pypi: ISA | Projects | Ecosyste.ms: Papers

10.1093/gigascience/gix037

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics
Cited by: 48
Author(s): Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R. Fernie
Software Mentions: 12
Published: over 7 years ago

10.1186/1471-2105-15-S1-S11

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again
Cited by: 19
Author(s): Alejandra N. González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 11
Published: almost 11 years ago

10.1186/s12859-017-1487-1

A systematic comparative evaluation of biclustering techniques
Cited by: 94
Author(s): Victor Alexandre Padilha, Ricardo J. G. B. Campello
Software Mentions: 10
Published: almost 8 years ago

10.1093/gigascience/giz064

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer
Cited by: 6
Author(s): Amartya Singh, Gyan Bhanot, Hossein Khiabanian
Software Mentions: 10
Published: over 5 years ago

10.1007/s11306-017-1242-7

Navigating freely-available software tools for metabolomics analysis
Cited by: 165
Author(s): Rachel Spicer, Reza M. Salek, Pablo Moreno-Ger, Daniel Cañueto, Christoph Steinbeck
Software Mentions: 8
Published: over 7 years ago

10.3389/fmicb.2021.569791

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem
Cited by: 15
Author(s): Yaqi You, Ken Aho, Kathleen A. Lohse, Stacy G. Schwabedissen, Rhesa N. Ledbetter, Timothy S. Magnuson
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-12-452

eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Cited by: 5
Author(s): Amit Sinha, Emily Merrill, Scott A. Armstrong, Tim W. Clark, Sudeshna Das
Software Mentions: 7
Published: about 13 years ago

10.1186/1756-0381-5-8

A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data
Cited by: 24
Author(s): Li Li, Yang Guo, Wenwu Wu, Yinggang Shi, Jian Cheng, Shiheng Tao
Software Mentions: 7
Published: over 12 years ago

10.1093/gigascience/giab060

ISA API: An open platform for interoperable life science experimental metadata
Cited by: 13
Author(s): David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra González-Beltrán, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno-Ger, Venkata Chandrasekhar Nainala, Claire O’Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 7
Published: over 3 years ago

10.3390/plants9121700

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots
Cited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0167265

Evidence of Facilitation Cascade Processes as Drivers of Successional Patterns of Ecosystem Engineers at the Upper Altitudinal Limit of the Dry Puna
Cited by: 13
Author(s): Luca Malatesta, Federico Maria Tardella, Karina Piermarteri, Andrea Catorci
Software Mentions: 7
Published: about 8 years ago

10.1371/journal.pntd.0003240

Noma Affected Children from Niger Have Distinct Oral Microbial Communities Based on High-Throughput Sequencing of 16S rRNA Gene Fragments
Cited by: 13
Author(s): Katrine Whiteson, Vladimir Lazarević, Manuela Tangomo-Bento, Myriam Girard, Heather Maughan, Didier Pittet, Patrice François, Jacques Schrenzel
Software Mentions: 6
Published: about 10 years ago

10.1038/sdata.2017.51

Transcriptomic analysis of gene signatures associated with sickle pain
Cited by: 8
Author(s): Jinny Paul, Anupam Aich, Juan E. Abrahante, Ying Wang, Rebecca S. LaRue, Susan K. Rathe, Krystina R. Kalland, Aditya Mittal, Ritu Jha, Fei Peng, David A. Largaespada, Anindya Bagchi, Kalpna Gupta
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0090801

Biclustering Methods: Biological Relevance and Application in Gene Expression Analysis
Cited by: 77
Author(s): Ali Oghabian, Sami Kilpinen, Sampsa Hautaniemi, Elena Czeizler
Software Mentions: 6
Published: almost 11 years ago

10.1186/s13015-014-0027-z

BicPAM: Pattern-based biclustering for biomedical data analysis
Cited by: 57
Author(s): Rui Henriques, Sara C. Madeira
Software Mentions: 5
Published: about 10 years ago

10.4056/sigs.1353455

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9
Cited by: 4
Author(s): Tanja Davidsen, Ramana Madupu, Peter J. Sterk, Dawn Field, George M Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Eugene Kolker, Renzo Kottmann, Nikos C. Kyrpides, Patrick Meyer, Norman Morrison, Lynn M. Schriml, Tatiana Tatusova, John Wooley
Software Mentions: 5
Published: almost 15 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: about 6 years ago

