cran: gridExtra | Projects | Ecosyste.ms: Papers

10.1186/1471-2156-15-81

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations
Cited by: 16
Author(s): Robert B. Scharpf, Lynn Mireles, Qiong Yang, Anna Köttgen, Ingo Ruczinski, Katalin Suszták, Eitan Halper-Stromberg, Adrienne Tin, Stephen Cristiano, Aravinda Chakravarti, Eric Boerwinkle, Caroline S. Fox, Josef Coresh, W. H. Linda Kao
Software Mentions: 56
Published: almost 11 years ago

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.1371/journal.pcbi.1007912

bigPint: A Bioconductor visualization package that makes big data pint-sized
Cited by: 3
Author(s): Lindsay Rutter, Dianne Cook
Software Mentions: 47
Published: over 4 years ago

10.1038/s41598-020-76683-1

Revisiting potential associations between brain morphology, fear acquisition and extinction through new data and a literature review
Cited by: 7
Author(s): Mana R. Ehlers, Janne Nold, Manuel Kuhn, Maren Klingelhöfer-Jens, Tina B. Lonsdorf
Software Mentions: 44
Published: about 4 years ago

10.15252/msb.20209539

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago

10.1371/journal.pcbi.1005752

mixOmics: An R package for ‘omics feature selection and multiple data integration
Cited by: 1,902
Author(s): Florian Rohart, Benoît Gautier, Amrit Singh, Kim‐Anh Lê Cao
Software Mentions: 29
Published: about 7 years ago

10.3389/fmicb.2018.01474

Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar Current
Cited by: 24
Author(s): Flavia Flaviani, Declan C. Schroeder, Karen Lebret, Cecilia Balestreri, Andrea Highfield, Joanna L. Schroeder, Sally Thorpe, Karen Moore, Konrad Pasckiewicz, Maya C. Pfaff, Edward P. Rybicki
Software Mentions: 27
Published: over 6 years ago

10.1186/s13073-021-00910-1

Landscape and selection of vaccine epitopes in SARS-CoV-2
Cited by: 21
Author(s): Christof C. Smith, Kelly Olsen, Kaylee M. Gentry, Maria J. Sambade, Wolfgang Beck, Jason Garness, Sarah Entwistle, Caryn Willis, Steven Vensko, Allison Woods, Misha Fini, Brandon Carpenter, Eric D. Routh, Julia Kodysh, Timothy J. O’Donnell, Carsten Haber, Kirsten Heiß, Volker Stadler, Erik Garrison, Adam Sandor, Jenny P.-Y. Ting, Jared Weiss, Krzysztof Krajewski, Oliver C. Grant, Robert J. Woods, Mark T. Heise, Benjamin G. Vincent, Alex Rubinsteyn
Software Mentions: 27
Published: over 3 years ago

10.1371/journal.pcbi.1006242

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
Cited by: 29
Author(s): Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard
Software Mentions: 27
Published: over 6 years ago

10.1038/s41598-021-96198-7

Cross-modal auditory priors drive the perception of bistable visual stimuli with reliable differences between individuals
Cited by: 2
Author(s): Zsófia Pálffy, Kinga Farkas, Gábor Csukly, Szabolcs Kéri, Bertalan Polner
Software Mentions: 25
Published: over 3 years ago

10.1016/j.cell.2019.07.038

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana
Cited by: 237
Author(s): Anna-Lena Van de Weyer, Freddy Monteiro, Oliver J. Furzer, Marc T. Nishimura, Volkan Çevik, Kamil Witek, Jonathan D. G. Jones, Jeffery L. Dangl, Detlef Weigel, Felix Bemm
Software Mentions: 23
Published: over 5 years ago

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: about 4 years ago

10.1038/s41421-020-00226-1

Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo
Cited by: 68
Author(s): Hang‐Ping Yao, Xiangyun Lu, Qiong Chen, Kaijin Xu, Yu Chen, Ming-Hui Cheng, Keda Chen, Linfang Cheng, Tian-Hao Weng, Danrong Shi, Fumin Liu, Zhigang Wu, Mingjie Xie, Haibo Wu, Changzhong Jin, Min Zheng, Nanping Wu, Chao Jiang, Lanjuan Li
Software Mentions: 21
Published: about 4 years ago

