10.1371/journal.ppat.1009280

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: about 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: almost 6 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.ppat.1008645

The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence
Cited by: 23
Author(s): Laure Nicolas Annick Ries, Lakhansing Pardeshi, Zhiqiang Dong, Kaeling Tan, Jacob L. Steenwyk, Ana Cristina Colabardini, Jaire Alves Ferreira Filho, Patrícia Alves de Castro, Lilian Pereira Silva, Nycolas Willian Preite, Fausto Almeida, Leandro José de Assis, Renato Augusto Corrêa dos Santos, Paul Bowyer, Michael Bromley, Rebecca A. Owens, Seán Doyle, Marilene Demasi, Diego Hernández, Luís Eduardo Soares Netto, Mônica Tallarico Pupo, Antonis Rokas, Flávio Vieira Loures, Koon Ho Wong, Gustavo H. Goldman
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pgen.1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Cited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0254607

Disseminated disease due to non-tuberculous mycobacteria in HIV positive patients: A retrospective case control study
Cited by: 3
Author(s): Nils Wetzstein, Ari Geil, Gerrit Kann, Annette Lehn, Gundolf Schüttfort, Johanna Kessel, Tobias M. Bingold, Claus P. Küpper-Tetzel, Annette Haberl, Christiana Graf, Maria J. G. T. Vehreschild, Christoph Stephan, Michael Hogardt, Thomas A. Wichelhaus, Timo Wolf
Software Mentions: 6
Published: over 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: almost 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: almost 6 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: about 6 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.pcbi.1008372

Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game
Cited by: 13
Author(s): Joseph M Barnby, Vaughan Bell, Mitul A. Mehta, Michael Moutoussis
Software Mentions: 6
Published: about 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.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.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: over 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.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: about 5 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.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: almost 7 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: about 6 years ago

10.1371/journal.pgen.1009027

Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD
Cited by: 5
Author(s): Christian Groß, Chiara Bortoluzzi, Dick de Ridder, Hendrik‐Jan Megens, Martien A. M. Groenen, Marcel J. T. Reinders, Mirte Bosse
Software Mentions: 6
Published: about 6 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.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.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 6 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 5 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 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: about 5 years ago

10.1371/journal.pgen.1009645

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: over 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 5 years ago

10.1371/journal.ppat.1008686

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes
Cited by: 7
Author(s): Laura Jackson, Barney Potter, Sean E. Schneider, Matthew Fitzgibbon, Kris M. Blair, Hajirah Farah, U. Murali Krishna, Trevor Bedford, Richard M. Peek, Nina R. Salama
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: about 6 years ago

10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat
Cited by: 16
Author(s): Liangjie Lv, Wenying Zhang, Lijing Sun, Aiju Zhao, Yingjun Zhang, Limei Wang, Yuping Liu, Ziqian Li, Xiyong Chen
Software Mentions: 6
Published: about 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.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 6 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: 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 5 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.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.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: 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.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: over 6 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.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: 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: 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: about 5 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.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 5 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.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.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 5 years ago

10.1371/journal.pone.0238304

Investigation of gene-gene interactions in cardiac traits and serum fatty acid levels in the LURIC Health Study
Cited by: 5
Author(s): Jiayan Zhou, Kristin Passero, Nicole Palmiero, Bertram Müller‐Myhsok, Marcus E. Kleber, Winfried Maerz, Molly A. Hall
Software Mentions: 5
Published: about 6 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 6 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: about 6 years ago

10.1371/journal.pone.0237066

Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways
Cited by: 12
Author(s): Juan R. Ureña‐Peralta, Raúl Pérez-Moraga, Francisco García‐García, Consuelo Guerri
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pmed.1003076

Comprehensive infectious disease screening in a cohort of unaccompanied refugee minors in Germany from 2016 to 2017: A cross-sectional study
Cited by: 18
Author(s): Aleš Janda, Kristin Eder, Roland Fressle, Anne Geweniger, Natalie Diffloth, Maximilian Heeg, Nadine Binder, Ana-Gabriela Sitaru, Jan Rohr, Philipp Henneke, Markus Hufnagel, Roland Elling
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0236796

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management
Cited by: 9
Author(s): Antonio J. Fernández‐González, Nuria M. Wentzien, Pablo J. Villadas, Antonio Valverde-Corredor, Ana V. Lasa, Carmen Gómez-Lama Cabanás, Jesús Mercado‐Blanco, Manuel Fernández‐López
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0228880

