10.1371/journal.pone.0231875

Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador
Cited by: 10
Author(s): M. V. Rao, Robert A. Rice, Robert C. Fleischer, Carly R. Muletz‐Wolz
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0248628

TriatoDex, an electronic identification key to the Triatominae (Hemiptera: Reduviidae), vectors of Chagas disease: Development, description, and performance
Cited by: 6
Author(s): Rodrigo Gurgel-Gonçalves, Fernando Abad‐Franch, Maxwell Ramos de Almeida, Marcos Takashi Obara, Rita de Cássia Moreira de Souza, Jainaine Abrantes de Sena Batista, Douglas de Almeida Rocha
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pcbi.1008716

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
Cited by: 14
Author(s): Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam‐Rudloff, Christian Brandt
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pcbi.1007666

Methods detecting rhythmic gene expression are biologically relevant only for strong signal
Cited by: 22
Author(s): David Laloum, Marc Robinson‐Rechavi
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0244122

Easyreporting simplifies the implementation of Reproducible Research layers in R software
Cited by: 0
Author(s): Dario Righelli, Claudia Angelini
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0231744

Combining genetic and demographic monitoring better informs conservation of an endangered urban snake
Cited by: 11
Author(s): Dustin A. Wood, Jonathan P. Rose, Brian J. Halstead, Ricka E. Stoelting, Karen E. Swaim, Amy G. Vandergast
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pcbi.1007832

Flux-based hierarchical organization of Escherichia coli’s metabolic network
Cited by: 2
Author(s): Semidán Robaina-Estévez, Zoran Nikoloski
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008205

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
Cited by: 43
Author(s): Tony Tran, Gary D. Bader
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pcbi.1008605

Machine learning based CRISPR gRNA design for therapeutic exon skipping
Cited by: 5
Author(s): Wilson Louie, Max W. Shen, Zakir Tahiry, Sophia Zhang, Daniel Worstell, Christopher A. Cassa, Richard I. Sherwood, David K. Gifford
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0220164

Disaggregated level child morbidity in Bangladesh: An application of small area estimation method
Cited by: 0
Author(s): Sumonkanti Das, Bappi Kumar, Luthful Alahi Kawsar
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pgen.1009744

The Integrity of the HMR complex is necessary for centromeric binding and reproductive isolation in Drosophila
Cited by: 25
Author(s): A. Lukacs, Andreas W. Thomae, P. Krueger, Tamás Schauer, Anuroop Venkateswaran Venkatasubramani, Natalia Y. Kochanova, Wasim Aftab, Rupam Choudhury, Ignasi Forné, Axel Imhof
Software Mentions: 8
Published: almost 4 years ago

10.1371/journal.pone.0251280

Middle ratings rise regardless of grammatical construction: Testing syntactic variability in a repeated exposure paradigm
Cited by: 3
Author(s): J. M. M. Brown, Gisbert Fanselow, R. Vance Hall, Reinhold Kliegl
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0235451

Is YouTube promoting the exotic pet trade? Analysis of the global public perception of popular YouTube videos featuring threatened exotic animals
Cited by: 14
Author(s): Georgia Kate Moloney, Jonathan Tuke, Eleonora Dal Grande, Torben Nielsen, Anne‐Lise Chaber
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0240824

A novel computational approach for predicting complex phenotypes in Drosophila (starvation-sensitive and sterile) by deriving their gene expression signatures from public data
Cited by: 0
Author(s): Dobril Ivanov, Gerrit Bostelmann, Benoît Lan-Leung, Julie Williams, Linda Partridge, Valentina Escott‐Price, Janet M. Thornton
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pone.0231526

Disentangling the influence of ecological and historical factors on seed germination and seedling types in a Neotropical dry forest
Cited by: 5
Author(s): Jorge Cortés‐Flores, Guadalupe Cornejo‐Tenorio, María Esther Sánchez‐Coronado, Alma Orozco‐Segovia, Guillermo Ibarra‐Manríquez
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0228782

