cran: XML | Projects | Ecosyste.ms: Papers

10.1038/s41598-019-54004-5

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 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

10.7717/peerj.8059

Exploring snake occurrence records: Spatial biases and marginal gains from accessible social media
Cited by: 9
Author(s): Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 24
Published: almost 5 years ago

10.7554/eLife.70086

Gaps in global wildlife trade monitoring leave amphibians vulnerable
Cited by: 22
Author(s): Alice C. Hughes, Benjamin Michael Marshall, Colin Thomas Strine
Software Mentions: 23
Published: over 3 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.pone.0197176

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation
Cited by: 12
Author(s): Selçuk Korkmaz, José M. Duarte, Andreas Prlić, Dinçer Göksülük, Gökmen Zararsız, Osman Saraçbaşı, S.K. Burley, Peter W. Rose
Software Mentions: 12
Published: over 6 years ago

10.1371/journal.pone.0251323

The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases
Cited by: 2
Author(s): Weijun Shi, Xincan Li, Shuai Xu, Hexin Wen, Tianwen Chen, Huazhang Wu, Mulin Liu
Software Mentions: 12
Published: over 3 years ago

10.1016/j.epidem.2014.04.003

OutbreakTools: A new platform for disease outbreak analysis using the R software
Cited by: 37
Author(s): Thibaut Jombart, David M. Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Caitlin Collins, Anne Cori, Xavier Didelot, Christophe Fraser, Simon D. W. Frost, Niel Hens, Joseph Hugues, Michael Höhle, Lulla Opatowski, Andrew Rambaut, Oliver Ratmann, Samuel Soubeyrand, Marc A. Suchard, Jacco Wallinga, Rolf J. F. Ypma, Neil M. Ferguson
Software Mentions: 11
Published: over 10 years ago

10.1186/1471-2105-10-74

RGG: A general GUI Framework for R scripts
Cited by: 7
Author(s): Ilhami Visne, Erkan Dilaveroǧlu, Klemens Vierlinger, Martin Lauss, Ahmet Yıldız, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner
Software Mentions: 11
Published: over 15 years ago

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: almost 15 years ago

10.1093/gigascience/gix119

funRiceGenes dataset for comprehensive understanding and application of rice functional genes
Cited by: 69
Author(s): Wen Yao, Guangwei Li, Yiming Yu, Yidan Ouyang
Software Mentions: 9
Published: almost 7 years ago

10.1371/journal.pone.0242142

'Tiny numbers' are actually tiny: Evidence from gestures in the TV News Archive
Cited by: 13
Author(s): Greg Woodin, Bodo Winter, Marcus Perlman, Jeannette Littlemore, Teenie Matlock
Software Mentions: 8
Published: about 4 years ago

10.3389/fninf.2013.00045

The Design of SimpleITK
Cited by: 402
Author(s): Bradley Lowekamp, David T. Chen, Luis Ibáñez, Daniel J. Blezek
Software Mentions: 7
Published: almost 12 years ago

10.1371/journal.pone.0200565

Using social media to quantify spatial and temporal dynamics of nature-based recreational activities
Cited by: 60
Author(s): Francesca Mancini, George M. Coghill, David Lusseau
Software Mentions: 7
Published: over 6 years ago

10.3897/BDJ.7.e31511

rMyCoPortal - an R package to interface with the Mycology Collections Portal
Cited by: 3
Author(s): Franz‐Sebastian Krah, Scott T. Bates, Andrew N. Miller
Software Mentions: 6
Published: almost 6 years ago

10.1186/s12934-016-0456-0

Diversity of flux distribution in central carbon metabolism of S. cerevisiae strains from diverse environments
Cited by: 24
Author(s): Thibault Nidelet, Pascale Brial, Carole Camarasa, Sylvie Dequin
Software Mentions: 6
Published: over 8 years ago

10.2196/27633

Web-Based Survival Analysis Tool Tailored for Medical Research (KMplot): Development and Implementation
Cited by: 716
Author(s): András Lánczky, Balázs Győrffy
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-017-1934-z

ImageJ2: ImageJ for the next generation of scientific image data
Cited by: 4,051
Author(s): Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
Software Mentions: 5
Published: almost 7 years ago

