Ecosyste.ms: Papers

10.12688/f1000research.17824.2

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

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: about 14 years ago

10.1136/jitc-2020-000705

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Cited by: 17
Author(s): Siwen Hu‐Lieskovan, Srabani Bhaumik, Kavita M. Dhodapkar, Jean‐Charles Grivel, Sumati Gupta, Brent A. Hanks, Sylvia Janetzki, Thomas O. Kleen, Yoshinobu Koguchi, Amanda W. Lund, Cristina Maccalli, Yolanda D. Mahnke, Ruslan D. Novosiadly, Senthamil R. Selvan, Tasha N. Sims, Yingdong Zhao, Holden T. Maecker
Software Mentions: 15
Published: almost 4 years ago

10.1186/s12859-016-0971-3

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data
Cited by: 20
Author(s): Kévin Rue-Albrecht, Paul A. McGettigan, Belinda Hernández, Nicolas C. Nalpas, David A. Magee, Andrew Parnell, Stephen V. Gordon, David E. MacHugh
Software Mentions: 14
Published: over 8 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago

10.3390/cancers11091248

Gastric Normal Adjacent Mucosa Versus Healthy and Cancer Tissues: Distinctive Transcriptomic Profiles and Biological Features
Cited by: 28
Author(s): Sabino Russi, Giovanni Calice, Vitalba Ruggieri, Simona Laurino, Francesco La Rocca, Elena Amendola, Cinzia Lapadula, Debora Compare, Gerardo Nardone, Pellegrino Musto, Mario De Felice, Geppino Falco, Pietro Zoppoli
Software Mentions: 12
Published: about 5 years ago

10.1186/s13059-019-1790-4

Identifying significantly impacted pathways: a comprehensive review and assessment
Cited by: 113
Author(s): Tuan-Minh Nguyen, Adib Shafi, Tin Nguyen, Sorin Drăghici
Software Mentions: 12
Published: about 5 years ago

10.1038/srep18871

LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights
Cited by: 37
Author(s): Xinran Dong, Yun Huang, Xiao Wang, Weidong Tian
Software Mentions: 12
Published: almost 9 years ago

10.1371/journal.pone.0079217

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
Cited by: 154
Author(s): Adi L. Tarca, Gaurav Bhatti, Roberto Romero
Software Mentions: 12
Published: about 11 years ago

10.1534/g3.120.401309

CeMbio - The<i>Caenorhabditis elegans</i>Microbiome Resource
Cited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 4 years ago

10.3389/fphys.2013.00278

Methods and approaches in the topology-based analysis of biological pathways
Cited by: 162
Author(s): Cristina Mitrea, Zeinab Taghavi, Behzad Bokanizad, Samer Najeeb Hanoudi, Rebecca Tagett, Michèle Donato, Călin Voichiţa, Sorin Drăghici
Software Mentions: 9
Published: almost 12 years ago

10.1186/s12859-014-0408-9

Kiwi: a tool for integration and visualization of network topology and gene-set analysis
Cited by: 12
Author(s): Leif Väremo, Francesco Gatto, Jens Nielsen
Software Mentions: 9
Published: almost 10 years ago

10.1186/1471-2105-13-136

Down-weighting overlapping genes improves gene set analysis
Cited by: 120
Author(s): Adi L. Tarca, Sorin Drăghici, Gaurav Bhatti, Roberto Romero
Software Mentions: 9
Published: over 12 years ago

10.1186/s13040-017-0125-9

Gene set analysis controlling for length bias in RNA-seq experiments
Cited by: 7
Author(s): Xing Ren, Qiang Hu, Song Liu, Jianmin Wang, Jeffrey C. Miecznikowski
Software Mentions: 9
Published: almost 8 years ago

10.1038/s41598-020-71521-w

Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples
Cited by: 9
Author(s): Leah C. Wehmas, Susan Hester, Charles E. Wood
Software Mentions: 9
Published: about 4 years ago

10.1186/s12950-020-00260-6

Anatabine ameliorates intestinal inflammation and reduces the production of pro-inflammatory factors in a dextran sulfate sodium mouse model of colitis
Cited by: 11
Author(s): Pedro A. Ruiz-Castro, Ulrike Kogel, Giuseppe Lo Sasso, Blaine Phillips, Alain Sewer, Bjoern Titz, Llenalia Garcia, Athanasios Kondylis, Emmanuel Guedj, Dariusz Peric, David Bornand, Rémi Dulize, Céline Merg, Maica Corciulo, Nikolai V. Ivanov, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pone.0069624

