cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1186/s12859-019-2879-1

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
Cited by: 146
Author(s): Fédérico Marini, Harald Binder
Software Mentions: 18
Published: over 7 years ago

flowEMMi: an automated model-based clustering tool for microbial cytometric data
Cited by: 16
Author(s): Joachim Ludwig, Christian Höner zu Siederdissen, Zishu Liu, Peter F. Stadler, Susann Müller
Software Mentions: 18
Published: almost 7 years ago

10.3390/genes12030413

Spt4 Promotes Pol I Processivity and Transcription Elongation
Cited by: 5
Author(s): Abigail K. Huffines, Yvonne J. K. Edwards, David A. Schneider
Software Mentions: 18
Published: over 5 years ago

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 5 years ago

10.1371/journal.pbio.3000673

“Frozen evolution” of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence
Cited by: 15
Author(s): David Pascall, Kyriaki Nomikou, Emmanuel Bréard, Stéphan Zientara, Ana da Silva Filipe, Bernd Hoffmann, Maude Jacquot, Joshua B. Singer, Kris De Clercq, Anette Bøtner, Corinne Sailleau, Cyril Viarouge, Carrie Batten, Giantonella Puggioni, Ciriaco Ligios, Giovanni Savini, Piet A. van Rijn, Peter Mertens, Roman Biek, Massimo Palmarini
Software Mentions: 18
Published: over 6 years ago

10.3390/ijms21228837

Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer
Cited by: 6
Author(s): Anni Kääriäinen, Vilma Pesola, Annalena Dittmann, Juho A. J. Kontio, Jarkko Koivunen, Taina Pihlajaniemi, Valerio Izzi
Software Mentions: 18
Published: almost 6 years ago

10.1002/1878-0261.12960

KRAS mutant rectal cancer cells interact with surrounding fibroblasts to deplete the extracellular matrix
Cited by: 6
Author(s): Jin K. Kim, Michael R. Marco, Seo‐Hyun Choi, Xuan Qu, Chin-Tung Chen, Moshe Elkabets, Lauren Fairchild, Oliver Chow, Francisco M. Barriga, Lukas E. Dow, Kevin P. O’Rourke, Bryan Szeglin, Dmitry Yarilin, Sho Fujisawa, Katia Manova‐Todorova, Philip B. Paty, Jinru Shia, Christina Leslie, J. Joshua Smith, Scott W. Lowe, Raphael Pelossof, Francisco Sánchez-Vega, Julio García-Aguilar
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: over 6 years ago

10.1186/s12859-020-03577-4

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 6 years ago

10.1186/s12859-020-03819-5

ideal: an R/Bioconductor package for interactive differential expression analysis
Cited by: 18
Author(s): Fédérico Marini, Jan Linke, Harald Binder
Software Mentions: 17
Published: almost 6 years ago

10.1371/journal.pcbi.1003531

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
Cited by: 2,083
Author(s): Paul J. McMurdie, Susan Holmes
Software Mentions: 17
Published: over 12 years ago

10.1371/journal.pcbi.1006245

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
Cited by: 213
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 17
Published: over 8 years ago

10.1001/jamanetworkopen.2020.37227

Trends in US Pediatric Hospital Admissions in 2020 Compared With the Decade Before the COVID-19 Pandemic
Cited by: 115
Author(s): Jonathan Pelletier, Jaskaran Rakkar, Alicia K. Au, Dana Y. Fuhrman, Robert S. B. Clark, Christopher M. Horvat
Software Mentions: 17
Published: over 5 years ago

10.3389/fonc.2021.658165

Using Tumor-Infiltrating Immune Cells and a ceRNA Network Model to Construct a Prognostic Analysis Model of Thyroid Carcinoma
Cited by: 11
Author(s): Fan Zhang, Xiao‐Juan Yu, Zheyu Lin, Xichang Wang, Tengteng Gao, Di Teng, Weiping Teng
Software Mentions: 17
Published: over 5 years ago

10.7717/peerj.9539

The importance of open science for biological assessment of aquatic environments
Cited by: 15
Author(s): Marcus W. Beck, Casey C. O’Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
Software Mentions: 17
Published: over 6 years ago

