Works matching IS 1553734X AND DT 2023 AND VI 19 AND IP 1

Results: 58

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010863

By:

Cazares, Tareian A.;
Rizvi, Faiz W.;
Iyer, Balaji;
Chen, Xiaoting;
Kotliar, Michael;
Bejjani, Anthony T.;
Wayman, Joseph A.;
Donmez, Omer;
Wronowski, Benjamin;
Parameswaran, Sreeja;
Kottyan, Leah C.;
Barski, Artem;
Weirauch, Matthew T.;
Prasath, V. B. Surya;
Miraldi, Emily R.

Publication type:

Article

Tissue specific LRRK2 interactomes reveal a distinct striatal functional unit.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010847

By:

Zhao, Yibo;
Vavouraki, Nikoleta;
Lovering, Ruth C.;
Escott-Price, Valentina;
Harvey, Kirsten;
Lewis, Patrick A.;
Manzoni, Claudia

Publication type:

Article

Bayesian reconstruction of memories stored in neural networks from their connectivity.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010813

By:

Goldt, Sebastian;
Krzakala, Florent;
Zdeborová, Lenka;
Brunel, Nicolas

Publication type:

Article

Community composition exceeds area as a predictor of long-term conservation value.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010804

By:

O'Sullivan, Jacob D.;
Terry, J. Christopher D.;
Wilson, Ramesh;
Rossberg, Axel G.

Publication type:

Article

neuroWalknet, a controller for hexapod walking allowing for context dependent behavior.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010136

By:

Schilling, Malte;
Cruse, Holk

Publication type:

Article

Correction: Time to revisit the endpoint dilution assay and to replace the TCID<sub>50</sub> as a measure of a virus sample's infection concentration.

Published in:

2023

By:

Cresta, Daniel;
Warren, Donald C.;
Quirouette, Christian;
Smith, Amanda P.;
Lane, Lindey C.;
Smith, Amber M.;
Beauchemin, Catherine A. A.

Publication type:

Correction Notice

A dual graph neural network for drug–drug interactions prediction based on molecular structure and interactions.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010812

By:

Ma, Mei;
Lei, Xiujuan

Publication type:

Article

Environmental uncertainty and the advantage of impulsive choice strategies.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010873

By:

Burk, Diana C.;
Averbeck, Bruno B.

Publication type:

Article

A real-time regional model for COVID-19: Probabilistic situational awareness and forecasting.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010860

By:

Engebretsen, Solveig;
Diz-Lois Palomares, Alfonso;
Rø, Gunnar;
Kristoffersen, Anja Bråthen;
Lindstrøm, Jonas Christoffer;
Engø-Monsen, Kenth;
Kamineni, Meghana;
Hin Chan, Louis Yat;
Dale, Ørjan;
Midtbø, Jørgen Eriksson;
Stenerud, Kristian Lindalen;
Di Ruscio, Francesco;
White, Richard;
Frigessi, Arnoldo;
de Blasio, Birgitte Freiesleben

Publication type:

Article

Deciphering the RRM-RNA recognition code: A computational analysis.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010859

By:

Roca-Martínez, Joel;
Dhondge, Hrishikesh;
Sattler, Michael;
Vranken, Wim F.

Publication type:

Article

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010822

By:

von Bülow, Sören;
Sikora, Mateusz;
Blanc, Florian E. C.;
Covino, Roberto;
Hummer, Gerhard

Publication type:

Article

Modelling ribosome kinetics and translational control on dynamic mRNA.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010870

By:

Dykeman, Eric C.

Publication type:

Article

Information theoretic evidence for layer- and frequency-specific changes in cortical information processing under anesthesia.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010380

By:

Pinzuti, Edoardo;
Wollstadt, Patricia;
Tüscher, Oliver;
Wibral, Michael

Publication type:

Article

Injury-related cell death and proteoglycan loss in articular cartilage: Numerical model combining necrosis, reactive oxygen species, and inflammatory cytokines.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010337

By:

Kosonen, Joonas P.;
Eskelinen, Atte S. A.;
Orozco, Gustavo A.;
Nieminen, Petteri;
Anderson, Donald D.;
Grodzinsky, Alan J.;
Korhonen, Rami K.;
Tanska, Petri

Publication type:

Article

Mechanisms of hemoglobin cycling in anemia patients treated with erythropoiesis-stimulating agents.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010850

By:

Jörg, David J.;
Fuertinger, Doris H.;
Kotanko, Peter

Publication type:

Article

Relating local connectivity and global dynamics in recurrent excitatory-inhibitory networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010855