Transcriptomic Analysis of Insulin-Sensitive Tissues from Anti-Diabetic Drug Treated ZDF Rats, a T2DM Animal Model
Cited by: 4
Author(s): Yo Na Kim, Sangok Kim, Il Yong Kim, Jae Hoon Shin, Sooyoung Cho, Sun Shin Yi, Wankyu Kim, Kyung Sub Kim, Sanghyuk Lee, Je Kyung Seong
Software Mentions: 8
Published: over 11 years ago

10.3390/e23080945

Statistical Approach of Gene Set Analysis with Quantitative Trait Loci for Crop Gene Expression Studies
Cited by: 1
Author(s): Das S, N. Shesh
Software Mentions: 8
Published: over 3 years ago

10.1093/bib/bbv069

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
Cited by: 45
Author(s): Yasir Rahmatallah, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 8
Published: about 9 years ago

10.1093/bioinformatics/bts438

iBBiG: iterative binary bi-clustering of gene sets
Cited by: 44
Author(s): Daniel Gusenleitner, Eleanor Howe, Stefan Bentink, John Quackenbush, Aedín C. Culhane
Software Mentions: 8
Published: over 12 years ago

10.1186/s12859-021-04124-5

Popularity and performance of bioinformatics software: the case of gene set analysis
Cited by: 21
Author(s): Chengshu Xie, Shaurya Jauhari, Antonio M. Mora
Software Mentions: 8
Published: over 3 years ago

10.1186/s12859-016-1180-9

Statistical inference for time course RNA-Seq data using a negative binomial mixed-effect model
Cited by: 21
Author(s): Xiaoxiao Sun, David Dalpiaz, Di Wu, Jun S. Liu, Wenxuan Zhong, Ping Ma
Software Mentions: 7
Published: about 8 years ago

10.3390/e22040427

Fifteen Years of Gene Set Analysis for High-Throughput Genomic Data: A Review of Statistical Approaches and Future Challenges
Cited by: 30
Author(s): Das S, Craig J. McClain, N. Shesh
Software Mentions: 7
Published: over 4 years ago

10.1186/1471-2105-11-510

Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets
Cited by: 7
Author(s): Fabrice Berger, Bertrand De Meulder, Anthoula Gaigneaux, Sophie Depiereux, Eric Bareke, Michael St.Pierre, Benoît De Hertogh, Mauro Delorenzi, Eric Depiereux
Software Mentions: 7
Published: about 14 years ago

10.12688/f1000research.6030.2

AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses
Cited by: 3
Author(s): Michael Considine, Hilary S. Parker, Yingying Wei, Xaio Xia, Leslie Cope, Michael F. Ochs, Elana J. Fertig
Software Mentions: 7
Published: about 9 years ago

10.1371/journal.pcbi.1006042

The Pathway Coexpression Network: Revealing pathway relationships
Cited by: 40
Author(s): Yered Pita-Juárez, Gabriel Altschuler, Sokratis Kariotis, Wenbin Wei, Katjuša Koler, Claire Green, Rudolph E. Tanzi, Winston Hide
Software Mentions: 7
Published: over 6 years ago

10.3389/fimmu.2021.694680

Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients
Cited by: 5
Author(s): Teresa Domaszewska, Joanna Żyła, Raik Otto, Stefan H. E. Kaufmann, January Weiner
Software Mentions: 7
Published: over 3 years ago

10.1186/s13040-018-0166-8

Gene set analysis methods: a systematic comparison
Cited by: 57
Author(s): Ravi Mathur, Daniel M. Rotroff, Ma Jun, Ali Shojaie, Alison A. Motsinger‐Reif
Software Mentions: 7
Published: over 6 years ago

10.1038/s41436-018-0337-5

Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions
Cited by: 65
Author(s): Sulev Reisberg, Kristi Krebs, Maarja Lepamets, Mart Kals, Reedik Mägi, Kristjan Metsalu, Volker M. Lauschke, Jaak Vilo, Lili Milani
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-015-0729-3

htsint: a Python library for sequencing pipelines that combines data through gene set generation
Cited by: 1
Author(s): Adam Richards, Anthony Herrel, Camille Bonneaud
Software Mentions: 6
Published: about 9 years ago