10.3390/cells8091045

Systematic Assessment of Blood-Borne MicroRNAs Highlights Molecular Profiles of Endurance Sport and Carbohydrate Uptake
Cited by: 12
Author(s): Fabian Kern, Nicole Ludwig, Christina Backes, Esther Maldener, Tobias Fehlmann, Artur Suleymanov, Eckart Meese, Anne Hecksteden, Andreas Keller, Tim Meyer
Software Mentions: 21
Published: over 5 years ago

10.1038/s41598-019-55469-0

Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papers
Cited by: 6
Author(s): Sebastian von Huth, Louise B. Thingholm, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 20
Published: about 5 years ago

10.18632/aging.203108

Cognitive dedifferentiation as a function of cognitive impairment in the ADNI and MemClin cohorts
Cited by: 2
Author(s): John Wallert, Anna Rennie, Daniel Ferreira, J‐Sebastian Muehlboeck, Lars‐Olof Wahlund, Eric Westman, Urban Ekman
Software Mentions: 20
Published: over 3 years ago

10.7717/peerj.2836

Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons
Cited by: 273
Author(s): Ilias Lagkouvardos, Sandra E. Fischer, Neeraj Kumar, Thomas Clavel
Software Mentions: 20
Published: almost 8 years ago

10.1371/journal.pntd.0005121

Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control
Cited by: 20
Author(s): Christina Sunyoung Kim, Pierre Echaubard, Apiporn Suwannatrai, Sasithorn Kaewkes, Bruce A. Wilcox, Banchob Sripa
Software Mentions: 19
Published: about 8 years ago

10.3390/v12101142

A Diverse Virome of Leafroll-Infected Grapevine Unveiled by dsRNA Sequencing
Cited by: 24
Author(s): Mamadou L. Fall, De-Xiang Xu, Pierre Lemoyne, Issam Moussa, Carole Beaulieu, Odile Carisse
Software Mentions: 19
Published: about 4 years ago

10.1093/molbev/msaa311

A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance
Cited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: about 4 years ago

10.3389/fimmu.2020.01691

Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies
Cited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago

10.1371/journal.pone.0244384

Metropolitan age-specific mortality trends at borough and neighborhood level: The case of Mexico City
Cited by: 2
Author(s): Karol Baca-López, Cristóbal Fresno, Jesús Espinal-Enríquez, Miriam V. Flores-Merino, Miguel A. Camacho-López, Enrique Hernández‐Lemus
Software Mentions: 18
Published: almost 4 years ago

10.1111/eva.13237

A machine learning approach to integrating genetic and ecological data in tsetse flies ( <i>Glossina pallidipes</i> ) for spatially explicit vector control planning
Cited by: 5
Author(s): Anusha P Bishop, Giuseppe Amatulli, Chaz Hyseni, Evlyn Pless, Rosemary Bateta, Winnie A. Okeyo, Paul O. Mireji, Sylvance Okoth, Imna Malele, Grace Murilla, Serap Aksoy, Adalgisa Caccone, Norah P. Saarman
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pbio.3001296

Tapping into non-English-language science for the conservation of global biodiversity
Cited by: 79
Author(s): Tatsuya Amano, Violeta Berdejo‐Espinola, Alec P. Christie, Kate Willott, Munemitsu Akasaka, András Báldi, Anna Berthinussen, Sandro Bertolino, Andrew J. Bladon, Min Chen, Chang Yong Choi, Magda Bou Dagher Kharrat, Luís Guilherme de Oliveira, Perla Farhat, Marina Golivets, Nataly Hidalgo Aranzamendi, Kerstin Jantke, Joanna Kajzer‐Bonk, M. Çisel Kemahlı Aytekin, Igor Khorozyan, Kensuke Kito, Ko Konno, Da Li Lin, Nick A. Littlewood, Yang Liu, Yifan Liu, Matthias Claudio Loretto, Valentina Marconi, Philip A. Martin, William H. Morgan, Juan Pablo Narváez-Gómez, Pablo José Negret, Elham Nourani, José Manuel Ochoa Quintero, Nancy Ockendon, Rachel Rui Ying Oh, Silviu O. Petrovan, Ana Cláudia Piovezan-Borges, Ingrid L. Pollet, Danielle Leal Ramos, Ana L. Reboredo Segovia, A. Nayelli Rivera‐Villanueva, Ricardo Rocha, Marie Morgane Rouyer, Katherine A. Sainsbury, Richard Schuster, Dominik Schwab, Çaǧan H. Şekercioǧlu, Hae Min Seo, Gorm E. Shackelford, Yushin Shinoda, Rebecca K. Smith, Shan Dar Tao, Ming-shan Tsai, Elizabeth Tyler, Flóra Vajna, José O. Valdebenito, Svetlana Vozykova, Paweł Waryszak, Veronica Zamora‐Gutiérrez, Rafael Dudeque Zenni, Wenjun Zhou, William J. Sutherland
Software Mentions: 18
Published: about 3 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: over 5 years ago