Learning about the Ellsberg Paradox reduces, but does not abolish, ambiguity aversion
Cited by: 6
Author(s): Ruonan Jia, Ellen E. Furlong, Sean Gao, Laurie R. Santos, Ifat Levy
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1007814

Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibility
Cited by: 4
Author(s): Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado‐Sainz, Felipe Cortés‐Ledesma
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0229689

Population dynamics and biological feasibility of sustainable harvesting as a conservation strategy for tropical and temperate freshwater turtles
Cited by: 11
Author(s): Angga Rachmansah, D. Ryan Norris, James P. Gibbs
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pcbi.1009148

POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis
Cited by: 12
Author(s): Pol Castellano‐Escuder, Raúl González‐Domínguez, Francesc Carmona-Pontaque, Cristina Andrés‐Lacueva, Álex Sánchez-Pla
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0249148

Ethnically biased microsatellites contribute to differential gene expression and glutathione metabolism in Africans and Europeans
Cited by: 5
Author(s): Nicholas A. Kinney, Lin Kang, Harpal Bains, Elizabeth Lawson, Mesam Husain, Kumayl Husain, Inderjit Sandhu, Yongdeok Shin, Javan K. Carter, Ramu Anandakrishnan, Pawel Michalak, Harold R. Garner
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0253038

Striking between-population floral divergences in a habitat specialized plant
Cited by: 1
Author(s): Sumayya Abdul Rahim, Ullasa Kodandaramaiah, Aboli Kulkarni, Deepak Barua
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0251416

Compounds from plantar foot sweat, nesting material, and urine show strain patterns associated with agonistic and affiliative behaviors in group housed male mice, Mus musculus
Cited by: 4
Author(s): Amanda J. Barabas, Helena A. Soini, Miloš V. Novotný, David R. Williams, Jacob A. Desmond, Jeffrey R. Lucas, Marisa A. Erasmus, Heng-Wei Cheng, Brianna N. Gaskill
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0245029

Experimental warming influences species abundances in a Drosophila host community through direct effects on species performance rather than altered competition and parasitism
Cited by: 8
Author(s): Mélanie Thierry, Nicholas A. Pardikes, Chia‐Hua Lue, Owen T. Lewis, Jan Hrček
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0246052

Transcriptomic profiling of susceptible and resistant flax seedlings after Fusarium oxysporum lini infection
Cited by: 10
Author(s): Aleksandra Boba, Kamil Kostyń, Bartosz Kozak, Iwan Zalewski, Jan Szopa, Anna Kulma
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0249691

Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Cited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0234498

Landscape composition and local floral resources influence foraging behavior but not the size of Bombus impatiens Cresson (Hymenoptera: Apidae) workers
Cited by: 9
Author(s): Amélie Gervais, Ève Courtois, Valérie Fournier, Marc Bélisle
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0239189

Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation
Cited by: 8
Author(s): Hong Dang, Deepika Polineni, Rhonda G. Pace, Jaclyn R. Stonebraker, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Lisa J. Strug, Wanda K. O’Neal, Michael R. Knowles
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0238422

SSNdesign—An R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks
Cited by: 4
Author(s): Alan R. Pearse, James McGree, Nicholas A. Som, Catherine Leigh, Paul Maxwell, Jay M. Ver Hoef, Erin E. Peterson
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1009386

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus
Cited by: 39
Author(s): Thorsten Langner, Adeline Harant, Luis B. Gómez-Luciano, Ram-Krishna Shrestha, Angus Malmgren, Sergio M. Latorre, Hernán A. Burbano, Joe Win, Sophien Kamoun
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pntd.0008755

Combining natural language processing and metabarcoding to reveal pathogen-environment associations
Cited by: 2
Author(s): David Molik, DeAndre Tomlinson, Shane Davitt, Eric Lease Morgan, Matthew Sisk, Benjamin Roche, Natalie Meyers, Michael E. Pfrender
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0229146

Vegetation changes in temperate ombrotrophic peatlands over a 35 year period
Cited by: 20
Author(s): Nicolas Pinceloup, Monique Poulin, Marie‐Hélène Brice, Stéphanie Pellerin
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0248031