10.1186/s12859-017-1482-6

GSAR: Bioconductor package for Gene Set analysis in R
Cited by: 34
Author(s): Yasir Rahmatallah, Boris Zybailov, Frank Emmert‐Streib, Galina Glazko
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0212866

Dynamic changes in lung responses after single and repeated exposures to cigarette smoke in mice
Cited by: 10
Author(s): Michelle Engle, Justine N. Monk, Corey M. Jania, Jessica R. Martin, John C. Gomez, Hong Dang, Joel S. Parker, Claire M. Doerschuk
Software Mentions: 6
Published: over 5 years ago

10.3389/fphar.2021.692442

Development, Testing, Parameterisation and Calibration of a Human PBPK Model for the Plasticiser, Di-(2-propylheptyl) Phthalate (DPHP) Using in Silico, in vitro and Human Biomonitoring Data
Cited by: 6
Author(s): Kevin McNally, Craig Sams, Alex Hogg, Annie Lumen, George Loizou
Software Mentions: 6
Published: about 3 years ago

10.3389/fphar.2021.630457

Derivation of a Human In Vivo Benchmark Dose for Perfluorooctanoic Acid From ToxCast In Vitro Concentration–Response Data Using a Computational Workflow for Probabilistic Quantitative In Vitro to In Vivo Extrapolation
Cited by: 8
Author(s): George Loizou, Kevin McNally, Jean-Lou C.M. Dorne, Alex Hogg
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0019024

Functional Genomics Unique to Week 20 Post Wounding in the Deep Cone/Fat Dome of the Duroc/Yorkshire Porcine Model of Fibroproliferative Scarring
Cited by: 21
Author(s): Loren H. Engrav, Christopher K. Tuggle, Kathleen F. Kerr, Kehao Zhu, Surawej Numhom, Oliver Couture, Richard P. Beyer, Anne M. Hocking, Gretchen J. Carrougher, Maria Luiza Christóvão Ramos, Matthew B. Klein, Nicole S. Gibran
Software Mentions: 6
Published: over 13 years ago

10.3389/fphar.2019.01394

Development, Testing, Parameterization, and Calibration of a Human Physiologically Based Pharmacokinetic Model for the Plasticizer, Hexamoll® Diisononyl-Cyclohexane-1, 2-Dicarboxylate Using In Silico, In Vitro, and Human Biomonitoring Data
Cited by: 9
Author(s): Kevin McNally, Craig Sams, George Loizou
Software Mentions: 6
Published: almost 5 years ago

10.1186/1745-6150-7-44

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods
Cited by: 21
Author(s): Frank Emmert‐Streib, Shailesh Tripathi, Ricardo de Matos Simoes
Software Mentions: 6
Published: almost 13 years ago

10.1186/1471-2105-12-92

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies
Cited by: 5
Author(s): Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
Software Mentions: 6
Published: over 13 years ago

10.1186/1752-0509-8-S4-S5

Network-based biomarkers enhance classical approaches to prognostic gene expression signatures
Cited by: 18
Author(s): Rebecca Barter, Sarah-Jane Schramm, Graham J. Mann, Jean Yee Hwa Yang
Software Mentions: 6
Published: almost 10 years ago

10.1186/1752-0509-6-56

Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes
Cited by: 62
Author(s): Zuguang Gu, Jialin Liu, Kun-Ming Cao, Junfeng Zhang, Jin Wang
Software Mentions: 6
Published: over 12 years ago

10.1186/1471-2105-12-209

Multiple testing for gene sets from microarray experiments
Cited by: 6
Author(s): Insuk Sohn, Kouros Owzar, Jong-Tae Lim, Stephen L. George, Stephanie M. Cushman, Sin‐Ho Jung
Software Mentions: 5
Published: over 13 years ago

10.1186/1755-8794-6-2

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data
Cited by: 13
Author(s): Kristina Hettne, André Boorsma, Dorien A.M. van Dartel, Jelle J. Goeman, Esther de Jong, Aldert H. Piersma, Rob Stierum, Jos Kleinjans, Jan A. Kors
Software Mentions: 5
Published: almost 12 years ago

10.1371/journal.pcbi.1005187

MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways
Cited by: 24
Author(s): Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias
Software Mentions: 5
Published: about 8 years ago

