10.1371/journal.pone.0232120

Corticosterone and testosterone treatment influence expression of gene pathways linked to meiotic segregation in preovulatory follicles of the domestic hen
Cited by: 2
Author(s): E. Wróbel, Alexandra B. Bentz, W. Walter Lorenz, Steven T. Gardner, Mary T. Mendonça, Kristen J. Navara
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0235833

Main and interacting effects of physical activity and sedentary time on older adults’ BMI: The moderating roles of socio-demographic and environmental attributes
Cited by: 5
Author(s): Delfien Van Dyck, Anthony Barnett, Jelle Van Cauwenberg, Casper J. P. Zhang, Cindy H.P. Sit, Ester Cerin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0228094

Human and climatic drivers affect spatial fishing patterns in a multiple-use marine protected area: The Galapagos Marine Reserve
Cited by: 14
Author(s): Mauricio Castrejón, Anthony Charles
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1007988

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases
Cited by: 7
Author(s): Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0250235

Association of adverse prenatal exposure burden with child psychopathology in the Adolescent Brain Cognitive Development (ABCD) Study
Cited by: 18
Author(s): Joshua L. Roffman, Eren D. Sipahi, Kevin Dowling, Dylan Hughes, Casey E. Hopkinson, Hang Lee, Hamdi Eryilmaz, Lee S. Cohen, Jodi M. Gilman, Alysa E. Doyle, Erin C. Dunn
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227130

Community- and trophic-level responses of soil nematodes to removal of a non-native tree at different stages of invasion
Cited by: 2
Author(s): Guadalupe Peralta, Ian A. Dickie, G. W. Yeates, Duane A. Peltzer
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0233841

Whole blood transcriptional responses of very preterm infants during late-onset sepsis
Cited by: 16
Author(s): Sherrianne Ng, Tobias Strunk, Ahwon Lee, Erin E. Gill, Reza Falsafi, Tabitha Woodman, Julie Hibbert, Robert E. W. Hancock, Andrew Currie
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232736

Using species distribution models to locate the potential cradles of the allopolyploid Gypsophila bermejoi G. López (Caryophyllaceae)
Cited by: 2
Author(s): Miguel de Luis, Julio Álvarez-Jiménez, Francisco Javier Rejos, Carmen Bartolomé
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1009774

A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation
Cited by: 4
Author(s): Payel Ganguly, Landiso Madonsela, Jesse T. Chao, Christopher Loewen, Timothy P. O’Connor, Esther M. Verheyen, Douglas W. Allan
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0242520

On the agreement between bibliometrics and peer review: Evidence from the Italian research assessment exercises
Cited by: 5
Author(s): Alberto Baccini, Lucio Barabesi, Giuseppe De Nicolao
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1009477

Drivers of linkage disequilibrium across a species’ geographic range
Cited by: 10
Author(s): Kay Lucek, Yvonne Willi
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0227076

All of gene expression (AOE): An integrated index for public gene expression databases
Cited by: 29
Author(s): Hidemasa Bono
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0246869

Uniting against a common enemy: Perceived outgroup threat elicits ingroup cohesion in chimpanzees
Cited by: 8
Author(s): James Brooks, Ena Onishi, Isabelle R. Clark, Manuel Bohn, Shinya Yamamoto
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0254200

Contextualizing goal preferences in fear-avoidance models. Looking at fatigue as a disabling symptom in fibromyalgia patients
Cited by: 5
Author(s): Cecilia Peñacoba, Irene López‐Gómez, María Ángeles Pastor-Mira, Sofía López-Roig, Carmen Écija
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0255986

Stockpiled personal protective equipment and knowledge of pandemic plans as predictors of perceived pandemic preparedness among German general practitioners
Cited by: 9
Author(s): Arno Stöcker, Ibrahim Demirer, Sophie Gunkel, Jan Hoffmann, Laura Mause, Tim Ohnhäuser, Nadine Scholten
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0235748