10.3390/cells10082013

ChroMo, an Application for Unsupervised Analysis of Chromosome Movements in Meiosis
Cited by: 0
Author(s): Daniel León-Periñán, Alfonso Fernández-Álvarez
Software Mentions: 17
Published: about 5 years ago

10.1038/s41597-021-00998-5

A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression
Cited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: about 5 years ago

10.1038/s41598-020-58274-2

Pollen defenses negatively impact foraging and fitness in a generalist bee (Bombus impatiens: Apidae)
Cited by: 34
Author(s): Kristen Brochu, Maria T. van Dyke, Nelson J. Milano, Jessica D. Petersen, Scott H. McArt, Brian A. Nault, André Kessler, Bryan N. Danforth
Software Mentions: 17
Published: over 6 years ago

10.1038/s41597-019-0171-x

A multi-omics digital research object for the genetics of sleep regulation
Cited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: almost 7 years ago

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 7 years ago

10.1038/s41598-020-80340-y

Universal principles underlying segmental structures in parrot song and human speech
Cited by: 6
Author(s): Dan C. Mann, W. Tecumseh Fitch, Hsiao‐Wei Tu, Marisa Hoeschele
Software Mentions: 17
Published: almost 6 years ago

10.1186/s12913-019-4105-2

Testing the psychometric properties of the Finnish version of the cross-cultural competence instrument of healthcare professionals (CCCHP)
Cited by: 5
Author(s): Laura Hietapakka, Marko Elovainio, Karolina Wesołowska, Anna-Mari Aalto, Anu‐Marja Kaihlanen, Timo Sinervo, Tarja Heponiemi
Software Mentions: 17
Published: over 7 years ago

10.1016/j.cell.2015.01.006

Enhancer Evolution across 20 Mammalian Species
Cited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 12 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: about 5 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: almost 10 years ago

10.1371/journal.pone.0135831

CoGA: An R Package to Identify Differentially Co-Expressed Gene Sets by Analyzing the Graph Spectra
Cited by: 18
Author(s): Suzana de Siqueira Santos, Thais Fernanda de Almeida Galatro, Rodrigo Akira Watanabe, Sueli Mieko Oba-Shinjo, Suely Kazue Nagahashi Marie, André Fujita
Software Mentions: 17
Published: about 11 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: almost 6 years ago

10.1038/s42003-021-02025-0

SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy
Cited by: 23
Author(s): Marta Giovanetti, Eleonora Cella, Francesca Benedetti, Brittany Rife Magalis, Vagner Fonseca, Silvia Fabris, Giovanni Campisi, Alessandra Ciccozzi, Silvia Angeletti, Alessândra Borsetti, Vittoradolfo Tambone, Caterina Sagnelli, Stefano Pascarella, Alberto Riva, Giancarlo Ceccarelli, Alessandro Marcello, Taj Azarian, Eduan Wilkinson, Túlio de Oliveira, Luiz Carlos Júnior Alcântara, Roberto Cauda, Arnaldo Caruso, Natalie E. Dean, Cameron J. Browne, José Lourenço, Marco Salemi, Davide Zella, Massimo Ciccozzi
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pone.0200653

Cryopreservation of human mucosal tissues
Cited by: 13
Author(s): Sean M. Hughes, April L. Ferre, Sarah E Yandura, Cory Shetler, Chris A. R. Baker, Fernanda Calienes, Claire Levy, Rena D. Astronomo, Zhiquan Shu, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, M. Juliana McElrath, Elizabeth Sinclair, Lisa C. Rohan, Peter L. Anderson, Barbara L. Shacklett, Charlene S. Dezzutti, Dayong Gao, Florian Hladik
Software Mentions: 17
Published: about 8 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: over 5 years ago

10.3389/fmicb.2019.01726

Diversity, Distribution and Co-occurrence Patterns of Bacterial Communities in a Karst Cave System
Cited by: 66
Author(s): Hai-Zhen Zhu, Z.F. Zhang, Nan Zhou, Cheng‐Ying Jiang, Baojun Wang, Lei Cai, Shuang‐Jiang Liu
Software Mentions: 17
Published: about 7 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 7 years ago

10.12688/wellcomeopenres.16458.2

MethylDetectR: a software for methylation-based health profiling
Cited by: 14
Author(s): Robert F. Hillary, Riccardo E. Marioni
Software Mentions: 17
Published: over 5 years ago