10.1093/database/bau027

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Cited by: 11
Author(s): Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pcbi.1002228

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters
Cited by: 7
Author(s): Thadeous J. Kacmarczyk, Peter Waltman, Ashley R. Bate, Patrick Eichenberger, Richard Bonneau
Software Mentions: 5
Published: about 13 years ago

10.1186/s12918-015-0174-y

SEEK: a systems biology data and model management platform
Cited by: 79
Author(s): Katy Wolstencroft, Stuart Owen, Olga Krebs, Quyen Le Hoang Thuy To Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lin An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-019-3289-0

Identifying gene-specific subgroups: an alternative to biclustering
Cited by: 3
Author(s): Vincent Branders, Pierre Schaus, Pierre Dupont
Software Mentions: 5
Published: about 5 years ago

10.1186/2041-1480-5-41

Structuring research methods and data with the research object model: genomics workflows as a case study
Cited by: 26
Author(s): Kristina Hettne, Harish Dharuri, Jun Zhao, Katy Wolstencroft, Khalid Belhajjame, Stian Soiland‐Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, L. Verdes–Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C ‘t Hoen, Sean Bechhofer, Carole Goble, Marco Roos
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.562546

Bacterial Communities Are More Sensitive to Water Addition Than Fungal Communities Due to Higher Soil K and Na in a Degraded Karst Ecosystem of Southwestern China
Cited by: 4
Author(s): Muhammad Umair, Ning Sun, Hongmei Du, Nan Hui, Muhammad Altaf, Baoming Du, Shan Yin, Chunjiang Liu
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0082890

SiBIC: A Web Server for Generating Gene Set Networks Based on Biclusters Obtained by Maximal Frequent Itemset Mining
Cited by: 1
Author(s): Keiichiro Takahashi, Ichigaku Takigawa, Hiroshi Mamitsuka
Software Mentions: 4
Published: almost 11 years ago

10.1038/s42003-021-02244-5

Climate-driven divergence in plant-microbiome interactions generates range-wide variation in bud break phenology
Cited by: 19
Author(s): Ian M. Ware, Michael E. Van Nuland, Zamin K. Yang, Christopher W. Schadt, Jennifer A. Schweitzer, Joseph K. Bailey
Software Mentions: 4
Published: over 3 years ago

10.1093/cid/ciz906

Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth Cohort
Cited by: 19
Author(s): Saba Rouhani, Nicholas W. Griffin, Pablo Peñataro Yori, Maribel Paredes Olórtegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H. Moulton, Eric R. Houpt, Michael J. Barratt, Margaret Kosek, Jeffrey I. Gordon
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0159923

BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes
Cited by: 8
Author(s): Amir Lakizadeh, Saeed Jalili
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-12-71

LabKey Server: An open source platform for scientific data integration, analysis and collaboration
Cited by: 121
Author(s): Elizabeth Nelson, Britt Piehler, Josh Eckels, Adam Rauch, Matthew Bellew, Peter S. Hussey, Sarah Ramsay, Cory Nathe, Karl Lum, Kevin Krouse, David L. Stearns, B. Connolly, Tom Skillman, Mark Igra
Software Mentions: 4
Published: almost 14 years ago

10.3390/insects12010011

Olfactory Choice for Decomposition Stage in the Burying Beetle Nicrophorus vespilloides: Preference or Aversion?
Cited by: 4
Author(s): Pablo J. Delclós, Tammy L. Bouldin, Jeffery K. Tomberlin
Software Mentions: 4
Published: almost 4 years ago

10.3762/bjnano.6.202

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology
Cited by: 23
Author(s): Richard L. Marchese Robinson, Mark T.D. Cronin, Andrea-Nicole Richarz, Robert Ralló
Software Mentions: 4
Published: about 9 years ago

10.1093/gigascience/giaa041

Community standards for open cell migration data
Cited by: 11
Author(s): Alejandra González-Beltrán, Paola Masuzzo, Christophe Ampè, Gert-Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R. Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsky, Susanna Assunta Sansone, Lennart Martens
Software Mentions: 4
Published: over 4 years ago