By:

Shao, Yuxiu;
Ostojic, Srdjan

Publication type:

Article

Shape-specific characterization of colorectal adenoma growth and transition to cancer with stochastic cell-based models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010831

By:

Simonetto, Cristoforo;
Mansmann, Ulrich;
Kaiser, Jan Christian

Publication type:

Article

Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010815

By:

Kimmel, Gregory J.;
Beck, Richard J.;
Yu, Xiaoqing;
Veith, Thomas;
Bakhoum, Samuel;
Altrock, Philipp M.;
Andor, Noemi

Publication type:

Article

Improving the validity of neuroimaging decoding tests of invariant and configural neural representation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010819

By:

Soto, Fabian A.;
Narasiwodeyar, Sanjay

Publication type:

Article

Pyfectious: An individual-level simulator to discover optimal containment policies for epidemic diseases.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010799

By:

Mehrjou, Arash;
Soleymani, Ashkan;
Abyaneh, Amin;
Bhatt, Samir;
Schölkopf, Bernhard;
Bauer, Stefan

Publication type:

Article

Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010841

By:

Newman, Kahlan E.;
Khalid, Syma

Publication type:

Article

Geometric analysis enables biological insight from complex non-identifiable models using simple surrogates.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010844

By:

Browning, Alexander P.;
Simpson, Matthew J.

Publication type:

Article

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010457

By:

Gueto-Tettay, Carlos;
Tang, Di;
Happonen, Lotta;
Heusel, Moritz;
Khakzad, Hamed;
Malmström, Johan;
Malmström, Lars

Publication type:

Article

Surround suppression in mouse auditory cortex underlies auditory edge detection.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010861

By:

Gilday, Omri David;
Praegel, Benedikt;
Maor, Ido;
Cohen, Tav;
Nelken, Israel;
Mizrahi, Adi

Publication type:

Article

Modelling continual learning in humans with Hebbian context gating and exponentially decaying task signals.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010808

By:

Flesch, Timo;
Nagy, David G.;
Saxe, Andrew;
Summerfield, Christopher

Publication type:

Article

Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009989

By:

Sugiyama, Yuki;
Uno, Kohei;
Matsui, Yusuke

Publication type:

Article

A new model of Notch signalling: Control of Notch receptor cis-inhibition via Notch ligand dimers.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010169

By:

Chen, Daipeng;
Forghany, Zary;
Liu, Xinxin;
Wang, Haijiang;
Merks, Roeland M. H.;
Baker, David A.

Publication type:

Article

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010851

By:

Cai, Tian;
Xie, Li;
Zhang, Shuo;
Chen, Muge;
He, Di;
Badkul, Amitesh;
Liu, Yang;
Namballa, Hari Krishna;
Dorogan, Michael;
Harding, Wayne W.;
Mura, Cameron;
Bourne, Philip E.;
Xie, Lei

Publication type:

Article

Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009499

By:

Phillips, Caleb M.;
Lima, Ernesto A. B. F.;
Gadde, Manasa;
Jarrett, Angela M.;
Rylander, Marissa Nichole;
Yankeelov, Thomas E.

Publication type:

Article

Systematic design of pulse dosing to eradicate persister bacteria.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010243

By:

Singh, Garima;
Orman, Mehmet A.;
Conrad, Jacinta C.;
Nikolaou, Michael

Publication type:

Article

Examining the efficacy of localised gemcitabine therapy for the treatment of pancreatic cancer using a hybrid agent-based model.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010104

By:

Jenner, Adrianne L.;
Kelly, Wayne;
Dallaston, Michael;
Araujo, Robyn;
Parfitt, Isobelle;
Steinitz, Dominic;
Pooladvand, Pantea;
Kim, Peter S.;
Wade, Samantha J.;
Vine, Kara L.

Publication type:

Article

Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009061

By:

Thomas, Oshane O.;
Shen, Hongyu;
Raaum, Ryan L.;
Harcourt-Smith, William E. H.;
Polk, John D.;
Hasegawa-Johnson, Mark

Publication type:

Article

Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010833

By:

Murphy, Ryan J.;
Gunasingh, Gency;
Haass, Nikolas K.;
Simpson, Matthew J.