10.1093/gigascience/giaa010

Interpretable and accurate prediction models for metagenomics data
Cited by: 29
Author(s): Edi Prifti, Yann Chevaleyre, Blaise Hanczar, Eugeni Belda, Antoine Danchin, Karine Clément, Jean-Daniel Zucker
Software Mentions: 18
Published: almost 5 years ago

10.1371/journal.pone.0238665

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains
Cited by: 19
Author(s): Anastasis Oulas, Maria Zanti, Marios Tomazou, Margarita Zachariou, George Minadakis, Marilena M. Bourdakou, Margarita Zachariou, George M. Spyrou
Software Mentions: 18
Published: almost 4 years ago

10.3389/fimmu.2020.565730

Class I HLA Allele Predicted Restricted Antigenic Coverages for Spike and Nucleocapsid Proteins Are Associated With Deaths Related to COVID-19
Cited by: 22
Author(s): Marco Antônio M. Pretti, Rômulo Gonçalves Galvani, Gustavo Fioravanti Vieira, Adriana Bonomo, Martín Bonamino, Mariana Boroni
Software Mentions: 17
Published: about 4 years ago

10.31744/einstein_journal/2020AO6127

COVID-19 information exposure in digital media and implications for employees in the health care sector: findings from an online survey
Cited by: 7
Author(s): Paulo Rodrigo Bazán, Raymundo Machado de Azevedo Neto, Julia Abou Dias, Vanessa Gil Salvatierra, Liana Guerra Sanches, Sheylla Nadjane Batista Lacerda, Edson Amaro, Elisa Harumi Kozasa, Joana Bisol Balardin
Software Mentions: 17
Published: almost 5 years ago

10.3390/brainsci11081017

Facial Signals and Social Actions in Multimodal Face-to-Face Interaction
Cited by: 14
Author(s): Naomi Nota, James P. Trujillo, Judith Holler
Software Mentions: 17
Published: over 3 years ago

10.1084/jem.20200920

Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment
Cited by: 57
Author(s): Kristen E. Pauken, Osmaan Shahid, Kaitlyn A. Lagattuta, Kelly Mahuron, Jacob M. Luber, Margaret M. Lowe, Lüping Huang, Conor P. Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum, Adil Daud, Arlene H. Sharpe, Meromit Singer
Software Mentions: 17
Published: almost 4 years ago

10.1371/journal.pone.0151935

Novel and Lost Forests in the Upper Midwestern United States, from New Estimates of Settlement-Era Composition, Stem Density, and Biomass
Cited by: 48
Author(s): Simon Goring, David J. Mladenoff, Charles V. Cogbill, Sydne Record, Christopher J. Paciorek, Stephen T. Jackson, Michael C. Dietze, Andria Dawson, Jaclyn Hatala Matthes, J. S. McLachlan, John W. Williams
Software Mentions: 17
Published: about 8 years ago

10.1093/molbev/msab006

Compatibility of Evolutionary Responses to Constituent Antibiotics Drive Resistance Evolution to Drug Pairs
Cited by: 14
Author(s): Leonie Johanna Jahn, Daniel Simon, Mia Jensen, Charles B. Bradshaw, Mostafa Mostafa Hashim Ellabaan, Morten Otto Alexander Sommer
Software Mentions: 16
Published: almost 4 years ago

