Works matching IS 1553734X AND DT 2022 AND VI 18 AND IP 4

Results: 66

Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010066

By:

Giliberti, Renato;
Cavaliere, Sara;
Mauriello, Italia Elisa;
Ercolini, Danilo;
Pasolli, Edoardo

Publication type:

Article

phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010056

By:

De Maio, Nicola;
Boulton, William;
Weilguny, Lukas;
Walker, Conor R.;
Turakhia, Yatish;
Corbett-Detig, Russell;
Goldman, Nick

Publication type:

Article

Inferring ongoing cancer evolution from single tumour biopsies using synthetic supervised learning.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010007

By:

Ouellette, Tom W.;
Awadalla, Philip

Publication type:

Article

Mechanisms of ventricular arrhythmias elicited by coexistence of multiple electrophysiological remodeling in ischemia: A simulation study.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009388

By:

Liang, Cuiping;
Li, Qince;
Wang, Kuanquan;
Du, Yimei;
Wang, Wei;
Zhang, Henggui

Publication type:

Article

Optimizing interneuron circuits for compartment-specific feedback inhibition.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009933

By:

Keijser, Joram;
Sprekeler, Henning

Publication type:

Article

Calcium modeling of spine apparatus-containing human dendritic spines demonstrates an "all-or-nothing" communication switch between the spine head and dendrite.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010069

By:

Rosado, James;
Duc Bui, Viet;
Haas, Carola A.;
Beck, Jürgen;
Queisser, Gillian;
Vlachos, Andreas

Publication type:

Article

Learning the rules of collective cell migration using deep attention networks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009293

By:

LaChance, Julienne;
Suh, Kevin;
Clausen, Jens;
Cohen, Daniel J.

Publication type:

Article

Multi-targeting of K-Ras domains and mutations by peptide and small molecule inhibitors.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009962

By:

Poorebrahim, Mansour;
Abazari, Mohammad Foad;
Moradi, Leila;
Shahbazi, Behzad;
Mahmoudi, Reza;
Kalhor, Hourieh;
Askari, Hassan;
Teimoori-Toolabi, Ladan

Publication type:

Article

Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010053

By:

Kumata, Ryuichi;
Iwanami, Shoya;
Mar, Katrina B.;
Kakizoe, Yusuke;
Misawa, Naoko;
Nakaoka, Shinji;
Koyanagi, Yoshio;
Perelson, Alan S.;
Schoggins, John W.;
Iwami, Shingo;
Sato, Kei

Publication type:

Article

Multiple nutrient transporters enable cells to mitigate a rate-affinity tradeoff.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010060

By:

Montaño-Gutierrez, Luis Fernando;
Correia, Kevin;
Swain, Peter S.

Publication type:

Article

Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010040

By:

Li, Hongyang;
Eksi, Ridvan;
Yi, Daiyao;
Godfrey, Bradley;
Mathew, Lisa R.;
O'Connor, Christopher L.;
Bitzer, Markus;
Kretzler, Matthias;
Menon, Rajasree;
Guan, Yuanfang

Publication type:

Article

Distinguishing excess mutations and increased cell death based on variant allele frequencies.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010048

By:

Tibély, Gergely;
Schrempf, Dominik;
Derényi, Imre;
Szöllősi, Gergely J.

Publication type:

Article

Bioactivity assessment of natural compounds using machine learning models trained on target similarity between drugs.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010029

By:

Periwal, Vinita;
Bassler, Stefan;
Andrejev, Sergej;
Gabrielli, Natalia;
Patil, Kaustubh Raosaheb;
Typas, Athanasios;
Patil, Kiran Raosaheb

Publication type:

Article

Updating age-specific contact structures to match evolving demography in a dynamic mathematical model of tuberculosis vaccination.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010002

By:

Weerasuriya, Chathika Krishan;
Harris, Rebecca Claire;
McQuaid, Christopher Finn;
Gomez, Gabriela B.;
White, Richard G.

Publication type:

Article

Cell type-specific mechanisms of information transfer in data-driven biophysical models of hippocampal CA3 principal neurons.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010071

By:

Linaro, Daniele;
Levy, Matthew J.;
Hunt, David L.

Publication type:

Article

Phylogenetic analysis of migration, differentiation, and class switching in B cells.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009885

By:

Hoehn, Kenneth B.;
Pybus, Oliver G.;
Kleinstein, Steven H.

Publication type:

Article

Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009977

By:

Peiffer, Amanda L.;
Garlick, Julie M.;
Joy, Stephen T.;
Mapp, Anna K.;
Brooks III, Charles L.

