10.1371/journal.pone.0244637

metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics
Cited by: 5
Author(s): Romuald Laso-Jadart, Christophe Ambroise, Pierre Peterlongo, Mohammed‐Amin Madoui
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0230888

Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada
Cited by: 13
Author(s): Zonlehoua Coulibali, Athyna N. Cambouris, Léon‐Étienne Parent
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.pgen.1009294

Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0241691

Succinivibrionaceae is dominant family in fecal microbiota of Behçet’s Syndrome patients with uveitis
Cited by: 12
Author(s): Duygu Tecer, Feride Göğüş, Ayşe Kalkancı, Merve Erdoğan, Murat Hasanreisoğlu, Çağrı Ergin, Tarkan Karakan, Ramazan Kozan, Serhat Emre Coban, Kadir Serdar Diker
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0229146

Vegetation changes in temperate ombrotrophic peatlands over a 35 year period
Cited by: 20
Author(s): Nicolas Pinceloup, Monique Poulin, Marie‐Hélène Brice, Stéphanie Pellerin
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0223141

Attenuation correction using 3D deep convolutional neural network for brain 18F-FDG PET/MR: Comparison with Atlas, ZTE and CT based attenuation correction
Cited by: 36
Author(s): Paul Blanc-Durand, Maya Khalifé, B. Sgard, Sandeep Kaushik, Marine Soret, Tiss Amal, Georges El Fakhri, Marie‐Odile Habert, Florian Wiesinger, Aurélie Kas
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pcbi.1007625

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Cited by: 14
Author(s): Jordan A. Berg, Jonathan R Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0257011

Curiosity or savouring? Information seeking is modulated by both uncertainty and valence
Cited by: 12
Author(s): Lieke L. F. van Lieshout, Iris J. Traast, Floris P. de Lange, Roshan Cools
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0219807

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm
Cited by: 12
Author(s): Korin Eckstrom, John W. Barlow
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0246656

Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile
Cited by: 10
Author(s): Daniel Kurth, Darío Elías, María Cecilia Rasuk, Manuel Contreras, Marı́a Eugenia Farı́as
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0235328

Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections
Cited by: 10
Author(s): Liang Dong, Joshua R. Watson, Sha Cao, Samuel Arregui, Vijay Saxena, John Ketz, Abduselam K. Awol, Daniel M. Cohen, Jeffrey M. Caterino, David S. Hains, Andrew L. Schwaderer
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0219874

Decision-making flexibility in New Caledonian crows, young children and adult humans in a multi-dimensional tool-use task
Cited by: 7
Author(s): Rachael Miller, Romana Gruber, Anna Frohnwieser, Martina Schiestl, Sarah A. Jelbert, Russell D. Gray, Markus Boeckle, Alexander Taylor, Nicola S. Clayton
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0250282

Understanding interactions between risk factors, and assessing the utility of the additive and multiplicative models through simulations
Cited by: 5
Author(s): Lina-Marcela Diaz-Gallo, Boel Brynedal, Helga Westerlind, Rickard Sandberg, Daniel Ramsköld
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008769

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Cited by: 1
Author(s): Song He, Xinyu Song, Xisheng Yang, Jianyang Yu, Yao Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0252069

A machine learning prediction model for waiting time to kidney transplant
Cited by: 7
Author(s): Juliana Feiman Sapiertein Silva, Gustavo Fernandes Ferreira, Marcelo Perosa, Hong Si Nga, Luís Gustavo Modelli de Andrade
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008807

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
Cited by: 7
Author(s): Andreas Haahr Larsen, Lilya Tata, Laura John, Mark S. P. Sansom
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0246663

An open-sourced, web-based application to analyze weekly excess mortality based on the Short-term Mortality Fluctuations data series
Cited by: 38
Author(s): László Németh, Dmitri A. Jdanov, Vladimir M. Shkolnikov
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1008804