10.1038/s41598-017-11514-4

Microbial communities in placentas from term normal pregnancy exhibit spatially variable profiles
Cited by: 121
Author(s): Lindsay A. Parnell, Catherine Briggs, Bin Cao, Omar Delannoy-Bruno, Andrew E. Schrieffer, Indira U. Mysorekar
Software Mentions: 16
Published: over 7 years ago

10.1038/s41419-021-03909-z

Diagnostic and prognostic potential of the proteomic profiling of serum-derived extracellular vesicles in prostate cancer
Cited by: 14
Author(s): Michele Signore, Romina Alfonsi, Giulia Federici, Simona Nanni, Antonio Addario, Lucia Bertuccini, Aurora Aiello, Anna Pace, Isabella Sperduti, Giovanni Muto, Alessandro Giacobbe, Devis Collura, Lidia Brunetto, Giuseppe Simone, Manuela Costantini, Lucio Crinò, Stefania Rossi, Claudio Tabolacci, Marco Diociaiuti, Tania Merlino, Michele Gallucci, Steno Sentinelli, Rocco Papalia, Ruggero De Maria, Dèsirèe Bonci
Software Mentions: 16
Published: over 3 years ago

10.3389/fimmu.2021.668391

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
Cited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: over 3 years ago

10.1186/s12866-019-1598-0

Characterization of Salmonella Dublin isolated from bovine and human hosts
Cited by: 35
Author(s): Narayan Paudyal, Hang Pan, Mohammed Elbediwi, Xiao Hua Zhou, Xianqi Peng, Xiaoliang Li, Weihuan Fang, Min Yue
Software Mentions: 15
Published: about 5 years ago

10.1371/journal.pntd.0009232

Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-Bissau
Cited by: 8
Author(s): Sebastian von Huth, Louise B. Thingholm, Poul Erik Kofoed, Corinna Bang, Malte Rühlemann, André Franke, Uffe Holmskov
Software Mentions: 15
Published: almost 4 years ago

10.1038/s41598-019-46510-3

Differential prognostic impact of platelet-derived growth factor receptor expression in NSCLC
Cited by: 19
Author(s): Thomas K. Kilvaer, Mehrdad Rakaee, Turid Hellevik, Jørg Vik, Luigi De Petris, Tom Dønnem, Carina Strell, Arne Östman, Lill-Tove Busund, Iñigo Martínez-Zubiaurre
Software Mentions: 15
Published: over 5 years ago

10.3390/microorganisms9051050

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum
Cited by: 5
Author(s): Jing Zhu, Xiang Sun, Zhidong Zhang, Qi-Yong Tang, Minghong Gu, Lijuan Zhang, Min Hou, Amir Sharon, Hongli Yuan
Software Mentions: 15
Published: over 3 years ago

10.2196/24889

A Novel Machine Learning Framework for Comparison of Viral COVID-19–Related Sina Weibo and Twitter Posts: Workflow Development and Content Analysis
Cited by: 7
Author(s): Shi Chen, Lina Zhou, Yunya Song, Qian Xu, Ping Wang, Kanlun Wang, Yaorong Ge, Daniel Janies
Software Mentions: 15
Published: almost 4 years ago

10.1128/mBio.02120-17

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients
Cited by: 95
Author(s): Matthew K. Doherty, Tao Ding, Charlie C. Koumpouras, Shannon Telesco, Calixte S. Monast, Anuk Das, Carrie Brodmerkel, Patrick D. Schloss
Software Mentions: 15
Published: over 6 years ago

10.3390/biom10081095

Glutenin and Gliadin, a Piece in the Puzzle of their Structural Properties in the Cell Described through Monte Carlo Simulations
Cited by: 26
Author(s): Joel Markgren, Mikael S. Hedenqvist, Faiza Rasheed, Marie Skepö, Eva Johansson
Software Mentions: 15
Published: over 4 years ago

10.1186/s13007-018-0376-6

PhenoFly Planning Tool: flight planning for high-resolution optical remote sensing with unmanned areal systems
Cited by: 43
Author(s): Lukas Roth, Andreas Hund, Helge Aasen
Software Mentions: 15
Published: about 6 years ago