10.1093/gigascience/giy149

PhenoMeNal: processing and analysis of metabolomics data in the cloud
Cited by: 58
Author(s): Kristian Peters, J. H. Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M. D. Ebbels, Carles Foguet, Robert C. Glen, Alejandra González-Beltrán, Ulrich L. Günther, Evangelos Handakas, Thomas Hankemeier, Kenneth Haug, Stephanie Herman, Petr Holub, Massimiliano Izzo, Daniel Jacob, David Johnson, Fabien Jourdan, Namrata Kale, Íbrahím Karaman, Bita Khalili, Payam Emami Khonsari, Kim Kultima, Samuel Lampa, Anders Larsson, Christian Ludwig, Pablo Moreno-Ger, Steffen Neumann, Jon Ander Novella, Claire O’Donovan, Jake T M Pearce, Alina Peluso, Marco Piras, Luca Pireddu, Michelle A.C. Reed, Philippe Rocca-Serra, Pierrick Roger, Antonio Rosato, Rico Rueedi, Christoph Ruttkies, Noureddin Sadawi, Reza M. Salek, Susanna-Assunta Sansone, Vitaly A. Selivanov, Ola Spjuth, Daniel Schober, Etienne Thévenot, Mattia Tomasoni, Merlijn van Rijswijk, Michael Van Vliet, Mark R. Viant, Ralf Weber, Gianluigi Zanetti, Christoph Steinbeck
Software Mentions: 5
Published: almost 6 years ago

10.7150/thno.63416

Mapping the landscape of synthetic lethal interactions in liver cancer
Cited by: 7
Author(s): Chen Yang, Yuchen Guo, Ruolan Qian, Yi‐Wen Huang, Linmeng Zhang, Jun Wang, Xiaowen Huang, Zhicheng Liu, Wenxin Qin, Cun Wang, Huimin Chen, Xuhui Ma, Dayong Zhang
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2018.00696

A Comprehensive RNA Expression Signature for Cervical Squamous Cell Carcinoma Prognosis
Cited by: 5
Author(s): Jie Xiong, Shengyu Guo, Zhitong Bing, Yanlin Su, Le Guo
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0141719

Potential Compounds for Oral Cancer Treatment: Resveratrol, Nimbolide, Lovastatin, Bortezomib, Vorinostat, Berberine, Pterostilbene, Deguelin, Andrographolide, and Colchicine
Cited by: 37
Author(s): Saurabh Bundela, Anjana Sharma, Prakash S. Bisen
Software Mentions: 4
Published: about 9 years ago

10.1186/1471-2105-14-334

Fastphylo: Fast tools for phylogenetics
Cited by: 17
Author(s): Muhammad Alam Zaib Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Valls Guimerà, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
Software Mentions: 4
Published: about 11 years ago

10.3389/fninf.2014.00090

Automatic analysis (aa): efficient neuroimaging workflows and parallel processing using Matlab and XML
Cited by: 91
Author(s): Rhodri Cusack, Alejandro Vicente-Grabovetsky, D. N. Mitchell, Conor Wild, Tibor Auer, Annika C. Linke, Jonathan E. Peelle
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijerph17207529

Do Spatial Boundaries Matter for Exploring the Impact of Community Green Spaces on Health?
Cited by: 9
Author(s): Jong Cheol Shin, Mei‐Po Kwan, Diana S. Grigsby-Toussaint
Software Mentions: 3
Published: about 4 years ago

10.3390/s120912026

Using SWE Standards for Ubiquitous Environmental Sensing: A Performance Analysis
Cited by: 16
Author(s): Alain Tamayo, Carlos Granell, Joaquín Huerta
Software Mentions: 3
Published: about 12 years ago

10.1186/1758-2946-3-44

CML: Evolution and design
Cited by: 36
Author(s): Peter Murray‐Rust, Rzepa Henry S.
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2105-7-229

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data
Cited by: 38
Author(s): Bertrand R. Huber, Martha L. Bulyk
Software Mentions: 3
Published: over 18 years ago

10.1186/1471-2105-9-311

Function2Gene: A gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge
Cited by: 5
Author(s): Don Armstrong, Chaim O. Jacob, Raphael Zidovetzki
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-10-2

GenomeGraphs: integrated genomic data visualization with R
Cited by: 67
Author(s): Steffen Durinck, James Bullard, Paul T. Spellman, Sandrine Dudoit
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2164-13-S4-S10