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Cited by: 24
Author(s): Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, F. Schmitz‐Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, R. Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0236878

Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes
Cited by: 12
Author(s): Daniela Vergara, Reggie Gaudino, Thomas Blank, Brian Keegan
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pgen.1009038

Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas
Cited by: 40
Author(s): Erin Calfee, Marcelo Nicolás Agra, Marí­a Alejandra Palacio, Santiago R. Ramírez, Graham Coop
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0256457

Colombia’s bioregions as a source of useful plants
Cited by: 3
Author(s): Nadia Bystriakova, Carolina Tovar, Alexandre K. Monro, Justin Moat, Pablo Hendrigo, Julia Carretero, Germán Torres-Morales, Mauricio Diazgranados
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0225556

IL-18/IL-37/IP-10 signalling complex as a potential biomarker for discriminating active and latent TB
Cited by: 20
Author(s): Sebastian Wawrocki, Michał Seweryn, Grzegorz Kielnierowski, Wiesława Rudnicka, Marcin Włodarczyk, Magdalena Druszczyńska
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1009353

Fitness landscape of a dynamic RNA structure
Cited by: 5
Author(s): Valerie W. C. Soo, Jacob B. Swadling, Aline Faure, Tobias Warnecke
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0233211

Molecular diversity and genetic structure of Saccharum complex accessions
Cited by: 15
Author(s): Carolina Medeiros, Thiago Willian Almeida Balsalobre, Monalisa Sampaio Carneiro
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0244877

Towards remote monitoring in pediatric care and clinical trials—Tolerability, repeatability and reference values of candidate digital endpoints derived from physical activity, heart rate and sleep in healthy children
Cited by: 10
Author(s): Matthijs D Kruizinga, N van der Heide, A. C. Moll, Ahnjili Zhuparris, Yalçin Yavuz, Marieke L. de Kam, Frederik E. Stuurman, Adam F. Cohen, Gertjan J. Driessen
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0237881

Identification of key odorants in honeysuckle by headspace-solid phase microextraction and solvent-assisted flavour evaporation with gas chromatography-mass spectrometry and gas chromatograph-olfactometry in combination with chemometrics
Cited by: 6
Author(s): Keran Su, Xin Zhang, Shao-Quan Liu, LiHui Jia, Benjamin Lassabliere, Kim Huey Ee, Aileen Pua, Rui Min Vivian Goh, Jingcan Sun, Bin Yu, XiaoXue Hu
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0222898

Bayesian hierarchical models for disease mapping applied to contagious pathologies
Cited by: 7
Author(s): Sylvain Coly, Myriam Garrido, David Abrial, Anne-Françoise Yao
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0233823

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1
Cited by: 8
Author(s): Gina Chaput, Andrew F. Billings, Lani DeDiego, Roberto Orellana, Joshua N. Adkins, Carrie Nicora, Young Mo Kim, Rosalie K. Chu, Blake A. Simmons, Kristen M. DeAngelis
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pgen.1008546

Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation
Cited by: 53
Author(s): Máté Pálfy, G Schulze, Eivind Valen, Nadine L. Vastenhouw
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0257726

Specificity of spiders among fear- and disgust-eliciting arthropods: Spiders are special, but phobics not so much
Cited by: 11
Author(s): Eva Landová, Markéta Janovcová, Iveta Štolhoferová, Silvie Rádlová, Petra Frýdlová, Kristýna Sedláčková, Daniel Frynta
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1009591

RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility
Cited by: 17
Author(s): Peiwei Chen, Yicheng Luo, Alexei A. Aravin
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0232648

Climatic drivers of Verticillium dahliae occurrence in Mediterranean olive-growing areas of southern Spain
Cited by: 1
Author(s): Juan M. Requena‐Mullor, José Manuel Garcı́a-Garrido, Pilar Garcı́a Garcı́a, Estefanı́a Rodrı́guez
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0240010

