10.1371/journal.pone.0236495

An unbiased template of the Drosophila brain and ventral nerve cord
Cited by: 57
Author(s): John A. Bogovic, Hideo Otsuna, Larissa Heinrich, Masayoshi Ito, Jennifer Jeter, Geoffrey W. Meissner, Aljoscha Nern, Jennifer Colonell, Oz Malkesman, Kei Ito, Stephan Saalfeld
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008387

RNA structure prediction using positive and negative evolutionary information
Cited by: 39
Author(s): Elena Rivas
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008061

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

10.1371/journal.pcbi.1008310

Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
Cited by: 12
Author(s): Marco Aqil, Selen Atasoy, Morten L. Kringelbach, Rikkert Hindriks
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0236001

Germination response of diverse wild and landrace chile peppers (Capsicum spp.) under drought stress simulated with polyethylene glycol
Cited by: 2
Author(s): Vivian Bernau, Lev Jardón Barbolla, Leah K. McHale, Kristin L. Mercer
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1009770

The genetics and evolution of eye color in domestic pigeons (Columba livia)
Cited by: 5
Author(s): Si Si, Xiao Xu, Yan Zhuang, Xiao‐Dong Gao, Honghai Zhang, Zhengting Zou, Shu‐Jin Luo
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1009146

Crumbs and the apical spectrin cytoskeleton regulate R8 cell fate in the Drosophila eye
Cited by: 4
Author(s): Jonathan M. Pojer, Abdul Jabbar Saiful Hilmi, Shu Kondo, Ken Harvey
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pcbi.1008114

HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data
Cited by: 9
Author(s): Sára Saray, Christian Rössert, Shailesh Appukuttan, Rosanna Migliore, Paola Vitale, Carmen Alina Lupaşcu, Luca Bologna, Werner Van Geit, Armando Romani, Andrew Davison, Eilif Müller, Tamás F. Freund, Szabolcs Káli
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1009227

Relating simulation studies by provenance—Developing a family of Wnt signaling models
Cited by: 5
Author(s): Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0243704

Cyberchondria in the age of COVID-19
Cited by: 53
Author(s): Nataša Jokić‐Begić, Anita Lauri Korajlija, Una Mikac
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009390

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition
Cited by: 11
Author(s): Luis Enrique Cabrera-Quio, Alexander Schleiffer, Karl Mechtler, Andrea Pauli
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0238876

Identification and validation of early genetic biomarkers for apple replant disease
Cited by: 11
Author(s): Annmarie-Deetja Rohr, Jessica Schimmel, Benye Liu, Georg Guggenberger, Traud Winkelmann
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008537

Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation
Cited by: 33
Author(s): Gregory R. Keele, Bryan C. Quach, Jennifer W. Israel, Grace A. Chappell, Lauren Lewis, Alexias Safi, Jeremy M. Simon, Paul Cotney, Gregory E. Crawford, William Valdar, Ivan Rusyn, Terrence S. Furey
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008422

Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells
Cited by: 2
Author(s): Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008466

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines
Cited by: 59
Author(s): Barbara De Kegel, Colm J. Ryan
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1009041

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

10.1371/journal.pcbi.1008286

Breaking the circularity in circular analyses: Simulations and formal treatment of the flattened average approach
Cited by: 8
Author(s): Howard Bowman, Joseph Brooks, Omid Hajilou, Alexia Zoumpoulaki, Vladimir Litvak
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0252987

Morus alba: Host reaction for Meloidogyne javanica, biological nematicides assessment and study of these relationships with yield and quality of leaves, cocoon and health of the silkworm
Cited by: 0
Author(s): Santino Aleandro da Silva, Renata da Rosa, Rachel Colauto Milanezi Aguiar, Cristianne Cordeiro Nascimento, Andressa Cristina Zamboni Machado
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0224695

Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology
Cited by: 13
Author(s): Lisa Sakamoto, Hiromi Kajiya‐Kanegae, Koji Noshita, Hideki Takanashi, Mariko Kobayashi, Toru Kudo, Kentarô Yano, Tsuyoshi Tokunaga, Nobuhiro Tsutsumi, Hiroyoshi Iwata
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232609

The two types of society: Computationally revealing recurrent social formations and their evolutionary trajectories
Cited by: 3
Author(s): Lux Miranda, Jacob Freeman
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1009014

Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine
Cited by: 8
Author(s): Qiang Gu, Anup Kumar, Simon Bray, Allison Creason, Alireza Khanteymoori, Vahid Jalili, Björn Grüning, Jeremy Goecks
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0237170

