Stop the war!Остановите войну!
for scientists:
default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDPLoS Computational Biology, Volume 18
Volume 18, Number 1, January 2022
- Stevie A. Bain
, Heleen Plaisier, Felicity Anderson, Nicola Cook, Kathryn Crouch, Thomas R. Meagher, Michael G. Ritchie, Edward W. J. Wallace, Daniel Barker:
Bringing bioinformatics to schools with the 4273pi project. - Thomas Sauter, Tamara Bintener, Ali Kishk, Luana Presta, Tessy Prohaska, Daniel Guignard, Ni Zeng, Claudia Cipriani, Sundas Arshad, Thomas Pfau, Patricia Martins Conde, Maria Pires Pacheco:
Project-based learning course on metabolic network modelling in computational systems biology.
- Elizabeth Dupre, Chris Holdgraf, Agah Karakuzu, Loïc Tetrel, Pierre Bellec, Nikola Stikov, Jean-Baptiste Poline:
Beyond advertising: New infrastructures for publishing integrated research objects. - Sheila M. Saia, Natalie G. Nelson, Sierra N. Young, Stanton Parham, Micah Vandegrift:
Ten simple rules for researchers who want to develop web apps.
- George Courcoubetis, Manasi S. Gangan, Sean Lim, Xiaokan Guo, Stephan Haas, James Q. Boedicker:
Formation, collective motion, and merging of macroscopic bacterial aggregates. - István Z. Reguly, Dávid Csercsik, János Juhász, Kálmán Tornai, Zsófia Bujtár, Gergely Horváth, Bence Keömley-Horváth, Tamás Kós, György Cserey, Kristóf Iván, Sándor Pongor, Gábor Szederkényi, Gergely Röst, Attila Csikász-Nagy:
Microsimulation based quantitative analysis of COVID-19 management strategies. - He Li, Yixiang Deng, Konstantina Sampani, Shengze Cai, Zhen Li, Jennifer K. Sun, George E. Karniadakis:
Computational investigation of blood cell transport in retinal microaneurysms. - Raga Krishnakumar, Anne M. Ruffing:
OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. - Nathan C. L. Kong, Eshed Margalit, Justin L. Gardner, Anthony M. Norcia:
Increasing neural network robustness improves match to macaque V1 eigenspectrum, spatial frequency preference and predictivity. - Gautam Reddy, Laura Desban, Hidenori Tanaka, Julian Roussel, Olivier Mirat, Claire Wyart:
A lexical approach for identifying behavioural action sequences. - Spencer Farrell, Arnold Mitnitski, Kenneth Rockwood, Andrew D. Rutenberg:
Interpretable machine learning for high-dimensional trajectories of aging health. - Benjamin Martin, Pablo D. Dans, Milosz Wieczór, Núria Villegas, Isabelle Brun-Heath, Federica Battistini, Montserrat Terrazas, Modesto Orozco:
Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation. - Yan Wu, Lingfeng Xue, Wen Huang, Minghua Deng, Yihan Lin:
Profiling transcription factor activity dynamics using intronic reads in time-series transcriptome data. - Eline R. Kupers, Noah C. Benson, Marisa Carrasco, Jonathan Winawer:
Asymmetries around the visual field: From retina to cortex to behavior. - Marina Papadopoulou, Hanno Hildenbrandt, Daniel W. E. Sankey, Steven J. Portugal, Charlotte K. Hemelrijk:
Self-organization of collective escape in pigeon flocks. - Jennifer Yihong Tan, Ana Claudia Marques:
The activity of human enhancers is modulated by the splicing of their associated lncRNAs. - Arno Strouwen, Bart M. Nicolaï, Peter Goos:
Robust dynamic experiments for the precise estimation of respiration and fermentation parameters of fruit and vegetables. - Georgy Antonov, Christopher Gagne, Eran Eldar, Peter Dayan:
Optimism and pessimism in optimised replay. - Le Khanh Ngan Nguyen, Itamar Megiddo, Susan Howick:
Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff. - Yushi Yang, Francesco Turci, Erika Kague, Chrissy L. Hammond, John Russo, C. Patrick Royall:
Dominating lengthscales of zebrafish collective behaviour. - Zhi Ming Xu, Sina Rüeger, Michaela Zwyer, Daniela Brites, Hellen Hiza, Miriam Reinhard, Liliana K. Rutaihwa, Sonia Borrell, Faima Isihaka, Hosiana Temba, Thomas Maroa, Rastard Naftari, Jerry Hella, Mohamed Sasamalo, Klaus Reither, Damien Portevin, Sebastien Gagneux, Jacques Fellay:
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations. - William F. Turner, Daniel Feuerriegel, Robert Hester, Stefan Bode:
An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind. - Ulrike Münzner, Tomoya Mori, Marcus Krantz, Edda Klipp, Tatsuya Akutsu:
Identification of periodic attractors in Boolean networks using a priori information. - Jann Paul Mattern, Kristof Glauninger, Gregory L. Britten, John R. Casey, Sangwon Hyun, Zhen Wu, E. Virginia Armbrust, Zaïd Harchaoui, Francois Ribalet:
A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series. - Xiangyu Kuang, Guoye Guan, Ming-Kin Wong, Lu-Yan Chan, Zhongying Zhao, Chao Tang, Lei Zhang:
Computable early Caenorhabditis elegans embryo with a phase field model. - Joanna E. Handzlik, Manu:
Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. - Rory M. Donovan-Maiye, Eva Maxfield Brown, K. Caleb Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg, Gregory R. Johnson:
A deep generative model of 3D single-cell organization. - Winston Campeau, Andrew M. Simons, Brett Stevens:
The evolutionary maintenance of Lévy flight foraging. - Md Zulfikar Ali, Robert C. Brewster:
Controlling gene expression timing through gene regulatory architecture. - Marcell Miski, Bence Márk Keömley-Horváth, Dorina Rákóczi Megyeriné, Attila Csikász-Nagy, Zoltán Gáspári:
Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach. - Chenfei Zhang, David Hofmann, Andreas Neef, Fred Wolf:
Ultrafast population coding and axo-somatic compartmentalization. - Gorka Lasso, Saad Khan, Stephanie A. Allen, Margarette Mariano, Catalina Florez, Erika P. Orner, Jose A. Quiroz, Gregory Quevedo, Aldo Massimi, Aditi Hegde, Ariel S. Wirchnianski, Robert H. Bortz III, Ryan J. Malonis, George I. Georgiev, Karen Tong, Natalia G. Herrera, Nicholas C. Morano, Scott J. Garforth, Avinash Malaviya, Ahmed Khokhar, Ethan Laudermilch, M. Eugenia Dieterle, J. Maximilian Fels, Denise Haslwanter, Rohit K. Jangra, Jason Barnhill, Steven C. Almo, Kartik Chandran, Jonathan R. Lai, Libusha Kelly, Johanna P. Daily, Olivia Vergnolle:
Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes. - Alexander J. Bryer, Tyler Reddy, Edward Lyman, Juan R. Perilla:
Full scale structural, mechanical and dynamical properties of HIV-1 liposomes. - Anton V. Chizhov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev:
Ictal wavefront propagation in slices and simulations with conductance-based refractory density model. - Maggie Wisniewska, Ivan Puga-Gonzalez, Phyllis Lee, Cynthia Moss, Gareth Russell, Simon Garnier, Cédric Sueur:
Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants - An exemplar of how human disturbance impacts group-living species. - Chen Jia, Abhyudai Singh, Ramon Grima:
Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach. - Owen M. O'Connor, Razan N. Alnahhas, Jean-Baptiste Lugagne, Mary J. Dunlop:
DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics. - Tadamune Kaneko, Macoto Kikuchi:
Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution. - Shun Sakuraba, Qilin Xie, Kota Kasahara, Junichi Iwakiri, Hidetoshi Kono:
Extended ensemble simulations of a SARS-CoV-2 nsp1-5'-UTR complex. - Vladimír Palivec, Christian Johannessen, Jakub Kaminský, Hector Martinez-Seara:
Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution. - Janet Ong, Stacy Soh, Soon Hoe Ho, Annabel Seah, Borame Sue Dickens, Ken Wei Tan, Joel Ruihan Koo, Alex R. Cook, Daniel Rex Richards, Leon Yan-Feng Gaw, Ng Lee Ching, Jue Tao Lim:
Fine-scale estimation of effective reproduction numbers for dengue surveillance. - Mengting Niu, Quan Zou, Chen Lin:
CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach. - Arish Alreja, Ilya Nemenman, Christopher J. Rozell:
Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices. - Priyan Bhattacharya, Karthik Raman, Arun K. Tangirala:
Discovering adaptation-capable biological network structures using control-theoretic approaches. - Fabien Laporte, Alain Charcosset, Tristan Mary-Huard:
Efficient ReML inference in variance component mixed models using a Min-Max algorithm. - André Bogdanowski, Thomas Banitz, Linea Katharina Muhsal, Christian Kost, Karin Frank:
McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems. - Ryan R. Wick, Kathryn E. Holt:
Polypolish: Short-read polishing of long-read bacterial genome assemblies. - Alasdair D. F. Clarke, Amelia R. Hunt, Anna E. Hughes:
Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection. - Eduard Porta-Pardo, Victoria Ruiz-Serra, Samuel Valentini, Alfonso Valencia:
The structural coverage of the human proteome before and after AlphaFold. - Qi Jiang, Shuo Zhang, Lin Wan:
Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data. - Alexander Byers Brummer, Xin Yang, Eric Ma, Margarita Gutova, Christine E. Brown, Russell C. Rockne:
Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy. - Elodie Goldwaser, Catherine Laurent, Nathalie Lagarde, Sylvie Fabrega, Laure Nay, Bruno O. Villoutreix, Christian Jelsch, Arnaud B. Nicot, Marie-Anne Loriot, Maria A. Miteva:
Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9. - Tianwei Yu:
AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments. - Quinn Dickinson, Jesse G. Meyer:
Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences. - Nina Kudryashova, Theoklitos Amvrosiadis, Nathalie Dupuy, Nathalie Rochefort, Arno Onken:
Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships. - Alexander Nestor-Bergmann, Guy B. Blanchard, Nathan Hervieux, Alexander G. Fletcher, Jocelyn Étienne, Bénédicte Sanson:
Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model. - Chloé Dequeker, Yasser Mohseni Behbahani, Laurent David, Elodie Laine, Alessandra Carbone:
From complete cross-docking to partners identification and binding sites predictions. - Sayak Bhattacharya, Scott L. Brincat, Mikael Lundqvist, Earl K. Miller:
Traveling waves in the prefrontal cortex during working memory. - Chunrui Xu, Henry Hollis, Michelle Dai, Xiangyu Yao, Layne T. Watson, Yang Cao, Minghan Chen:
Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle. - Kaushik N. Shankar, Yiyuan Zhang, Talid Sinno, Scott L. Diamond:
A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution. - Dave Osthus:
Fast and accurate influenza forecasting in the United States with Inferno. - Tomiko Oskotsky, Ruchika Bajaj, Jillian Burchard, Taylor Cavazos, Ina Chen, William T. Connell, Stephanie Eaneff, Tianna Grant, Ishan Kanungo, Karla Lindquist, Douglas Myers-Turnbull, Zun Zar Chi Naing, Alice Tang, Bianca Vora, Jon Wang, Isha Karim, Claire Swadling, Janice Yang, AI4ALL Student Cohort, Bill Lindstaedt, Marina Sirota:
Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students. - Sina Tootoonian, Andreas T. Schaefer, Peter E. Latham:
Sparse connectivity for MAP inference in linear models using sister mitral cells. - Vatsala Chauhan, Mohamed N. M. Bahrudeen, Cristina S. D. Palma, Ines S. C. Baptista, Bilena Almeida, Suchintak Dash, Vinodh Kandavalli, Andre S. Ribeiro:
Analytical kinetic model of native tandem promoters in E. coli. - Richard M. Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander, Linda R. Petzold:
Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods. - Junhao Liang, Changsong Zhou:
Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks. - Yuan Gao, Jeff Gaither, Julia Chifman, Laura Salter Kubatko:
A phylogenetic approach to inferring the order in which mutations arise during cancer progression. 1010560
- Jing Qi, Yang Zhou, Zicen Zhao, Shuilin Jin:
Correction: SDImpute: A statistical block imputation method based on cell-level and gene-level information for dropouts in single-cell RNA-seq data. - Chintan J. Joshi, Song-Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O'Rourke, Nathan E. Lewis:
Correction: StanDep: Capturing transcriptomic variability improves context-specific metabolic models.