10.1093/database/bau068

yStreX: yeast stress expression database
Cited by: 11
Author(s): Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranović
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pcbi.1004847

Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Cited by: 40
Author(s): Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James Stevens
Software Mentions: 5
Published: over 8 years ago

10.1186/1471-2105-11-311

FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases
Cited by: 25
Author(s): Stephen J. Goodswen, Cedric Gondro, Nathan S. Watson-Haigh, Haja N. Kadarmideen
Software Mentions: 5
Published: over 14 years ago

10.1186/s12864-015-2188-7

Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples
Cited by: 16
Author(s): Xiangtian Yu, Tao Zeng, Guojun Li
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0159182

LPEseq: Local-Pooled-Error Test for RNA Sequencing Experiments with a Small Number of Replicates
Cited by: 6
Author(s): Jungsoo Gim, Sungho Won, Taesung Park
Software Mentions: 5
Published: over 8 years ago

10.1534/g3.119.400044

HSB-1 Inhibition and HSF-1 Overexpression Trigger Overlapping Transcriptional Changes To Promote Longevity in <i>Caenorhabditis elegans</i>
Cited by: 20
Author(s): Surojit Sural, Tzu-Chiao Lu, Seung Ah Jung, Ao Lin Hsu
Software Mentions: 5
Published: over 5 years ago

10.3389/fgene.2021.620453

STATegra: Multi-Omics Data Integration – A Conceptual Scheme With a Bioinformatics Pipeline
Cited by: 21
Author(s): Núria Planell, Vincenzo Lagani, Patricia Sebastián-León, Frans van der Kloet, Ewoud Ewing, Nestoras Karathanasis, Arantxa Urdangarin, Imanol Arozarena, Maja Jagodic, Ioannis Tsamardinos, Sonia Tarazona, Ana Conesa, Jesper Tegnér, David Green
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0055635

Functional-Network-Based Gene Set Analysis Using Gene-Ontology
Cited by: 6
Author(s): Billy Chang, Rafal Kustra, Weidong Tian
Software Mentions: 5
Published: almost 12 years ago

10.1074/mcp.TIR118.001251

MOGSA: Integrative Single Sample Gene-set Analysis of Multiple Omics Data
Cited by: 49
Author(s): Chen Meng, Azfar Basunia, Bjoern Peters, Amin Moghaddas Gholami, Bernhard Küster, Aedín C. Culhane
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-016-0928-6

Gene set analysis using sufficient dimension reduction
Cited by: 7
Author(s): Huey-Miin Hsueh, Tsai Chen-An
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0086299

Functional Module Connectivity Map (FMCM): A Framework for Searching Repurposed Drug Compounds for Systems Treatment of Cancer and an Application to Colorectal Adenocarcinoma
Cited by: 33
Author(s): Feng Hsiang Chung, Yun Ru Chiang, Ai Lun Tseng, Yung Chuan Sung, Jean Lu, Min Chang Huang, Nianhan Ma, Hoong Chien Lee
Software Mentions: 5
Published: almost 11 years ago

10.1371/journal.pone.0146469

Large-Scale Spatio-Temporal Patterns of Mediterranean Cephalopod Diversity
Cited by: 11
Author(s): Stefanie Keller, Valerio Bartolino, Manuel Hidalgo, Isabella Bitetto, Loredana Casciaro, Danila Cuccu, Antonio Esteban, Carlos Martín García, Germana Garofalo, Marios Josephides, Angélique Jadaud, Eugenia Lefkaditou, Porzia Maiorano, Chiara Manfredi, Bojan Marčeta, Enric Massutí, Reno Micallef, Panagiota Peristeraki, Giulio Rélini, Paolo Sartor, María Teresa Spedicato, George Tserpes, Antoni Quetglas
Software Mentions: 5
Published: almost 9 years ago

10.1186/s12864-019-5738-6

GScluster: network-weighted gene-set clustering analysis
Cited by: 11
Author(s): Susan A. Yoon, Jinhwan Kim, Seon‐Kyu Kim, Bukyung Baik, Sang-Mun Chi, Seon‐Young Kim, Dougu Nam
Software Mentions: 4
Published: over 5 years ago

10.1186/1752-0509-6-65

Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases
Cited by: 49
Author(s): Yu Liu, Mehmet Koyutürk, Jill S. Barnholtz‐Sloan, Mark R. Chance
Software Mentions: 4
Published: over 12 years ago

