10.1371/journal.pone.0221543

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
Cited by: 18
Author(s): Paltu Kumar Dhal, Gérmán A. Kopprio, Astrid Gärdes
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: almost 6 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: over 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: almost 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: almost 6 years ago

10.1371/journal.pntd.0009500

Lay attitudes and misconceptions and their implications for the control of brucellosis in an agro-pastoral community in Kilombero district, Tanzania
Cited by: 6
Author(s): Caroline M. Mburu, Salome A. Bukachi, Kathrin H. Tokpa, Gilbert Fokou, Khamati Shilabukha, Mangi J. Ezekiel, Bassirou Bonfoh, Rudovick Kazwala, Katharina Kreppel
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pntd.0008962

Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination
Cited by: 14
Author(s): Lucas E. Buyon, Ana María Santamaría, Angela M. Early, Mario Quijada, Itza Barahona, José Lasso, Mario Ávila, Sarah K. Volkman, Matthias Marti, Daniel E. Neafsey, Nicanor Obaldía
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pntd.0008179

Predicting disease risk areas through co-production of spatial models: The example of Kyasanur Forest Disease in India’s forest landscapes
Cited by: 26
Author(s): Bethan V. Purse, Narayanaswamy Darshan, Gudadappa S. Kasabi, F. Gerard, Abhishek Samrat, Charles George, Abi Tamim Vanak, Meera Anna Oommen, Mujeeb Rahman, Sarah J. Burthe, Juliette Young, Prashanth Nuggehalli Srinivas, Stefanie Schäfer, Peter A. Henrys, Vijay K. Sandhya, Mohammed Mudassar Chanda, Manoj Murhekar, S.L. Hoti, Shivani K. Kiran
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pntd.0009567

Inequalities of visceral leishmaniasis case-fatality in Brazil: A multilevel modeling considering space, time, individual and contextual factors
Cited by: 18
Author(s): Gláucia Cota, Astrid Erber, Eva Schernhammer, Taynãna César Simões
Software Mentions: 6
Published: over 4 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: almost 5 years ago

10.1371/journal.pgen.1009035

The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations
Cited by: 12
Author(s): Fredrika Åsenius, T.J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah Marzi, David Williams
Software Mentions: 6
Published: about 5 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: over 4 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: about 5 years ago

10.1371/journal.pntd.0009537

Spatio-temporal modelling of the first Chikungunya epidemic in an intra-urban setting: The role of socioeconomic status, environment and temperature
Cited by: 10
Author(s): Laís Picinini Freitas, Alexandra M. Schmidt, William Cossich, Oswaldo Gonçalves Cruz, Marília Sá Carvalho
Software Mentions: 6
Published: over 4 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 5 years ago

10.1371/journal.pone.0239154

Assessing the low complexity of protein sequences via the low complexity triangle
Cited by: 4
Author(s): Pablo Mier, Miguel A. Andrade‐Navarro
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: over 4 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: over 5 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: over 4 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: about 5 years ago

10.1371/journal.pone.0244175

Rapid detection of fast innovation under the pressure of COVID-19
Cited by: 11
Author(s): Nicola Melluso, Andrea Bonaccorsi, Filippo Chiarello, Gualtiero Fantoni
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pgen.1009574

Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets
Cited by: 13
Author(s): Matthew R. Hass, Daniel Brissette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
Software Mentions: 6
Published: over 4 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: over 5 years ago

10.1371/journal.pgen.1009737

Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver
Cited by: 9
Author(s): Benjamin P. Flynn, Matthew T. Birnie, Yvonne M. Kershaw, Audrys G Pauža, Sohyoung Kim, Songjoon Baek, Mark F. Rogers, Alex Paterson, Diana A. Stavreva, David Murphy, Gordon L. Hager, Stafford Lightman, Becky Conway-Campbell
Software Mentions: 6
Published: over 4 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: about 5 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: almost 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: over 4 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: about 5 years ago

10.1371/journal.pgen.1009506

Comparative analysis reveals distinctive epigenetic features of the human cerebellum
Cited by: 11
Author(s): Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Software Mentions: 6
Published: over 4 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: about 5 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: over 4 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: over 4 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: over 4 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: almost 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: almost 6 years ago