10.1186/s12864-015-2140-x

GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data
Cited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: about 9 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: over 7 years ago

10.1371/journal.pone.0248202

Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils
Cited by: 1
Author(s): Ava Mackay-Smith, Mary Kate Dornon, R.E. Lucier, Annalisa Okimoto, Flavia Mendonca de Sousa, Marcela Silvina Rodriguero, Viviana A. Confalonieri, Analía Alicia Lanteri, Andrea S. Sequeira
Software Mentions: 14
Published: over 3 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.3390/ani10071151

Tenebrio molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs
Cited by: 8
Author(s): Sandra De Meyer, Denise K. Geßner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis, Klaus Eder
Software Mentions: 14
Published: over 4 years ago

10.3390/pathogens9100841

Diverse Epidemiology of Leptospira Serovars Notified in New Zealand, 1999–2017
Cited by: 12
Author(s): Shahista Nisa, David A. Wilkinson, Olivia Angelin‐Bonnet, Shevaun Paine, Karen Weber Cullen, Jackie Wight, Michael G Baker, Jackie Benschop
Software Mentions: 14
Published: about 4 years ago

10.3389/fonc.2020.573295

Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal Cancer
Cited by: 11
Author(s): Fang-Ze Wei, Shiwen Mei, Zhijie Wang, Jianan Chen, Huan Shen, Fen Zhao, Juan Li, Zheng Liu, Qian Liu
Software Mentions: 14
Published: about 4 years ago

10.1186/s12889-021-11060-9

Identifying US County-level characteristics associated with high COVID-19 burden
Cited by: 9
Author(s): Daniel Li, Sheila M. Gaynor, Corbin Quick, Jarvis T. Chen, Briana Stephenson, Brent A. Coull, Xihong Lin
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pgen.1008405

Causal relationships between obesity and the leading causes of death in women and men
Cited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 years ago

10.1186/s13227-020-0147-0

Elongation during segmentation shows axial variability, low mitotic rates, and synchronized cell cycle domains in the crustacean, Thamnocephalus platyurus
Cited by: 9
Author(s): Savvas J. Constantinou, Nicole Duan, Lisa M. Nagy, Ariel D. Chipman, Terri A. Williams
Software Mentions: 13
Published: almost 5 years ago

10.1038/s41598-019-49160-7

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children
Cited by: 27
Author(s): Silvia Gschwendtner, Hani Kang, Elisabeth Thiering, Susanne Kublik, Bärbel U. Foesel, Holger Schulz, Susanne Krauss‐Etschmann, Joachim Heinrich, Anne Schöler, Michael Schloter, Marie Standl
Software Mentions: 13
Published: over 5 years ago

10.1186/s13072-020-00343-x

BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Cited by: 29
Author(s): Lőrinc Sándor Pongor, Jacob M. Gross, Roberto Vera Alvarez, Junko Murai, Sang‐Min Jang, Hongliang Zhang, Christophe E. Redon, Haiqing Fu, Shar-yin N. Huang, Bhushan Thakur, Adrian Baris, Leonardo Mariño‐Ramírez, David Landsman, Mirit I. Aladjem, Yves Pommier
Software Mentions: 13
Published: over 4 years ago

10.1007/s00248-020-01635-1

Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition
Cited by: 12
Author(s): Irina Tanuwidjaja, Cordula Vogel, Geertje Johanna Pronk, Anne Schöler, Susanne Kublik, Gisle Vestergaard, Ingrid Kögel‐Knabner, Mirna Mrkonjić Fuka, Michael Schloter, Stefanie Schulz
Software Mentions: 13
Published: about 4 years ago

10.3389/fpls.2021.628439

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions
Cited by: 19
Author(s): Marta Liber, Isabel Margarida Duarte, Ana-Teresa Maia, Hugo R. Oliveira
Software Mentions: 13
Published: over 3 years ago