10.1186/1471-2105-12-273

Gene set analysis for longitudinal gene expression data
Cited by: 11
Author(s): Ke Zhang, Haiyan Wang, Arne C. Bathke, Solomon W. Harrar, Hans‐Peter Piepho, Youping Deng
Software Mentions: 4
Published: over 13 years ago

10.1038/s42003-019-0748-0

Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations
Cited by: 35
Author(s): C. Keith Cassidy, Benjamin A. Himes, Dapeng Sun, Jun Ma, Gongpu Zhao, John S. Parkinson, Phillip J. Stansfeld, Zaida Luthey‐Schulten, P. Zhang
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms22116159

Virus–Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1vir Infection
Cited by: 2
Author(s): Grzegorz M. Cech, Agnieszka Szalewska-Pałasz, Katarzyna Potrykus, Anna Kłoska
Software Mentions: 4
Published: over 3 years ago

10.1155/2018/3028290

Stress-Adaptive Responses Associated with High-Level Carbapenem Resistance in KPC-ProducingKlebsiella pneumoniae
Cited by: 4
Author(s): Sheila Adams‐Sapper, Adam Gayoso, Lee W. Riley
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2105-12-29

Investigating the effect of paralogs on microarray gene-set analysis
Cited by: 0
Author(s): Aline Faure, Cathal Seoighe, Nicola Mulder
Software Mentions: 4
Published: almost 14 years ago

10.1038/s41598-020-60981-9

NBIA: a network-based integrative analysis framework – applied to pathway analysis
Cited by: 7
Author(s): Tin Nguyen, Adib Shafi, Tuan-Minh Nguyen, A. Grant Schissler, Sorin Drăghici
Software Mentions: 4
Published: over 4 years ago

10.3390/s21155214

Cat and Mouse Based Optimizer: A New Nature-Inspired Optimization Algorithm
Cited by: 47
Author(s): Mohammad Dehghani, Štěpán Hubálovský, Pavel Trojovský
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1007530

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
Cited by: 31
Author(s): Ryan Sun, Shirley Hui, Gary D. Bader, Xihong Lin, Peter Kraft
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6390-x

High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis
Cited by: 8
Author(s): Nirupama Benis, Jerry M. Wells, M.A. Smits, Soumya K. Kar, Bart van der Hee, Vítor A. P. Martins dos Santos, María Suárez-Diez, Dirkjan Schokker
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40246-021-00357-w

Evaluation of low-pass genome sequencing in polygenic risk score calculation for Parkinson’s disease
Cited by: 2
Author(s): Sung-Jae Kim, Jong-Yeon Shin, Nak‐Jung Kwon, Chang-Uk Kim, Changhoon Kim, Chong Sik Lee, Jeong‐Sun Seo
Software Mentions: 4
Published: about 3 years ago

10.1534/genetics.119.302089

<i>beditor</i>: A Computational Workflow for Designing Libraries of Guide RNAs for CRISPR-Mediated Base Editing
Cited by: 32
Author(s): Rohan Dandage, Philippe Després, Nozomu Yachie, Christian R. Landry
Software Mentions: 4
Published: over 5 years ago

10.1534/genetics.120.303474

Age and Genetic Background Modify Hybrid Male Sterility in House Mice
Cited by: 17
Author(s): Samuel J. Widmayer, Mary Ann Handel, David L. Aylor
Software Mentions: 4
Published: about 4 years ago

10.1152/physiolgenomics.00057.2018

Salt stress in the renal tubules is linked to TAL-specific expression of uromodulin and an upregulation of heat shock genes
Cited by: 7
Author(s): Lesley Graham, Alisha Aman, Desmond Campbell, Julian J. Augley, Delyth Graham, Martin W. McBride, Niall J. Fraser, Nicholas R. Ferreri, Anna F. Dominiczak, Sandosh Padmanabhan
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-12-S1-S25

GARNET – gene set analysis with exploration of annotation relations
Cited by: 10
Author(s): Kyoohyoung Rho, Bumjin Kim, Yeongjun Jang, Sang‐Hyun Lee, Taejeong Bae, Jihae Seo, Chae Hwa Seo, Ji‐Hyun Lee, Hyun‐Jung Kang, Ungsik Yu, Sung Hoon Kim, Sanghyuk Lee, Wankyu Kim
Software Mentions: 4
Published: almost 14 years ago