10.1371/journal.pone.0241704

Evaluating the effectiveness of a group-based resilience intervention versus psychoeducation for emergency responders in England: A randomised controlled trial
Cited by: 19
Author(s): Jennifer Wild, Shama El-Salahi, Michelle Degli Esposti, Graham R. Thew
Software Mentions: 6
Published: about 5 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: over 4 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: over 5 years ago

10.1371/journal.pone.0251385

Improving the diagnostic recognition of thoracic endometriosis: Spotlight on a new histo-morphological indicator
Cited by: 1
Author(s): Okechukwu Charles Okafor, N Ezemba, Nnaemeka Thaddeus Onyishi, Kevin Nwabueze Ezike
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0239122

DArTSeq SNP-based markers revealed high genetic diversity and structured population in Ethiopian cowpea [Vigna unguiculata (L.) Walp] germplasms
Cited by: 26
Author(s): Selamawit Ketema, Bizuayehu Tesfaye, Gemechu Keneni, Berhanu Amsalu Fenta, Ermias Assefa, Nicolas Greliche, Eunice Machuka, Nasser Yao
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pcbi.1008495

Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology
Cited by: 5
Author(s): Ivan I. Borisov, Eugeniy Metelkin
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0252207

Genomic diversity of 39 samples of Pyropia species grown in Japan
Cited by: 4
Author(s): Yukio Nagano, Kei Kimura, Genta Kobayashi, Yoshio Kawamura
Software Mentions: 6
Published: over 4 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: over 5 years ago

10.1371/journal.pone.0236574

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya
Cited by: 11
Author(s): Edward Nderitu Karanja, Andreas Fließbach, Noah Adamtey, Anne Kelly Kambura, Martha W. Musyoka, Komi K. M. Fiaboe, Romano Mwirichia
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: over 4 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 5 years ago

10.1371/journal.pcbi.1007939

Iterative point set registration for aligning scRNA-seq data
Cited by: 3
Author(s): Amir Alavi, Ziv Bar‐Joseph
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0237713

Isn’t high school bad enough already? Rates of gender harassment and institutional betrayal in high school and their association with trauma-related symptoms
Cited by: 9
Author(s): Monika N Lind, Alexis A. Adams-Clark, Jennifer J. Freyd
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0243857

Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in NAc and PFC
Cited by: 7
Author(s): Eric Vornholt, John W. Drake, Mohammed Mamdani, Gowon O. McMichael, Zachary N. Taylor, Silviu‐Alin Bacanu, Michael F. Miles, Vladimir I. Vladimirov
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1007866

Learning clinical networks from medical records based on information estimates in mixed-type data
Cited by: 8
Author(s): Vincent Cabeli, Louis Verny, Nadir Sella, Guido Uguzzoni, Marc Verny, Hervé Isambert
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1009256

Computational identification and experimental characterization of preferred downstream positions in human core promoters
Cited by: 2
Author(s): René Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bücher, Tamar Juven‐Gershon
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008195

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution
Cited by: 9
Author(s): Wei Wen, Adam J. Mead, Supat Thongjuea
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0255436

Global distribution of sporadic sapovirus infections: A systematic review and meta-analysis
Cited by: 8
Author(s): Marta Diez‐Valcarce, Anita Kambhampati, Laura Calderwood, Aron J. Hall, Sara Mirza, Jan Vinjé
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1009316

A probabilistic model for the ultradian timing of REM sleep in mice
Cited by: 6
Author(s): Sung-Ho Park, Justin Baik, June Seok Hong, Hanna Antila, Benjamin Kurland, Shinjae Chung, Franz Weber
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0232963

Identifying the key regulators that promote cell-cycle activity in the hearts of early neonatal pigs after myocardial injury
Cited by: 11
Author(s): Eric Zhang, Thanh Nguyen, Meng Zhao, Son Do Hai Dang, Jake Y. Chen, Weihua Bian, Gregory P. Walcott
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0238285

