pypi: PACE | Projects | Ecosyste.ms: Papers

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 3 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: over 3 years ago

10.1371/journal.pone.0250629

Epiphytic diatom community structure and richness is determined by macroalgal host and location in the South Shetland Islands (Antarctica)
Cited by: 3
Author(s): Andrea M. Burfeid-Castellanos, Rafael P. Martín–Martín, Michael Kloster, Carlos Angulo‐Preckler, Conxita Àvila, Bánk Beszteri
Software Mentions: 8
Published: about 3 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: about 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: about 4 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: over 2 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: about 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: almost 3 years ago

10.1371/journal.pone.0245639

Are we missing the forest for the trees? Conspecific negative density dependence in a temperate deciduous forest
Cited by: 3
Author(s): Kathryn E. Barry, Stefan A. Schnitzer
Software Mentions: 8
Published: almost 3 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: almost 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 3 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: about 3 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 3 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 3 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: almost 3 years ago

10.1371/journal.pone.0255849

Literary runaway: Increasingly more references cited per academic research article from 1980 to 2019
Cited by: 1
Author(s): Chaoyang Dai, Chen Quan, Tao Wan, Fan Liu, Ya‐Jun Gong, Qingfeng Wang
Software Mentions: 8
Published: almost 3 years ago

10.1371/journal.pone.0230262

So far, so good… Similar fitness consequences and overall energetic costs for short and long-distance migrants in a seabird
Cited by: 10
Author(s): David Pelletier, Yannick Seyer, Stefan Garthe, Salomé Bonnefoi, Richard A. Phillips, Magella Guillemette
Software Mentions: 8
Published: about 4 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 3 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 3 years ago

10.1371/journal.pmed.1003413

Body mass index and risk of dying from a bloodstream infection: A Mendelian randomization study
Cited by: 14
Author(s): Tormod Rogne, Erik Solligård, Stephen Burgess, Ben Brumpton, Julie Paulsen, Hallie C. Prescott, Randi Marie Mohus, Lise Tuset Gustad, Arne Mehl, Bjørn Olav Åsvold, Andrew T. DeWan, Jan Kristian Damås
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pone.0247476

Small area estimation and childhood obesity surveillance using electronic health records
Cited by: 5
Author(s): Ying‐Qi Zhao, Derek Norton, Larry Hanrahan
Software Mentions: 8
Published: about 3 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: almost 3 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 3 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 4 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: over 2 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 3 years ago

10.1371/journal.pone.0240996

Biological invasions alter environmental microbiomes: A meta-analysis
Cited by: 11
Author(s): Antonino Malacrinò, Victoria A Sadowski, Tvisha Martin, Nathalia Cavichiolli de Oliveira, Ian J. Brackett, James D. Feller, Kira Harris, ORLANDO COMBITA-HEREDIA, Rosa Vescio, Alison E. Bennett
Software Mentions: 8
Published: over 3 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 3 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: about 4 years ago

10.1371/journal.pone.0234336

Gamble for the needy! Does identifiability enhances donation?
Cited by: 5
Author(s): Marc Wyszynski, Adele Diederich, Ilana Ritov
Software Mentions: 8
Published: almost 4 years ago

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: about 4 years ago

10.1371/journal.pgen.1009303

Creating artificial human genomes using generative neural networks
Cited by: 51
Author(s): Burak Yelmen, Aurélien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, Flora Jay
Software Mentions: 7
Published: over 3 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: almost 3 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 3 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 3 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: almost 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 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: over 2 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 4 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: about 4 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 3 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 4 years ago

10.1371/journal.pone.0222822

Range of motion and between-measurement variation of spinal kinematics in sound horses at trot on the straight line and on the lunge
Cited by: 8
Author(s): A. M. Hardeman, Anna Byström, L. Roepstorff, J. H. Swagemakers, P. R. van Weeren, F. M. Serra Bragança
Software Mentions: 7
Published: about 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: about 3 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 3 years ago

10.1371/journal.pone.0254749

Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node
Cited by: 2
Author(s): Christopher Schölzel, Valeria Blesius, Gernot Ernst, Alexander Goesmann, Andreas Dominik
Software Mentions: 7
Published: almost 3 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: over 3 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: about 3 years ago

10.1371/journal.pgen.1009331

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Cited by: 20
Author(s): Young Lim Lee, Hitoshi Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Erik Mullaart, Wouter Coppieters, Ruth Appeltant, R.F. Veerkamp, Martien A. M. Groenen, Michel Georges, Mirte Bosse, Tom Druet, A.C. Bouwman, Carole Charlier
Software Mentions: 7
Published: almost 3 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: almost 3 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 3 years ago

10.1371/journal.pone.0233282

Can we decode phonetic features in inner speech using surface electromyography?
Cited by: 8
Author(s): Ladislas Nalborczyk, Romain Grandchamp, Ernst H. W. Koster, Marcela Perrone‐Bertolotti, Hélène Lœvenbruck
Software Mentions: 7
Published: almost 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: over 4 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: almost 3 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: almost 3 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 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 4 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 4 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: over 2 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: almost 3 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: over 2 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 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: over 3 years ago

10.1371/journal.pone.0226527

Increased performance of DNA metabarcoding of macroinvertebrates by taxonomic sorting
Cited by: 22
Author(s): Kevin K. Beentjes, Arjen G.C.L. Speksnijder, Menno Schilthuizen, Marten Hoogeveen, Rob Pastoor, Berry B. van der Hoorn
Software Mentions: 7
Published: over 4 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: almost 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: almost 3 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: almost 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 3 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: over 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 4 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: over 3 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: about 4 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 3 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 4 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: about 3 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 3 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: over 2 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: about 3 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 4 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: about 3 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: over 3 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: about 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: almost 3 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: almost 3 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: over 4 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 3 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: over 2 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 3 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 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: about 3 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: 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: over 2 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: almost 3 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: over 2 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 3 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 3 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 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 3 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: over 2 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: about 3 years ago

Projects: pypi: PACE

Papers Mentioning PACE 13,779