bioconductor: GOSim | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/btw763

ontologyX: a suite of R packages for working with ontological data
Cited by: 66
Author(s): Daniel Greene, Sylvia Richardson, Ernest Turro
Software Mentions: 9
Published: almost 8 years ago

10.1186/1471-2105-9-559

WGCNA: an R package for weighted correlation network analysis
Cited by: 14,193
Author(s): Peter Langfelder, Steve Horvath
Software Mentions: 8
Published: almost 16 years ago

Genomic Profiling of Collaborative Cross Founder Mice Infected with Respiratory Viruses Reveals Novel Transcripts and Infection-Related Strain-Specific Gene and Isoform Expression
Cited by: 22
Author(s): Hao Xiong, Juliet Morrison, Martin T. Ferris, Lisa E. Gralinski, Alan C. Whitmore, Richard Green, Matthew Thomas, Jennifer Tisoncik-Go, Gary P. Schroth, Fernando P Pardo Manuel De Villena, Ralph S. Baric, Mark T. Heise, Xinxia Peng, Michael G. Katze
Software Mentions: 7
Published: over 10 years ago

10.1038/s41416-018-0236-1

Phenotype-independent DNA methylation changes in prostate cancer
Cited by: 11
Author(s): Davide Pellacani, Alastair Droop, Fiona M. Frame, Matthew Simms, Vincent M. Mann, Anne T. Collins, Connie J. Eaves, Norman J. Maitland
Software Mentions: 6
Published: about 6 years ago

10.1038/srep26947

Variation in serum biomarkers with sex and female hormonal status: implications for clinical tests
Cited by: 29
Author(s): Jordan M. Ramsey, Jason D. Cooper, Brenda W. J. H. Penninx, Sabine Bahn
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0115692

HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology
Cited by: 49
Author(s): Yue Deng, Lin Gao, Bingbo Wang, Guo Xia-zhen
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-016-1160-0

TopoICSim: a new semantic similarity measure based on gene ontology
Cited by: 24
Author(s): Rezvan Ehsani, Finn Drabløs
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0192613

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples
Cited by: 17
Author(s): Hua Yu, Bingke Jiao, Lu Lu, Pengfei Wang, Shuangcheng Chen, Chengzhi Liang, Wei Liu
Software Mentions: 4
Published: over 6 years ago

10.1186/s12918-017-0420-6

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks
Cited by: 196
Author(s): Juan A. Botía, Jana Vandrovcová, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten, Michael E. Weale
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-8-166

GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products
Cited by: 178
Author(s): Holger Fröhlich, N. Speer, Annemarie Poustka, Tim Beißbarth
Software Mentions: 3
Published: over 17 years ago

10.1186/s12859-020-3515-9

Comparative analysis of similarity measurements in miRNAs with applications to miRNA-disease association predictions
Cited by: 12
Author(s): Hailin Chen, Ruiyu Guo, Guanghui Li, Wei Zhang, Zuping Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-018-2546-y

Measures of co-expression for improved function prediction of long non-coding RNAs
Cited by: 10
Author(s): Rezvan Ehsani, Finn Drabløs
Software Mentions: 3
Published: almost 6 years ago

10.1038/cddis.2015.241

IMP2/p62 induces genomic instability and an aggressive hepatocellular carcinoma phenotype
Cited by: 61
Author(s): Sonja M. Kessler, Stephan Laggai, Ahmad Barghash, Christina S. Schultheiss, Eva Lederer, Monika Artl, Volkhard Helms, Johannes Haybaeck, Alexandra K. Kiemer
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2105-14-284

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures
Cited by: 30
Author(s): Gaston K. Mazandu, Nicola Mulder
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0235670

UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization
Cited by: 8
Author(s): Duc-Hau Le
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0079118

Discovering Transcription and Splicing Networks in Myelodysplastic Syndromes
Cited by: 11
Author(s): Hongyan Wang, Jianguo Wen, Chung‐Che Chang, Xiaobo Zhou
Software Mentions: 3
Published: almost 11 years ago