10.1073/pnas.2006024117

Diel variability of methane emissions from lakes
Cited by: 46
Author(s): Anna Sieczko, Nguyen Thanh Duc, Jonathan Schenk, Gustav Pajala, David Rudberg, Henrique O. Sawakuchi, David Bastviken
Software Mentions: 17
Published: about 6 years ago

10.1038/s41598-020-71344-9

Twentieth-century emergence of antimicrobial resistant human- and bovine-associated Salmonella enterica serotype Typhimurium lineages in New York State
Cited by: 9
Author(s): Laura M. Carroll, Jana S. Huisman
Software Mentions: 17
Published: about 6 years ago

10.7554/eLife.53350

The natverse, a versatile toolbox for combining and analysing neuroanatomical data
Cited by: 128
Author(s): Alexander Shakeel Bates, James D. Manton, Sridhar R. Jagannathan, Marta Costa, Philipp Schlegel, Torsten Rohlfing, Gregory Jefferis
Software Mentions: 17
Published: over 6 years ago

10.3389/fvets.2021.620327

Detection of Mycobacterium avium ssp. paratuberculosis in Cultures From Fecal and Tissue Samples Using VOC Analysis and Machine Learning Tools
Cited by: 6
Author(s): Philipp Vitense, Elisa Kasbohm, Anne Klassen, Peter Gierschner, Phillip Trefz, M. Weber, Wolfram Miekisch, Jochen K. Schubert, Petra Möbius, Petra Reinhold, Volkmar Liebscher, Heike Köhler
Software Mentions: 17
Published: over 5 years ago

10.1371/journal.pone.0195112

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats
Cited by: 43
Author(s): Edna Chiang, Marian L. Schmidt, Michelle A. Berry, Bopaiah A. Biddanda, Ashley M. Burtner, Thomas H. Johengen, Danna Palladino, Vincent J. Denef
Software Mentions: 16
Published: over 8 years ago

10.3389/fimmu.2017.00445

Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations
Cited by: 15
Author(s): Michael T. Zimmermann, Richard B. Kennedy, Diane E. Grill, Ann L. Oberg, Krista M. Goergen, Inna G. Ovsyannikova, Iana H. Haralambieva, Gregory A. Poland
Software Mentions: 16
Published: over 9 years ago

10.1371/journal.pone.0230416

The citation advantage of linking publications to research data
Cited by: 131
Author(s): Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray
Software Mentions: 16
Published: over 6 years ago

10.1186/s40168-019-0725-3

Baseline microbiota composition modulates antibiotic-mediated effects on the gut microbiota and host
Cited by: 43
Author(s): Aonghus Lavelle, Thomas Hoffmann, Hang-Phuong Pham, Philippe Langella, Éric Guédon, Harry Sokol
Software Mentions: 16
Published: about 7 years ago

10.1186/s13059-021-02335-w

Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits
Cited by: 15
Author(s): Lindsay F. Rizzardi, Peter Hickey, Adrian Idrizi, Rakel Tryggvadóttir, Colin M. Callahan, K Stephens, Sean D. Taverna, Hao Zhang, Sinan Ramazanoglu, Kasper D. Hansen, Andrew P. Feinberg
Software Mentions: 16
Published: over 5 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: about 6 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: over 6 years ago

10.3389/fpsyg.2021.627561

Automatic Facial Expression Recognition in Standardized and Non-standardized Emotional Expressions
Cited by: 41
Author(s): Theresa Küntzler, T. Tim A. Höfling, Georg W. Alpers
Software Mentions: 16
Published: over 5 years ago

10.1186/s13059-020-02020-4

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Cited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 6 years ago

10.3389/fvets.2020.00068

Near Real-Time Monitoring of Clinical Events Detected in Swine Herds in Northeastern Spain
Cited by: 3
Author(s): Ana Alba-Casals, Eduard Allue, Vicens Tarancón, Jordi Baliellas, Elena Novell, Sebastián Napp, Lorenzo Fraile
Software Mentions: 16
Published: over 6 years ago

10.1128/MRA.00129-19

omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection
Cited by: 12
Author(s): Connor R. Tiffany, Andreas J. Bäumler
Software Mentions: 16
Published: over 7 years ago