Spatio-temporal variation of Cerambycidae-host tree interaction networks
Cited by: 8
Author(s): Michelle Ramos‐Robles, Orthon Ricardo Vargas‐Cardoso, Angélica María Corona‐López, Alejandro Flores‐Palacios, Víctor Hugo Toledo‐Hernández
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pmed.1003229

Maternal dysglycaemia, changes in the infant’s epigenome modified with a diet and physical activity intervention in pregnancy: Secondary analysis of a randomised control trial
Cited by: 52
Author(s): Elie Antoun, Negusse Tadesse Kitaba, Philip Titcombe, Kathryn V. Dalrymple, Emma Garratt, Sheila J. Barton, Robert Murray, Paul Seed, Joanna D. Holbrook, Michael S. Kobor, David T.S. Lin, Julia L. MacIsaac, Graham C. Burdge, Sara L. White, Lucilla Poston, Keith M. Godfrey, Karen A. Lillycrop
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0227486

The effect of storage conditions on microbial communities in stool
Cited by: 20
Author(s): Kristien Nel Van Zyl, Andrew Whitelaw, Mae Newton-Foot
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1009121

A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome
Cited by: 20
Author(s): Benjamin L. S. Furman, Caroline M S Cauret, Martin Knytl, Xuhong Song, Tharindu Premachandra, Caleb Ofori‐Boateng, Danielle C. Jordan, Marko E. Horb, Ben Evans
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0237412

The impact of different negative training data on regulatory sequence predictions
Cited by: 3
Author(s): Louisa-Marie Krützfeldt, Max Schubach, Martin Kircher
Software Mentions: 5
Published: almost 6 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: almost 6 years ago

10.1371/journal.pone.0242879

Validation of models using basic parameters to differentiate intestinal tuberculosis from Crohn’s disease: A multicenter study from Asia
Cited by: 9
Author(s): Julajak Limsrivilai, Choon Kin Lee, Piyapan Prueksapanich, Kamin Harinwan, Asawin Sudcharoen, Natcha Cheewasereechon, Satimai Aniwan, Pimsiri Sripongpan, Panu Wetwittayakhlang, Ananya Pongpaibul, Anapat Sanpavat, Nonthalee Pausawasdi, Phunchai Charatcharoenwitthaya, Peter Higgins, Siew C. Ng
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1009140

Drosophila Caliban preserves intestinal homeostasis and lifespan through regulating mitochondrial dynamics and redox state in enterocytes
Cited by: 12
Author(s): Zhaoxia Dai, Dong Liu, Xiao Du, Ying Ge, Deborah A. Hursh, Xiaolin Bi
Software Mentions: 5
Published: about 6 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: about 5 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: over 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: about 5 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: almost 7 years ago

10.1371/journal.pone.0254514

Reaching to inhibit a prepotent response: A wearable 3-axis accelerometer kinematic analysis
Cited by: 2
Author(s): Alessia Angeli, Irene Valori, Teresa Farroni, Gustavo Marfia
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pgen.1008799

BRM-SWI/SNF chromatin remodeling complex enables functional telomeres by promoting co-expression of TRF2 and TRF1
Cited by: 9
Author(s): Shu Wu, Yuanlong Ge, Xiaocui Li, Yiding Yang, Huan Zhou, Kaixuan Lin, Zepeng Zhang, Yong Zhao
Software Mentions: 5
Published: over 6 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 5 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 6 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: about 5 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 7 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 5 years ago

10.1371/journal.pgen.1008502

Ancestral male recombination in Drosophila albomicans produced geographically restricted neo-Y chromosome haplotypes varying in age and onset of decay
Cited by: 26
Author(s): Kevin H.-C. Wei, Doris Bachtrog
Software Mentions: 5
Published: almost 7 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: over 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 5 years ago

10.1371/journal.ppat.1009701

Control of SARS-CoV-2 infection after Spike DNA or Spike DNA+Protein co-immunization in rhesus macaques
Cited by: 11
Author(s): Margherita Rosati, Mahesh Agarwal, Xintao Hu, Santhi Devasundaram, Dimitris Stellas, Bhabadeb Chowdhury, Jenifer Bear, Robert T. Burns, Duncan Donohue, Laurent Pessaint, Hanné Andersen, Mark G. Lewis, Evangelos Terpos, Meletios A. Dimopoulos, Alexander Wlodawer, James I. Mullins, David Venzon, George N. Pavlakis, Barbara K. Felber
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1009389

