10.1371/journal.ppat.1009674

Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection
Cited by: 5
Author(s): Michelle Y.H. Lee, Amit A. Upadhyay, Hasse Walum, Chi N. Chan, Reem A. Dawoud, Christine Grech, Justin Harper, Kirti A. Karunakaran, Sydney A. Nelson, Ernestine Mahar, Kyndal Goss, Diane G. Carnathan, Barbara Cervasi, Kiran Gill, Gregory K. Tharp, Elizabeth R. Wonderlich, Vijayakumar Velu, Simon M. Barratt‐Boyes, Mirko Paiardini, Guido Silvestri, Jacob D. Estes, Steven E. Bosinger
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.ppat.1009349

PD-1 is imprinted on cytomegalovirus-specific CD4+ T cells and attenuates Th1 cytokine production whilst maintaining cytotoxicity
Cited by: 15
Author(s): Helen Parry, Alexander C. Dowell, Jianmin Zuo, Kriti Verma, Francesca Kinsella, Jusnara Begum, Wayne Croft, Archana Sharma-Oates, Guy Pratt, Paul Moss
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0257151

Replicating the Disease framing problem during the 2020 COVID-19 pandemic: A study of stress, worry, trust, and choice under risk
Cited by: 11
Author(s): Nikolay R. Rachev, Hyemin Han, David Lacko, Rebekah Gelpí, Yuki Yamada, Andreas Lieberoth
Software Mentions: 5
Published: about 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.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: 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.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.pone.0245824

MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction
Cited by: 51
Author(s): Otília Menyhárt, Boglárka Weltz, Balázs Győrffy
Software Mentions: 5
Published: over 4 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 4 years ago

10.1371/journal.ppat.1009528

Virus shedding kinetics and unconventional virulence tradeoffs
Cited by: 4
Author(s): Andrew R. Wargo, Gael Kurath, Robert J. Scott, Benjamin Kerr
Software Mentions: 5
Published: over 4 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: over 5 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 5 years ago

10.1371/journal.ppat.1009769

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections
Cited by: 11
Author(s): Kai Fang, Jie Zhou, Lin Chen, Yuxuan Li, Ai-Ling Yang, Xing-Fan Dong, Hanbo Zhang
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0223549

Quantifying normal and parkinsonian gait features from home movies: Practical application of a deep learning–based 2D pose estimator
Cited by: 46
Author(s): Kenichiro Sato, Yu Nagashima, Tatsuo Mano, Atsushi Iwata, Tatsushi Toda
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0244724

Geography as non-genetic modulation factor of chicken cecal microbiota
Cited by: 8
Author(s): Natalia Daniela Pin Viso, Enzo A. Redondo, Juan María Díaz Carrasco, Leandro M. Redondo, Javier García, Mariano E. Fernández‐Miyakawa, Marisa Diana Farber
Software Mentions: 5
Published: almost 5 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: almost 5 years ago

10.1371/journal.pone.0240614

Interspecific interactions among functionally diverse frugivores and their outcomes for plant reproduction: A new approach based on camera-trap data and tailored null models
Cited by: 16
Author(s): M. Arthur Selwyn, Pedro J. Garrote, Antonio R. Castilla, José M. Fedriani
Software Mentions: 5
Published: about 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: almost 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: 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.0241231

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica
Cited by: 7
Author(s): Joel H. Nitta, Atsushi Ebihara, Alan Р. Smith
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0236631

Citizen science for predicting spatio-temporal patterns in seabird abundance during migration
Cited by: 5
Author(s): Beatriz Martín, Alejandro Onrubia, Julio González-Arias, Juan Antonio Vicente-Virseda
Software Mentions: 5
Published: about 5 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: about 4 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.0239480

Horizontal and vertical movements of starry smooth-hound Mustelus asterias in the northeast Atlantic
Cited by: 4
Author(s): Christopher A. Griffiths, Serena Wright, Joana F. Silva, Jim R. Ellis, David Righton, Sophy R. McCully Phillips
Software Mentions: 5
Published: about 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: about 4 years ago

10.1371/journal.pone.0246297

Rhabdomyolysis related to acute recreational drug toxicity—A Euro-DEN study
Cited by: 9
Author(s): W. James Waldman, Piotr Maciej Kabata, Alison Dines, David M. Wood, Chris Yates, Fridtjof Heyerdahl, Knut Erik Hovda, Isabelle Giraudon, Jacek Sein Anand
Software Mentions: 5
Published: over 4 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 5 years ago

10.1371/journal.pone.0245324

InsectOR—Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes
Cited by: 10
Author(s): Snehal D. Karpe, Vikas Tiwari, R. Sowdhamini
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0243446