10.1038/s41598-020-69683-8

Concomitant DNA methylation and transcriptome signatures define epidermal responses to acute solar UV radiation
Cited by: 5
Author(s): Nicholas Holzscheck, Jörn Söhle, T. Schläger, Cassandra Falckenhayn, Elke Grönniger, Ludger Kolbe, Horst Wenck, Lara Terstegen, Lars Kaderali, Marc Winnefeld, Katharina Gorges
Software Mentions: 16
Published: about 6 years ago

10.3389/fmicb.2019.00240

Changes in Trophic Groups of Protists With Conversion of Rainforest Into Rubber and Oil Palm Plantations
Cited by: 38
Author(s): Garvin Schulz, Dominik Schneider, Nicole Brinkmann, Nur Edy, Rolf Daniel, Andrea Polle, Stefan Scheu, Valentyna Krashevska
Software Mentions: 16
Published: over 7 years ago

10.3390/cancers12040957

Pan-Cancer Analysis of Radiotherapy Benefits and Immune Infiltration in Multiple Human Cancers
Cited by: 10
Author(s): Pengbo Wen, Yang Gao, Bin Chen, Xiaojing Qi, Guanshuo Hu, An Xu, Junfeng Xia, Lijun Wu, Lu Han, Guoping Zhao
Software Mentions: 16
Published: over 6 years ago

10.3390/cells10092367

The Emerging Plasticizer Alternative DINCH and Its Metabolite MINCH Induce Oxidative Stress and Enhance Inflammatory Responses in Human THP-1 Macrophages
Cited by: 16
Author(s): Alexandra Schaffert, Josi Arnold, Isabel Karkossa, Matthias Blüher, Martin von Bergen, Kristin Schubert
Software Mentions: 16
Published: about 5 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: about 9 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: about 6 years ago

10.3389/fcell.2020.596679

Development and Validation of a Combined Ferroptosis and Immune Prognostic Classifier for Hepatocellular Carcinoma
Cited by: 77
Author(s): Yang Liu, Xi Zhang, Junjun Zhang, Juan Tan, Jie Li, Zewen Song
Software Mentions: 16
Published: almost 6 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 5 years ago

10.3389/fonc.2021.644416

An Inflammatory Response-Related Gene Signature Can Impact the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma
Cited by: 62
Author(s): Zhuo Lin, Xu Qian, Dan Miao, Fang Yu
Software Mentions: 16
Published: over 5 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: over 5 years ago

10.1186/s12935-020-01571-7

RETRACTED ARTICLE: Aging-related tumor associated fibroblasts changes could worsen the prognosis of GBM patients
Cited by: 7
Author(s): Hongwang Song, Xiaojun Fu, Chenxing Wu, Shouwei Li
Software Mentions: 16
Published: about 6 years ago

10.1038/s41598-021-81688-5

Fungal diversity and community structure from coastal and barrier island beaches in the United States Gulf of Mexico
Cited by: 14
Author(s): Allison K. Walker, Brent M. Robicheau
Software Mentions: 16
Published: over 5 years ago

10.3390/ijms22052244

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis
Cited by: 4
Author(s): Anton E. Shikov, Yury V. Malovichko, Arseniy Lobov, Maria Belousova, Anton A. Nizhnikov, Kirill S. Antonets
Software Mentions: 16
Published: over 5 years ago

10.1093/gigascience/giz061

LION/web: a web-based ontology enrichment tool for lipidomic data analysis
Cited by: 110
Author(s): Martijn R. Molenaar, Aike Jeucken, Tsjerk A. Wassenaar, Chris H.A. van de Lest, Jos F. Brouwers, J. Bernd Helms
Software Mentions: 16
Published: over 7 years ago

10.1155/2018/6587049

Data Association Methodology to Improve Spatial Predictions in Alternative Marketing Circuits in Ecuador
Cited by: 1
Author(s): Washington R. Padilla, Juan Francisco Blanco García
Software Mentions: 16
Published: almost 8 years ago

10.1080/17453674.2020.1846956

Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size
Cited by: 7
Author(s): Yosef Tyson, Christer Hillman, Norbert Majenburg, Olof Sköldenberg, Ola Rolfson, Johan Kärrholm, Maziar Mohaddes, Nils P Hailer
Software Mentions: 16
Published: almost 6 years ago