Predicting gene regulatory regions with a convolutional neural network for processing double-strand genome sequence information
Cited by: 8
Author(s): Koh Onimaru, Osamu Nishimura, Shigehiro Kuraku
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0255298

Northern bobwhite select for shrubby thickets interspersed in grasslands during fall and winter
Cited by: 2
Author(s): Alisha R. Mosloff, Mitch D. Weegman, Frank R. Thompson, Thomas R. Thompson
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008837

Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model
Cited by: 36
Author(s): Gregory L. Watson, Dayuan Xiong, Lu Zhang, Joseph A. Zoller, John Shamshoian, Phillip Sundin, Teresa Bufford, Anne W. Rimoin, Marc A. Suchard, Christina M. Ramirez
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0251502

“Know your epidemic, know your response”: Epidemiological assessment of the substance use disorder crisis in the United States
Cited by: 8
Author(s): Andrés Hernández, Minxuan Lan, Neil J. MacKinnon, Adam J. Branscum, Diego F. Cuadros
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009526

Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication
Cited by: 5
Author(s): Ignacio Soriano, Enrique Vázquez, Nagore de León, Sibyl Bertrand, Ellen Heitzer, Sophia Toumazou, Zhihan Bo, Claire Palles, Chen-Chun Pai, Timothy C. Humphrey, Ian Tomlinson, Sue Cotterill, Stephen Kearsey
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0255076

A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction
Cited by: 9
Author(s): Teng Ruei Chen, Sheng Hung Juan, Yu Huang, Lianfang Tian, Wei-Cheng Lo
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0246473

The forests of the midwestern United States at Euro-American settlement: Spatial and physical structure based on contemporaneous survey data
Cited by: 6
Author(s): Paciorek Cj, Charles V. Cogbill, Jody A. Peters, John W. Williams, David J. Mladenoff, Andria Dawson, J. S. McLachlan
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0249254

Large-scale analysis of SARS-CoV-2 spike-glycoprotein mutants demonstrates the need for continuous screening of virus isolates
Cited by: 32
Author(s): Barbara Schrörs, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Thomas Bukur, Thomas W. Rösler, Martin Löwer, Uğur Şahin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008926

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads
Cited by: 6
Author(s): Ramila Shah, Alexander J. Ruthenburg
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008870

Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death
Cited by: 10
Author(s): Irina Veith, Arianna Mencattini, Valentin Picant, Marco Serra, Marine Leclerc, Maria Colomba Comes, Fathia Mami‐Chouaib, Jacques Camonis, Stéphanie Descroix, Hamasseh Shirvani, Fatima Mechta‐Grigoriou, Gérard Zalcman, Maria Carla Parrini, Eugenio Martinelli
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008955

Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder
Cited by: 12
Author(s): Mads Lund Pedersen, Maria Ironside, Ken‐ichi Amemori, Callie L. McGrath, Min Su Kang, Ann M. Graybiel, Diego A. Pizzagalli, Michael J. Frank
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007909

Perturbation biology links temporal protein changes to drug responses in a melanoma cell line
Cited by: 14
Author(s): Elin Nyman, Richard R. Stein, Xin Jing, Weiqing Wang, Benjamin Marks, Ioannis K. Zervantonakis, Anil Korkut, Nicholas Paul Gauthier, Chris Sander
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008935

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes
Cited by: 82
Author(s): Shelbi L. Russell, Evan Pepper-Tunick, Jesper Svedberg, Ashley Byrne, Jennie Ruelas Castillo, Christopher Vollmers, Roxanne A. Beinart, Russell Corbett-Detig
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1008833

PDKit: A data science toolkit for the digital assessment of Parkinson’s Disease
Cited by: 2
Author(s): Cosmin Stamate, Joan Saez Pons, David Weston, George Roussos
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0226691

