Works matching IS 1553734X AND DT 2023 AND VI 19 AND IP 5

Results: 49

Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011197

By:

Wang, Seunghyun;
Lee, Doheon

Publication type:

Article

Contact-number-driven virus evolution: A multi-level modeling framework for the evolution of acute or persistent RNA virus infection.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011173

By:

Sunagawa, Junya;
Komorizono, Ryo;
Park, Hyeongki;
Hart, William S.;
Thompson, Robin N.;
Makino, Akiko;
Tomonaga, Keizo;
Iwami, Shingo;
Yamaguchi, Ryo

Publication type:

Article

Predicting yield of individual field-grown rapeseed plants from rosette-stage leaf gene expression.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011161

By:

De Meyer, Sam;
Cruz, Daniel Felipe;
De Swaef, Tom;
Lootens, Peter;
De Block, Jolien;
Bird, Kevin;
Sprenger, Heike;
Van de Voorde, Michael;
Hawinkel, Stijn;
Van Hautegem, Tom;
Inzé, Dirk;
Nelissen, Hilde;
Roldán-Ruiz, Isabel;
Maere, Steven

Publication type:

Article

Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011157

By:

Smith, Matthew Beauregard;
Simpson, Zack Booth;
Marcotte, Edward M.

Publication type:

Article

Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011138

By:

Arbona, Jean-Michel;
Kabalane, Hadi;
Barbier, Jeremy;
Goldar, Arach;
Hyrien, Olivier;
Audit, Benjamin

Publication type:

Article

CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011137

By:

Sanvicente-García, Marta;
García-Valiente, Albert;
Jouide, Socayna;
Jaraba-Wallace, Jessica;
Bautista, Eric;
Escobosa, Marc;
Sánchez-Mejías, Avencia;
Güell, Marc

Publication type:

Article

Tight basis cycle representatives for persistent homology of large biological data sets.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010341

By:

Aggarwal, Manu;
Periwal, Vipul

Publication type:

Article

Enabling interpretable machine learning for biological data with reliability scores.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011175

By:

Ahlquist, K. D.;
Sugden, Lauren A.;
Ramachandran, Sohini

Publication type:

Article

Two modes of fusogenic action for influenza virus fusion peptide.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011174

By:

Michalski, Michal;
Setny, Piotr

Publication type:

Article

AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010263

By:

Essegian, Derek J.;
Chavez, Valery;
Khurshid, Rabia;
Merchan, Jaime R.;
Schürer, Stephan C.

Publication type:

Article

Design of an adaptable intrafascicular electrode (AIR) for selective nerve stimulation by model-based optimization.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011184

By:

Ciotti, Federico;
Cimolato, Andrea;
Valle, Giacomo;
Raspopovic, Stanisa

Publication type:

Article

The proportion of resistant hosts in mixtures should be biased towards the resistance with the lowest breaking cost.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011146

By:

Clin, Pauline;
Grognard, Frédéric;
Andrivon, Didier;
Mailleret, Ludovic;
Hamelin, Frédéric M.

Publication type:

Article

Mesoscale, long-time mixing of chromosomes and its connection to polymer dynamics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011142

By:

Bajpai, Gaurav;
Safran, Samuel

Publication type:

Article

Inferring evolutionary trajectories from cross-sectional transcriptomic data to mirror lung adenocarcinoma progression.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011122

By:

Huang, Kexin;
Zhang, Yun;
Gong, Haoran;
Qiao, Zhengzheng;
Wang, Tiangang;
Zhao, Weiling;
Huang, Liyu;
Zhou, Xiaobo

Publication type:

Article

Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011105

By:

Miller, Kai J.;
Müller, Klaus-Robert;
Valencia, Gabriela Ojeda;
Huang, Harvey;
Gregg, Nicholas M.;
Worrell, Gregory A.;
Hermes, Dora

Publication type:

Article

Four guiding principles for effective trainee-led STEM community engagement through high school outreach.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011072

By:

Luecke, Stefanie;
Schiffman, Allison;
Singh, Apeksha;
Huang, Helen;
Shannon, Barbara;
Wilder, Catera L.