10.3390/md17110601

Fungal Diversity in Intertidal Mudflats and Abandoned Solar Salterns as a Source for Biological Resources
Cited by: 18
Author(s): Young Mok Heo, Hanbyul Lee, Kyeongwon Kim, Sun Lul Kwon, Min Young Park, Ji Eun Kang, Gyu Hyeok Kim, Beom Seok Kim, Jae Jin Kim
Software Mentions: 4
Published: about 5 years ago

10.4056/sigs.1423520

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10
Cited by: 8
Author(s): Elizabeth M. Glass, Patrick Meyer, Jack A. Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos C. Kyrpides, Susanna Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Owen White, John Wooley
Software Mentions: 4
Published: almost 15 years ago

10.1101/2021.06.22.449395

Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks
Cited by: 3
Author(s): Meghana Venkata Palukuri, Edward M. Marcotte
Software Mentions: 4
Published: over 3 years ago

10.1186/1752-0509-2-33

Extracting expression modules from perturbational gene expression compendia
Cited by: 16
Author(s): Steven Maere, Patrick Van Dijck, Martin Kuiper
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-15-S14-S4

linkedISA: semantic representation of ISA-Tab experimental metadata
Cited by: 55
Author(s): Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 3
Published: about 10 years ago

10.1093/database/bau018

GigaDB: promoting data dissemination and reproducibility
Cited by: 19
Author(s): Tam P. Sneddon, Sizhe Xiao, Scott Edmunds, Peter Li, Laurie Goodman, Chris Hunter
Software Mentions: 3
Published: almost 11 years ago

10.1186/1756-0381-2-9

A biclustering algorithm based on a Bicluster Enumeration Tree: application to DNA microarray data
Cited by: 66
Author(s): Wassim Ayadi, Mourad Elloumi, Jin‐Kao Hao
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pone.0102445

biDCG: A New Method for Discovering Global Features of DNA Microarray Data via an Iterative Re-Clustering Procedure
Cited by: 4
Author(s): Chia-Pei Chen, Fushing Hsieh, Rob Atwill, Patrice Koehl
Software Mentions: 3
Published: over 10 years ago

10.3389/fbioe.2015.00038

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses
Cited by: 33
Author(s): Takeshi Ara, Mitsuo Enomoto, Masanori Arita, Chiaki Ikeda, Kota Kera, Manabu Yamada, Takaaki Nishioka, Tasuku Ikeda, Yoshito Nihei, Daisuke Shibata, Shigehiko Kanaya, Nozomu Sakurai
Software Mentions: 3
Published: over 9 years ago

10.1155/2016/3059767

Evaluation of Plaid Models in Biclustering of Gene Expression Data
Cited by: 3
Author(s): Hamid Alavi Majd, Soodeh Shahsavari, Ahmad Reza Baghestani, Seyyed Mohammad Tabatabaei, Naghme Khadem Bashi, Mostafa Rezaei Tavirani, Mohsen Hamidpour
Software Mentions: 3
Published: almost 9 years ago

10.1186/1748-7188-8-4

Configurable pattern-based evolutionary biclustering of gene expression data
Cited by: 33
Author(s): Beatriz Pontes, Raúl Giráldez, Jesús S. Aguilar–Ruiz
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2021.654820

REW-ISA V2: A Biclustering Method Fusing Homologous Information for Analyzing and Mining Epi-Transcriptome Data
Cited by: 5
Author(s): Lin Zhang, Shutao Chen, Jiani Ma, Zhaoyang Liu, Hui Liu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations
Cited by: 228
Author(s): Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, F. Gibson, Alejandra González-Beltrán, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez‐Boussard, Mark A. Jensen, Yuling Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa Soldatova, Christian J. Stoeckert, Chris Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
Software Mentions: 3
Published: over 8 years ago

10.1186/1748-7188-6-18

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach
Cited by: 61
Author(s): Akdes Serin, Martin Vingron
Software Mentions: 3
Published: over 13 years ago

10.1038/s41597-019-0048-z

High-resolution global urban growth projection based on multiple applications of the SLEUTH urban growth model
Cited by: 87
Author(s): Yuerong Zhou, Alvin C. G. Varquez, Manabu Kanda
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-13-85