Genomic and morphological evidence of distinct populations in the endemic common (weedy) seadragon Phyllopteryx taeniolatus (Syngnathidae) along the east coast of Australia
Cited by: 9
Author(s): O. Selma Klanten, Michelle R. Gaither, Samuel E. Greaves, Kade Mills, Kristine O’Keeffe, John Turnbull, Rob McKinnon, David J. Booth
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0255598

A Bayesian approach to reveal the key role of mask wearing in modulating projected interpersonal distance during the first COVID-19 outbreak
Cited by: 20
Author(s): Matteo P. Lisi, Marina Scattolin, Martina Fusaro, Salvatore Maria Aglioti
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0246544

Swab pooling: A new method for large-scale RT-qPCR screening of SARS-CoV-2 avoiding sample dilution
Cited by: 21
Author(s): Ana Paula Christoff, Giuliano Netto Flores Cruz, Aline Fernanda Rodrigues Sereia, Dellyana Rodrigues Boberg, Daniela Carolina de Bastiani, Laís Eiko Yamanaka, Gislaine Fongaro, Patrícia Hermes Stoco, Maria Luiza Bazzo, Edmundo C. Grisard, Camila Hernandes, Luiz Felipe Valter de Oliveira
Software Mentions: 5
Published: over 4 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: over 4 years ago

10.1371/journal.pone.0256554

Is it easier to use one language variety at a time, or mix them? An investigation of voluntary language switching with bidialectals
Cited by: 1
Author(s): Mathieu Declerck, Neil W. Kirk
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0250385

What proportion of people have a follow-up biopsy in randomized trials of treatments for non-alcoholic steatohepatitis?: A systematic review and meta-analysis
Cited by: 1
Author(s): Dimitrios A. Koutoukidis, Elizabeth Morris, John A. Henry, Yusra Shammoon, Matthew C. Zimmerman, Moscho Michalopoulou, Susan A. Jebb, Paul Aveyard
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0242662

Assessing roost disturbance of straw-coloured fruit bats (Eidolon helvum) through tri-axial acceleration
Cited by: 2
Author(s): Tânia Domingues Costa, Carlos David Santos, Ana Rainho, Michael Abedi-Lartey, Jakob Fahr, Martin Wikelski, Dina K. N. Dechmann
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0251458

Statistical privacy-preserving message broadcast for peer-to-peer networks
Cited by: 1
Author(s): David Mödinger, Jan-Hendrik Lorenz, Franz J. Hauck
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008893

Computation of the electroencephalogram (EEG) from network models of point neurons
Cited by: 19
Author(s): Pablo Martínez‐Cañada, Torbjørn V. Ness, Gaute T. Einevoll, Tommaso Fellin, Stefano Panzeri
Software Mentions: 5
Published: over 4 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: about 4 years ago

10.1371/journal.pone.0255648

The reciprocal relationships between social media self-control failure, mindfulness and wellbeing: A longitudinal study
Cited by: 13
Author(s): Jie Du, P.C.M. van de Kerkhof, Guido M. van Koningsbruggen
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0244363

Backbone: An R package for extracting the backbone of bipartite projections
Cited by: 20
Author(s): Rachel Domagalski, Zachary P. Neal, Bruce E. Sagan
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0252685

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis
Cited by: 0
Author(s): Gibum Yi, Hosub Shin, Kyeonglim Min, Eun Jin Lee
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0249633

Climatic change and extinction risk of two globally threatened Ethiopian endemic bird species
Cited by: 13
Author(s): Andrew J. Bladon, Paul F. Donald, Nigel Collar, Jarso Denge, Galgalo Dadacha, Mengistu Wondafrash, Rhys E. Green
Software Mentions: 5
Published: over 4 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 4 years ago

10.1371/journal.pcbi.1008735

From heterogeneous healthcare data to disease-specific biomarker networks: A hierarchical Bayesian network approach
Cited by: 9
Author(s): Ann‐Kristin Becker, Marcus Dörr, Stephan B. Felix, Fabian Frost, Hans J. Grabe, Markus M. Lerch, Matthias Nauck, Uwe Völker, Henry Völzke, Lars Kaderali
Software Mentions: 5
Published: over 4 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.pgen.1009820

Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature
Cited by: 7
Author(s): Mark Achtman, Frederik Van den Broeck, Kerry K. Cooper, Philippe Lemey, Craig T. Parker, Zhemin Zhou
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0234552

Multiple measures derived from 3D photonic body scans improve predictions of fat and muscle mass in young Swiss men
Cited by: 8
Author(s): Roman Sager, Sabine Güsewell, Frank J Rühli, Nicole Bender, Kaspar Staub
Software Mentions: 5
Published: over 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: about 4 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.pcbi.1008988

Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
Cited by: 10
Author(s): Nikolina Šoštarić, Vera van Noort
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0236827