Distribution of aerophilous diatom communities associated with terrestrial green macroalgae in the South Shetland Islands, Maritime Antarctica
Cited by: 2
Author(s): Juliana Ferreira da Silva, Maria Angélica Oliveira Linton, Raylane Ribeiro da Anunciação, Eduardo Pereira da Silva, Rodrigo Paidano Alves, Adriano Luís Schünemann, Filipe de Carvalho Victória, Margéli Pereira de Albuquerque, Antônio Batista Pereira
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1007840

An open source tool to infer epidemiological and immunological dynamics from serological data: serosolver
Cited by: 12
Author(s): James A. Hay, Amanda Minter, Kylie E. C. Ainslie, Justin Lessler, Bingyi Yang, Derek A. T. Cummings, Adam J. Kucharski, Steven Riley
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008786

Physiologically based pharmacokinetic/pharmacodynamic model for the prediction of morphine brain disposition and analgesia in adults and children
Cited by: 9
Author(s): Laurens F. M. Verscheijden, Carlijn H. C. Litjens, Jan B. Koenderink, Ron H.J. Mathijssen, Marcel M. Verbeek, Saskia N. de Wildt, Frans G. M. Rüssel
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0254852

Ward-level factors associated with methicillin-resistant Staphylococcus aureus acquisition–an electronic medical records study in Singapore
Cited by: 2
Author(s): Zaw Tun, Dale Fisher, Sharon Salmon, Clarence C. Tam
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0253814

Mortality and morbidity of asthma and chronic obstructive pulmonary disease associated with ambient environment in metropolitans in Taiwan
Cited by: 9
Author(s): Yasmin Zafirah, Yu‐Kai Lin, Gerry Andhikaputra, Liwen Deng, Fung‐Chang Sung, Yu Chun Wang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1009298

Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
Cited by: 8
Author(s): Natalie Schaworonkow, Bradley Voytek
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008377

Active probing to highlight approaching transitions to ictal states in coupled neural mass models
Cited by: 2
Author(s): Vinícius Rezende Carvalho, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo M. A. M. Mendes
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007851

LMSM: A modular approach for identifying lncRNA related miRNA sponge modules in breast cancer
Cited by: 16
Author(s): Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007249

Predicting Meridian in Chinese traditional medicine using machine learning approaches
Cited by: 33
Author(s): Yinyin Wang, Mohieddin Jafari, Yun Tang, Jing Tang
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0243422

Socioeconomic and behavioral determinants of cardiovascular diseases among older adults in Belgium and France: A longitudinal analysis from the SHARE study
Cited by: 6
Author(s): Hamid Yimam Hassen, Hilde Bastiaens, Kathleen Van Royen, Steven Abrams
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008489

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication in vitro
Cited by: 40
Author(s): Haiping Zhang, Yang Yang, Junxin Li, Min Wang, Konda Mani Saravanan, Jinli Wei, Jiawei Ng, Tofazzal Hossain, Maoxuan Liu, Huiling Zhang, Xiaohu Ren, Yi Pan, Yin Peng, Yi Shi, Xiaochun Wan, Yingxia Liu, Yanjie Wei
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007634

Doubting what you already know: Uncertainty regarding state transitions is associated with obsessive compulsive symptoms
Cited by: 12
Author(s): Isaac Fradkin, Casimir J. H. Ludwig, Eran Eldar, Jonathan D. Huppert
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009824

pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread
Cited by: 12
Author(s): Tomasz H. Benedyk, Julia Muenzner, Viv Connor, Yue Han, Katherine A. Brown, Kaveesha J. Wijesinghe, Yunhui Zhuang, Susanna Colaco, Guido A. Stoll, Owen S. Tutt, Stanislava Svobodova, Dmitri I. Svergun, Neil Bryant, Janet E. Deane, Andrew E. Firth, Cy M. Jeffries, Colin M. Crump, Stephen C. Graham
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0255370