Volume 18, Number 2, February 2022
- Arkarachai Fungtammasan, Alexandra Lee, Jaclyn N. Taroni, Kurt Wheeler, Chen-Shan Chin, Sean R. Davis, Casey S. Greene:
Ten simple rules for large-scale data processing. - Nicole Contaxis, Jason A. Clark, Anthony Dellureficio, Sara Gonzales, Sara Mannheimer, Peter R. Oxley, Melissa A. Ratajeski, Alisa Surkis, Amy M. Yarnell, Michelle Yee, Kristi L. Holmes:
Ten simple rules for improving research data discovery. - Mark Baillie, Saskia le Cessie, Carsten Oliver Schmidt, Lara Lusa, Marianne Huebner:
Ten simple rules for initial data analysis.
- Camilo Fuentes-Beals, Alejandro Valdés-Jiménez, Gonzalo Riadi:
Hidden Markov Modeling with HMMTeacher. - Greg Wilson:
Twelve quick tips for software design.
- Jon Zelner, Nina B. Masters, Ramya Naraharisetti, Sanyu A. Mojola, Merlin Chowkwanyun, Ryan Malosh:
There are no equal opportunity infectors: Epidemiological modelers must rethink our approach to inequality in infection risk.
- Mathieu Desroches, John Rinzel, Serafim Rodrigues:
Classification of bursting patterns: A tale of two ducks.
- Stefan Müller, Diana Széliová, Jürgen Zanghellini:
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth. - Myo T. Naung, Elijah Martin, Jacob E. Munro, Somya Mehra, Andrew J. Guy, Moses Laman, G. L. Abby Harrison, Livingstone Tavul, Manuel Hetzel, Dominic Kwiatkowski, Ivo Mueller, Melanie Bahlo, Alyssa E. Barry:
Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. - Ignacio Sanchez-Burgos, Jorge R. Espinosa, Jerelle A. Joseph, Rosana Collepardo-Guevara:
RNA length has a non-trivial effect in the stability of biomolecular condensates formed by RNA-binding proteins. - Gabriela Canto-Encalada, Diego Tec-Campos, Juan D. Tibocha-Bonilla, Karsten Zengler, Alejandro Zepeda, Cristal Zuñiga:
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds. - Cristian Buc Calderon, Tom Verguts, Michael J. Frank:
Thunderstruck: The ACDC model of flexible sequences and rhythms in recurrent neural circuits. - Narmin Ghaffari Laleh, Chiara Maria Lavinia Loeffler, Julia Grajek, Katerina Stanková, Alexander T. Pearson, Hannah Sophie Muti, Christian Trautwein, Heiko Enderling, Jan Poleszczuk, Jakob Nikolas Kather:
Classical mathematical models for prediction of response to chemotherapy and immunotherapy. - Daniel Kaiser, Arthur M. Jacobs, Radoslaw Martin Cichy:
Modelling brain representations of abstract concepts. - Anca R. Radulescu, Gabrielle C. Todd, Cassandra L. Williams, Benjamin A. Bennink, Alex A. Lemus, Haley E. Chesbro, Justin R. Bourgeois, Ashley M. Kopec, Damian G. Zuloaga, Annalisa Scimemi:
Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes. - Benjamin J. Livesey, Joseph A. Marsh:
The properties of human disease mutations at protein interfaces. - Aleksey V. Zimin, Steven L. Salzberg:
The SAMBA tool uses long reads to improve the contiguity of genome assemblies. - Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani:
INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. - Thomas J. Moutinho Jr., Benjamin C. Neubert, Matthew L. Jenior, Jason A. Papin:
Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. - Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud:
Evaluating supervised and unsupervised background noise correction in human gut microbiome data. - David E. Chen Kersen, Gaia Tavoni, Vijay Balasubramanian:
Connectivity and dynamics in the olfactory bulb. - Haiting Chai, Quan Gu, Joseph Hughes, David L. Robertson:
In silico prediction of HIV-1-host molecular interactions and their directionality. - Lovemore Tenha, Mingzhou Song:
Inference of trajectory presence by tree dimension and subset specificity by subtree cover. - Ramin Khajeh, Francesco Fumarola, L. F. Abbott:
Sparse balance: Excitatory-inhibitory networks with small bias currents and broadly distributed synaptic weights. - György Abrusán, David B. Ascher, Michael Inouye:
Known allosteric proteins have central roles in genetic disease. - Reza Yaesoubi, Ted Cohen, Katherine Hsu, Thomas L. Gift, Sancta B. St. Cyr, Joshua A. Salomon, Yonatan H. Grad:
Evaluating spatially adaptive guidelines for the treatment of gonorrhea to reduce the incidence of gonococcal infection and increase the effective lifespan of antibiotics. - Qi Sun, Ali Nematbakhsh, Prashant Kumar Kuntala, Gretta Kellogg, B. Franklin Pugh, William K. M. Lai:
STENCIL: A web templating engine for visualizing and sharing life science datasets. - Sevan K. Harootonian, Arne D. Ekstrom, Robert C. Wilson:
Combination and competition between path integration and landmark navigation in the estimation of heading direction. - Anna Foix, Daniel López, Francisco Diez-Fuertes, Michael J. McConnell, Antonio J. Martin-Galiano:
Predicted impact of the viral mutational landscape on the cytotoxic response against SARS-CoV-2. - Robert C. Mines, Tomasz Lipniacki, Xiling Shen:
Slow nucleosome dynamics set the transcriptional speed limit and induce RNA polymerase II traffic jams and bursts. - Júlia V. Gallinaro, Nebojsa Gasparovic, Stefan Rotter:
Homeostatic control of synaptic rewiring in recurrent networks induces the formation of stable memory engrams. - Samuel Goldman, Ria Das, Kevin K. Yang, Connor W. Coley:
Machine learning modeling of family wide enzyme-substrate specificity screens. - Siyu Wang, Stephanie M. Reeve, Graham T. Holt, Adegoke A. Ojewole, Marcel S. Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G. Fowler, Dennis L. Wright, Bruce Randall Donald:
Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus. - Alexander Eugene Zarebski, Louis du Plessis, Kris V. Parag, Oliver George Pybus:
A computationally tractable birth-death model that combines phylogenetic and epidemiological data. - Liron Sheintuch, Alon Rubin, Ziv Yaniv:
Bias-free estimation of information content in temporally sparse neuronal activity. - Shubham Tripathi, Jun Hyoung Park, Shivanand Pudakalakatti, Pratip K. Bhattacharya, Benny Abraham Kaipparettu, Herbert Levine:
A mechanistic modeling framework reveals the key principles underlying tumor metabolism. - Leonie van Steijn, Inge M. N. Wortel, Clément Sire, Loïc Dupré, Guy Theraulaz, Roeland M. H. Merks:
Computational modelling of cell motility modes emerging from cell-matrix adhesion dynamics.