Publication type:

Article

The stochastic logistic model with correlated carrying capacities reproduces beta-diversity metrics of microbial communities.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010043

By:

Zaoli, Silvia;
Grilli, Jacopo

Publication type:

Article

Ten simple rules for getting started with statistics in graduate school.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010033

By:

Zitomer, Rachel A.;
Karr, Jessica;
Kerstens, Mark;
Perry, Lindsey;
Ruth, Kayla;
Adrean, Lindsay;
Austin, Suzanne;
Cornelius, Jamie;
Dachenhaus, Jonathan;
Dinkins, Jonathan;
Harrington, Alan;
Kim, Hankyu;
Owens, Terrah;
Revekant, Claire;
Schroeder, Vanessa;
Sink, Chelsea;
Valente, Jonathon J.;
Woodis, Ethan;
Rivers, James W.

Publication type:

Article

Predicting the functional impact of KCNQ1 variants with artificial neural networks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010038

By:

Phul, Saksham;
Kuenze, Georg;
Vanoye, Carlos G.;
Sanders, Charles R.;
George Jr., Alfred L.;
Meiler, Jens

Publication type:

Article

BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009987

By:

Poole, William;
Pandey, Ayush;
Shur, Andrey;
Tuza, Zoltan A.;
Murray, Richard M.

Publication type:

Article

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009487

By:

Sarangi, Vivekananda;
Jang, Yeongjun;
Suvakov, Milovan;
Bae, Taejeong;
Fasching, Liana;
Sekar, Shobana;
Tomasini, Livia;
Mariani, Jessica;
Vaccarino, Flora M.;
Abyzov, Alexej

Publication type:

Article

Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009391

By:

Conti, Simone;
Ovchinnikov, Victor;
Faris, Jonathan G.;
Chakraborty, Arup K.;
Karplus, Martin;
Sprenger, Kayla G.

Publication type:

Article

Application of modular response analysis to medium- to large-size biological systems.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009312

By:

Mekedem, Meriem;
Ravel, Patrice;
Colinge, Jacques

Publication type:

Article

Alpha blocking and 1/fβ spectral scaling in resting EEG can be accounted for by a sum of damped alpha band oscillatory processes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010012

By:

Evertz, Rick;
Hicks, Damien G.;
Liley, David T. J.

Publication type:

Article

A general framework for predicting the transcriptomic consequences of non-coding variation and small molecules.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010028

By:

Abdalla, Moustafa;
Abdalla, Mohamed

Publication type:

Article

Ten simple rules to ruin a collaborative environment.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009957

By:

Lawrence-Dill, Carolyn J.;
Allscheid, Robyn L.;
Boaitey, Albert;
Bauman, Todd;
Buckler IV, Edward S.;
Clarke, Jennifer L.;
Cullis, Christopher;
Dekkers, Jack;
Dorius, Cassandra J.;
Dorius, Shawn F.;
Ertl, David;
Homann, Matthew;
Hu, Guiping;
Losch, Mary;
Lyons, Eric;
Murdoch, Brenda;
Navabi, Zahra-Katy;
Punnuri, Somashekhar;
Rafiq, Fahad;
Reecy, James M.

Publication type:

Article

Dissecting recurrent waves of pertussis across the boroughs of London.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009898

By:

Saeidpour, Arash;
Bansal, Shweta;
Rohani, Pejman

Publication type:

Article

Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009879

By:

Kar, Anuradha;
Petit, Manuel;
Refahi, Yassin;
Cerutti, Guillaume;
Godin, Christophe;
Traas, Jan

Publication type:

Article

Chaotic and stochastic dynamics of epileptiform-like activities in sclerotic hippocampus resected from patients with pharmacoresistant epilepsy.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010027

By:

Araújo, Noemi S.;
Reyes-Garcia, Selvin Z.;
Brogin, João A. F.;
Bueno, Douglas D.;
Cavalheiro, Esper A.;
Scorza, Carla A.;
Faber, Jean

Publication type:

Article

Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010051

By:

Di Leo, Simone;
Marni, Stefano;
Plata, Carlos A.;
Fraccia, Tommaso P.;
Smith, Gregory P.;
Maritan, Amos;
Suweis, Samir;
Bellini, Tommaso

Publication type:

Article

Microbiome-based disease prediction with multimodal variational information bottlenecks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010050

By:

Grazioli, Filippo;
Siarheyeu, Raman;
Alqassem, Israa;
Henschel, Andreas;
Pileggi, Giampaolo;
Meiser, Andrea

Publication type:

Article

RNA folding using quantum computers.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010032

By:

Fox, Dillion M.;
MacDermaid, Christopher M.;
Schreij, Andrea M. A.;
Zwierzyna, Magdalena;
Walker, Ross C.