DIPSBC - data integration platform for systems biology collaborations
Cited by: 13
Author(s): Felix Dreher, Thomas Kreitler, Christopher Hardt, Atanas Kamburov, Reha Yildirimman, K. Schellander, Hans Lehrach, Bodo Lange, Ralf Herwig
Software Mentions: 3
Published: over 12 years ago

10.1186/1742-4682-8-39

Construction of gene regulatory networks using biclustering and bayesian networks
Cited by: 20
Author(s): Fadhl Alakwaa, Nahed H. Solouma, Yasser M. Kadah
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0159595

Incorporating and Compensating Cerebrospinal Fluid in Surface-Based Forward Models of Magneto- and Electroencephalography
Cited by: 52
Author(s): Matti Stenroos, Aapo Nummenmaa
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0009058

Lack of nAChR Activity Depresses Cochlear Maturation and Up-Regulates GABA System Components: Temporal Profiling of Gene Expression in α9 Null Mice
Cited by: 17
Author(s): Şevin Turcan, Donna K. Slonim, Douglas E. Vetter
Software Mentions: 3
Published: almost 15 years ago

10.1038/s41598-020-68785-7

Effects of vegetation restoration and environmental factors on understory vascular plants in a typical karst ecosystem in southern China
Cited by: 17
Author(s): Ou Zhiyang, Pang Shilong, He Qinfei, Yungui Peng, Huang Xiao-rong, Wenhui Shen
Software Mentions: 3
Published: over 4 years ago

10.1155/2013/731969

Navigating Traditional Chinese Medicine Network Pharmacology and Computational Tools
Cited by: 65
Author(s): Moon-Sik Yang, Jia-Lei Chen, Liwen Xu, Guang Ji
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13015-016-0074-8

BicNET: Flexible module discovery in large-scale biological networks using biclustering
Cited by: 29
Author(s): Rui Henriques, Sara C. Madeira
Software Mentions: 2
Published: over 8 years ago

10.1186/1748-7188-5-23

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms
Cited by: 27
Author(s): Burton Kuan Hui Chia, R. Krishna Murthy Karuturi
Software Mentions: 2
Published: over 14 years ago

10.3390/antibiotics10030279

Phage φAB6-Borne Depolymerase Combats Acinetobacter baumannii Biofilm Formation and Infection
Cited by: 33
Author(s): Md. Shahed-Al-Mahmud, Rakesh Roy, Febri Gunawan Sugiokto, Md. Nazmul Islam, Ming‐Der Lin, Ling-Chun Lin, Ning Lin
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-16-S4-S7

Analysis of miRNA expression profiles in breast cancer using biclustering
Cited by: 29
Author(s): Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo, Alfonso Urso
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-9-247

A visual analytics approach for understanding biclustering results from microarray data
Cited by: 53
Author(s): Rodrigo Santamaría, Roberto Therón, Luis Quintales
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-11-477

A bi-ordering approach to linking gene expression with clinical annotations in gastric cancer
Cited by: 4
Author(s): Fan Shi, Christopher Leckie, Geoff Macintyre, Izhak Haviv, Alex Boussioutas, Adam Kowalczyk
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2105-12-351

Knowledge engineering tools for reasoning with scientific observations and interpretations: a neural connectivity use case
Cited by: 35
Author(s): Thomas A. Russ, C. R. Ramakrishnan, Eduard Hovy, Mihail Bota, Gully A. P. C. Burns
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-014-0355-5

A framework for generalized subspace pattern mining in high-dimensional datasets
Cited by: 4
Author(s): Ed Curry
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2105-9-458

Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
Cited by: 56
Author(s): Peter A. DiMaggio, Scott R. McAllister, Christodoulos A. Floudas, Feng Xiao, Joshua D. Rabinowitz, Herschel Rabitz
Software Mentions: 2
Published: about 16 years ago

10.1186/s12859-016-1234-z

Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis
Cited by: 6
Author(s): José María González-Calabozo, Francisco J. Valverde-Albacete, Carmen Peláez-Moreno
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-15-130

BicSPAM: flexible biclustering using sequential patterns
Cited by: 37
Author(s): Rui Henriques, Sara C. Madeira
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-9-S1-S4

Bayesian biclustering of gene expression data
Cited by: 134
Author(s): Jian Gu, Jun S. Liu
Software Mentions: 2
Published: almost 17 years ago