Physiological and morphological correlates of blood parasite infection in urban and non-urban house sparrow populations
Cited by: 5
Author(s): Coraline Bichet, François Brischoux, Cécile Ribout, Charline Parenteau, Alizée Meillère, Frédéric Angelier
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1007847

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

10.1371/journal.pgen.1009713

Multitrait GWAS to connect disease variants and biological mechanisms
Cited by: 12
Author(s): Hanna Julienne, Vincent Laville, Zachary R. McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Cyril Nerin, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie‐Pierre Dubé, Peter Kraft, Iuliana Ionita‐Laza, Bjarni J. Vilhjálmsson, Hugues Aschard
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1007731

AncesTree: An interactive immunoglobulin lineage tree visualizer
Cited by: 13
Author(s): Mathilde Foglierini, Leontios Pappas, Antonio Lanzavecchia, Davide Corti, Laurent Perez
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1009370

Protein structural features predict responsiveness to pharmacological chaperone treatment for three lysosomal storage disorders
Cited by: 4
Author(s): Jaie Woodard, Wei Zheng, Zifeng Yang
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1008377

Active probing to highlight approaching transitions to ictal states in coupled neural mass models
Cited by: 2
Author(s): Vinícius Rezende Carvalho, Márcio Flávio Dutra Moraes, Sydney S. Cash, Eduardo M. A. M. Mendes
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1008617

Inhibition of the oligosaccharyl transferase in Caenorhabditis elegans that compromises ER proteostasis suppresses p38-dependent protection against pathogenic bacteria
Cited by: 8
Author(s): Dae‐Eun Jeong, Yujin Lee, Seokjin Ham, Dong-Yeop Lee, Sujeong Kwon, Hae‐Eun H. Park, Sunyoung Hwang, Joo‐Yeon Yoo, Tae-Young Roh, Seung-Jae Lee
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008914

WormPose: Image synthesis and convolutional networks for pose estimation in C. elegans
Cited by: 29
Author(s): Laetitia Hebert, Tosif Ahamed, Á. S. Costa, Liam O’Shaughnessy, Greg J. Stephens
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009440

A more accurate method for colocalisation analysis allowing for multiple causal variants
Cited by: 87
Author(s): Chris Wallace
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0247320

Effects of entrepreneurial orientation on social media adoption and SME performance: The moderating role of innovation capabilities
Cited by: 33
Author(s): Mingyue Fan, Sikandar Ali Qalati, Muhammad Aamir Shafique Khan, Syed Mir Muhammad Shah, Muhammad Ramzan, Raza Saleem Khan
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008830

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

10.1371/journal.pone.0254852

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

10.1371/journal.pone.0239026

Impact of COVID-19 epidemic curtailment strategies in selected Indian states: An analysis by reproduction number and doubling time with incidence modelling
Cited by: 14
Author(s): Arun Mitra, Abhijit Pakhare, Adrija Roy, Ankur Joshi
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1007982

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

10.1371/journal.pcbi.1009127

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

10.1371/journal.pgen.1008452

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania
Cited by: 12
Author(s): Megan A. Sloan, Karen Brooks, Thomas D. Otto, Mandy Sanders, James A. Cotton, Petros Ligoxygakis
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0243422

Socioeconomic and behavioral determinants of cardiovascular diseases among older adults in Belgium and France: A longitudinal analysis from the SHARE study
Cited by: 6
Author(s): Hamid Yimam Hassen, Hilde Bastiaens, Kathleen Van Royen, Steven Abrams
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0246501

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

10.1371/journal.pcbi.1009298

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

10.1371/journal.pcbi.1009040

A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila
Cited by: 0
Author(s): Claudio D. T. Barros, Maira Arruda Cardoso, Paulo Mascarello Bisch, Helena Araujo, Francisco J. P. Lopes
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1009734

Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans
Cited by: 10
Author(s): Delaney C Pagliuso, Devavrat M Bodas, Amy E. Pasquinelli
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1009164

The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition
Cited by: 7
Author(s): Gloria González Curto, Audrey Der Vartanian, Youcef El-Mokhtar Frarma, Line Manceau, Lorenzo Baldi, Selene Prisco, Nabila Elarouci, Frédéric Causeret, Daniil Korenkov, Muriel Rigolet, Frédéric Auradé, Aurélien de Reyniès, Vincent Contremoulins, Frédéric Relaix, Orestis Faklaris, James Briscoe, Pascale Gilardi-Hebenstreit, Vanessa Ribes
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0233182