Automated extraction and semantic analysis of mutation impacts from the biomedical literature
Cited by: 30
Author(s): Nona Naderi, René Witte
Software Mentions: 3
Published: almost 13 years ago

10.1186/s40709-016-0038-7

NaCl stress-induced transcriptomics analysis of Salix linearistipularis (syn. Salix mongolica)
Cited by: 7
Author(s): Nan Gui-xian, Yan Zhang, Song Li, Imshik Lee, Tetsuo Takano, Shenkui Liu
Software Mentions: 2
Published: over 8 years ago

10.1186/s12859-018-2119-0

JAMI: a Java library for molecular interactions and data interoperability
Cited by: 6
Author(s): M. Sivade, Maximilian Koch, Anjali Shrivastava, Diego Alonso-López, Javier De Las Rivas, Noemi del-Toro, Colin Combe, Birgit Meldal, Joshua Heimbach, Juri Rappsilber, Julie Sullivan, Yo Yehudi, Sandra Orchard
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-8-320

Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation
Cited by: 6
Author(s): Kathrin Klee, Rebecca Ernst, Manuel Spannagl, Klaus Mayer
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2229-11-104

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles
Cited by: 54
Author(s): Hélène Ferry‐Dumazet, Laurent Gil, Catherine Deborde, Annick Moing, Stéphane Bernillon, Dominique Rolin, Macha Nikolski, Antoine de Daruvar, Daniel Jacob
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pcbi.0020061

Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis
Cited by: 142
Author(s): Samiul Hasan, Sabine Daugelat, P. S. Srinivasa Rao, Mark Schreiber
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0240047

Analysis of data dictionary formats of HIV clinical trials
Cited by: 6
Author(s): Craig S. Mayer, Nick Williams, Vojtech Huser
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2018.01538

Prediction of Lime Tolerance in Rhododendron Based on Herbarium Specimen and Geochemical Data
Cited by: 5
Author(s): Shusheng Wang, Leen Leus, Marie-Christine Van Labeke, Johan Van Huylenbroeck
Software Mentions: 2
Published: about 6 years ago

10.1038/sdata.2018.125

The Chemical and Products Database, a resource for exposure-relevant data on chemicals in consumer products
Cited by: 113
Author(s): Kathie L. Dionisio, Katherine A. Phillips, Paul S. Price, Christopher M. Grulke, Antony J. Williams, Derya Biryol, Tao Hong, Kristin Isaacs
Software Mentions: 2
Published: over 6 years ago

10.1007/978-3-030-57764-3_7

Snap4City Platform to Speed Up Policies
Cited by: 1
Author(s): Nicola Mitolo, Paolo Nesi, Gianni Pantaleo, Michela Paolucci
Software Mentions: 2
Published: almost 4 years ago

10.5195/jmla.2018.319

Research Electronic Data Capture (REDCap)
Cited by: 182
Author(s): Emily Patridge, Tania Bardyn
Software Mentions: 2
Published: almost 7 years ago

10.6028/jres.120.016

A Journey in Standard Development: The Core Manufacturing Simulation Data (CMSD) Information Model
Cited by: 6
Author(s): Yung-Tsun Tina Lee
Software Mentions: 2
Published: about 9 years ago

10.1120/jacmp.v16i4.5363

Use of TrueBeam developer mode for imaging QA
Cited by: 30
Author(s): Gilmer Valdés, Olivier Morin, Y. Valenciaga, Niel Kirby, Jean Pouliot, Cynthia Chuang
Software Mentions: 1
Published: over 9 years ago

10.1002/acm2.12222

Normalize the response of <scp>EPID</scp> in pursuit of linear accelerator dosimetry standardization
Cited by: 10
Author(s): Bin Cai, S Goddu, S Yaddanapudi, D. Caruthers, J. Wen, C. Noël, Sasa Mutic, Baozhou Sun
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0199242

ODM Data Analysis—A tool for the automatic validation, monitoring and generation of generic descriptive statistics of patient data
Cited by: 6
Author(s): Tobias Brix, Philipp Bruland, Saad Sarfraz, Jan Ernsting, Philipp Neuhaus, Michael Storck, Justin Doods, Sonja Ständer, Martin Dugas
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj-cs.440