10.1186/s12864-021-07542-0

Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn
Cited by: 8
Author(s): Songlin Guo, Shouxiong Huang, Xi Jiang, Haiyang Hu, Dingding Han, Carlos S. Moreno, Genevieve Fairbrother, David A. Hughes, Mark Stoneking, Philipp Khaitovich
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.8986.2

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 years ago

10.1186/s12915-016-0258-1

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model
Cited by: 283
Author(s): Philipp Dirksen, Sarah Arnaud Marsh, Ines Braker, Nele Heitland, Sophia Wagner, Rania Nakad, Sebastian Mäder, Carola Petersen, Vienna Kowallik, Philip Rosenstiel, Marie‐Anne Félix, Hinrich Schulenburg
Software Mentions: 12
Published: over 8 years ago

10.1186/s13567-021-00981-3

Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogens
Cited by: 8
Author(s): Christine Weiße, Denise Dittmar, Beata Jakóbczak, Volker Florian, Nicole Schütze, Gottfried Alber, Kristin Klose, Stephan Michalik, Peter Valentin‐Weigand, Uwe Völker, Christoph Georg Baums
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-018-1563-5

CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis
Cited by: 27
Author(s): Vivien A.C. Schoonenberg, Mitchel A Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello, Daniel E. Bauer
Software Mentions: 12
Published: about 6 years ago

10.1111/1462-2920.14621

Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes
Cited by: 22
Author(s): Pavla Debeljak, Ève Toulza, Sara Beier, Stéphane Blain, Ingrid Obernosterer
Software Mentions: 12
Published: over 5 years ago

10.1186/s12974-021-02235-7

Sex differences and similarities in the neuroimmune response to central administration of poly I:C
Cited by: 14
Author(s): Caitlin K. Posillico, Rosa E. Garcia-Hernandez, Natalie C. Tronson
Software Mentions: 12
Published: over 3 years ago

10.3389/fgene.2019.01200

Dysregulation of MicroRNA Regulatory Network in Lower Extremities Arterial Disease
Cited by: 22
Author(s): Anna Bogucka‐Kocka, Daniel Zalewski, Karol P Ruszel, Andrzej Stępniewski, Dariusz Gałkowski, Jacek Bogucki, Łukasz Komsta, Przemysław Kołodziej, Tomasz Zubilewicz, Marcin Feldo, Janusz Kocki
Software Mentions: 12
Published: about 5 years ago

10.7554/eLife.25062

High-intensity training enhances executive function in children in a randomized, placebo-controlled trial
Cited by: 51
Author(s): David Moreau, Ian J. Kirk, Karen E. Waldie
Software Mentions: 12
Published: over 7 years ago

10.1371/journal.pgen.1006111

Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes
Cited by: 109
Author(s): Sébastian Lequime, Albin Fontaine, Meriadeg Ar Gouilh, Isabelle Moltini-Conclois, Louis Lambrechts
Software Mentions: 12
Published: over 8 years ago

10.7554/eLife.34409

General decapping activators target different subsets of inefficiently translated mRNAs
Cited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0195065

Dengue forecasting in São Paulo city with generalized additive models, artificial neural networks and seasonal autoregressive integrated moving average models
Cited by: 48
Author(s): Oswaldo Santos Baquero, Lidia Maria Reis Santana, Francisco Chiaravalloti Neto
Software Mentions: 12
Published: over 6 years ago

10.3390/biom11020338

Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations
Cited by: 1
Author(s): Maroua Ben Amira, Mohamed Faize, Magnus Karlsson, Mukesh Dubey, Magdalena Frąc, Jacek Panek, Boris Fumanal, Aurélie Gousset-Dupont, Jean-Louis Julien, Hatem Chaar, Daniel Auguin, Robin Mom, Philippe Label, Jean-Stéphane Venisse
Software Mentions: 12
Published: almost 4 years ago

10.7717/peerj.9850

lcc: an R package to estimate the concordance correlation, Pearson correlation and accuracy over time
Cited by: 5
Author(s): Thiago Pires Oliveira, Rafael de Andrade Moral, Sílvio Sandoval Zocchi, Clarice Garcia Borges Demétrio, John Hinde
Software Mentions: 12
Published: over 4 years ago