Over 13,000 elements from a single bonebed help elucidate disarticulation and transport of an Edmontosaurus thanatocoenosis
Cited by: 2
Author(s): Keith Snyder, Matthew A. McLain, Jared P. Wood, Arthur V. Chadwick
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1009448

Recent loss of the Dim2 DNA methyltransferase decreases mutation rate in repeats and changes evolutionary trajectory in a fungal pathogen
Cited by: 27
Author(s): Mareike Möller, Michael Habig, Cécile Lorrain, Alice Feurtey, Janine Haueisen, Wagner C. Fagundes, A. Alizadeh, Michael Freitag, Eva H. Stukenbrock
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1007756

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

10.1371/journal.pcbi.1008003

Biological network growth in complex environments: A computational framework
Cited by: 6
Author(s): Torsten Johann Paul, Philip Kollmannsberger
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0256353

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Cited by: 6
Author(s): Claus M. Zacho, Martina Abenhus Bager, Ashot Margaryan, Peter Gravlund, Anders Galatius, Arne Redsted Rasmussen, Morten E. Allentoft
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0234939

Effect of bovine leukemia virus (BLV) infection on bovine mammary epithelial cells RNA-seq transcriptome profile
Cited by: 4
Author(s): Lucia Martínez Cuesta, Juan Pedro Lirón, María Victoria Nieto Farias, Guillermina Laura Dolcini, María Carolina Ceriani
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0246473

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

10.1371/journal.pcbi.1008789

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes
Cited by: 0
Author(s): Grace Hui Ting Yeo, Oscar Juez, Qing Chen, Budhaditya Banerjee, Lendy Chu, Max W. Shen, May Sabry, Ive Logister, Richard I. Sherwood, David K. Gifford
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008919

Detecting adherence to the recommended childhood vaccination schedule from user-generated content in a US parenting forum
Cited by: 5
Author(s): Lorenzo Betti, Gianmarco De Francisci Morales, Laetitia Gauvin, Kyriaki Kalimeri, Yelena Mejova, Daniela Paolotti, Michele Starnini
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0223031

Lipidomics analysis of juveniles’ blue mussels (Mytilus edulis L. 1758), a key economic and ecological species
Cited by: 13
Author(s): Vincenzo Alessandro Laudicella, Christine Beveridge, Stefano Carboni, Sofia C. Franco, Mary K. Doherty, Nina Long, Elaine Mitchell, Michele S. Stanley, Phillip D. Whitfield, Adam D. Hughes
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008243

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

10.1371/journal.pcbi.1007988

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases
Cited by: 7
Author(s): Bojan Krtenic, Adrian Drazic, Thomas Arnesen, Nathalie Reuter
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009036

Polygenic risk for autism spectrum disorder associates with anger recognition in a neurodevelopment-focused phenome-wide scan of unaffected youths from a population-based cohort
Cited by: 5
Author(s): Frank R. Wendt, Carolina Muniz Carvalho, Gita A Pathak, Joel Gelernter, Renato Polimanti
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1008955

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

10.1371/journal.pone.0242941

Effects of transcranial magnetic stimulation over the left posterior superior temporal gyrus on picture-word interference
Cited by: 2
Author(s): Vitória Piai, Laura Nieberlein, Gesa Hartwigsen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0245222

Early Holocene Scandinavian foragers on a journey to affluence: Mesolithic fish exploitation, seasonal abundance and storage investigated through strontium isotope ratios by laser ablation (LA‐MC-ICP‐MS)
Cited by: 9
Author(s): Adam Boëthius, Mathilda Kjällquist, Melanie Kielman‐Schmitt, Torbjörn Ahlström, Lars Larsson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008924

Incorporating the speciation process into species delimitation
Cited by: 48
Author(s): Jeet Sukumaran, Mark T. Holder, L. Lacey Knowles
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0236791

Eradicating the large white butterfly from New Zealand eliminates a threat to endemic Brassicaceae
Cited by: 6
Author(s): C.B. Phillips, Kerry Brown, Christopher Green, Richard Toft, G.P. Walker, Keith Broome
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0234142

The child’s pantheon: Children’s hierarchical belief structure in real and non-real figures
Cited by: 5
Author(s): Rohan Kapitány, Nicole L. Nelson, Emily Burdett, Thalia R. Goldstein
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0248489

Enhanced streamflow prediction with SWAT using support vector regression for spatial calibration: A case study in the Illinois River watershed, U.S.
Cited by: 10
Author(s): Liang Yuan, Kenneth J. Forshay
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008837

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

10.1371/journal.pgen.1009221

Short-range template switching in great ape genomes explored using pair hidden Markov models
Cited by: 10
Author(s): Conor R Walker, Aylwyn Scally, Nicola De Maio, Nick Goldman
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0233841