10.3390/genes12050702

Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests
Cited by: 3
Author(s): Simon Jansen, Ulrich Baulain, Christin Habig, Faisal Ramzan, Jens Schauer, Armin O. Schmitt, Armin M. Scholz, Ahmad Sharifi, Annett Weigend, Steffen Weigend
Software Mentions: 4
Published: over 3 years ago

10.1186/gb-2013-14-11-r125

Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts
Cited by: 176
Author(s): Adam D. Pfefferle, Jason I. Herschkowitz, Jerry Usary, J. Chuck Harrell, Benjamin T. Spike, Jessica R. Adams, Maria I. Torres-Arzayus, Myles Brown, Sean E. Egan, Geoffrey M. Wahl, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2164-11-26

1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1
Cited by: 80
Author(s): Pavlo L. Kovalenko, Zhentao Zhang, Min Cui, S. Clinton, James C. Fleet
Software Mentions: 4
Published: almost 15 years ago

10.3389/fphar.2021.646701

Aripiprazole as a Candidate Treatment of COVID-19 Identified Through Genomic Analysis
Cited by: 22
Author(s): Benedicto Crespo‐Facorro, Miguel Ruiz‐Veguilla, Javier Vázquez-Bourgon, Ana C. Sánchez-Hidalgo, Nathalia Garrido-Torres, José Miguel Cisneros, Carlos Prieto, Jesús Sainz
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0056657

Significance and Suppression of Redundant IL17 Responses in Acute Allograft Rejection by Bioinformatics Based Drug Repositioning of Fenofibrate
Cited by: 15
Author(s): Silke Roedder, Naoyuki Kimura, Homare Okamura, Szu‐Chuan Hsieh, Yongquan Gong, Minnie M. Sarwal
Software Mentions: 4
Published: almost 12 years ago

10.3389/fphar.2018.00588

Applying a Global Sensitivity Analysis Workflow to Improve the Computational Efficiencies in Physiologically-Based Pharmacokinetic Modeling
Cited by: 51
Author(s): Nan‐Hung Hsieh, Brad Reisfeld, Frédéric Bois, Weihsueh A. Chiu
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-020-3366-4

A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Cited by: 4
Author(s): Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich A. Maus, Thomas Illig, David S. DeLuca
Software Mentions: 4
Published: almost 5 years ago

10.1016/j.ejps.2011.10.026

Model-based global sensitivity analysis as applied to identification of anti-cancer drug targets and biomarkers of drug resistance in the ErbB2/3 network
Cited by: 33
Author(s): Galina Lebedeva, Anatoly Sorokin, Dana Faratian, Peter Mullen, Alexey Goltsov, Simon P. Langdon, David J. Harrison, Igor Goryanin
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pgen.1007890

Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability
Cited by: 15
Author(s): Isabella Cera, Laura Whitton, Gary Donohoe, Derek W. Morris, Georg Dechant, Galina Apostolova
Software Mentions: 4
Published: almost 6 years ago

10.1155/2014/346074

MAVTgsa: An R Package for Gene Set (Enrichment) Analysis
Cited by: 5
Author(s): Chih-Yi Chien, Ching‐Wei Chang, Chen‐An Tsai, James J. Chen
Software Mentions: 4
Published: almost 11 years ago

10.1155/2019/8912961

Curcumin Inhibits ERK/c-Jun Expressions and Phosphorylation against Endometrial Carcinoma
Cited by: 25
Author(s): Zhenxue Zhang, Pengfei Yi, Changchun Tu, Jiejie Zhan, Liping Jiang, Fanglin Zhang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-021-04110-x

Gene-set distance analysis (GSDA): a powerful tool for gene-set association analysis
Cited by: 0
Author(s): Xueyuan Cao, Stan Pounds
Software Mentions: 4
Published: over 3 years ago

10.1186/s13040-015-0059-z

Principal component gene set enrichment (PCGSE)
Cited by: 20
Author(s): H. Robert Frost, Zhigang Li, Jason H. Moore
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2105-10-358

ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization
Cited by: 90
Author(s): Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor
Software Mentions: 4
Published: about 15 years ago

10.1186/s12859-016-1403-0

Robust multi-group gene set analysis with few replicates
Cited by: 4
Author(s): Pashupati P. Mishra, Alan Medlar, Liisa Holm, Petri Törönen
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0013954

