"Renata",
""
],
[
"Liang",
"Shuang",
"... | With the ongoing global pandemic of coronavirus disease 2019 (COVID-19), there is an increasing quest for more accessible, easy-to-use, rapid, inexpensive, and high accuracy diagnostic tools. Traditional disease diagnostic methods such as qRT-PCR (quantitative reverse transcription-PCR) and ELISA (enzyme-linked immunos... |
1902.03739 | Nasim Nematzadeh | Nasim Nematzadeh, David M. W. Powers | Prediction of Dashed Caf\'e Wall illusion by the Classical Receptive
Field Model | 6 pages, 6 figures. Accepted in ICECCE2020 conference | null | null | null | q-bio.NC cs.CV | http://creativecommons.org/publicdomain/zero/1.0/ | The Caf\'e Wall illusion is one of a class of tilt illusions where lines that
are parallel appear to be tilted. We demonstrate that a simple Differences of
Gaussian model provides an explanatory mechanism for the illusory tilt
perceived in a family of Caf\'e Wall illusion generalizes to the dashed
versions of Caf\'e ... | [
{
"created": "Fri, 8 Feb 2019 03:23:22 GMT",
"version": "v1"
},
{
"created": "Mon, 11 May 2020 07:59:53 GMT",
"version": "v2"
}
] | 2020-05-12 | [
[
"Nematzadeh",
"Nasim",
""
],
[
"Powers",
"David M. W.",
""
]
] | The Caf\'e Wall illusion is one of a class of tilt illusions where lines that are parallel appear to be tilted. We demonstrate that a simple Differences of Gaussian model provides an explanatory mechanism for the illusory tilt perceived in a family of Caf\'e Wall illusion generalizes to the dashed versions of Caf\'e Wa... |
1105.4751 | Armita Nourmohammad | Armita Nourmohammad and Michael Laessig | Formation of regulatory modules by local sequence duplication | null | null | 10.1371/journal.pcbi.1002167 | null | q-bio.PE q-bio.GN | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Turnover of regulatory sequence and function is an important part of
molecular evolution. But what are the modes of sequence evolution leading to
rapid formation and loss of regulatory sites? Here, we show that a large
fraction of neighboring transcription factor binding sites in the fly genome
have formed from a com... | [
{
"created": "Tue, 24 May 2011 12:48:06 GMT",
"version": "v1"
}
] | 2015-03-19 | [
[
"Nourmohammad",
"Armita",
""
],
[
"Laessig",
"Michael",
""
]
] | Turnover of regulatory sequence and function is an important part of molecular evolution. But what are the modes of sequence evolution leading to rapid formation and loss of regulatory sites? Here, we show that a large fraction of neighboring transcription factor binding sites in the fly genome have formed from a commo... |
2209.06865 | Gabriele Scheler | Gabriele Scheler | Sketch of a novel approach to a neural model | null | null | null | null | q-bio.NC cond-mat.dis-nn cs.AI cs.NE q-bio.MN | http://creativecommons.org/licenses/by-nc-nd/4.0/ | In this paper, we lay out a novel model of neuroplasticity in the form of a
horizontal-vertical integration model of neural processing. The horizontal
plane consists of a network of neurons connected by adaptive transmission
links. This fits with standard computational neuroscience approaches. Each
individual neuron ... | [
{
"created": "Wed, 14 Sep 2022 18:28:39 GMT",
"version": "v1"
},
{
"created": "Sat, 8 Oct 2022 08:43:55 GMT",
"version": "v2"
},
{
"created": "Tue, 1 Nov 2022 13:20:18 GMT",
"version": "v3"
},
{
"created": "Thu, 10 Nov 2022 09:14:05 GMT",
"version": "v4"
},
{
"cre... | 2023-01-09 | [
[
"Scheler",
"Gabriele",
""
]
] | In this paper, we lay out a novel model of neuroplasticity in the form of a horizontal-vertical integration model of neural processing. The horizontal plane consists of a network of neurons connected by adaptive transmission links. This fits with standard computational neuroscience approaches. Each individual neuron al... |
1410.1475 | Zachary Kilpatrick PhD | Paul C. Bressloff and Zachary P. Kilpatrick | Nonlinear Langevin equations for wandering patterns in stochastic neural
fields | 28 pages, 8 figures | null | null | null | q-bio.NC nlin.PS | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | We analyze the effects of additive, spatially extended noise on
spatiotemporal patterns in continuum neural fields. Our main focus is how
fluctuations impact patterns when they are weakly coupled to an external
stimulus or another equivalent pattern. Showing the generality of our approach,
we study both propagating f... | [
{
"created": "Mon, 6 Oct 2014 17:49:00 GMT",
"version": "v1"
},
{
"created": "Wed, 7 Jan 2015 03:29:00 GMT",
"version": "v2"
}
] | 2015-01-08 | [
[
"Bressloff",
"Paul C.",
""
],
[
"Kilpatrick",
"Zachary P.",
""
]
] | We analyze the effects of additive, spatially extended noise on spatiotemporal patterns in continuum neural fields. Our main focus is how fluctuations impact patterns when they are weakly coupled to an external stimulus or another equivalent pattern. Showing the generality of our approach, we study both propagating fro... |
2407.00566 | Shruthi Viswanath | Kartik Majila, Shreyas Arvindekar, Muskaan Jindal, and Shruthi
Viswanath | Frontiers in integrative structural biology: modeling disordered
proteins and utilizing in situ data | null | null | null | null | q-bio.BM | http://creativecommons.org/licenses/by-sa/4.0/ | Integrative modeling enables structure determination for large macromolecular