Inclusion of photoautotrophic cultivated diatom biomass in salmon feed can deter lice
Cited by: 2
Author(s): Hans Christian Eilertsen, Edel O. Elvevoll, Ingeborg Hulda Giæver, Jon Brage Svenning, Lars Dalheim, Ragnhild Aven Svalheim, Birthe Vang, Sten Ivar Siikavuopio, Ragnhild Dragøy, Richard Andre Ingebrigtsen, Espen Hansen, Anette Hustad, Karl‐Erik Eilertsen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009734

Divergent metabolism between Trypanosoma congolense and Trypanosoma brucei results in differential sensitivity to metabolic inhibition
Cited by: 10
Author(s): Pieter C. Steketee, Emily A. Dickie, James Iremonger, Kathryn Crouch, Edith Paxton, Siddharth Jayaraman, Omar A. Alfituri, Georgina Awuah‐Mensah, Ryan Ritchie, Achim Schnaufer, T.G. Rowan, Harry P. de Koning, Catarina Gadelha, Bill Wickstead, Michael P. Barrett, Liam J. Morrison
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1009250

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA
Cited by: 7
Author(s): Zhonghe Shao, Ting Wang, Meng Zhang, Zhou Jiang, Shuiping Huang, Ping Zeng
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008018

Visual perception of liquids: Insights from deep neural networks
Cited by: 11
Author(s): Jan Jaap R. van Assen, Shin’ya Nishida, Roland W. Fleming
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0235741

Changes in infant non-nutritive sucking throughout a suck sample at 3-months of age
Cited by: 6
Author(s): Emily Zimmerman, Thomas Carpenito, Alaina Martens
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0254072

Changes in the structure and composition of the ‘Mexical’ scrubland bee community along an elevational gradient
Cited by: 5
Author(s): Sergio Osorio-Canadas, Noé Flores-Hernández, Tania Sánchez-Ortiz, Alfonso Valiente‐Banuet
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0244408

Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep
Cited by: 13
Author(s): Seyed Mehdi Esmaeili-Fard, Mohsen Gholizadeh, Seyed Hasan Hafezian, Rostam Abdollahi-Arpanahi
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0225658

Highly multiplexed quantitative PCR-based platform for evaluation of chicken immune responses
Cited by: 15
Author(s): Dominika Borowska, Richard Kuo, Richard Bailey, Kellie Watson, Pete Kaiser, Lonneke Vervelde, Mark P. Stevens
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0245064

Racial and geographic variation in effects of maternal education and neighborhood-level measures of socioeconomic status on gestational age at birth: Findings from the ECHO cohorts
Cited by: 19
Author(s): Anne L. Dunlop, Alicynne Glazier Essalmi, Lyndsay Alvalos, Carrie V. Breton, Carlos A. Camargo, Whitney Cowell, Dana Dabelea, Stephen R. Dager, Cristiane S. Duarte, Amy J. Elliott, Raina N. Fichorova, James E. Gern, Monique M. Hedderson, Elizabeth Hom Thepaksorn, Kathi Huddleston, Margaret R. Karagas, Ken Kleinman, Leslie D. Leve, Ximin Li, Yijun Li, Augusto A. Litonjua, Yunin Ludena-Rodriguez, Juliette C. Madan, Julio Mateus Nino, Cynthia McEvoy, Thomas G. O’Connor, Amy Padula, Nigel Paneth, Frederica P. Perera, Sheela Sathyanarayana, Rebecca J. Schmidt, Robert T. Schultz, Jessica Snowden, Joseph B. Stanford, Leonardo Trasande, Heather E. Volk, William Wheaton, Rosalind J. Wright, Monica McGrath
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007453

TAPES: A tool for assessment and prioritisation in exome studies
Cited by: 15
Author(s): Alexandre Xavier, Rodney J. Scott, Bente A. Talseth‐Palmer
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0234494

