Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: EBarrays

https://packages.ecosyste.ms/registries/bioconductor.org/packages/EBarrays

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
1 version
Latest release: 10 months ago
6 dependent packages
45,243 downloads total

Papers Mentioning EBarrays 26

10.1155/2017/5310198

Robust Significance Analysis of Microarrays by Minimum <i>β</i>-Divergence Method
Cited by: 10
Author(s): Shahjaman, Nishith Kumar, Md. Manir Hossain Mollah, Shakil Ahmed, Anjuman Ara Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 7
Published: over 7 years ago

10.3390/bios3030238

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach
Cited by: 20
Author(s): Sergiusz Wesołowski, Marc R. Birtwistle, Grzegorz A. Rempała
Software Mentions: 7
Published: about 11 years ago

10.1186/s12859-015-0664-3

Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
Cited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: almost 9 years ago

10.1371/journal.ppat.1004959

Fungal Morphology, Iron Homeostasis, and Lipid Metabolism Regulated by a GATA Transcription Factor in Blastomyces dermatitidis
Cited by: 16
Author(s): Amber J. Marty, Aimee Teo Broman, Robert Żarnowski, Teigan G. Dwyer, Laura M. Bond, Anissa Lounès-Hadj Sahraoui, Joël Fontaine, James M. Ntambi, Sündüz Keleş, Christina Kendziorski, Gregory M. Gauthier
Software Mentions: 4
Published: about 9 years ago

10.6026/97320630013202

Serum and Plasma Metabolomic Biomarkers for Lung Cancer
Cited by: 42
Author(s): Nishith Kumar, Md. Shahjaman, Md. Nurul Haque Mollah, Shahidul Islam, Hongxia Ma
Software Mentions: 4
Published: about 7 years ago

10.3389/fnagi.2014.00044

Transcriptomics of Post-Stroke Angiogenesis in the Aged Brain
Cited by: 84
Author(s): Ana-Maria Buga, Claudiu Mărgăritescu, Claus‐Jürgen Scholz, Eugen Radu, Christine Zelenak, Aurel Popa‐Wagner
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0123791

Robust Modeling of Differential Gene Expression Data Using Normal/Independent Distributions: A Bayesian Approach
Cited by: 4
Author(s): Mojtaba Ganjali, Taban Baghfalaki, Damon Berridge
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-8-464

Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
Cited by: 50
Author(s): Brian D. Eads, John K. Colbourne, Elizabeth A. Bohuski, Justen Andrews
Software Mentions: 3
Published: over 17 years ago

10.1371/journal.pgen.1003034

A Dominantly Acting Murine Allele of Mcm4 Causes Chromosomal Abnormalities and Promotes Tumorigenesis
Cited by: 35
Author(s): Bruce N. Bagley, Thomas M. Keane, Vilena I. Maklakova, Jonathon G. Marshall, Rachael Lester, Michelle M. Cancel, Alex R. Paulsen, Laura Bendzick, Raha A. Been, Scott C. Kogan, Robert T. Cormier, Christina Kendziorski, David J. Adams, Lara S. Collier
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0050985

Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke
Cited by: 50
Author(s): Ana-Maria Buga, Claus‐Jürgen Scholz, Krishan Kumar, James G. Herndon, Dragoş Ovidiu Alexandru, Gabriel Radu Cojocaru, Thomas Dandekar, Aurel Popa‐Wagner
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-6-173

Normal uniform mixture differential gene expression detection for cDNA microarrays
Cited by: 74
Author(s): Nema Dean, Adrian E. Raftery
Software Mentions: 3
Published: about 19 years ago

10.3389/fnins.2020.00732

Electric Stimulation of Neurogenesis Improves Behavioral Recovery After Focal Ischemia in Aged Rats
Cited by: 14
Author(s): Adrian Tudor Bălșeanu, Monica Grigore, Leonard-Radu Pinosanu, Mark Slevin, Dirk M. Hermann, Daniela Glăvan, Aurel Popa‐Wagner
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-16-S5-S3