10.7150/ijms.53531

Identification novel prognostic signatures for Head and Neck Squamous Cell Carcinoma based on ceRNA network construction and immune infiltration analysis
Cited by: 18
Author(s): Haiting Zhou, Yi He, Lingling Li, Cheng Wu, Guoqing Hu
Software Mentions: 16
Published: almost 6 years ago

10.1038/s41598-021-81583-z

Foraging niche partitioning in sympatric seabird populations
Cited by: 11
Author(s): Christina Petalas, Thomas Lazarus, Richard Lavoie, Kyle H. Elliott, Mélanie F. Guigueno
Software Mentions: 16
Published: over 5 years ago

10.7554/eLife.61812

Reproducible analysis of disease space via principal components using the novel R package syndRomics
Cited by: 18
Author(s): Abel Torres-Espín, Austin Chou, J. Russell Huie, Nikos Kyritsis, Pavan S. Upadhyayula, Adam R. Ferguson
Software Mentions: 16
Published: almost 6 years ago

10.1002/ece3.6959

In the shadows of snow leopards and the Himalayas: density and habitat selection of blue sheep in Manang, Nepal
Cited by: 11
Author(s): Marc Filla, Rinzin Phunjok Lama, Tashi Rapte Ghale, Johannes Signer, Tim Filla, Raja Ram Aryal, Marco Heurich, Matthias Waltert, Niko Balkenhol, Igor Khorozyan
Software Mentions: 16
Published: almost 6 years ago

10.7554/eLife.21883

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex
Cited by: 72
Author(s): Lucas T. Gray, Zizhen Yao, Thuc Nghi Nguyen, Tae Kyung Kim, Hongkui Zeng, Bosiljka Tasic
Software Mentions: 16
Published: almost 10 years ago

10.12688/f1000research.22139.2

scRepertoire: An R-based toolkit for single-cell immune receptor analysis
Cited by: 121
Author(s): Nicholas Borcherding, Nicholas L. Bormann, Gloria Kraus
Software Mentions: 16
Published: over 6 years ago

10.1371/journal.pone.0244876

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes
Cited by: 12
Author(s): Moamen M. Elmassry, Sunghwan Kim, Ben Busby
Software Mentions: 16
Published: almost 6 years ago

10.3389/fgene.2021.719204

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization
Cited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: about 5 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 8 years ago

10.3390/cancers13123089

A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer
Cited by: 12
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 15
Published: over 5 years ago

10.3389/fchem.2021.734132

The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary Data
Cited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: about 5 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 5 years ago

10.1186/s40168-020-00961-3

Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach
Cited by: 30
Author(s): Wang Ya, Yan Yan, Kelsey N. Thompson, Sena Bae, Emma K. Accorsi, Yancong Zhang, Jiaxian Shen, Hera Vlamakis, Erica M. Hartmann, Curtis Huttenhower
Software Mentions: 15
Published: almost 6 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 7 years ago

10.1186/s12864-020-06856-9

mitch: multi-contrast pathway enrichment for multi-omics and single-cell profiling data
Cited by: 28
Author(s): Antony Kaspi, Mark Ziemann
Software Mentions: 15
Published: over 6 years ago

10.1038/s41598-021-81200-z

MuSA: a graphical user interface for multi-OMICs data integration in radiogenomic studies
Cited by: 11
Author(s): Mario Zanfardino, Rossana Castaldo, Katia Pane, Ornella Affinito, Marco Aiello, Marco Salvatore, Monica Franzese
Software Mentions: 15
Published: almost 6 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 5 years ago

10.3389/fcell.2020.00790

The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer
Cited by: 4
Author(s): Runzhi Huang, Jian Guo, Penghui Yan, Suna Zhai, Peng Hu, Xiaolong Zhu, Jiayao Zhang, Yannan Qiao, Yu Zhang, Hui Liu, Ling Huang, Jie Zhang, Daoke Yang, Zongqiang Huang
Software Mentions: 15
Published: about 6 years ago

10.1128/mBio.00034-20

Proposal of a Taxonomic Nomenclature for the Bacillus cereus Group Which Reconciles Genomic Definitions of Bacterial Species with Clinical and Industrial Phenotypes
Cited by: 98
Author(s): Laura M. Carroll, Martin Wiedmann, Jasna Kovač
Software Mentions: 15
Published: over 6 years ago