Publication type:

Article

Random walk informed heterogeneity detection reveals how the lymph node conduit network influences T cells collective exploration behavior.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011168

By:

Song, Solène;
Senoussi, Malek;
Escande, Paul;
Villoutreix, Paul

Publication type:

Article

Deep self-supervised learning for biosynthetic gene cluster detection and product classification.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011162

By:

Rios-Martinez, Carolina;
Bhattacharya, Nicholas;
Amini, Ava P.;
Crawford, Lorin;
Yang, Kevin K.

Publication type:

Article

Correction: A computational modeling approach for predicting multicell spheroid patterns based on signaling-induced differential adhesion.

Published in:

2023

By:

Sivakumar, Nikita;
Warner, Helen V.;
Peirce, Shayn M.;
Lazzara, Matthew J.

Publication type:

Correction Notice

The MAPK/ERK channel capacity exceeds 6 bit/hour.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011155

By:

Nałęcz-Jawecki, Paweł;
Gagliardi, Paolo Armando;
Kochańczyk, Marek;
Dessauges, Coralie;
Pertz, Olivier;
Lipniacki, Tomasz

Publication type:

Article

Filter inference: A scalable nonlinear mixed effects inference approach for snapshot time series data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011135

By:

Augustin, David;
Lambert, Ben;
Wang, Ken;
Walz, Antje-Christine;
Robinson, Martin;
Gavaghan, David

Publication type:

Article

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010680

By:

Sheffler, William;
Yang, Erin C.;
Dowling, Quinton;
Hsia, Yang;
Fries, Chelsea N.;
Stanislaw, Jenna;
Langowski, Mark D.;
Brandys, Marisa;
Li, Zhe;
Skotheim, Rebecca;
Borst, Andrew J.;
Khmelinskaia, Alena;
King, Neil P.;
Baker, David

Publication type:

Article

Modelling the structures of frameshift-stimulatory pseudoknots from representative bat coronaviruses.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011124

By:

Sekar, Rohith Vedhthaanth;
Oliva, Patricia J.;
Woodside, Michael T.

Publication type:

Article

Shadow enhancers mediate trade-offs between transcriptional noise and fidelity.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011071

By:

Fletcher, Alvaro;
Wunderlich, Zeba;
Enciso, German

Publication type:

Article

Stochastic modelling of a three-dimensional glycogen granule synthesis and impact of the branching enzyme.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010694

By:

Rousset, Yvan;
Ebenhöh, Oliver;
Raguin, Adélaïde

Publication type:

Article

Structure Learning for Gene Regulatory Networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011118

By:

Federico, Anthony;
Kern, Joseph;
Varelas, Xaralabos;
Monti, Stefano

Publication type:

Article

Binding pocket dynamics along the recovery stroke of human β-cardiac myosin.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011099

By:

Akter, Fariha;
Ochala, Julien;
Fornili, Arianna

Publication type:

Article

An approximate diffusion process for environmental stochasticity in infectious disease transmission modelling.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011088

By:

Ghosh, Sanmitra;
Birrell, Paul J.;
De Angelis, Daniela

Publication type:

Article

Knowledge-guided data mining on the standardized architecture of NRPS: Subtypes, novel motifs, and sequence entanglements.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011100

By:

He, Ruolin;
Zhang, Jinyu;
Shao, Yuanzhe;
Gu, Shaohua;
Song, Chen;
Qian, Long;
Yin, Wen-Bing;
Li, Zhiyuan

Publication type:

Article

Targeting operational regimes of interest in recurrent neural networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011097

By:

Ekelmans, Pierre;
Kraynyukovas, Nataliya;
Tchumatchenko, Tatjana

Publication type:

Article

Self-assembly coupled to liquid-liquid phase separation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010652

By:

Hagan, Michael F.;
Mohajerani, Farzaneh

Publication type:

Article

Modelling novelty detection in the thalamocortical loop.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1009616

By:

Han, Chao;
English, Gwendolyn;
Saal, Hannes P.;
Indiveri, Giacomo;
Gilra, Aditya;
von der Behrens, Wolfger;
Vasilaki, Eleni

Publication type:

Article

Understanding the impact of mobility on COVID-19 spread: A hybrid gravity-metapopulation model of COVID-19.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011123

By:

Iyaniwura, Sarafa A.;
Ringa, Notice;
Adu, Prince A.;
Mak, Sunny;
Janjua, Naveed Z.;
Irvine, Michael A.;
Otterstatter, Michael

Publication type:

Article

Learning to predict future locations with internally generated theta sequences.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011101