10.1242/bio.20134408

An integrative computational analysis provides evidence for FBN1-associated network deregulation in trisomy 21
Cited by: 3
Author(s): Mireia Vilardell, Sergi Civit, Ralf Herwig
Software Mentions: 2
Published: over 11 years ago

10.1007/s11306-015-0810-y

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access
Cited by: 122
Author(s): Reza M. Salek, Steffen Neumann, Daniel Schober, Jan Hummel, Kenny Billiau, Joachim Kopka, Elon Correa, Theo H. Reijmers, Antonio Rosato, Leonardo Tenori, Paola Turano, Silvia Marín, Catherine Deborde, Daniel Jacob, Dominique Rolin, Benjamin Dartigues, Pablo Conesa, Kenneth Haug, Philippe Rocca-Serra, Steve O’Hagan, Jie Hao, Michael Van Vliet, Marko Sysi-Aho, Christian Ludwig, Jildau Bouwman, Marta Cascante, Timothy M. D. Ebbels, Julian L. Griffin, Annick Moing, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Mark R. Viant, Royston Goodacre, Ulrich L. Günther, Thomas Hankemeier, Claudio Luchinat, Dirk Walther, Christoph Steinbeck
Software Mentions: 2
Published: over 9 years ago

10.1016/j.ymeth.2018.02.004

Bi-clustering of metabolic data using matrix factorization tools
Cited by: 7
Author(s): Quan Gu, Kirill Veselkov
Software Mentions: 2
Published: about 6 years ago

10.1007/s12253-018-0418-4

Aspects of Modern Biobank Activity – Comprehensive Review
Cited by: 72
Author(s): Wiktor Paskal, Adriana M. Paskal, Tomasz Dębski, Maciej Gryziak, Janusz Jaworowski
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.8903

Palustrine forested wetland vegetation communities change across an elevation gradient, Washington State, USA
Cited by: 2
Author(s): Nate Hough‐Snee
Software Mentions: 2
Published: over 4 years ago

10.7717/peerj.9126

An improved similarity-based approach to predicting and mapping soil organic carbon and soil total nitrogen in a coastal region of northeastern China
Cited by: 4
Author(s): Shuai Wang, Kabindra Adhikari, Qianlai Zhuang, Zijiao Yang, Xinxin Jin, Qiubing Wang, Zhenxing Bian
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pbio.1001088

The Genomic Standards Consortium
Cited by: 180
Author(s): Dawn Field, Linda Amaral‐Zettler, Guy Cochrane, James R. Cole, Peter Dawyndt, George M Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Ilene Karsch-Mizrachi, Hans‐Peter Klenk, Rob Knight, Renzo Kottmann, Nikos C. Kyrpides, Patrick Meyer, Inigo San Gil, Susanna-Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Tatiana Tatusova, David W. Ussery, Owen White, John Wooley
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0227337

Vegetation change over seven years in the largest protected Pacific Northwest Bunchgrass Prairie remnant
Cited by: 9
Author(s): Joshua P. Averett, Lesley R. Morris, Bridgett J. Naylor, R B Taylor, Bryan A. Endress
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0010910

Gene Set-Based Module Discovery Decodes cis-Regulatory Codes Governing Diverse Gene Expression across Human Multiple Tissues
Cited by: 2
Author(s): Atsushi Niida, Seiya Imoto, Rui Yamaguchi, Masao Nagasaki, Satoru Miyano
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0151436

Understory Plant Community Composition Is Associated with Fine-Scale Above- and Below-Ground Resource Heterogeneity in Mature Lodgepole Pine (Pinus contorta) Forests
Cited by: 16
Author(s): Anne C.S. McIntosh, S. Ellen Macdonald, Sylvie A. Quideau
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0199214

Gauging the influence of increased search effort on reporting rates of bottlenose dolphin (Tursiops truncatus) strandings following the deepwater horizon oil spill
Cited by: 4
Author(s): Jonathan L. Pitchford, Michael Cristian Garcia, Eric E. Pulis, Ashley Millan Ambert, Andrew Heaton, Moby Solangi
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0141707