A Role for the Retinoblastoma Protein As a Regulator of Mouse Osteoblast Cell Adhesion: Implications for Osteogenesis and Osteosarcoma Formation
Cited by: 30
Author(s): Bernadette Sosa‐García, Volkan Gündüz, Viviana Vázquez‐Rivera, W. Douglas Cress, Gabriëla Wright, Haikuo Bian, Philip W. Hinds, Pedro G. Santiago‐Cardona
Software Mentions: 4
Published: about 14 years ago

10.3389/fonc.2013.00184

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways
Cited by: 13
Author(s): Alexander J. Trevarton, Michael B. Mann, Christoph Knapp, Hiromitsu Araki, Jonathan D. Wren, Steven Stones-Havas, Michael A. Black, Cristin G. Print
Software Mentions: 4
Published: almost 12 years ago

10.1155/2018/7690435

A Water-Area Recognition Approach Based on “Tuned” Texture Mask and Cuckoo Search Algorithm
Cited by: 4
Author(s): Zhongwei Chen, Kangbo Peng, Hong‐Jian Lai, Yichao Wang, Xiaolong Wu, Zhifeng Xiao
Software Mentions: 3
Published: almost 6 years ago

10.1155/2016/8179670

A “Tuned” Mask Learnt Approach Based on Gravitational Search Algorithm
Cited by: 5
Author(s): Youchuan Wan, Mingwei Wang, Zhiwei Ye, Xudong Lai
Software Mentions: 3
Published: almost 9 years ago

10.1155/2016/9063065

Training Feedforward Neural Networks Using Symbiotic Organisms Search Algorithm
Cited by: 55
Author(s): Haizhou Wu, Yongquan Zhou, Qifang Luo, Mohamed Abdel Basset
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12859-019-3221-7

Longitudinal linear combination test for gene set analysis
Cited by: 2
Author(s): Elham Khodayari Moez, Morteza Hajihosseini, Jeffrey L. Andrews, Irina Dinu
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-12-411

EPEPT: A web service for enhanced P-value estimation in permutation tests
Cited by: 5
Author(s): Theo Knijnenburg, Jake Lin, Hector Rovira, John P. Boyle, Ilya Shmulevich
Software Mentions: 3
Published: about 13 years ago

10.1155/2015/704301

Fuzzy Controller Design Using Evolutionary Techniques for Twin Rotor MIMO System: A Comparative Study
Cited by: 21
Author(s): Hashim A. Hashim, M. A. Abido
Software Mentions: 3
Published: almost 10 years ago

10.1016/j.csbj.2021.06.040

A survey of direct-to-consumer genotype data, and quality control tool (GenomePrep) for research
Cited by: 6
Author(s): Chang Lu, Bastian Greshake Tzovaras, Julian Gough
Software Mentions: 3
Published: almost 4 years ago

10.1186/1755-8794-1-38

Tobacco use induces anti-apoptotic, proliferative patterns of gene expression in circulating leukocytes of Caucasian males
Cited by: 13
Author(s): Peter C. Charles, Brian D Alder, Eleanor Hilliard, Jonathan C. Schisler, Robert E. Lineberger, Joel S. Parker, Sabeen Mapara, Samuel S. Wu, Andrea L. Portbury, Cam Patterson, George A. Stouffer
Software Mentions: 3
Published: over 16 years ago

10.3390/cancers13010158

Novel Epigenetic Eight-Gene Signature Predictive of Poor Prognosis and MSI-Like Phenotype in Human Metastatic Colorectal Carcinomas
Cited by: 12
Author(s): Valentina Condelli, Giovanni Calice, Alessandra Cassano, Michele Basso, Maria Grazia Rodriquenz, Angela Zupa, Francesca Maddalena, Fabiana Crispo, Michele Pietrafesa, Michele Aieta, Alessandro Sgambato, Giampaolo Tortora, Pietro Zoppoli, Matteo Landriscina
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-10-26

A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets
Cited by: 8
Author(s): Chien Yi Tung, Chih Hung Jen, Ming Hsu, Hsei Wei Wang, Chi Lin
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2105-14-212

Linear combination test for gene set analysis of a continuous phenotype
Cited by: 8
Author(s): Irina Dinu, Xiaoming Wang, Linda E. Kelemen, Shabnam Vatanpour, Saumyadipta Pyne
Software Mentions: 3
Published: over 11 years ago