Formal verification of Matrix based MATLAB models using interactive theorem proving
Cited by: 3
Author(s): Ayesha Gauhar, Adnan Rashid, Osman Hasan, João Bispo, João M. P. Cardoso
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-7-281

MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
Cited by: 43
Author(s): Irena Spasić, Warwick B. Dunn, Giles Velarde, Andy Tseng, Howard J. Jenkins, Nigel Hardy, Stephen G. Oliver, Douglas B. Kell
Software Mentions: 1
Published: over 18 years ago

10.1038/sdata.2018.237

Phase contrast time-lapse microscopy datasets with automated and manual cell tracking annotations
Cited by: 30
Author(s): Dai Fei Elmer Ker, Sungeun Eom, Sho Sanami, Ryoma Bise, Corinne Pascale, Zhaozheng Yin, Seung Il Huh, Elvira Osuna-Highley, Silvina N. Junkers, Casey J. Helfrich, Peter Liang, Jiyan Pan, Soojin Jeong, Seung-Min Kang, Jinyu Liu, Ritchie Nicholson, Michael F. Sandbothe, Phu T. Van, An-An Liu, Mei Chen, Takeo Kanade, Lee E. Weiss, Phil G. Campbell
Software Mentions: 1
Published: about 6 years ago

10.1186/1756-0500-4-86

A DIGE study on the effects of salbutamol on the rat muscle proteome - an exemplar of best practice for data sharing in proteomics
Cited by: 6
Author(s): Jenna Kenyani, J. Alberto Medina-Auñón, Salvador Martínez‐Bartolomé, Juan-Pablo Albar, Jonathan M. Wastling, Andrew R. Jones
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-10-87

Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens
Cited by: 72
Author(s): Qi Zheng, Yong Zhang, Runsheng Chen, Ning Yang, Xiu‐Jie Wang, Dahai Zhu
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-13-213

Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens
Cited by: 111
Author(s): Huanxian Cui, Ranran Liu, Guiping Zhao, Maiqing Zheng, Jilan Chen, Jie Wen
Software Mentions: 1
Published: over 12 years ago

10.1186/1751-0473-3-2

LSID Tester, a tool for testing Life Science Identifier resolution services
Cited by: 9
Author(s): Roderic Page
Software Mentions: 1
Published: almost 17 years ago

10.1186/s12864-018-5191-y

CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes
Cited by: 2
Author(s): Andres Benavides, Juan Pablo Isaza, Juan Pablo Niño-García, Juan F. Alzate, Felipe Cabarcas
Software Mentions: 1
Published: almost 6 years ago

10.3390/toxins5091597

Canine Cyanotoxin Poisonings in the United States (1920s–2012): Review of Suspected and Confirmed Cases from Three Data Sources
Cited by: 106
Author(s): Lorraine C. Backer, Jan H. Landsberg, Melissa A. Miller, Kevin Keel, Tegwin K. Taylor
Software Mentions: 1
Published: about 11 years ago

10.3389/fphys.2018.00004

Reticuloendotheliosis Virus Inhibits the Immune Response Acting on Lymphocytes from Peripheral Blood of Chicken
Cited by: 12
Author(s): Yue Bi, Liping Xu, Lingling Qiu, Shasha Wang, Xiangping Liu, Yani Zhang, Yang Chen, Yang Zhang, Qi Xu, Guobin Chang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-017-4292-3

Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens
Cited by: 45
Author(s): Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu, Jie Wen
Software Mentions: 1
Published: almost 7 years ago

10.3389/fphar.2019.00923

Xinmailong Modulates Platelet Function and Inhibits Thrombus Formation via the Platelet αIIbβ3-Mediated Signaling Pathway
Cited by: 9
Author(s): Huawei Wang, Yujia Ye, Wen Wan, Luqiao Wang, Ruijie Li, Longjun Li, Lihong Yang, Lai Yang, Yajuan Gu, Ling Dong, Ziyang Meng
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0037847

Results and Outcome Reporting In ClinicalTrials.gov, What Makes it Happen?
Cited by: 13
Author(s): Olga Kirillova
Software Mentions: 1
Published: over 12 years ago

10.1186/s40104-020-0433-7

Salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens
Cited by: 59
Author(s): Samiullah Khan, Kapil K. Chousalkar
Software Mentions: 1
Published: over 4 years ago

Projects: cran: XML

Papers Mentioning XML 60