By:

Parra-Barrero, Eloy;
Cheng, Sen

Publication type:

Article

Pupillary response is associated with the reset and switching of functional brain networks during salience processing.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011081

By:

He, Hengda;
Hong, Linbi;
Sajda, Paul

Publication type:

Article

Noise improves the association between effects of local stimulation and structural degree of brain networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010866

By:

Zheng, Yi;
Tang, Shaoting;
Zheng, Hongwei;
Wang, Xin;
Liu, Longzhao;
Yang, Yaqian;
Zhen, Yi;
Zheng, Zhiming

Publication type:

Article

Temporal novelty detection and multiple timescale integration drive Drosophila orientation dynamics in temporally diverse olfactory environments.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010606

By:

Jayaram, Viraaj;
Sehdev, Aarti;
Kadakia, Nirag;
Brown, Ethan A.;
Emonet, Thierry

Publication type:

Article

Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011115

By:

Rokhsar, Jennifer L.;
Raynor, Brinkley;
Sheen, Justin;
Goldstein, Neal D.;
Levy, Michael Z.;
Castillo-Neyra, Ricardo

Publication type:

Article

A unitary mechanism underlies adaptation to both local and global environmental statistics in time perception.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011116

By:

Wang, Tianhe;
Luo, Yingrui;
Ivry, Richard B.;
Tsay, Jonathan S.;
Pöppel, Ernst;
Bao, Yan

Publication type:

Article

Coherent noise enables probabilistic sequence replay in spiking neuronal networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1010989

By:

Bouhadjar, Younes;
Wouters, Dirk J.;
Diesmann, Markus;
Tetzlaff, Tom

Publication type:

Article

Target-agnostic drug prediction integrated with medical record analysis uncovers differential associations of statins with increased survival in COVID-19 patients.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011050

By:

Sperry, Megan M.;
Oskotsky, Tomiko T.;
Marić, Ivana;
Kaushal, Shruti;
Takeda, Takako;
Horvath, Viktor;
Powers, Rani K.;
Rodas, Melissa;
Furlong, Brooke;
Soong, Mercy;
Prabhala, Pranav;
Goyal, Girija;
Carlson, Kenneth E.;
Wong, Ronald J.;
Kosti, Idit;
Le, Brian L.;
Logue, James;
Hammond, Holly;
Frieman, Matthew;
Stevenson, David K.

Publication type:

Article

Matrix prior for data transfer between single cell data types in latent Dirichlet allocation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011049

By:

Min, Alan;
Durham, Timothy;
Gevirtzman, Louis;
Noble, William Stafford

Publication type:

Article

An integrated model for predicting KRAS dependency.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011095

By:

Tsai, Yihsuan S.;
Chareddy, Yogitha S.;
Price, Brandon A.;
Parker, Joel S.;
Pecot, Chad V.

Publication type:

Article

Predicting partner fitness based on spatial structuring in a light-driven microbial community.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011045

By:

Sakkos, Jonathan K.;
Santos-Merino, María;
Kokarakis, Emmanuel J.;
Li, Bowen;
Fuentes-Cabrera, Miguel;
Zuliani, Paolo;
Ducat, Daniel C.

Publication type:

Article

A convolutional neural network provides a generalizable model of natural sound coding by neural populations in auditory cortex.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011110

By:

Pennington, Jacob R.;
David, Stephen V.

Publication type:

Article

Data-driven segmentation of cortical calcium dynamics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011085

By:

Weiser, Sydney C.;
Mullen, Brian R.;
Ascencio, Desiderio;
Ackman, James B.

Publication type:

Article

Predicting anti-cancer drug combination responses with a temporal cell state network model.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011082

By:

Sarmah, Deepraj;
Meredith, Wesley O.;
Weber, Ian K.;
Price, Madison R.;
Birtwistle, Marc R.

Publication type:

Article

Generative models of birdsong learning link circadian fluctuations in song variability to changes in performance.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011051

By:

Brudner, Samuel;
Pearson, John;
Mooney, Richard

Publication type:

Article

ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 5, p. 1, doi. 10.1371/journal.pcbi.1011001

By:

Mineeva, Olga;
Danciu, Daniel;
Schölkopf, Bernhard;
Ley, Ruth E.;
Rätsch, Gunnar;
Youngblut, Nicholas D.

Publication type:

Article