Evaluating the effects of embedded self-massage practice on strength performance: A randomized crossover pilot trial
Cited by: 4
Author(s): Yann Kerautret, Aymeric Guillot, Franck Di Rienzo
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0242486

Altered feeding behavior and immune competence in paper wasps: A case of parasite manipulation?
Cited by: 3
Author(s): L. Beani, Marta Mariotti Lippi, Nadia Mulinacci, Fabio Manfredini, Lorenzo Cecchi, C. Giuliani, Corrado Tani, Niccolò Meriggi, Duccio Cavalieri, Federico Cappa
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0219723

Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima
Cited by: 10
Author(s): Gareth A. Pearson, Neusa Martins, Pedro M Madeira, Ester Á. Serrão, Inka Bartsch
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0257386

(DIGSS) Determination of Intervals using Georeferenced Survey Simulation: An R package for subsurface survey
Cited by: 0
Author(s): William J. Pestle, Cara Hubbell, Mark Hübbe
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0230767

The design and implementation of restraint devices for the injection of pathogenic microorganisms into Galleria mellonella
Cited by: 8
Author(s): Lance R. Fredericks, Mark D. Lee, Cooper R. Roslund, Angela Crabtree, Peter B. Allen, Paul A. Rowley
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0244637

metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics
Cited by: 5
Author(s): Romuald Laso-Jadart, Christophe Ambroise, Pierre Peterlongo, Mohammed‐Amin Madoui
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0234190

Positive attitudes towards feline obesity are strongly associated with ownership of obese cats
Cited by: 2
Author(s): Kendy Tzu-Yun Teng, Paul McGreevy, Jenny‐Ann L.M.L. Toribio, Navneet K. Dhand
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0234669

netboxr: Automated discovery of biological process modules by network analysis in R
Cited by: 2
Author(s): Eric Minwei Liu, Augustin Luna, Guanlan Dong, Chris Sander
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0250783

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores
Cited by: 12
Author(s): John K. Pearman, Georgia Thomson‐Laing, Jamie Howarth, Marcus J. Vandergoes, L. M. Thompson, Andrew Rees, Susanna A. Wood
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0224693

ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells
Cited by: 15
Author(s): Samuel A. Danziger, David L. Gibbs, Ilya Shmulevich, Mark McConnell, Matthew Trotter, Frank Schmitz, David J Reiss, Alexander V. Ratushny
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0222977

No relationship between fornix and cingulum degradation and within-network decreases in functional connectivity in prodromal Alzheimer’s disease
Cited by: 10
Author(s): Therese Gilligan, Francesca Sibilia, Dervla Farrell, Declan Lyons, Sean Kennelly, Arun L.W. Bokde
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0230945

Timescales of variation in diversity and production of bacterioplankton assemblages in the Lower Mississippi River
Cited by: 3
Author(s): Jason T. Payne, Colin R. Jackson, Justin Millar, Clifford A. Ochs
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0242943

Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy
Cited by: 7
Author(s): Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0237419

Development and validation of a model for individualized prediction of hospitalization risk in 4,536 patients with COVID-19
Cited by: 106
Author(s): Lara Jehi, Xinge Ji, Alex Milinovich, Serpil C. Erzurum, Amy Merlino, Steve Gordon, James B. Young, Michael W. Kattan
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0231773

Perceived socio-economic impacts of the marbled crayfish invasion in Madagascar
Cited by: 19
Author(s): Ranja Andriantsoa, Julia P. G. Jones, Vlad Achimescu, Heriniaina Randrianarison, Miary Raselimanana, Manjary Andriatsitohaina, Jeanne Rasamy, Frank Lyko
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0227760

A graph-based algorithm for RNA-seq data normalization
Cited by: 2
Author(s): Diem-Trang Tran, Aditya Bhaskara, Balagurunathan Kuberan, Matthew Might
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0254293

easyFulcrum: An R package to process and analyze ecological sampling data generated using the Fulcrum mobile application
Cited by: 4
Author(s): Matteo Di Bernardo, Timothy A. Crombie, Daniel E. Cook, Erik C. Andersen
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0230218

Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11
Cited by: 10
Author(s): Takahiro Yamada, Yusuke Hiki, Noriko Hiroi, Elena Shagimardanova, Oleg Gusev, Richard Cornette, Takahiro Kikawada, Akira Funahashi
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0236890

Defining the nutritional input for genome-scale metabolic models: A roadmap
Cited by: 21
Author(s): Γεώργιος Μαρίνος, Christoph Kaleta, Silvio Waschina
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0237893

The response of culturally important plants to experimental warming and clipping in Pakistan Himalayas
Cited by: 2
Author(s): Saira Karimi, Muhammad Ali Nawaz, Saadia Naseem, Ahmed Akrem, Hussain Ali, Olivier Dangles, Zahid Ali
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0239247

Trust and transparency in times of crisis: Results from an online survey during the first wave (April 2020) of the COVID-19 epidemic in the UK
Cited by: 78
Author(s): Luisa Enria, Naomi R. Waterlow, Nina Trivedy Rogers, Hannah Brindle, Sham Lal, Rosalind M Eggo, Shelley Lees, Chrissy h. Roberts
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0253411

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0256990

Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
Cited by: 11
Author(s): Joe G Greener, David T. Jones
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0258157

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
Cited by: 4
Author(s): Matthew S. Tucker, Celia O’Brien, Mark C. Jenkins, Benjamin M. Rosenthal
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1008375

DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
Cited by: 29
Author(s): Sheila Lutz, Christian Brion, Margaret Kliebhan, Frank W. Albert
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0230888

Site-specific machine learning predictive fertilization models for potato crops in Eastern Canada
Cited by: 13
Author(s): Zonlehoua Coulibali, Athyna N. Cambouris, Léon‐Étienne Parent
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0249735

Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA
Cited by: 10
Author(s): Kanae Nishii, Michael Möller, Hidetoshi Iida
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0255012

Hierarchical modelling of immunoglobulin coated bacteria in dogs with chronic enteropathy shows reduction in coating with disease remission but marked inter-individual and treatment-response variability
Cited by: 0
Author(s): Lina María Martínez-López, Alexis Perez‐Gonzalez, Elizabeth A. Washington, Andrew Woodward, Alexandra J. Roth‐Schulze, Julien Dandrieux, Thurid Johnstone, Nathalee Prakash, Aaron R. Jex, Caroline Mansfield
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0225216

Abundance of ethnically biased microsatellites in human gene regions
Cited by: 3
Author(s): Nicholas A. Kinney, Lin Kang, Laurel Eckstrand, Arichanah Pulenthiran, Peter Samuel, Ramu Anandakrishnan, Robin Varghese, Pawel Michalak, Harold R. Garner
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0248398

Productive wetlands restored for carbon sequestration quickly become net CO2 sinks with site-level factors driving uptake variability
Cited by: 27
Author(s): Amy Valach, Kuno Kasak, Kyle S. Hemes, Tyler L. Anthony, Iryna Dronova, Sophie Taddeo, Whendee L. Silver, Daphne Szutu, Joseph Verfaillie, Dennis Baldocchi
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0239381

Short k-mer abundance profiles yield robust machine learning features and accurate classifiers for RNA viruses
Cited by: 8
Author(s): Nafis Ul Alam, Umar Faruq Chowdhury
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0239864

Hybrid algorithms for generating optimal designs for discriminating multiple nonlinear models under various error distributional assumptions
Cited by: 6
Author(s): Chih-Chia Chen, Ping Yang Chen, Cheng Lin Hsu, Weng Kee Wong
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0243672

Characterisation and chemometric evaluation of 17 elements in ten seaweed species from Greenland
Cited by: 11
Author(s): Katharina Kreissig, Lisbeth Truelstrup Hansen, Pernille Erland Jensen, Susse Wegeberg, Ole Geertz‐Hansen, Jens Jørgen Sloth
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1009566

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
Cited by: 19
Author(s): James R. Whiting, Josephine R. Paris, Mijke J. van der Zee, Paul J. Parsons, Detlef Weigel, Bonnie A. Fraser
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0256038