Extraction of radiographic findings from unstructured thoracoabdominal computed tomography reports using convolutional neural network based natural language processing
Cited by: 12
Author(s): Mohit Pandey, Zhuoran Xu, Evan Sholle, Gabriel Maliakal, Gurpreet Singh, Zahra Fatima, Daria Larine, Benjamin C. Lee, Jing Wang, Alexander R. van Rosendael, Leslee J. Shaw, James K. Min, Subhi J. Al’Aref
Software Mentions: 5
Published: over 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 6 years ago

10.1371/journal.pcbi.1008473

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease
Cited by: 7
Author(s): Pamela N. Luna, Jonathan M. Mansbach, Chad A. Shaw
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0237601

Impact of calculated plasma volume status on all-cause and cardiovascular mortality: 4-year nationwide community-based prospective cohort study
Cited by: 14
Author(s): Yoichiro Otaki, Tetsu Watanabe, Tsuneo Konta, Masafumi Watanabe, Koichi Asahi, Kunihiro Yamagata, Shouichi Fujimoto, Kazuhiko Tsuruya, Ichiei Narita, Masato Kasahara, Yugo Shibagaki, Kunitoshi Iseki, Toshiki Moriyama, Masahide Kondo, Tsuyoshi Watanabe
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1008770

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone
Cited by: 19
Author(s): Stine M. Præstholm, Majken Siersbæk, Ronni Nielsen, Xuguang Zhu, Anthony N. Hollenberg, Sheue-yann Cheng, Lars Grøntved
Software Mentions: 5
Published: over 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 4 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 5 years ago

10.1371/journal.pcbi.1007764

StanDep: Capturing transcriptomic variability improves context-specific metabolic models
Cited by: 19
Author(s): Chintan Joshi, Song‐Min Schinn, Anne Richelle, Isaac Shamie, Eyleen J. O’Rourke, Nathan E. Lewis
Software Mentions: 5
Published: over 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: about 5 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 5 years ago

10.1371/journal.pone.0252074

Development and psychometric evaluation of the CO-PARTNER tool for collaboration and parent participation in neonatal care
Cited by: 8
Author(s): Nicole R. van Veenendaal, Jennifer N. Auxier, Sophie R D van der Schoor, Linda S. Franck, Mireille Stelwagen, Femke de Groof, Johannes B. van Goudoever, Iris Eekhout, Henrica C.W. de Vet, Anna Axelin, Anne A. M. W. van Kempen
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0256902

Classifying patients with depressive and anxiety disorders according to symptom network structures: A Gaussian graphical mixture model-based clustering
Cited by: 1
Author(s): Jun Kashihara, Yoshitake Takebayashi, Yoshihiko Kunisato, Masaya Ito
Software Mentions: 5
Published: about 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.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.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.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 5 years ago

10.1371/journal.pone.0226616

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses
Cited by: 25
Author(s): Ka−Lai Pang, Sheng−Yu Guo, I-An Chen, Gaëtan Burgaud, Zengwei Luo, Hans-Uwe Dahms, Jiang‐Shiou Hwang, Yi-Li Lin, Jian-Shun Huang, Tsz-Wai Ho, Ling Ming Tsang, Michael Chiang, Hyojung Cha
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0253587

HIV-1 Gag gene mutations, treatment response and drug resistance to protease inhibitors: A systematic review and meta-analysis protocol
Cited by: 1
Author(s): Alex Durand Nka, Georges Této, Maria Mercedes Santoro, Valantine Ngum Ndze, Désiré Takou, Béatrice Dambaya, Ezéchiel Ngoufack Jagni Semengue, Lavinia Fabeni, Carlo Federico Perno, Vittorio Colizzi, Francesca Ceccherini‐Silberstein, Joseph Fokam
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0250831

Environmentally triggered shifts in steelhead migration behavior and consequences for survival in the mid-Columbia River
Cited by: 5
Author(s): Jared E. Siegel, Lisa G. Crozier, Lauren E. Wiesebron, Daniel L. Widener
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0255290

High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz)
Cited by: 7
Author(s): Bright Gyamfi Adu, R. Akromah, Stephen Amoah, Daniel Nyadanu, Alex Yeboah, L. M. Aboagye, R. Adu Amoah, Eva Gyamfuaa Owusu
Software Mentions: 5
Published: over 4 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 5 years ago

10.1371/journal.pone.0229277

Habitat selection in natural and human-modified landscapes by capybaras (Hydrochoerus hydrochaeris), an important host for Amblyomma sculptum ticks
Cited by: 12
Author(s): Thiago C. Dias, Jared A. Stabach, Qiongyu Huang, Marcelo B. Labruna, Peter Leimgruber, Kátia Maria Paschoaletto Micchi de Barros Ferraz, Beatriz Lopes, Hermes Ribeiro Luz, Francisco Borges Costa, Hector Ribeiro Benatti, Lucas Ribeiro Correa, Ana Maria Nievas, Patrícia Ferreira Monticelli, Ubiratan Piovezan, Matias Pablo Juán Szabó, Daniel Moura de Aguiar, José Brites-Neto, Márcio Port-Carvalho, Vlamir José Rocha
Software Mentions: 5
Published: about 5 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 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.0248967