A cost efficient spatially balanced hierarchical sampling design for monitoring boreal birds incorporating access costs and habitat stratification
Cited by: 10
Author(s): Steven L. Van Wilgenburg, C. Lisa Mahon, Greg Campbell, Logan J. T. McLeod, Margaret Campbell, Dean R. Evans, Wendy E. Easton, Charles M. Francis, Samuel Haché, Craig S. Machtans, Caitlin Mader, C. Lisa Mahon, Robert Rußell, Adam C. Smith, Peter Thomas, Judith D. Toms, Junior A. Tremblay
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0245525

Water quality assessment and source identification of the Shuangji River (China) using multivariate statistical methods
Cited by: 19
Author(s): Junzhao Liu, Dong Zhang, Qiuju Tang, Hongbin Xu, Shanheng Huang, Dan Shang, Ruxue Liu
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008061

Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
Cited by: 16
Author(s): Brian Coventry, David Baker
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0235263

Visualisation tools for dependent peptide searches to support the exploration of in vitro protein modifications
Cited by: 2
Author(s): George W. Preston, Liping Yang, David H. Phillips, Claudia S. Maier
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1009041

Ten simple rules for making a vocabulary FAIR
Cited by: 19
Author(s): Simon J. Cox, Alejandra N. González-Beltrán, Barbara Magagna, Maria-Cristina Marinescu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008219

A simple, scalable approach to building a cross-platform transcriptome atlas
Cited by: 12
Author(s): Paul W. Angel, Nadia Rajab, Yidi Deng, Chris M. Pacheco, Tyrone Chen, Kim‐Anh Lê Cao, Jarny Choi, Christine A. Wells
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1008114

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data
Cited by: 9
Author(s): Sára Saray, Christian Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen Alina Lupaşcu, Luca Bologna, Werner Van Geit, Armando Romani, Andrew Davison, Eilif Müller, Tamás F. Freund, Szabolcs Káli
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0236944

Impact of time and temperature on gut microbiota and SCFA composition in stool samples
Cited by: 9
Author(s): Janet L. Cunningham, Ludvig Bramstång, Abhijeet Singh, Shishanthi Jayarathna, Annica J. Rasmusson, Ali A. Moazzami, Bettina Müller
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007847

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions
Cited by: 18
Author(s): Gregory L. Medlock, Thomas J. Moutinho, Jason A. Papin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008003

Biological network growth in complex environments: A computational framework
Cited by: 6
Author(s): Torsten Johann Paul, Philip Kollmannsberger
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008422

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
Cited by: 2
Author(s): Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0227530

Soil solution in Swiss forest stands: A 20 year's time series
Cited by: 11
Author(s): Sabine Braun, Simon Tresch, Sabine Augustin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232835

Effects of arthropod inquilines on growth and reproductive effort among metacommunities of the purple pitcher plant (Sarracenia purpurea var. montana)
Cited by: 1
Author(s): Rebecca E. Hale, Elise Powell, Leila Beikmohamadi, Mara L. Alexander
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007982

It’s about time: Analysing simplifying assumptions for modelling multi-step pathways in systems biology
Cited by: 17
Author(s): Niklas Korsbo, Henrik Jönsson
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1009127

Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread
Cited by: 2
Author(s): J. R. Giles, Derek A. T. Cummings, Bryan T. Grenfell, Andrew J. Tatem, Elisabeth zu Erbach-Schoenberg, C Jessica E Metcalf, Amy Wesolowski
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0230254

Forecasting severe grape downy mildew attacks using machine learning
Cited by: 26
Author(s): Mathilde Chen, François Brun, M. Raynal, David Makowski
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pmed.1003703

The latent tuberculosis cascade-of-care among people living with HIV: A systematic review and meta-analysis
Cited by: 17
Author(s): Mayara Lisboa Bastos, Luca Melnychuk, Jonathon R. Campbell, Olivia Oxlade, Dick Menzies
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pmed.1003115

The association of innate and adaptive immunity, subclinical atherosclerosis, and cardiovascular disease in the Rotterdam Study: A prospective cohort study
Cited by: 24
Author(s): Lana Fani, Kimberly D. van der Willik, Daniël Bos, Maarten J.G. Leening, Peter J. Koudstaal, Dimitris Rizopoulos, Rikje Ruiter, Bruno H. Ch. Stricker, Maryam Kavousi, M. Arfan Ikram
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008734