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

10.1371/journal.pgen.1009802

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

10.1371/journal.pcbi.1007770

A framework for integrating directed and undirected annotations to build explanatory models of cis-eQTL data
Cited by: 2
Author(s): David Lamparter, Rajat Bhatnagar, Katja Hebestreit, T. Grant Belgard, Alice Zhang, Victor Hanson-Smith
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008551

Aspergillus fumigatus calcium-responsive transcription factors regulate cell wall architecture promoting stress tolerance, virulence and caspofungin resistance
Cited by: 32
Author(s): Patrícia Alves de Castro, Ana Cristina Colabardini, Adriana Oliveira Manfiolli, Jéssica Chiaratto, Lilian Pereira Silva, Eliciane Cevolani Mattos, Giuseppe Palmisano, Fausto Almeida, Gabriela Félix Persinoti, Laure Nicolas Annick Ries, Laura Mellado, Marina Campos Rocha, Michael Bromley, Roberto Nascimento Silva, Gabriel Scalini de Souza, Flávio Vieira Loures, Iran Malavazi, Neil Andrew Brown, Gustavo H. Goldman
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0237950

Individual response to antidepressants for depression in adults-a meta-analysis and simulation study
Cited by: 10
Author(s): Klaus Munkholm, Stephanie Winkelbeiner, Philipp Homan
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0243595

Extreme value theory as a framework for understanding mutation frequency distribution in cancer genomes
Cited by: 2
Author(s): Natsuki Tokutomi, Kenta Nakai, Sumio Sugano
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0253264

Dietary vitamin E reaches the mitochondria in the flight muscle of zebra finches but only if they exercise
Cited by: 6
Author(s): Clara Cooper-Mullin, Wales A. Carter, Ronald S. Amato, David W. Podlesak, Scott R. McWilliams
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0230941

Demarcating geographic regions using community detection in commuting networks with significant self-loops
Cited by: 14
Author(s): Mark He, Joseph Glasser, Nathaniel Pritchard, Shankar Bhamidi, Nikhil Kaza
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1008347

Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability
Cited by: 30
Author(s): Javier Rasero, A. Sentis, Fang‐Cheng Yeh, Timothy Verstynen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0245596

Space-time smoothing of mortality estimates in children aged 5-14 in Sub-Saharan Africa
Cited by: 1
Author(s): Benjamin-Samuel Schlüter, Bruno Masquelier
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0245103

Disease progression of 213 patients hospitalized with Covid-19 in the Czech Republic in March–October 2020: An exploratory analysis
Cited by: 1
Author(s): Martin Modrák, Paul - Christian Bürkner, Tomáš Sieger, Tomás Slisz, Martina Vašáková, Grigorij Mesežnikov, Luis Fernando Casas-Mendez, Jaromír Vajter, J Táborský, Viktor Kubricht, Daniel Suk, Jan Horejsek, M. Jedlička, Adriana Mifková, Adam Jaroš, Miroslav Kubiska, Jana Váchalová, Robin Šín, Markéta Veverková, Zbysek Pospísil, Julie Vohryzková, Rebeka Pokrievková, Kristián Hrusák, Kristína Christozova, Vianey Leos‐Barajas, Karel Fišer, Tomáš Hyánek
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1008908

An expanded cell wall damage signaling network is comprised of the transcription factors Rlm1 and Sko1 in Candida albicans
Cited by: 19
Author(s): Marienela Y. Heredia, Mélanie Ikeh, Deepika Gunasekaran, Karen A. Conrad, Sviatlana Filimonava, Dawn H. Marotta, Clarissa J. Nobile, Jason M. Rauceo
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1008361

An osteocalcin-deficient mouse strain without endocrine abnormalities
Cited by: 74
Author(s): Cassandra R. Diegel, Steven Hann, Ugur M. Ayturk, Jennifer C. W. Hu, Kyung-Eun Lim, Casey J. Droscha, Zachary Madaj, Gabrielle E. Foxa, Isaac Izaguirre, Vai Vivarium And Transgenics Core, Noorulain Paracha, Bohdan Pidhaynyy, Terry L. Dowd, Alexander G. Robling, Matthew L. Warman, Bart O. Williams
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pcbi.1008647

Independent component analysis recovers consistent regulatory signals from disparate datasets
Cited by: 24
Author(s): Anand V. Sastry, Alyssa Hu, David Heckmann, Saugat Poudel, Erol Kavvas, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008904