Analyse multiple disease subtypes and build associated gene networks using genome-wide expression profiles
Cited by: 17
Author(s): Sara Aibar, Celia Fontanillo, Conrad Droste, Beatriz Rosón-Burgo, Francisco J. Campos‐Laborie, Jesús María Hernández-Rivas, Javier De Las Rivas
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-46245-1

Genome-scale metabolic model of the rat liver predicts effects of diet restriction
Cited by: 7
Author(s): Priyanka Baloni, Vineet Sangar, James T. Yurkovich, Max Robinson, Scott L. Taylor, Christine M. Karbowski, Hisham K. Hamadeh, Yudong He, Nathan D. Price
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0138810

A Hybrid One-Way ANOVA Approach for the Robust and Efficient Estimation of Differential Gene Expression with Multiple Patterns
Cited by: 10
Author(s): Mohammad Manir Hossain Mollah, Rahman Jamal, Norfilza Mohd Mokhtar, Roslan Harun, Md. Nurul Haque Mollah
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0181242

Identification of a serum-induced transcriptional signature associated with metastatic cervical cancer
Cited by: 10
Author(s): Anna Palatnik, Shuyun Ye, Christina Kendziorski, Marissa Iden, Jessica S. Zigman, Martin J. Hessner, Janet S. Rader
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2105-7-353

A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates
Cited by: 12
Author(s): Anne-Mette K. Hein, Sylvia Richardson
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0112997

Comparison of Temporal Transcriptomic Profiles from Immature Lungs of Two Rat Strains Reveals a Viral Response Signature Associated with Chronic Lung Dysfunction
Cited by: 8
Author(s): Elizabeth A. Hines, Renee J. Szakaly, Ning Leng, A. Webster, Jamie M. Verheyden, Amber J. Lashua, Christina Kendziorski, Louis A. Rosenthal, James E. Gern, Ronald L. Sorkness, Xin Sun, Robert F. Lemanske
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2407-10-343

Neoplastic transformation of breast epithelial cells by genotoxic stress
Cited by: 6
Author(s): Mahendran Botlagunta, Paul T. Winnard, Venu Raman
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0017738

Advanced Computational Biology Methods Identify Molecular Switches for Malignancy in an EGF Mouse Model of Liver Cancer
Cited by: 16
Author(s): Philip Stegmaier, Nico Voss, Tatiana Meier, Alexander Kel, Edgar Wingender, Jürgen Borlak
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0019734

Metabolic Changes in Skin Caused by Scd1 Deficiency: A Focus on Retinol Metabolism
Cited by: 36
Author(s): Matthew T. Flowers, Chad M. Paton, Sheila M. O’Byrne, Kevin J. Schiesser, John A. Dawson, William S. Blaner, Christina Kendziorski, James M. Ntambi
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-8-80

Gene expression profiling of aging reveals activation of a p53-mediated transcriptional program
Cited by: 166
Author(s): Michael G. Edwards, Rozalyn M. Anderson, Ming Yuan, Christina Kendziorski, Richard Weindruch, Tomas A. Prolla
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-15-859

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia
Cited by: 68
Author(s): Lev Y. Yampolsky, Erliang Zeng, Jacqueline Lopez, Patricia J. Williams, Kenneth B. Dick, John K. Colbourne, Michael E. Pfrender
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0076567

Transcriptome Changes Associated with Anaerobic Growth in Yersinia intermedia (ATCC29909)
Cited by: 6
Author(s): Lavanya Babujee, Vallath Balakrishnan, Patricia J. Kiley, Jeremy D. Glasner, Nicole T. Perna
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-13-110

Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria
Cited by: 35
Author(s): Lavanya Babujee, Jennifer Apodaca, Vallath Balakrishnan, Paul Liss, Patricia J. Kiley, Amy O. Charkowski, Jeremy D. Glasner, Nicole T. Perna
Software Mentions: 1
Published: over 12 years ago