10.1111/tran.12131

Regional surnames and genetic structure in Great Britain
Cited by: 14
Author(s): Jens Kandt, James Cheshire, Paul Longley
Software Mentions: 15
Published: over 10 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: almost 11 years ago

10.3389/fneur.2019.01366

Prediction of Early TBI Mortality Using a Machine Learning Approach in a LMIC Population
Cited by: 39
Author(s): Robson Luís Oliveira de Amorim, Louise Makarem Oliveira, Luis Marcelo Malbouisson, Márcia Mitie Nagumo, Marcela Simoes, Leandro Miranda, Edson Bor‐Seng‐Shu, André Beer‐Furlan, Almir Ferreira de Andrade, Andrés M. Rubiano, Manoel Jacobsen Teixeira, Angelos G. Kolias, Wellingson Silva Paiva
Software Mentions: 15
Published: over 6 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: over 5 years ago

10.3389/fimmu.2020.00082

Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection
Cited by: 7
Author(s): Kazuhito Honjo, Woong-Jai Won, R. Glenn King, Lara Ianov, David K. Crossman, Juliet Easlick, Mikhail A. Shakhmatov, Mohamed Khass, André M. Vale, Robert P. Stephan, Ran Li, Randall S. Davis
Software Mentions: 15
Published: over 6 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 6 years ago

10.1093/jas/skaa402

ASAS-NANP SYMPOSIUM: prospects for interactive and dynamic graphics in the era of data-rich animal science1
Cited by: 4
Author(s): Gota Morota, Hao Cheng, Dianne Cook, Emi Tanaka
Software Mentions: 15
Published: over 5 years ago

10.21105/joss.03073

mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines
Cited by: 22
Author(s): Begüm D. Topçuoğlu, Zena Lapp, Kelly L Sovacool, Evan S. Snitkin, Jenna Wiens, Patrick D. Schloss
Software Mentions: 15
Published: over 5 years ago

10.1371/journal.pgen.1009538

Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae
Cited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 5 years ago

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: almost 6 years ago

10.3389/fmicb.2020.580691

No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods
Cited by: 20
Author(s): Laura M. Carroll, Rachel A. Cheng, Jasna Kovač
Software Mentions: 15
Published: about 6 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: about 7 years ago

10.2196/12875

Developing the National Usability-Focused Health Information System Scale for Physicians: Validation Study
Cited by: 26
Author(s): Hannele Hyppönen, Johanna Kaipio, Tarja Heponiemi, Tinja Lääveri, Anna Mari Aalto, Jukka Vänskä, Marko Elovainio
Software Mentions: 15
Published: over 7 years ago

10.1038/s42003-021-01796-w

Temporal association between human upper respiratory and gut bacterial microbiomes during the course of COVID-19 in adults
Cited by: 73
Author(s): Rong Xu, Renfei Lu, Tao Zhang, Qian Wu, Wei Cai, Xudong Han, Zhenzhou Wan, Xia Jin, Zhigang Zhang, Chiyu Zhang
Software Mentions: 15
Published: over 5 years ago

10.1038/s41598-020-72571-w

Persistent fire foci in all biomes undermine the Paris Agreement in Brazil
Cited by: 51
Author(s): Carlos Antônio da Silva, Paulo Eduardo Teodoro, Rafael Coll Delgado, Larissa Pereira Ribeiro Teodoro, Mendelson Lima, Ariane de Andréa Pantaleão, Fábio Henrique Rojo Baio, Gileno Brito de Azevedo, Glauce Táıs de Oliveira Sousa Azevedo, Guilherme Fernando Capristo-Silva, Damien Arvor, Cassiele Uliana Facco
Software Mentions: 15
Published: about 6 years ago

10.1098/rsos.191609

Spatial heterogeneity of the shorebird gastrointestinal microbiome
Cited by: 17
Author(s): Kirsten Grond, Hannah Guilani, Sarah M. Hird
Software Mentions: 15
Published: almost 7 years ago

10.1186/s12885-021-08598-7

Cannabinoid exposure as a major driver of pediatric acute lymphoid Leukaemia rates across the USA: combined geospatial, multiple imputation and causal inference study
Cited by: 24
Author(s): Albert Stuart Reece, Gary Kenneth Hulse
Software Mentions: 15
Published: about 5 years ago

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Papers Mentioning ggplot2 11,441