Evolution of heterogeneous perceptual limits and indifference in competitive foraging
Cited by: 2
Author(s): Richard P. Mann
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008222

Genome Complexity Browser: Visualization and quantification of genome variability
Cited by: 1
Author(s): Alexander I. Manolov, Dmitry N. Konanov, Dmitry E. Fedorov, Ivan Osmolovsky, Rinat Vereshchagin, Elena N. Ilina
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1008243

Inferring a complete genotype-phenotype map from a small number of measured phenotypes
Cited by: 7
Author(s): Zachary Sailer, Sarah H. Shafik, Robert L. Summers, Alex Joule, Alice Patterson-Robert, R. L. Martin
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0231840

Commercial integrated crop-livestock systems achieve comparable crop yields to specialized production systems: A meta-analysis
Cited by: 37
Author(s): Caitlin A. Peterson, Leonardo Deiss, Amélie C. M. Gaudin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0219652

Drone-based effective counting and ageing of hippopotamus (Hippopotamus amphibius) in the Okavango Delta in Botswana
Cited by: 16
Author(s): Victoria L. Inman, Richard T. Kingsford, Michael J. Chase, Keith E. A. Leggett
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1009409

Widespread misregulation of inter-species hybrid transcriptomes due to sex-specific and sex-chromosome regulatory evolution
Cited by: 24
Author(s): Santiago Sánchez‐Ramírez, Jörg G Weiss, Cristel G. Thomas, Asher D. Cutter
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1008277

Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly
Cited by: 42
Author(s): Robert A. Dick, Chaoyi Xu, Dustin R. Morado, Vladyslav Kravchuk, C.L. Ricana, Terri D. Lyddon, Arianna M. Broad, J. Ryan Feathers, Marc C. Johnson, Volker M. Vogt, Juan R. Perilla, John Briggs, F.K.M. Schur
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1008256

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)
Cited by: 13
Author(s): Shuonan Chen, Jackson Loper, Xiaoyin Chen, Alex Vaughan, Anthony M. Zador, Liam Paninski
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009802

Endothelial lipase mediates efficient lipolysis of triglyceride-rich lipoproteins
Cited by: 12
Author(s): Sumeet A. Khetarpal, Cecilia Vitali, Michael G. Levin, Derek Klarin, Joseph Park, Akhil Pampana, John S. Millar, Takashi Kuwano, Dhavamani Sugasini, Papasani V. Subbaiah, Jeffrey T. Billheimer, Pradeep Natarajan, Daniel J. Rader
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1009411

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Cited by: 5
Author(s): Juan L. Trincado, Marina Reixachs‐Solé, Judith Pérez-Granado, Tim Fugmann, Ferrán Sanz, Jun Yokota, Eduardo Eyras
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1009349

Acetyltransferase Enok regulates transposon silencing and piRNA cluster transcription
Cited by: 3
Author(s): Shih-Ying Tsai, Fu Huang
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1008401

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
Cited by: 35
Author(s): Jérémie Bazin, Kadarkaraisamy Mariappan, Yunhe Jiang, Thomas Blein, Ronny Völz, Martín Crespi, Heribert Hirt
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0229531

Frailty predicts surgical complications after kidney transplantation. A propensity score matched study
Cited by: 19
Author(s): Milena dos Santos Mantovani, Nyara Coelho de Carvalho, Thomáz Archangelo, Luís Gustavo Modelli de Andrade, Sebastião Pires Ferreira Filho, Ricardo de Souza Cavalcante, Paulo Roberto Kawano, Sílvia Justina Papini, Nara Aline Costa, Ricardo Augusto Monteiro de Barros Almeida
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007219

Revisiting the “satisfaction of spatial restraints” approach of MODELLER for protein homology modeling
Cited by: 11
Author(s): Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0246508