The pulmonary mycobiome—A study of subjects with and without chronic obstructive pulmonary disease
Cited by: 13
Author(s): Einar Marius Hjellestad Martinsen, Tomas Mikal Eagan, Elise Orvedal Leiten, Ingvild Haaland, Gunnar Reksten Husebø, Kristel Svalland Knudsen, Christine Drengenes, Walter Sanseverino, Andreu Paytuví-Gallart, Rune Nielsen
Software Mentions: 5
Published: over 4 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: almost 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 6 years ago

10.1371/journal.pcbi.1007904

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Cited by: 7
Author(s): Agata P. Perlinska, Adam Stasiulewicz, Ewa K. Nawrocka, Krzysztof Kazimierczuk, Piotr Setny, Joanna I. Sułkowska
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0244377

A methodology and theoretical taxonomy for centrality measures: What are the best centrality indicators for student networks?
Cited by: 7
Author(s): Kristel Vignery, Wim Laurier
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0238689

Assessment of transcriptomic constraint-based methods for central carbon flux inference
Cited by: 3
Author(s): Siddharth Bhadra-Lobo, Min Kyung Kim, Desmond S. Lun
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1007799

ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
Cited by: 12
Author(s): Pierre Millard, Uwe Schmitt, Patrick Kiefer, Julia A. Vorholt, Stéphanie Heux, Jean‐Charles Portais
Software Mentions: 5
Published: over 5 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.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.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: over 4 years ago

10.1371/journal.pone.0236874

What’s all that racket! Soundscapes, phenology, and biodiversity in estuaries
Cited by: 10
Author(s): Agnieszka Monczak, Bradshaw McKinney, Claire Mueller, Eric W. Montie
Software Mentions: 5
Published: about 5 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 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 5 years ago

10.1371/journal.pone.0257564

Tree species identity and composition shape the epiphytic lichen community of structurally simple boreal forests over vast areas
Cited by: 7
Author(s): Julian Klein, Matthew Low, Göran Thor, Jörgen Sjögren, Eva Lindberg, Sönke Eggers
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0255838

Optimal distribution-preserving downsampling of large biomedical data sets (opdisDownsampling)
Cited by: 9
Author(s): Jörn Lötsch, Sebastian Malkusch, Alfred Ultsch
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0229502

A background correction method to compensate illumination variation in hyperspectral imaging
Cited by: 6
Author(s): Jonghee Yoon, Alexandru Grigoroiu, Sarah E. Bohndiek
Software Mentions: 5
Published: over 5 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 5 years ago

10.1371/journal.pone.0234489

Application of network analysis and cluster analysis for better prevention and control of swine diseases in Argentina
Cited by: 11
Author(s): Jerome N. Baron, María Natalia Aznar, M. Monterubbianesi, Beatriz Martínez‐López
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pcbi.1009274

Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
Cited by: 0
Author(s): Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gómez-Sjöberg
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pntd.0009397

Global patterns of aegyptism without arbovirus
Cited by: 10
Author(s): Mark F. Olson, José G. Juárez, Moritz U. G. Kraemer, Jane P. Messina, Gabriel L. Hamer
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0007876

Microsatellite analysis reveals connectivity among geographically distant transmission zones of Plasmodium vivax in the Peruvian Amazon: A critical barrier to regional malaria elimination
Cited by: 11
Author(s): Paulo Manrique, Julio Miranda-Alban, Jhonatan Alarcon-Baldeon, Roberson Ramirez, Gabriel Carrasco-Escobar, Henry Herrera, Mitchel Guzmán-Guzmán, Ángel Rosas Aguirre, Alejandro Llanos‐Cuentas, Joseph M. Vinetz, Ananías A. Escalante, Dionicia Gamboa
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0239541

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)
Cited by: 14
Author(s): Nikolaj Vendelbo, Pernille Sarup, Jihad Orabi, Peter Skov Kristensen, A. Jahoor
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pcbi.1008806

VolPy: Automated and scalable analysis pipelines for voltage imaging datasets
Cited by: 17
Author(s): Changjia Cai, Johannes Friedrich, Amrita Singh, M. Hossein Eybposh, Eftychios A. Pnevmatikakis, Kaspar Podgorski, Andrea Giovannucci
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pntd.0008046

Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages
Cited by: 15
Author(s): Haoqiu Wang, Chao Yang, Sun Zhou, Wei Zheng, Wei Zhang, Hua Yu, Yarong Wu, Xavier Didelot, Ruifu Yang, Jinren Pan, Yu‐Jun Cui
Software Mentions: 5
Published: over 5 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 5 years ago