Contemporary Land Change Alters Fish Communities in a San Francisco Bay Watershed, California, U.S.A.
Cited by: 3
Author(s): Kristina Cervantes-Yoshida, Robert A. Leidy, Stephanie M. Carlson
Software Mentions: 2
Published: about 9 years ago

10.1289/ehp.1409157

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms
Cited by: 13
Author(s): Nehme El‐Hachem, Patrick Großmann, Alexis Blanchet-Cohen, Alain R. Bateman, Nicolas Bouchard, Jacques Archambault, Hugo J.W.L. Aerts, Benjamin Haibe‐Kains
Software Mentions: 2
Published: almost 9 years ago

10.1155/2015/909765

CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences
Cited by: 12
Author(s): Charalambos Chrysostomou, Hüseyin Şeker, Nizamettin Aydin
Software Mentions: 2
Published: almost 10 years ago

10.1111/eva.12368

Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew
Cited by: 81
Author(s): Chloé Delmas, Frédéric Fabre, Jérôme Jolivet, Isabelle D. Mazet, Sylvie Richart-Cervera, Laurent Delière, François Delmotte
Software Mentions: 2
Published: almost 9 years ago

10.12688/f1000research.27188.1

isa4j: a scalable Java library for creating ISA-Tab metadata
Cited by: 4
Author(s): Dennis Psaroudakis, Liqiang Feng, Patrick König, Uwe Scholz, Astrid Junker, Matthias Lange, Daniel Arend
Software Mentions: 2
Published: about 4 years ago

10.12688/f1000research.12342.2

The future of metabolomics in ELIXIR
Cited by: 4
Author(s): Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Domínguez Del Angel, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra González-Beltrán, Thomas Hankemeier, Kenneth Haug, José Luis Izquierdo-García, Rafael C. Jiménez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Pablo Moreno-Ger, Nicholas Κ. Moschonas, Steffen Neumann, Claire O’Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel Spicer, Ola Spjuth, Etienne Thévenot, Mark R. Viant, Ralf Weber, Egon Willighagen, Gianluigi Zanetti, Christoph Steinbeck
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2012.00441

Eukaryotic diversity at pH extremes
Cited by: 40
Author(s): Linda Amaral‐Zettler
Software Mentions: 2
Published: almost 12 years ago

10.3389/frobt.2018.00051

Highly-Integrated Hydraulic Smart Actuators and Smart Manifolds for High-Bandwidth Force Control
Cited by: 42
Author(s): Victor Barasuol, Octavio Antonio Villarreal-Magaña, Dhinesh Sangiah, Marco Frigerio, Michael J. Baker, Robert Morgan, Gustavo A. Medrano-Cerda, Darwin G. Caldwell, Claudio Semini
Software Mentions: 2
Published: over 6 years ago

10.1111/gcb.15223

Climate change considerations are fundamental to management of deep‐sea resource extraction
Cited by: 57
Author(s): Lisa A. Levin, Chih‐Lin Wei, Daniel C. Dunn, Diva J. Amon, Oliver S. Ashford, William W. L. Cheung, Ana Colaço, Carlos Domínguez-Carrió, Elva Escobar, Harriet Harden‐Davies, Jeffrey C. Drazen, Khaira Ismail, Daniel O.B. Jones, David E. Johnson, Jennifer Le, Franck Lejzerowicz, Satoshi Mitarai, Telmo Morato, Sandor Mulsow, Paul V. R. Snelgrove, Andrew K. Sweetman, Moriaki Yasuhara
Software Mentions: 2
Published: over 4 years ago

10.1038/sdata.2016.18

The FAIR Guiding Principles for scientific data management and stewardship
Cited by: 7,743
Author(s): Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Olavo Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim W. Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra González-Beltrán, Alasdair J. G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C. ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost N. Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt L. Persson, Philippe Rocca-Serra, Marco Roos, René van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik M. van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katy Wolstencroft, Jun Zhao, Barend Mons
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41597-019-0286-0

Experiment design driven FAIRification of omics data matrices, an exemplar
Cited by: 12
Author(s): Philippe Rocca-Serra, Susanna-Assunta Sansone
Software Mentions: 2
Published: about 5 years ago

10.1038/srep23466

UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data
Cited by: 34
Author(s): Zhenjia Wang, Guojun Li, R. W. Robinson, Xiuzhen Huang
Software Mentions: 2
Published: almost 9 years ago