Framing COVID-19: How we conceptualize and discuss the pandemic on Twitter
Cited by: 135
Author(s): Philipp Wicke, Marianna Bolognesi
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0248756

Veteran trees have divergent effects on beetle diversity and wood decomposition
Cited by: 2
Author(s): Ross Wetherbee, Tone Birkemoe, Ryan C. Burner, Anne Sverdrup‐Thygeson
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0243807

Optimised generation of iPSC-derived macrophages and dendritic cells that are functionally and transcriptionally similar to their primary counterparts
Cited by: 17
Author(s): Susan J. Monkley, Jayendra Kumar Krishnaswamy, Melker Göransson, Maryam Clausen, Johan Meuller, Kristofer Thörn, Ryan Hicks, Stephen Delaney, Louise Stjernborg
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0232065

Tropical fishes vanished after the operation of a nuclear power plant was suspended in the Sea of Japan
Cited by: 3
Author(s): Reiji Masuda
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1007800

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
Cited by: 30
Author(s): Avtar Roopra
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0243746

Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs
Cited by: 7
Author(s): Ryuta Shioi, Fumika Karaki, Hirosuke Yoshioka, Tomomi Noguchi‐Yachide, Minoru Ishikawa, Kosuke Dodo, Yuichi Hashimoto, Mikiko Sodeoka, Kenji Ohgane
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0255667

Towards a better characterisation of deep-diving whales’ distributions by using prey distribution model outputs?
Cited by: 7
Author(s): Auriane Virgili, Laura Hedon, Matthieu Authier, Beatriz Calmettes, Diane Claridge, Timothy V. N. Cole, Peter J. Corkeron, Ghislain Dorémus, Charlotte Dunn, Timothy E. Dunn, Sophie Laran, Patrick Lehodey, Mark Lewis, Maité Louzao, Laura Mannocci, José Martínez‐Cedeira, Pascal Monestiez, Debra L. Palka, Emeline Pettex, Jason J. Roberts, Leire Ruiz, Camilo Saavedra, M.B. Santos, Olivier Van Canneyt, José Antonio Vázquez Bonales, Vincent Ridoux
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0241848

Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle)
Cited by: 3
Author(s): Hyo Jun Lee, Young Jin Chung, Sungbong Jang, Dongil Seo, Hak Kyo Lee, Duhak Yoon, Dajeong Lim, Seung Hwan Lee
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0238497

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)
Cited by: 2
Author(s): Nabil F. Saba, Ashok R. Dinasarapu, Kelly R. Magliocca, Bhakti Dwivedi, Sandra Seby, Zhaohui S. Qin, Mihir R. Patel, Christopher C. Griffith, Xu Wang, Mark W. El‐Deiry, Conor E. Steuer, Jeanne Kowalski, Dong M. Shin, Michael E. Zwick, Zhuo Georgia Chen
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1008864

­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods
Cited by: 52
Author(s): Samuel H. Lewis, Laura Ross, Stevie A. Bain, Eleni Pahita, Stephen A. Smith, Richard Cordaux, Eric A. Miska, Boris Lenhard, Francis M. Jiggins, Peter Sarkies
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0254366

A clinical prediction model to identify children at risk for revisits with serious illness to the emergency department: A prospective multicentre observational study
Cited by: 5
Author(s): Ruud Nijman, Dorine H. Borensztajn, Joany M Zachariasse, Carine Hajema, Paulo Freitas, Susanne Greber‐Platzer, Frank J Smit, Claudio F. Alves, Johan van der Lei, Ewout W. Steyerberg, Ian Maconochie, Henriëtte A. Moll
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1008531

ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1009801

Tramtrack acts during late pupal development to direct ant caste identity
Cited by: 6
Author(s): Karl M. Glastad, Linyang Ju, Shelley L. Berger
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0240538

Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate
Cited by: 5
Author(s): Jana Bürger, Andrey V. Malyshev, Nathalie Colbach
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1009398

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies
Cited by: 37
Author(s): Arjun Bhattacharya, Yun Li, Michael I. Love
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0224366

Horizontal seed dispersal by dung beetles reduced seed and seedling clumping, but did not increase short-term seedling establishment
Cited by: 12
Author(s): Lina Adonay Urrea‐Galeano, Ellen Andresen, Rosamond Coates, Francisco Mora Ardila, Alfonso Díaz Rojas, Gabriel Ramos‐Fernández
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pcbi.1008277

EventEpi—A natural language processing framework for event-based surveillance
Cited by: 11
Author(s): Auss Abbood, Alexander Ullrich, Rüdiger Busche, Stéphane Ghozzi
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pcbi.1008302

Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals
Cited by: 28
Author(s): Etienne Combrisson, Timothy Nest, Andrea Brovelli, Robin A. A. Ince, Juan L.P. Soto, Aymeric Guillot, Karim Jerbi
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0233645

Freewater estimatoR using iNtErpolated iniTialization (FERNET): Characterizing peritumoral edema using clinically feasible diffusion MRI data
Cited by: 24
Author(s): Drew Parker, Abdol Aziz Ould Ismail, Ronald L. Wolf, Steven Brem, Shelton S. Alexander, Wes Hodges, Ofer Pasternak, Emmanuel Caruyer, Ragini Verma
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1007553

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Cited by: 18
Author(s): David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0236732

Determining mean and standard deviation of the strong gravity prior through simulations
Cited by: 3
Author(s): Björn Jörges, Joan López‐Moliner
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pcbi.1008414

Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
Cited by: 4
Author(s): Rachael L. Sumner, Meg J. Spriggs, Alexander D Shaw
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pmed.1003795

Differences in outcomes of mandatory motorcycle helmet legislation by country income level: A systematic review and meta-analysis
Cited by: 9
Author(s): Jacob Lepard, Riccardo Spagiari, Jacquelyn Corley, Ernest J. Barthélemy, Eliana Kim, Rolvix H. Patterson, Sara Venturini, Megan Still, Yu Tung Lo, Gail Rosseau, Rania A. Mekary, Kee B. Park
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pntd.0009633

Identification of potential biomarkers in dengue via integrated bioinformatic analysis
Cited by: 5
Author(s): Lisha Xie, Xin Yin, Jie Bi, Hongyu Luo, Xun‐Jie Cao, Yu-Wen Ma, Ye-Ling Liu, Jianwen Su, Geng-Ling Lin, Xu‐Guang Guo
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1007973

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
Cited by: 9
Author(s): Will Xiao, Gabriel Kreiman
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0256929

Modelling the effects of the repellent scent marks of pollinators on their foraging efficiency and the plant-pollinator community
Cited by: 0
Author(s): Elise Verrier, Emmanuelle Baudry, Carmen Bessa‐Gomes
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1009263

A multi-objective genetic algorithm to find active modules in multiplex biological networks
Cited by: 7
Author(s): Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaı̈s Baudot
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0249231

Risk factors for in-hospital mortality in laboratory-confirmed COVID-19 patients in the Netherlands: A competing risk survival analysis
Cited by: 16
Author(s): Gerine Nijman, Maike H M Wientjes, Jordache Ramjith, Nico Janssen, Jacobien J. Hoogerwerf, Evertine J. Abbink, Marc Blaauw, Ton Dofferhoff, Marjan van Apeldoorn, Karin Veerman, Quirijn de Mast, Jaap ten Oever, Wouter Hoefsloot, Monique H. Reijers, Reinout van Crevel, Josephine S. van de Maat
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1009197

Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection
Cited by: 1
Author(s): Tessa Lloyd, Pia Steigler, Cheleka A M Mpande, Virginie Rozot, Boitumelo Mosito, Constance Schreuder, Timothy D. Reid, Mark Hatherill, Thomas J. Scriba, Francesca Little, Elisa Nemes
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pmed.1003084