Increased risk of adverse events in non-cancer patients with chronic and high-dose opioid use—A health insurance claims analysis
Cited by: 6
Author(s): Jakob M Burgstaller, Ulrike Held, Andri Signorell, Eva Blozik, Johann Steurer, Maria M. Wertli
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0230594

A Zipf-plot based normalization method for high-throughput RNA-seq data
Cited by: 6
Author(s): Bin Wang
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0233731

Eyebrow position in grammatical and emotional expressions in Kazakh-Russian Sign Language: A quantitative study
Cited by: 8
Author(s): Vadim Kimmelman, Alfarabi Imashev, Medet Mukushev, Anara Sandygulova
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0256503

PyPlutchik: Visualising and comparing emotion-annotated corpora
Cited by: 16
Author(s): Alfonso Semeraro, Salvatore Vilella, Giancarlo Ruffo
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0249899

A pseudomolecule assembly of the Rocky Mountain elk genome
Cited by: 2
Author(s): Rick E. Masonbrink, David P. Alt, Darrell O. Bayles, Paola M. Boggiatto, William H. Edwards, Fred M. Tatum, Jeffrey T. Williams, Jennifer H. Wilson-Welder, Aleksey V. Zimin, Andrew J. Severin, Steven C. Olsen
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008819

Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer
Cited by: 3
Author(s): Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, Dominique Stoppa‐Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0233077

Comparative transcriptomics of Diuraphis noxia and Schizaphis graminum fed wheat plants containing different aphid-resistance genes
Cited by: 2
Author(s): Lina Aguirre Rojas, Erin D. Scully, Laramy Enders, Alicia E. Timm, Deepak K. Sinha, C. Michael Smith
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1008517

Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities
Cited by: 1
Author(s): Marzia Antonella Scelsi, Valerio Napolioni, Michael D. Greicius, André Altmann
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1009350

Evaluating the effectiveness of ensemble voting in improving the accuracy of consensus signals produced by various DTWA algorithms from step-current signals generated during nanopore sequencing
Cited by: 0
Author(s): M. R. Smith, Rachel Chan, Maaz Khurram, Paul M. Gordon
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008889

Building blocks and blueprints for bacterial autolysins
Cited by: 9
Author(s): Spencer J. Mitchell, Deeptak Verma, Karl E. Griswold, Chris Bailey‐Kellogg
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1009300

MicrobeTrace: Retooling molecular epidemiology for rapid public health response
Cited by: 17
Author(s): Ellsworth Campbell, Anthony Boyles, Anupama Shankar, Jay Kim, S. P. Knyazev, Roxana Cintrón, William M. Switzer
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1007520

A novel network control model for identifying personalized driver genes in cancer
Cited by: 39
Author(s): Weifeng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao, Luonan Chen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0238557

eDNA metabarcoding as a biomonitoring tool for marine protected areas
Cited by: 67
Author(s): Zachary Gold, Joshua Sprague, David J. Kushner, Erick Zerecero Marin, Paul H. Barber
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1009108

Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis
Cited by: 5
Author(s): Necati Esener, Alexandre Maciel-Guerra, Katharina Giebel, Daniel Lea, Martin J. Green, Andrew J. Bradley, Tania Dottorini
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0236717

Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
Cited by: 6
Author(s): Deon de Jager, Cindy Kim Harper, Paulette Bloomer
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0252457

Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study
Cited by: 1
Author(s): Kimberly C. Olney, Joshua D. Gibson, Heini M. Natri, Avery Underwood, Juergen Gadau, Melissa A. Wilson
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1007481

Bayesian inference of neuronal assemblies
Cited by: 18
Author(s): Giovanni Diana, Thomas T. J. Sainsbury, Martin P. Meyer
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0248485

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya
Cited by: 21
Author(s): Edith M. Muwawa, Chinedu Christopher Obieze, Huxley Mae Makonde, Joyce Jefwa, James H. P. Kahindi, Damase Khasa
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pgen.1009455

MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity
Cited by: 19
Author(s): Anqi Zhu, Nana Matoba, Emmaleigh Wilson, Amanda L. Tapia, Yun Li, Joseph G. Ibrahim, Jason L. Stein, Michael I. Love
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0252154

Hydrological and topographic determinants of biomass and species richness in a Mediterranean-climate shrubland
Cited by: 1
Author(s): Samantha Díaz de León-Guerrero, Rodrigo Méndez‐Alonzo, Stephen H. Bullock, Enrique R. Vivoni
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0255391

Not just trash birds: Quantifying avian diversity at landfills using community science data
Cited by: 9
Author(s): Zachary J. Arnold, Seth J. Wenger, Richard J. Hall
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0220165

PS-SiZer map to investigate significant features of body-weight profile changes in HIV infected patients in the IeDEA Collaboration
Cited by: 0
Author(s): Jaroslaw Harezlak, Samiha Sarwat, Kara Wools‐Kaloustian, Michael Schomaker, Eric Balestre, Matthew Law, Sasisopin Kiertiburanakul, Matthew P. Fox, Diana Huis in ʼt Veld, Beverly Musick, Constantin T. Yiannoutsos
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1009138

Behavioral correlates of cortical semantic representations modeled by word vectors
Cited by: 6
Author(s): Shogo Nishida, Antione Blanc, Naoya Maeda, Masataka Kado, Shinji Nishimoto
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0229881

Impacts of climate change on agro-climatic suitability of major food crops in Ghana
Cited by: 38
Author(s): Abel Chemura, Bernhard Schauberger, Christoph Gornott
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0243105

Machine learning-based e-commerce platform repurchase customer prediction model
Cited by: 14
Author(s): Cheng-Ju Liu, Tienshou Huang, Ping-Tsan Ho, Jui-Chan Huang, Ching-Tang Hsieh
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1008182

MONET: Multi-omic module discovery by omic selection
Cited by: 9
Author(s): Nimrod Rappoport, Roy Safra, Ron Shamir
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0255304

Coral reefs in the Gilbert Islands of Kiribati: Resistance, resilience, and recovery after more than a decade of multiple stressors
Cited by: 22
Author(s): Sara E. Cannon, Erietera Aram, Toaea Beiateuea, A. Kiareti, Max Peter, Simon D. Donner
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1007663

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Cited by: 36
Author(s): Kosuke Hamazaki, Hiroyoshi Iwata
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pmed.1003151

Impact of physicians’ participation in non-interventional post-marketing studies on their prescription habits: A retrospective 2-armed cohort study in Germany
Cited by: 4
Author(s): Cora Koch, Jörn Schleeff, Franka Techen, Daniel Wollschläger, Gisela Schott, Ralf Kölbel, Klaus Lieb
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pntd.0009306

The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection
Cited by: 4
Author(s): Zhiyuan Yao, Fabio Zanini, Sathish Kumar, Marwah Karim, Sirle Saul, Nishank Bhalla, Nuttada Panpradist, Avery Muniz, Aarthi Narayanan, Stephen R. Quake, Shirit Einav
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0254881

Online activity of mosques and Muslims in the Netherlands: A study of Facebook, Instagram, YouTube and Twitter
Cited by: 2
Author(s): Frank van Tubergen, Tobias Cinjee, Anastasia Menshikova, Joran Veldkamp
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008537

Factors influencing estimates of HIV-1 infection timing using BEAST
Cited by: 3
Author(s): Bethany L. Dearlove, Sodsai Tovanabutra, Christopher L. Owen, Éric Lewitus, Yifan Li, Eric Sanders‐Buell, Meera Bose, Anne Marie O’Sullivan, Gustavo H. Kijak, Shana Miller, Kultida Poltavee, Jenica Lee, Lydia Bonar, Elizabeth A. Harbolick, Bahar Ahani, Phuc Pham, Hannah Kibuuka, Lucas Maganga, Sorachai Nitayaphan, Fred Sawe, Jerome H. Kim, Leigh Anne Eller, Sandhya Vasan, Robert A. Gramzinski, Nelson L. Michael, Merlin L. Robb, Morgane Rolland
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0228098