assemblies by combining data from multiple sources of experiment data with
theoretical and computational predictions. Recent advancements in AI-based
structure prediction and electron cryo-microscopy have sparked renewed
enthusiasm for inte... | [
{
"created": "Sun, 30 Jun 2024 02:36:45 GMT",
"version": "v1"
}
] | 2024-07-02 | [
[
"Majila",
"Kartik",
""
],
[
"Arvindekar",
"Shreyas",
""
],
[
"Jindal",
"Muskaan",
""
],
[
"Viswanath",
"Shruthi",
""
]
] | Integrative modeling enables structure determination for large macromolecular assemblies by combining data from multiple sources of experiment data with theoretical and computational predictions. Recent advancements in AI-based structure prediction and electron cryo-microscopy have sparked renewed enthusiasm for integr... |
2402.00054 | Arshmeet Kaur | Arshmeet Kaur and Morteza Sarmadi | Predicting loss-of-function impact of genetic mutations: a machine
learning approach | Index Terms: Machine Learning, Prediction Algorithms, Supervised
Learning, Support vector machines, K-Nearest Neighbors, RANSAC, Decision
Trees, Random Forest, Ge- netic mutations, LoFtool, Next Generation
Sequencing | null | 10.54364/AAIML.2024.41119 | null | q-bio.GN cs.LG stat.AP | http://creativecommons.org/licenses/by/4.0/ | The innovation of next-generation sequencing (NGS) techniques has
significantly reduced the price of genome sequencing, lowering barriers to
future medical research; it is now feasible to apply genome sequencing to
studies where it would have previously been cost-inefficient. Identifying
damaging or pathogenic mutati... | [
{
"created": "Fri, 26 Jan 2024 19:27:38 GMT",
"version": "v1"
}
] | 2024-06-06 | [
[
"Kaur",
"Arshmeet",
""
],
[
"Sarmadi",
"Morteza",
""
]
] | The innovation of next-generation sequencing (NGS) techniques has significantly reduced the price of genome sequencing, lowering barriers to future medical research; it is now feasible to apply genome sequencing to studies where it would have previously been cost-inefficient. Identifying damaging or pathogenic mutation... |
2402.05856 | Zuobai Zhang | Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aur\'elie Lozano,
Payel Das, Jian Tang | Structure-Informed Protein Language Model | null | null | null | null | q-bio.BM cs.LG | http://arxiv.org/licenses/nonexclusive-distrib/1.0/ | Protein language models are a powerful tool for learning protein
representations through pre-training on vast protein sequence datasets.
However, traditional protein language models lack explicit structural
supervision, despite its relevance to protein function. To address this issue,
we introduce the integration of ... | [
{
"created": "Wed, 7 Feb 2024 09:32:35 GMT",
"version": "v1"
}
] | 2024-02-09 | [
[
"Zhang",
"Zuobai",
""
],
[
"Lu",
"Jiarui",
""
],
[
"Chenthamarakshan",
"Vijil",
""
],
[
"Lozano",
"Aurélie",
""
],
[
"Das",
"Payel",
""
],
[
"Tang",
"Jian",
""
]
] | Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of re... |
q-bio/0310012 | Zoltan Dezso | Zoltan Dezso, Zoltan N. Oltvai and Albert-Laszlo Barabasi | Bioinformatics analysis of experimentally determined protein complexes
in the yeast, S. cerevisiae | Supplementary Material available at http://www.nd.edu/~networks | null | null | null | q-bio.MN cond-mat q-bio.GN | null | Many important cellular functions are implemented by protein complexes that
act as sophisticated molecular machines of varying size and temporal stability.
Here we demonstrate quantitatively that protein complexes in the yeast,
Saccharomyces cerevisiae, are comprised of a core in which subunits are highly
coexpressed... | [
{
"created": "Fri, 10 Oct 2003 17:08:54 GMT",
"version": "v1"
}
] | 2007-05-23 | [
[
"Dezso",
"Zoltan",
""
],
[
"Oltvai",
"Zoltan N.",
""
],
[
"Barabasi",
"Albert-Laszlo",
""
]
] | Many important cellular functions are implemented by protein complexes that act as sophisticated molecular machines of varying size and temporal stability. Here we demonstrate quantitatively that protein complexes in the yeast, Saccharomyces cerevisiae, are comprised of a core in which subunits are highly coexpressed, ... |
2310.08774 | Ming Yang Zhou | Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghuai
Zhang, Moksh Jain, Mathieu Blanchette, Yoshua Bengio | PhyloGFN: Phylogenetic inference with generative flow networks | null | null | null | null | q-bio.PE cs.LG stat.ML | http://creativecommons.org/licenses/by/4.0/ | Phylogenetics is a branch of computational biology that studies the
evolutionary relationships among biological entities. Its long history and
numerous applications notwithstanding, inference of phylogenetic trees from
sequence data remains challenging: the high complexity of tree space poses a
significant obstacle f... | [
{
"created": "Thu, 12 Oct 2023 23:46:08 GMT",
"version": "v1"
},
{
"created": "Mon, 25 Mar 2024 00:18:35 GMT",
"version": "v2"
}
] | 2024-03-26 | [
[
"Zhou",
"Mingyang",
""
],
[
"Yan",
"Zichao",
""
],
[
"Layne",
"Elliot",
""
],
[
"Malkin",
"Nikolay",
""
],
[
"Zhang",
"Dinghuai",
""
],
[
"Jain",
"Moksh",
""
],
[
"Blanchette",
"Mathieu",
""
],
[
"B... | Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.