10.3389/fgene.2021.689159

Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular Carcinoma
Cited by: 3
Author(s): Wenjie Zhu, Jian Xu, Zehao Chen, Jianxin Jiang
Software Mentions: 12
Published: over 3 years ago

10.1128/mSystems.00750-21

Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies
Cited by: 11
Author(s): Christoph Ammer‐Herrmenau, Nina Pfisterer, T. van den Berg, Ivana Gavrilova, Ahmad Amanzada, Shiv K. Singh, Alaa Mohamed, Rohia Alili, Eugeni Belda, Karine Clément, Ahmed Abd El Wahed, ElSagad Eltayeb Gady, Martin Haubrock, Tim Beißbarth, Volker Ellenrieder, Albrecht Neeße
Software Mentions: 12
Published: over 3 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: over 7 years ago

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0231500

Propensity score adjustment using machine learning classification algorithms to control selection bias in online surveys
Cited by: 23
Author(s): Ramón Ferri‐García, María del Mar Rueda
Software Mentions: 12
Published: over 4 years ago

10.1371/journal.ppat.1005548

Determinants of Arbovirus Vertical Transmission in Mosquitoes
Cited by: 90
Author(s): Sébastian Lequime, Paul Rácz, Louis Lambrechts
Software Mentions: 12
Published: over 8 years ago

10.1371/journal.pone.0207491

Feature selection and prediction of treatment failure in tuberculosis
Cited by: 30
Author(s): Christopher Martin Sauer, David Sasson, Kenneth E. Paik, Ned McCague, Leo Anthony Celi, Iván Sánchez Fernández, Ben Illigens
Software Mentions: 12
Published: about 6 years ago

10.1371/journal.pone.0144134

Personality and Situation Predictors of Consistent Eating Patterns
Cited by: 15
Author(s): Uku Vainik, Laurette Dubé, Jianjun Lu, Lesley K. Fellows
Software Mentions: 11
Published: about 9 years ago

10.3389/fimmu.2016.00339

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST
Cited by: 38
Author(s): Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie‐Paule Lefranc
Software Mentions: 11
Published: over 8 years ago

10.3389/fmicb.2018.02301

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach
Cited by: 38
Author(s): Wen Chen, Graham Wilkes, Izhar U. H. Khan, Katarina Pintar, Joseph P. Thomas, C. André Lévesque, Julie T. Chapados, Edward Topp, David R. Lapen
Software Mentions: 11
Published: about 6 years ago

10.3390/foods10010143

Intramuscular Fat Prediction Using Color and Image Analysis of Bísaro Pork Breed
Cited by: 7
Author(s): Alfredo Teixeira, Severiano Silva, Marianne Hasse, José Almeida, Luís G. Dias
Software Mentions: 11
Published: almost 4 years ago

10.3390/ijms19030742

Effect of Presence and Concentration of Plasticizers, Vegetable Oils, and Surfactants on the Properties of Sodium-Alginate-Based Edible Coatings
Cited by: 48
Author(s): Tugce Sentürk Parreidt, Michael Schott, Markus Schmid, Kajetan Müller
Software Mentions: 11
Published: almost 7 years ago

10.3390/plants8120547

New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences
Cited by: 12
Author(s): Hyoung Tae Kim, Ki-Byung Lim, Jung Sung Kim
Software Mentions: 11
Published: about 5 years ago

10.1093/rheumatology/keaa615

Changes in the illness perceptions of patients with rheumatoid arthritis over the first year of methotrexate therapy
Cited by: 7
Author(s): James M Gwinnutt, Sam Norton, Kimme L Hyrich, Mark Lunt, Anne Barton, Lis Cordingley, Suzanne Verstappen, Rams co-investigators
Software Mentions: 11
Published: about 4 years ago

10.1038/s41598-017-02464-y

UROPA: a tool for Universal RObust Peak Annotation
Cited by: 38
Author(s): Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
Software Mentions: 11
Published: over 7 years ago

10.7554/eLife.49064

Stepwise polarisation of developing bilayered epidermis is mediated by aPKC and E-cadherin in zebrafish
Cited by: 10
Author(s): Prateek Arora, Shivali Dongre, Renuka Raman, Mahendra Sonawane
Software Mentions: 11
Published: almost 5 years ago