10.1155/2014/252489

The Influences of Canopy Species and Topographic Variables on Understory Species Diversity and Composition in Coniferous Forests
Cited by: 18
Author(s): Huasheng Hong, Qi Feng, Yufang Su
Software Mentions: 2
Published: almost 11 years ago

10.3390/s18124372

Toward Security Enhanced Provisioning in Industrial IoT Systems
Cited by: 12
Author(s): Sungmoon Kwon, Jaehan Jeong, Taeshik Shon
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0043867

Post-Disturbance Plant Community Dynamics following a Rare Natural-Origin Fire in a Tsuga canadensis Forest
Cited by: 3
Author(s): Bryan D. Murray, Stacie A. Holmes, Christopher R. Webster, Jessica K. Witt
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0150117

Ideal Binocular Disparity Detectors Learned Using Independent Subspace Analysis on Binocular Natural Image Pairs
Cited by: 6
Author(s): David W. Hunter, Paul B. Hibbard
Software Mentions: 1
Published: almost 9 years ago

10.5966/sctm.2016-0087

Therapeutic Prospective of Infused Allogenic Cultured Mesenchymal Stem Cells in Traumatic Brain Injury Mice: A Longitudinal Proton Magnetic Resonance Spectroscopy Assessment
Cited by: 15
Author(s): Sushanta Kumar Mishra, Poonam Rana, Subash Khushu, Gurudutta Gangenahalli
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pgen.1000800

Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast
Cited by: 13
Author(s): Irit Gat‐Viks, Renana Meller, Martin Kupiec, Ron Shamir
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pcbi.1003468

Slowness and Sparseness Have Diverging Effects on Complex Cell Learning
Cited by: 13
Author(s): Jörn-Philipp Lies, Ralf M. Häfner, Matthias Bethge
Software Mentions: 1
Published: almost 11 years ago

10.3389/fmicb.2017.02118

Modeling Reveals the Role of Aging and Glucose Uptake Impairment in L1A1 Listeria monocytogenes Biofilm Life Cycle
Cited by: 5
Author(s): Eva Balsa‐Canto, Carlos Vilas, Alejandro López‐Núñez, M. Mosquera-Fernández, Romain Briandet, Marta López Cabo, Carlos Vázquez
Software Mentions: 1
Published: about 7 years ago

10.3389/fmicb.2020.00023

Stress Response of Vibrio parahaemolyticus and Listeria monocytogenes Biofilms to Different Modified Atmospheres
Cited by: 8
Author(s): Hui Qian, Wei Li, Liting Guo, Ling Ling Tan, Haiquan Liu, Jing Jing Wang, Yingjie Pan, Yong Zhao
Software Mentions: 1
Published: almost 5 years ago

10.3389/fmicb.2017.00055

xMAP Technology: Applications in Detection of Pathogens
Cited by: 76
Author(s): Nikol Reslová, Veronika Michna, Martin Kašný, Pavel Mikel, Petr Králík
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-018-2580-9

OMeta: an ontology-based, data-driven metadata tracking system
Cited by: 10
Author(s): Indresh Singh, Mehmet Kuscuoglu, Derek M. Harkins, Granger Sutton, Derrick E. Fouts, Karen E. Nelson
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.11004

Plyometric jump training effects on the physical fitness of individual-sport athletes: a systematic review with meta-analysis
Cited by: 17
Author(s): Sílvia Solé, Rodrigo Ramírez‐Campillo, David C. Andrade, Javier Sánchez-Sánchez
Software Mentions: 1
Published: almost 4 years ago

10.1093/gigascience/gix062

Automated assembly of species metabolomes through data submission into a public repository
Cited by: 8
Author(s): Reza M. Salek, Pablo Conesa, Keeva Cochrane, Kenneth Haug, Mark Williams, Namrata Kale, Pablo Moreno-Ger, Kalai Vanii Jayaseelan, José Ramón Macías, Venkata Chandrasekhar Nainala, Robert D. Hall, Laura K. Reed, Mark R. Viant, Claire O’Donovan, Christoph Steinbeck
Software Mentions: 1
Published: over 7 years ago

Projects: pypi: ISA

Papers Mentioning ISA 137