Exogenous corticosterone and melanin-based coloration explain variation in juvenile dispersal behaviour in the barn owl (Tyto alba)
Cited by: 3
Author(s): Bettina Almasi, Carolina Massa, Lukas Jenni, Alexandre Roulin
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pcbi.1009302

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge
Cited by: 5
Author(s): Zhitao Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug Dream Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1009294

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

10.1371/journal.pone.0254007

Text classification to streamline online wildlife trade analyses
Cited by: 7
Author(s): Oliver C. Stringham, Stephanie Moncayo, Katherine G. W. Hill, Adam Toomes, Lewis Mitchell, Joshua V. Ross, Phillip Cassey
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0235779

Prostate MRI added to CAPRA, MSKCC and Partin cancer nomograms significantly enhances the prediction of adverse findings and biochemical recurrence after radical prostatectomy
Cited by: 7
Author(s): Kevin Sandeman, Juho Eineluoto, Joona Pohjonen, Andrew Erickson, Tuomas P. Kilpeläinen, Petrus Järvinen, Henrikki Santti, Anssi Pétas, Mika Matikainen, Suvi Marjasuo, Anu Kenttämies, Tuomas Mirtti, Antti Rannikko
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pcbi.1008720

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity
Cited by: 4
Author(s): John P. Lloyd, Matthew B. Soellner, Sofía D. Merajver, Jun Z. Li
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.ppat.1009418

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity
Cited by: 10
Author(s): Cédric Lood, Charlotte Peeters, Quentin Lamy-Besnier, Jeroen Wagemans, Daniël De Vos, Marijke Proesmans, Jean‐Paul Pirnay, Fedoua Echahidi, Denis Piérard, M Thimmesch, Anca Boeras, Katrien Lagrou, Evelien De Canck, Elke De Wachter, Vera van Noort, Rob Lavigne, Peter Vandamme
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0250344

One dog’s waste is another dog’s wealth: A pilot study of fecal microbiota transplantation in dogs with acute hemorrhagic diarrhea syndrome
Cited by: 13
Author(s): Arnon Gal, Patrick C. Barko, Patrick J. Biggs, Kristene Gedye, Anne C. Midwinter, David A. Williams, Richard K. Burchell, P. Pazzi
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1008984

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model
Cited by: 16
Author(s): Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J.M. Walhout, Erik C. Andersen
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pcbi.1008551

DEER-PREdict: Software for efficient calculation of spin-labeling EPR and NMR data from conformational ensembles
Cited by: 39
Author(s): Giulio Tesei, João M. Martins, Micha B. A. Kunze, Yong Wang, Ramón Crehuet, Kresten Lindorff‐Larsen
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pcbi.1008329

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes
Cited by: 6
Author(s): Aleksei Mironov, Stepan Denisov, Alexander Greß, Olga V. Kalinina, Dmitri D. Pervouchine
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0254884

Spatial epidemiological study of the distribution, clustering, and risk factors associated with early COVID-19 mortality in Mexico
Cited by: 19
Author(s): Ricardo Ramírez‐Aldana, Juan Carlos Gómez-Verján, Omar Yaxmehen Bello‐Chavolla, Carmen García-Peña
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0250496

Optimizing the P balance: How do modern maize hybrids react to different starter fertilizers?
Cited by: 7
Author(s): Thea Mi Weiß, Willmar L. Leiser, Alice-Jacqueline Reineke, Dongdong Li, Wenxin Liu, Volker Hahn, Tobias Würschum
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0245989

Effect of pre-operative bicarbonate infusion on maternal and perinatal outcomes among women with obstructed labour in Mbale hospital: A double blind randomized controlled trial
Cited by: 5
Author(s): Milton W. Musaba, Julius Wandabwa, Grace Ndeezi, Andrew Weeks, David Mukunya, Paul Waako, Victoria Nankabirwa, Kenneth Mugabe, Daniel Semakula, James K Tumwine, Justus K. Barageine
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pcbi.1009290