How to use frailtypack for validating failure-time surrogate endpoints using individual patient data from meta-analyses of randomized controlled trials
Cited by: 2
Author(s): Casimir Ledoux Sofeu, Virginie Rondeau
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0242927

Novel methods for epistasis detection in genome-wide association studies
Cited by: 7
Author(s): Lotfi Slim, Clément Chatelain, Chloé-Agathe Azencott, Jean-Philippe Vert
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0251963

Factors indicating intention to vaccinate with a COVID-19 vaccine among older U.S. adults
Cited by: 55
Author(s): Janeta Nikolovski, Martin Koldijk, Gerrit Jan Weverling, John A. Spertus, Mintu P. Turakhia, Leslie A. Saxon, C. Michael Gibson, John Whang, Troy C. Sarich, Robert A. Zambon, Nnamdi Ezeanochie, Jennifer Turgiss, Robyn Jones, Jeff Stoddard, Paul R. Burton, Ann Marie Návar
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0239237

Preparing GIS data for analysis of stream monitoring data: The R package openSTARS
Cited by: 4
Author(s): Mira Kattwinkel, Eduard Szöcs, Erin E. Peterson, Ralf B. Schäfer
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1007786

Minimizing the number of optimizations for efficient community dynamic flux balance analysis
Cited by: 12
Author(s): James D. Brunner, Nicholas Chia
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0256568

The absence of fans removes the home advantage associated with penalties called by National Hockey League referees
Cited by: 6
Author(s): Joël Guérette, Caroline Blais, Daniel Fiset
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0009504

Developmental changes and metabolic reprogramming during establishment of infection and progression of Trypanosoma brucei brucei through its insect host
Cited by: 16
Author(s): Arunasalam Naguleswaran, Paula Fernandes, Shubha Bevkal, Ruth Rehmann, Pamela Nicholson, Isabel Roditi
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008856

Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment
Cited by: 26
Author(s): Benjamin Deneu, Maximilien Servajean, Pierre Bonnet, Christophe Botella, François Munoz, Alexis Joly
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1007636

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice
Cited by: 23
Author(s): Aleksandr Kovaltsuk, Matthew I. J. Raybould, Wing Ki Wong, Claire Marks, Sebastian Kelm, James Snowden, Johannes Trück, Charlotte M. Deane
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pntd.0009165

Heterogeneity in response to serological exposure markers of recent Plasmodium vivax infections in contrasting epidemiological contexts
Cited by: 14
Author(s): Jason Rosado, Michael White, Rhea J. Longley, Marcus Vinícius Guimarães Lacerda, Wuelton Marcelo Monteiro, Jessica Brewster, Jetsumon Sattabongkot, Mitchel Guzmán-Guzmán, Alejandro Llanos-Cuentas, Joseph M. Vinetz, Dionicia Gamboa, Ivo Müeller
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pntd.0007910

Dispersal patterns of Trypanosoma cruzi in Arequipa, Peru
Cited by: 4
Author(s): Alexander S. F. Berry, Renzo Salazar-Sánchez, Ricardo Castillo-Neyra, Katty Borrini-Mayorí, Claudia Arevalo-Nieto, Claudia Chipana-Ramos, Melina Vargas-Maquera, Jenny Ancca-Juárez, César Náquira-Velarde, Michael Z. Levy, Dustin Brisson
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1009726

The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
Cited by: 8
Author(s): Erik Axelsson, Ingrid Ljungvall, Priyasma Bhoumik, Laura Bas Conn, Eva Murén, Åsa Ohlsson, Lisbeth H. Olsen, Karolina Engdahl, Ragnvi Hagman, Jeanette Hanson, Dmytro Kryvokhyzha, Mats E. Pettersson, Olivier Grenet, Jonathan G. Moggs, Alberto Del Río-Espínola, Christian Epe, Bruce E. Taillon, Nilesh R. Tawari, Shrinivas Mane, Troy Hawkins, Åke Hedhammar, Philippe Gruet, Jens Häggström, Kerstin Lindblad‐Toh
Software Mentions: 5
Published: over 4 years ago