Gene disruption by structural mutations drives selection in US rice breeding over the last century
Cited by: 6
Author(s): Justin N. Vaughn, Walid Korani, Joshua C. Stein, Jeremy D. Edwards, Daniel G. Peterson, Sheron Simpson, Ramey C Youngblood, Jane Grimwood, Kapeel Chougule, Doreen Ware, Anna M. McClung, Brian E. Scheffler
Software Mentions: 5
Published: over 5 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: over 6 years ago

10.1371/journal.pgen.1009260

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage
Cited by: 43
Author(s): Marta Gianini, Aleix Bayona-Feliú, Daisy Sproviero, Sónia Barroso, Cristina Cereda, Andrés Aguilera
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pgen.1009443

Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology
Cited by: 27
Author(s): Eilís Hannon, Georgina Mansell, Emma Walker, Marta F. Nabais, Joe Burrage, Agnieszka Kepa, Janis Best-Lane, Anna Rose, Suzanne Heck, Terrie E. Moffitt, Avshalom Caspi, Louise Arseneault, Jonathan Mill
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0254876

Mapping the probability of forest snow disturbances in Finland
Cited by: 5
Author(s): Susanne Suvanto, Aleksi Lehtonen, Seppo Nevalainen, Ilari Lehtonen, Heli Viiri, Mikael Strandström, Mikko Peltoniemi
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 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: about 6 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 6 years ago

10.1371/journal.pgen.1008261

Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes
Cited by: 26
Author(s): Eliška Táborská, Josef Pasulka, Radek Malı́k, Filip Horvat, Irena Jenickova, Zoe Jelić Matošević, Petr Svoboda
Software Mentions: 5
Published: almost 7 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: about 6 years ago

10.1371/journal.ppat.1008346

Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells
Cited by: 28
Author(s): Tzu‐Chun Chen, Marc Talló-Parra, Qian M. Cao, Sebastián Kadener, René Böttcher, Gemma Pérez‐Vilaró, Pakpoom Boonchuen, Kunlaya Somboonwiwat, Juana Díez, Peter Sarnow
Software Mentions: 5
Published: about 6 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: about 6 years ago

10.1371/journal.ppat.1008717

Genomic and transcriptomic evidence for descent from Plasmodium and loss of blood schizogony in Hepatocystis parasites from naturally infected red colobus monkeys
Cited by: 17
Author(s): Eerik Aunin, Ulrike Böhme, Theo Sanderson, Noah D. Simons, Tony L. Goldberg, Nelson Ting, Colin A. Chapman, Chris Newbold, Matthew Berriman, Adam J. Reid
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1008986

Qualitative Differences Between the IFNα subtypes and IFNβ Influence Chronic Mucosal HIV-1 Pathogenesis
Cited by: 21
Author(s): Kejun Guo, Guannan Shen, Jon Kibbie, Tanía González, Stephanie M. Dillon, Harry A. Smith, Emily Cooper, Kerry J. Lavender, Kim J. Hasenkrug, Kathrin Sutter, Ulf Dittmer, Miranda Kroehl, Katerina Kechris, Cara C. Wilson, Mario L. Santiago
Software Mentions: 5
Published: about 6 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 5 years ago

10.1371/journal.pone.0257343

Analysis of potential genetic biomarkers and molecular mechanism of smoking-related postmenopausal osteoporosis using weighted gene co-expression network analysis and machine learning
Cited by: 7
Author(s): Shaoshuo Li, Baixing Chen, Hao Chen, Zhen Hua, Yang Shao, Heng Yin, Jianwei Wang
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1008687

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell
Cited by: 35
Author(s): Bogdan Sieriebriennikov, Shuai Sun, James W. Lightfoot, Hanh Witte, Eduardo Moreno, Christian Rödelsperger, Ralf J. Sommer
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0243609

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data
Cited by: 6
Author(s): Yi An Chen, Jonguk Park, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Attayeb Mohsen, Koji Hosomi, Kumpei Tanisawa, Harumi Ohno, Kana Konishi, Haruka Murakami, Motohiko Miyachi, Jun Kunisawa, Kenji Mizuguchi
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0226575

Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis
Cited by: 17
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Lars Etholm, Cecilie G. Nome, Erik Taubøll, Kjell Heuser, Kaja Kristine Selmer
Software Mentions: 5
Published: almost 7 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: over 6 years ago

10.1371/journal.pone.0245958

Testing the causal mechanism of the peninsular effect in passerine birds from South Korea
Cited by: 2
Author(s): Jin–Yong Kim, Man‐Seok Shin, Chang Ho Seo, Soo Hyung Eo, Seungbum Hong
Software Mentions: 5
Published: almost 6 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 5 years ago