High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING
Cited by: 15
Author(s): Wesley M. Marin, Ravi Dandekar, Danillo G. Augusto, Tasneem Yusufali, Bianca Heyn, Jan A. Hofmann, Vinzenz Lange, Jürgen Sauter, Paul J. Norman, Jill A. Hollenbach
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0238124

Elderly patients with cancer admitted to intensive care unit: A multicenter study in a middle-income country
Cited by: 0
Author(s): Antônio Paulo Nassar, Mariane da Silva Trevisani, Bárbara Beltrame Bettim, Fernando G. Zampieri, José Albani Carvalho, Amílton Silva, Flávio Geraldo Rezende Freitas, José Roberto Aparecido dos Santos Pinto, Edson Romano, Sílvia Regina Ramos, Guilherme Brenande Alves Faria, Ulysses V. Andrade e Silva, Robson Correa Santos, Edmundo de Oliveira Tommasi, Ana Paula Pierre de Moraes, Bruno Azevedo da Cruz, Fernando A. Bozza, Pedro Caruso, Jorge I. Salluh, Márcio Soares
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.1009055

Cis-regulatory differences in isoform expression associate with life history strategy variation in Atlantic salmon
Cited by: 25
Author(s): Jukka‐Pekka Verta, Paul V. Debes, Nikolai Piavchenko, Annukka Ruokolainen, Outi Ovaskainen, Jacqueline Emmanuel Moustakas-Verho, Seija Tillanen, Noora Parre, Tutku Aykanat, Jaakko Erkinaro, Craig R. Primmer
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008464

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

10.1371/journal.pcbi.1009078

lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0245589

Efficient neural spike sorting using data subdivision and unification
Cited by: 3
Author(s): Masood Hassan, Rakesh Veerabhadrappa, Asim Bhatti
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0254827

Habitat selection by wolves and mountain lions during summer in western Montana
Cited by: 5
Author(s): Collin J. Peterson, Michael S. Mitchell, Nicholas J. DeCesare, Chad J. Bishop, Sarah N. Sells
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0225623

Is un stylo sharper than une épée? Investigating the interaction of sound symbolism and grammatical gender in English and French speakers
Cited by: 2
Author(s): David M. Sidhu, Penny M. Pexman, Jean Saint‐Aubin
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1009526

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

10.1371/journal.pone.0227825

Detection and density of breeding marsh birds in Iowa wetlands
Cited by: 1
Author(s): Rachel A. Vanausdall, Stephen J. Dinsmore
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0232120

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

10.1371/journal.ppat.1009697

Listeria monocytogenes infection rewires host metabolism with regulatory input from type I interferons
Cited by: 3
Author(s): Duygu Demiröz, Ekaterini Platanitis, Marsha Bryant, Philipp Fischer, Michaela Prchal-Murphy, Alexander Lercher, Caroline Lassnig, Manuela Baccarini, Mathias Müller, Andréas Bergthaler, Veronika Sexl, Marlies Dolezal, Thomas Decker
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1009477

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

10.1371/journal.pgen.1009578

Functional-genomic analysis reveals intraspecies diversification of antiviral receptor transporter proteins in Xenopus laevis
Cited by: 1
Author(s): Ian N. Boys, Katrina B. Mar, John W. Schoggins
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1009409

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

10.1371/journal.pcbi.1009216

Topology-preserving smoothing of retinotopic maps
Cited by: 3
Author(s): Yanshuai Tu, Duyan Ta, Zhong-Lin Lü, Yalin Wang
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0238076

Deletion of Mediator 1 suppresses TGFβ signaling leading to changes in epidermal lineages and regeneration
Cited by: 3
Author(s): Yuko Oda, Thai Nguyen, Akiko Hata, Mark B. Meyer, J. Wesley Pike, Daniel Bikle
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1009774

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

10.1371/journal.pone.0237001

Highs and lows: Genetic susceptibility to daily events
Cited by: 9
Author(s): Maurizio Sicorello, Linda Dieckmann, Dirk Moser, Vanessa Lux, Maike Luhmann, A. Neubauer, Wolff Schlotz, Robert Kumsta
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.ppat.1009552

Intraspecific variation in immune gene expression and heritable symbiont density
Cited by: 8
Author(s): Holly L. Nichols, Elliott B. Goldstein, Omid Saleh Ziabari, Benjamin J. Parker
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pcbi.1008476

Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage
Cited by: 7
Author(s): Samuel Ingram, Nicholas Henthorn, John-William Warmenhoven, N.F. Kirkby, Ranald I Mackay, Karen J Kirkby, Michael J Merchant
Software Mentions: 4
Published: over 5 years ago