Publication type:

Article

A unitary model of auditory frequency change perception.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010307

By:

Siedenburg, Kai;
Graves, Jackson;
Pressnitzer, Daniel

Publication type:

Article

Chaotic dynamics in spatially distributed neuronal networks generate population-wide shared variability.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010843

By:

Mosheiff, Noga;
Ermentrout, Bard;
Huang, Chengcheng

Publication type:

Article

Spikebench: An open benchmark for spike train time-series classification.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010792

By:

Lazarevich, Ivan;
Prokin, Ilya;
Gutkin, Boris;
Kazantsev, Victor

Publication type:

Article

Interspecific comparison of gene expression profiles using machine learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010743

By:

Kasianov, Artem S.;
Klepikova, Anna V.;
Mayorov, Alexey V.;
Buzanov, Gleb S.;
Logacheva, Maria D.;
Penin, Aleksey A.

Publication type:

Article

Ecological landscapes guide the assembly of optimal microbial communities.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010570

By:

George, Ashish B.;
Korolev, Kirill S.

Publication type:

Article

A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010821

By:

Zhai, Hongxuan;
Fukuyama, Julia

Publication type:

Article

Galaxy Training: A powerful framework for teaching!

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010752

By:

Hiltemann, Saskia;
Rasche, Helena;
Gladman, Simon;
Hotz, Hans-Rudolf;
Larivière, Delphine;
Blankenberg, Daniel;
Jagtap, Pratik D.;
Wollmann, Thomas;
Bretaudeau, Anthony;
Goué, Nadia;
Griffin, Timothy J.;
Royaux, Coline;
Le Bras, Yvan;
Mehta, Subina;
Syme, Anna;
Coppens, Frederik;
Droesbeke, Bert;
Soranzo, Nicola;
Bacon, Wendi;
Psomopoulos, Fotis

Publication type:

Article

Diversity and evolution of computationally predicted T cell epitopes against human respiratory syncytial virus.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010360

By:

Chen, Jiani;
Tan, Swan;
Avadhanula, Vasanthi;
Moise, Leonard;
Piedra, Pedro A.;
De Groot, Anne S.;
Bahl, Justin

Publication type:

Article

Humans account for cognitive costs when finding shortcuts: An information-theoretic analysis of navigation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010829

By:

Lancia, Gian Luca;
Eluchans, Mattia;
D'Alessandro, Marco;
Spiers, Hugo J.;
Pezzulo, Giovanni

Publication type:

Article

One dimensional approximations of neuronal dynamics reveal computational strategy.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010784

By:

Brennan, Connor;
Aggarwal, Adeeti;
Pei, Rui;
Sussillo, David;
Proekt, Alex

Publication type:

Article

HiSV: A control-free method for structural variation detection from Hi-C data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010760

By:

Li, Junping;
Gao, Lin;
Ye, Yusen

Publication type:

Article

SurvivalPath:A R package for conducting personalized survival path mapping based on time-series survival data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010830

By:

Shen, Lujun;
Mo, Jinqing;
Yang, Changsheng;
Jiang, Yiquan;
Ke, Liangru;
Hou, Dan;
Yan, Jingdong;
Zhang, Tao;
Fan, Weijun

Publication type:

Article

Skilled motor control of an inverted pendulum implies low entropy of states but high entropy of actions.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010810

By:

Catenacci Volpi, Nicola;
Greaves, Martin;
Trendafilov, Dari;
Salge, Christoph;
Pezzulo, Giovanni;
Polani, Daniel

Publication type:

Article

Novel modelling approaches to predict the role of antivirals in reducing influenza transmission.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010797

By:

Asher, Jason;
Lemenuel-Diot, Annabelle;
Clay, Matthew;
Durham, David P.;
Mier-y-Teran-Romero, Luis;
Arguello, Carlos J.;
Jolivet, Sebastien;
Wong, Diana Y.;
Kuhlbusch, Klaus;
Clinch, Barry;
Charoin, Jean-Eric

Publication type:

Article

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010820

By:

Ullmann, Theresa;
Peschel, Stefanie;
Finger, Philipp;
Müller, Christian L.;
Boulesteix, Anne-Laure

Publication type:

Article

A quantitative model for human neurovascular coupling with translated mechanisms from animals.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010818

By:

Sten, Sebastian;
Podéus, Henrik;
Sundqvist, Nicolas;
Elinder, Fredrik;
Engström, Maria;
Cedersund, Gunnar

Publication type:

Article

RCFGL: Rapid Condition adaptive Fused Graphical Lasso and application to modeling brain region co-expression networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 1, p. 1, doi. 10.1371/journal.pcbi.1010758

By:

Seal, Souvik;
Li, Qunhua;
Basner, Elle Butler;
Saba, Laura M.;
Kechris, Katerina

Publication type:

Article