Relationships between fox populations and rabies virus spread in northern Canada
Cited by: 17
Author(s): Susan A. Nadin-Davis, Emilie Falardeau, Alex Flynn, Hugh Whitney, H. Dawn Marshall
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009669

Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids
Cited by: 5
Author(s): Romain Durand, Florence Deschênes, Vincent Burrus
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008286

Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach
Cited by: 8
Author(s): Howard Bowman, Joseph Brooks, Omid Hajilou, Alexia Zoumpoulaki, Vladimir Litvak
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0246501

Mental health stigma and professional help-seeking attitudes a comparison between Cuba and Germany
Cited by: 6
Author(s): Laura Nohr, Alexis Lorenzo Ruíz, Juan Emilio Sandoval Ferrer, Ulrike Buhlmann
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009773

CXCL1: A new diagnostic biomarker for human tuberculosis discovered using Diversity Outbred mice
Cited by: 15
Author(s): Deniz Koyuncu, M. Khalid Khan Niazi, Thomas E. Tavolara, Claudia Abeijón, Melanie Ginese, Yanghui Liao, Carolyn Mark, Aubrey G. Specht, Adam C. Gower, Blanca I. Restrepo, Daniel M. Gatti, Igor Kramnik, Metin N. Gürcan, Bülent Yener, Gillian Beamer
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008284

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants
Cited by: 5
Author(s): Adil Alsiyabi, Ariadna González-Solís, Edgar B. Cahoon, Rajib Saha
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1009768

Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages
Cited by: 6
Author(s): Ruth Forman, Larisa Logunova, Hannah Smith, Kelly Wemyss, Iris Mair, Louis Boon, Judith E. Allen, Werner Müller, Joanne L. Pennock, Kathryn J. Else
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008830

Using Hawkes Processes to model imported and local malaria cases in near-elimination settings
Cited by: 9
Author(s): H. Juliette T. Unwin, Isobel Routledge, Seth Flaxman, Marian-Andrei Rizoiu, Shengjie Lai, Justin M. Cohen, Daniel J. Weiss, Swapnil Mishra, Samir Bhatt
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1009131

MiDAS—Meaningful Immunogenetic Data at Scale
Cited by: 9
Author(s): Maciej Migdał, Dan Fu Ruan, William F. Forrest, Amir Horowitz, Christian Hammer
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0248341

Quantity and quality: Normative open-access neuroimaging databases
Cited by: 2
Author(s): S.J.S. Isherwood, Pierre‐Louis Bazin, Anneke Alkemade, Birte U. Forstmann
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1008334

Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)-driven pulmonary immunopathogenesis
Cited by: 32
Author(s): Junsong Zhang, Jun Li, Yuhong Yuan, Feng Huang, Rong Ma, Baohong Luo, Zhihui Xi, Ting Pan, Bingfeng Liu, Yiwen Zhang, Xu Zhang, Yong Luo, Jin Wang, Meng Zhao, Gen Liu, Kai Deng, Hui Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007819

DOT: Gene-set analysis by combining decorrelated association statistics
Cited by: 9
Author(s): Olga A. Vsevolozhskaya, Min Shi, Fengjiao Hu, Dmitri V. Zaykin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1008464

CRISPR editing of sftb-1/SF3B1 in Caenorhabditis elegans allows the identification of synthetic interactions with cancer-related mutations and the chemical inhibition of splicing
Cited by: 13
Author(s): Xènia Serrat, Dmytro Kukhtar, Eric Cornes, Anna Esteve‐Codina, Helena Benlloch, Germano Cecere, Julián Cerón
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pcbi.1007756

3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Cited by: 42
Author(s): Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, J. Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232384

Socio-ecological network structures from process graphs
Cited by: 11
Author(s): Angelyn R. Lao, Heriberto Cabezas, Ákos Orosz, Ferenc Friedler, Raymond R. Tan
Software Mentions: 4
Published: over 6 years ago