10.3390/ijms21218148

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pone.0220961

Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data
Cited by: 4
Author(s): Amanda H. Pendegraft, Boyi Guo, Nengjun Yi
Software Mentions: 11
Published: over 5 years ago

10.1017/S003329171800315X

A machine learning ensemble to predict treatment outcomes following an Internet intervention for depression
Cited by: 37
Author(s): Rahel Pearson, Derek Pisner, Björn Meyer, Jason Shumake, Christopher G. Beevers
Software Mentions: 11
Published: about 6 years ago

10.3389/fmicb.2021.633659

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast
Cited by: 14
Author(s): Maria Luis de Vilar Correia Brito Bôto, Catarina Magalhães, Rafaela Perdigão, Diogo A. M. Alexandrino, Joana P. Fernandes, Ana M. Bernabéu, Sandra Ramos, Maria F. Carvalho, Miguel Semedo, Julie LaRoche, C. Marisa R. Almeida, Ana P. Mucha
Software Mentions: 11
Published: over 3 years ago

10.1371/journal.pone.0235283

Targeting the oral plaque microbiome with immobilized anti-biofilm peptides at tooth-restoration interfaces
Cited by: 18
Author(s): Dina G. Moussa, Conrado Aparicio
Software Mentions: 11
Published: over 4 years ago

10.3390/ijerph18041816

Academic Achievement in Spanish Secondary School Students: The Inter-Related Role of Executive Functions, Physical Activity and Gender
Cited by: 7
Author(s): Elena Escolano Pérez, Marta Bestué
Software Mentions: 11
Published: almost 4 years ago

10.1007/s00228-020-03052-2

Potentially inappropriate prescribing in older hospitalized Dutch patients according to the STOPP/START criteria v2: a longitudinal study
Cited by: 9
Author(s): Birgit A. Damoiseaux-Volman, Stephanie Medlock, Kimmy Raven, Danielle Sent, Johannes A. Romijn, Nathalie van der Velde, Ameen Abu‐Hanna
Software Mentions: 10
Published: about 4 years ago

10.3389/fmicb.2021.642543

Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites
Cited by: 6
Author(s): Jorge Doña, Stephany Virrueta Herrera, Tommi Nyman, Mervi Kunnasranta, Kevin P. Johnson
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-020-62453-6

Patterns of Rift Valley fever virus seropositivity in domestic ruminants in central South Africa four years after a large outbreak
Cited by: 19
Author(s): Yusuf B. Ngoshe, Alida Avenant, Melinda K. Rostal, William B. Karesh, Janusz T. Pawęska, Whitney Bagge, Petrus Jansen van Vuren, Alan C. Kemp, Claudia Cordel, Veerle Msimang, Peter N. Thompson
Software Mentions: 10
Published: over 4 years ago

10.1186/s12940-021-00693-3

Examining the role of wind in human illness due to pesticide drift in Washington state, 2000–2015
Cited by: 3
Author(s): Edward J. Kasner, Joanne Bonnar Prado, Michael G. Yost, Richard A. Fenske
Software Mentions: 10
Published: almost 4 years ago

10.1371/journal.pone.0218773

Demand and level of service inflation in Floating Catchment Area (FCA) methods
Cited by: 34
Author(s): Antonio Páez, Christopher D. Higgins, Salvatore Vivona
Software Mentions: 10
Published: over 5 years ago

10.1093/aje/kwaa127

Conditional Cash Transfer Program and Leprosy Incidence: Analysis of 12.9 Million Families From the 100 Million Brazilian Cohort
Cited by: 15
Author(s): Júlia Moreira Pescarini, Elizabeth Williamson, Maria Yury Ichihara, Rosemeire Leovigildo Fiaccone, Laura Forastiere, Anna Ramond, Joilda Silva Nery, Maria Lúcia Fernandes Penna, Agostino Strina, Sandra Reis, Liam Smeeth, Laura C. Rodrigues, Elizabeth B Brickley, Gerson Oliveira Penna, Marcos Barreto
Software Mentions: 10
Published: over 4 years ago

Projects: cran: gridExtra

Papers Mentioning gridExtra 298