Quantification of glucose-6-phosphate dehydrogenase activity by spectrophotometry: A systematic review and meta-analysis
Cited by: 29
Author(s): Daniel Pfeffer, Benedikt Ley, Rosalind E. Howes, Patrick Adu, Mohammad Shafiul Alam, Pooja Bansil, Yap Boum, Marcelo Augusto Mota Brito, Pimlak Charoenkwan, Archie Clements, Liwang Cui, Zeshuai Deng, OJ Egesie, Fe Esperanza Espino, Michael E. von Fricken, Muzamil Mahdi Abdel Hamid, Yongshu He, Gisela Henriques, Wasif Ali Khan, Nimol Khim, Saorin Kim, Marcus Lacerda, Chanthap Lon, Asrat Hailu Mekuria, Didier Ménard, Wuelton Marcelo Monteiro, François Nosten, Nwe Nwe Oo, Sampa Pal, Duangdao Palasuwan, Sunil Parikh, Ayodhia Pitaloka Pasaribu, Jeanne Rini Poespoprodjo, David J. Price, Arantxa Roca-Feltrer, Michelle E. Roh, David Saunders, Michele Spring, Inge Sutanto, Kamala Ley-Thriemer, Thomas A. Weppelmann, Lorenz von Seidlein, Ari Winasti Satyagraha, Germana Bancone, Gonzalo J. Domingo, Ric Price
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0246464

Is it feasible to detect FLOSS version release events from textual messages? A case study on Stack Overflow
Cited by: 0
Author(s): Artur Sokolovsky, Thomas Groß, Jaume Bacardit
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008315

Leveraging functional annotation to identify genes associated with complex diseases
Cited by: 13
Author(s): Wei Liu, Mo Li, Wenfeng Zhang, Geyu Zhou, Weijie Xing, Jiawei Wang, Qiongshi Lu, Hongyu Zhao
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1009474

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps
Cited by: 6
Author(s): Floria M. K. Uy, Christopher M. Jernigan, Natalie C. Zaba, Eshan Mehrotra, Sara Miller, Michael J. Sheehan
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1008569

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
Cited by: 16
Author(s): Andreas Tjärnberg, Omar Mahmood, Christopher Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008044

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
Cited by: 15
Author(s): Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C Censin, Samantha Laber, Hanieh Yaghootkar, Nilüfer Rahmioğlu, Emilie Pastel, Katarina Kos, Andrew M. Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pone.0245157

A comparison of machine learning models versus clinical evaluation for mortality prediction in patients with sepsis
Cited by: 38
Author(s): William P T M van Doorn, Patricia M. Stassen, Hella F. Borggreve, Maaike J. Schalkwijk, Judith Stoffers, Otto Bekers, Steven J.R. Meex
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0252233

A novel method of screening combinations of angiostatics identifies bevacizumab and temsirolimus as synergistic inhibitors of glioma-induced angiogenesis
Cited by: 3
Author(s): Michael I. Dorrell, Heidi R. Kast-Woelbern, Ryan T. Botts, Stephen Bravo, Jacob R. Tremblay, Sarah Giles, Jessica F. Wada, MaryAnn Alexander, Eric Alejandro García, Gabriel Villegas, Caylor B. Booth, Kaitlyn J. Purington, Haylie M. Everett, Erik N. Siles, Michael Wheelock, Jordan A. Silva, Bridget M. Fortin, Connor A. Lowey, Allison L. Hale, Troy L. Kurz, Jack C. Rusing, Dawn M. Goral, Paul Thompson, Alec M. Johnson, Daniel J. Elson, Roujih Tadros, Charisa E. Gillette, Carley Coopwood, Amy L. Rausch, Jeffrey M. Snowbarger
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pgen.1009432

Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0238669

Protected areas network is not adequate to protect a critically endangered East Africa Chelonian: Modelling distribution of pancake tortoise, Malacochersus tornieri under current and future climates
Cited by: 9
Author(s): Abraham Eustace, Luíz Fernando Esser, Rudolf Mremi, Patrick K. Malonza, Reginald T. Mwaya
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0240802

OrganoidTracker: Efficient cell tracking using machine learning and manual error correction
Cited by: 32
Author(s): Rutger Nico Ulbe Kok, Laetitia Hebert, Guizela Huelsz-Prince, Yvonne J. Goos, Xuan Zheng, Katarzyna Bożek, Greg J. Stephens, Sander J. Tans, Jeroen S. van Zon
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0243916

Online biology degree program broadens access for women, first-generation to college, and low-income students, but grade disparities remain
Cited by: 17
Author(s): Chris Mead, K. Supriya, Yi Zheng, Ariel D. Anbar, James P. Collins, Paul C. LePore, Sara E. Brownell
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pcbi.1007549

BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
Cited by: 41
Author(s): Manoj Kumar, Cameron T. Ellis, Qingming Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk‐Browne, Kenneth A. Norman
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0226666

Habitat quality, configuration and context effects on roe deer fecundity across a forested landscape mosaic
Cited by: 7
Author(s): Valentina Zini, Kristin Wäber, Paul M. Dolman
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pntd.0009776

The association between tropical cyclones and dengue fever in the Pearl River Delta, China during 2013-2018: A time-stratified case-crossover study
Cited by: 7
Author(s): Chuanxi Li, Qi Zhao, Zhe Zhao, Qiyong Liu, Wei Ma
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0229001

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome
Cited by: 45
Author(s): Samuel J. Bowers, Fernando Vargas, Antonio González, Shannon He, Peng Jiang, Pieter C. Dorrestein, Rob Knight, Kenneth P. Wright, Christopher A. Lowry, Monika Fleshner, Martha Hotz Vitaterna, Fred W. Turek
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0256793

Designing and validating a Markov model for hospital-based addiction consult service impact on 12-month drug and non-drug related mortality
Cited by: 5
Author(s): Caroline King, Honora Englander, P Todd Korthuis, Joshua A. Barocas, K. John McConnell, Cynthia D. Morris, Ryan Cook
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0240995

Risk factors for surgical site infections using a data-driven approach
Cited by: 5
Author(s): Johan Magnus van Niekerk, Margreet C. Vos, Alfred Stein, Louise Marie Antoinette Braakman-Jansen, Anne F. Voor in ’t holt, Julia E.W.C. van Gemert-Pijnen
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0243301

Response of oat morphologies, root exudates, and rhizosphere fungal communities to amendments in a saline-alkaline environment
Cited by: 5
Author(s): Peina Lu, Tony Yang, Lijun Li, Baoping Zhao, Jinghui Liu
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pmed.1002984

Incidence of maternal peripartum infection: A systematic review and meta-analysis
Cited by: 64
Author(s): Susannah Woodd, Ana Montoya, María Barreix, Li Pi, Clara Calvert, Andrea M. Rehman, Doris Chou, Oona M. R. Campbell
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0254829

Tumor infiltrating lymphocytes associated competitive endogenous RNA networks as predictors of outcome in hepatic carcinoma based on WGCNA analysis
Cited by: 1
Author(s): Ying He, Xu Rui, Li Peng, Xiaoyu Hu
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0250725

Parrotfish corallivory on stress-tolerant corals in the Anthropocene
Cited by: 7
Author(s): Víctor Huertas, Renato A. Morais, Roberta M. Bonaldo, David R. Bellwood
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0239518

Peer review and preprint policies are unclear at most major journals
Cited by: 26
Author(s): Thomas Klebel, Stefan Reichmann, Jessica Polka, Gary S. McDowell, Naomi Penfold, Samantha Hindle, Tony Ross-Hellauer
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0239021