Publication type:

Article

Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010021

By:

Barsi, Szilvia;
Papp, Henrietta;
Valdeolivas, Alberto;
Tóth, Dániel J.;
Kuczmog, Anett;
Madai, Mónika;
Hunyady, László;
Várnai, Péter;
Saez-Rodriguez, Julio;
Jakab, Ferenc;
Szalai, Bence

Publication type:

Article

Are transient protein-protein interactions more dispensable?

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010013

By:

Ghadie, Mohamed Ali;
Xia, Yu

Publication type:

Article

Fundamental limits on inferring epidemic resurgence in real time using effective reproduction numbers.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010004

By:

Parag, Kris V.;
Donnelly, Christl A.

Publication type:

Article

Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009999

By:

Sundqvist, Nicolas;
Grankvist, Nina;
Watrous, Jeramie;
Mohit, Jain;
Nilsson, Roland;
Cedersund, Gunnar

Publication type:

Article

Digital contact tracing and network theory to stop the spread of COVID-19 using big-data on human mobility geolocalization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009865

By:

Serafino, Matteo;
Monteiro, Higor S.;
Luo, Shaojun;
Reis, Saulo D. S.;
Igual, Carles;
Lima Neto, Antonio S.;
Travizano, Matías;
Andrade Jr, José S.;
Makse, Hernán A.

Publication type:

Article

Construction of disease-specific cytokine profiles by associating disease genes with immune responses.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009497

By:

Liu, Tianyun;
Wang, Shiyin;
Wornow, Michael;
Altman, Russ B.

Publication type:

Article

DGCyTOF: Deep learning with graphic cluster visualization to predict cell types of single cell mass cytometry data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1008885

By:

Cheng, Lijun;
Karkhanis, Pratik;
Gokbag, Birkan;
Liu, Yueze;
Li, Lang

Publication type:

Article

Blind demixing methods for recovering dense neuronal morphology from barcode imaging data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009991

By:

Chen, Shuonan;
Loper, Jackson;
Zhou, Pengcheng;
Paninski, Liam

Publication type:

Article

Using topic modeling to detect cellular crosstalk in scRNA-seq.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009975

By:

Pancheva, Alexandrina;
Wheadon, Helen;
Rogers, Simon;
Otto, Thomas D.

Publication type:

Article

Ten simple rules for using entrepreneurship skills to improve research careers and culture.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009946

By:

Bawn, Matt;
Dent, David;
Bourne, Philip E.

Publication type:

Article

Deep learning for robust and flexible tracking in behavioral studies for C. elegans.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009942

By:

Bates, Kathleen;
Le, Kim;
Lu, Hang

Publication type:

Article

A particle-based computational model to analyse remodelling of the red blood cell cytoskeleton during malaria infections.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009509

By:

Jäger, Julia;
Patra, Pintu;
Sanchez, Cecilia P.;
Lanzer, Michael;
Schwarz, Ulrich S.

Publication type:

Article

Effective population size for culturally evolving traits.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009430

By:

Deffner, Dominik;
Kandler, Anne;
Fogarty, Laurel

Publication type:

Article

Simulated actin reorganization mediated by motor proteins.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010026

By:

Ciocanel, Maria-Veronica;
Chandrasekaran, Aravind;
Mager, Carli;
Ni, Qin;
Papoian, Garegin A.;
Dawes, Adriana

Publication type:

Article

Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1010006

By:

Ose, Nicholas J.;
Butler, Brandon M.;
Kumar, Avishek;
Kazan, I. Can;
Sanderford, Maxwell;
Kumar, Sudhir;
Ozkan, S. Banu

Publication type:

Article

Ten simple rules for building a successful science start-up.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009982

By:

Reichmuth, Tobias;
Ewald, Collin Y.

Publication type:

Article

Adaptive and optimized COVID-19 vaccination strategies across geographical regions and age groups.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 4, p. 1, doi. 10.1371/journal.pcbi.1009974

By:

Molla, Jeta;
Ponce de León Chávez, Alejandro;
Hiraoka, Takayuki;
Ala-Nissila, Tapio;
Kivelä, Mikko;
Leskelä, Lasse

Publication type:

Article