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Cited by: 23
Author(s): Ariel A. Hippen, Matías M. Falco, Lukas M. Weber, Erdoğan Pekcan Erkan, Kaiyang Zhang, Jennifer A. Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0231824

Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis
Cited by: 0
Author(s): Simone Lederer, Tom Heskes, Simon J. van Heeringen, Cornelis A. Albers
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0237435

Translating episodic future thinking manipulations for clinical use: Development of a clinical control
Cited by: 6
Author(s): Jillian M. Rung, Leonard H. Epstein
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0237079

A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand
Cited by: 17
Author(s): Anya Sophia Noble, Stevie Noe, Michael J. Clearwater, Charles K. Lee
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0233235

Dominance rank but not body size influences female reproductive success in mountain gorillas
Cited by: 19
Author(s): Edward Wright, Jordi Galbany, Shannon C. McFarlin, Eric Ndayishimiye, Tara S. Stoinski, Martha M. Robbins
Software Mentions: 7
Published: about 5 years ago

10.1371/journal.pone.0257510

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment
Cited by: 17
Author(s): Jeanine Brantschen, Rosetta C. Blackman, Jean‐Claude Walser, Florian Altermatt
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0252448

Predicting direct and indirect non-target impacts of biocontrol agents using machine-learning approaches
Cited by: 3
Author(s): Hannah J. Kotula, Guadalupe Peralta, Carol M. Frost, Jacqui H. Todd, Jason M. Tylianakis
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0219235

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data
Cited by: 17
Author(s): Stephen Woloszynek, Joshua Chang Mell, Zhengqiao Zhao, Gideon Simpson, Michael O’Connor, Gail Rosen
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pntd.0009607

One hundred years of zoonoses research in the Horn of Africa: A scoping review
Cited by: 17
Author(s): Lisa Cavalerie, Maya Wardeh, Ophélie Lebrasseur, Mark Nanyingi, K. Marie McIntyre, Mirgissa Kaba, Daniel Asrat, Robert M. Christley, Gina Pinchbeck, Matthew Baylis, Siobhan M. Mor
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pcbi.1008354

Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines
Cited by: 5
Author(s): Chen Xie, Cemalettin Bekpen, Sven Künzel, Maryam Keshavarz, Rebecca Krebs-Wheaton, Neva Škrabar, Kristian K. Ullrich, Wenyu Zhang, Diethard Tautz
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0253277

Dogs fail to reciprocate the receipt of food from a human in a food-giving task
Cited by: 1
Author(s): Jim McGetrick, Lisa Poncet, Marietta Amann, Johannes Schullern-Schrattenhofen, Leona Fux, Mayte Martínez, Friederike Range
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pcbi.1009382

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Cited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0222749

Brettanomyces bruxellensis wine isolates show high geographical dispersal and long persistence in cellars
Cited by: 12
Author(s): Alice Cibrario, Marta Avramova, Maria Dimopoulou, Maura Magani, Cécile Miot-Sertier, Albert Mas, María del Carmen Portillo Guisado, Patricia Ballestra, Warren Albertin, Isabelle Masneuf‐Pomarède, Marguerite Dols‐Lafargue
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0241691

Succinivibrionaceae is dominant family in fecal microbiota of Behçet’s Syndrome patients with uveitis
Cited by: 12
Author(s): Duygu Tecer, Feride Göğüş, Ayşe Kalkancı, Merve Erdoğan, Murat Hasanreisoğlu, Çağrı Ergin, Tarkan Karakan, Ramazan Kozan, Serhat Emre Coban, Kadir Serdar Diker
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0223141

Attenuation correction using 3D deep convolutional neural network for brain 18F-FDG PET/MR: Comparison with Atlas, ZTE and CT based attenuation correction
Cited by: 36
Author(s): Paul Blanc-Durand, Maya Khalifé, B. Sgard, Sandeep Kaushik, Marine Soret, Tiss Amal, Georges El Fakhri, Marie‐Odile Habert, Florian Wiesinger, Aurélie Kas
Software Mentions: 7
Published: almost 6 years ago