Estimating the effect of a scanner upgrade on measures of grey matter structure for longitudinal designs
Cited by: 8
Author(s): Evelyn Medawar, Ronja Thieleking, Iryna Manuilova, Maria Paerisch, Arno Villringer, A. Veronica Witte, Frauke Beyer
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.ppat.1009539

Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis
Cited by: 8
Author(s): Jae Hak Son, Brian L. Weiss, Daniela Schneider, Kiswend-Sida Mikhailou Dera, Fabian Gstöttenmayer, Robert Opiro, Richard Echodu, Norah P. Saarman, Geoffrey M. Attardo, Maria G Onyango, Adly M. M. Abd-Alla, Serap Aksoy
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.ppat.1009063

Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis
Cited by: 20
Author(s): Nathan D. Hicks, Samantha R. Giffen, Peter H. Culviner, Michael C. Chao, Charles L. Dulberger, Qingyun Liu, Sydney Stanley, J. A. Brown, Jaimie Sixsmith, Ian D. Wolf, Sarah M. Fortune
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0238396

Comparison between flaming, mowing and tillage weed control in the vineyard: Effects on plant community, diversity and abundance
Cited by: 22
Author(s): Matia Mainardis, Francesco Boscutti, Maria del Mar Rubio Cebolla, Gianfranco Pergher
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.ppat.1009029

Drivers of within-host genetic diversity in acute infections of viruses
Cited by: 22
Author(s): Maoz Gelbart, Sheri Harari, Ya’ara Ben-Ari, Talia Kustin, Dana Wolf, Michal Mandelboim, Orna Mor, Pleuni S. Pennings, Adi Stern
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.ppat.1009916

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Cited by: 6
Author(s): Gonché Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0240041

Towards an open and decentralized case law curation ecosystem
Cited by: 1
Author(s): Eleni Panagou, Manolis Vavalis
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.ppat.1008754

JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glands
Cited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: about 6 years ago

10.1038/s41598-018-31866-9

Child Weight Gain Trajectories Linked To Oral Microbiota Composition
Cited by: 38
Author(s): Sarah Jane Craig, Daniel Blankenberg, Alice Parodi, Ian M. Paul, Leann L. Birch, Jennifer S. Savage, Michele Marini, Jennifer L. Stokes, Anton Nekrutenko, Matthew Reimherr, Francesca Chiaromonte, Kateryna D. Makova
Software Mentions: 6
Published: about 8 years ago

10.1371/journal.pone.0227639

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Cited by: 15
Author(s): Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pmed.1003750

The prevalence of mental disorders among homeless people in high-income countries: An updated systematic review and meta-regression analysis
Cited by: 80
Author(s): Stefan Gutwinski, Stefanie Schreiter, Karl Deutscher, Seena Fazel
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.ppat.1009875

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis
Cited by: 14
Author(s): Ian J. Groves, Emma L A Drane, Marco Michalski, Jack Monahan, Cinzia G. Scarpini, Stephen Smith, Giovanni Bussotti, Csilla Várnai, Stefan Schoenfelder, Peter Fraser, Anton J. Enright, Nicholas Coleman
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0229087

Risk factors for loneliness: The high relative importance of age versus other factors
Cited by: 59
Author(s): Bridget Shovestul, Han Jian-guo, Laura Germine, David Dodell-Feder
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1007869

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Cited by: 8
Author(s): Magali Richard, Clémentine Decamps, Florent Chuffart, Élisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0235726

Diversity of mosquitoes (Diptera: Culicidae) collected in different types of larvitraps in an Amazon rural settlement
Cited by: 8
Author(s): João Aprígio Guerra de Almeida, Heliana Christy Matos Belchior, Claudia María Ríos-Velásquez, Felipe Arley Costa Pessoa
Software Mentions: 6
Published: almost 6 years ago