10.18632/oncotarget.10439

Elevated expression of the <i>IGF2</i> mRNA binding protein 2 (IGF2BP2/IMP2) is linked to short survival and metastasis in esophageal adenocarcinoma
Cited by: 43
Author(s): Ahmad Barghash, Nicole Golob-Schwarzl, Volkhard Helms, Johannes Haybaeck, Sonja M. Kessler
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-12-266

DOSim: An R package for similarity between diseases based on Disease Ontology
Cited by: 85
Author(s): Jiang Li, Binsheng Gong, Xi Chen, Tao Liu, Chao Wu, Fan Zhang, Chunquan Li, Xiang Li, Shaoqi Rao, Xia Li
Software Mentions: 2
Published: over 13 years ago

10.1186/s12920-017-0288-8

Integrative model of leukocyte genomics and organ dysfunction in heart failure patients requiring mechanical circulatory support: a prospective observational study
Cited by: 5
Author(s): N. Wisniewski, G. Bondar, Christoph Rau, J. Chittoor, En‐Ting Chang, Azadeh Esmaeili, Martín Cadeiras, Mario C. Deng
Software Mentions: 2
Published: about 7 years ago

10.1155/2014/509149

FSim: A Novel Functional Similarity Search Algorithm and Tool for Discovering Functionally Related Gene Products
Cited by: 2
Author(s): Qiang Hu, Zhigang Wang, Zhengguo Zhang
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pcbi.1003210

How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation
Cited by: 68
Author(s): Kathrin Poos, Jan Smida, Michaela Nathrath, Doris Maugg, Daniel Baumhoer, Eberhard Korsching
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0015068

Analysis of Kinase Gene Expression Patterns across 5681 Human Tissue Samples Reveals Functional Genomic Taxonomy of the Kinome
Cited by: 45
Author(s): Sami Kilpinen, K. Ojala, Olli Kallioniemi
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0001440

Gene Characterization Index: Assessing the Depth of Gene Annotation
Cited by: 9
Author(s): Danielle Kemmer, Raf M. Podowski, Dimas Yusuf, Jochen Brumm, Warren A. Cheung, Claes Wahlestedt, Boris Lenhard, Wyeth W. Wasserman
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0101903

Identification of a Core miRNA-Pathway Regulatory Network in Glioma by Therapeutically Targeting miR-181d, miR-21, miR-23b, β-Catenin, CBP, and STAT3
Cited by: 18
Author(s): Ronghong Li, Xiang Li, Shangwei Ning, Jingrun Ye, Lei Han, Chunsheng Kang, Xia Li
Software Mentions: 2
Published: over 10 years ago

10.18632/oncotarget.9577

Identification of associations between small molecule drugs and miRNAs based on functional similarity
Cited by: 29
Author(s): Jing Wang, Fengyan Meng, Erfu Dai, Feng Yang, Shuyuan Wang, Xiaowen Chen, Lei Yang, Yuwen Wang, Wei Jiang
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-11-526

A statistical approach to finding overlooked genetic associations
Cited by: 2
Author(s): Andrew K. Rider, Geoffrey H. Siwo, Nitesh V. Chawla, Michael T. Ferdig, Scott J. Emrich
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0039662

Neighbor Overlap Is Enriched in the Yeast Interaction Network: Analysis and Implications
Cited by: 3
Author(s): Ariel Feiglin, John Moult, Byung Kook Lee, Yishai Ofran, Ron Unger
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.10008

FMLNCSIM: fuzzy measure-based lncRNA functional similarity calculation model
Cited by: 91
Author(s): Chen Xing, Yuan Huang, Xuesong Wang, Zhu-Hong You, Kwong Chan
Software Mentions: 1
Published: over 8 years ago

10.1186/1752-0509-6-S1-S7

Inferring domain-domain interactions from protein-protein interactions in the complex network conformation
Cited by: 6
Author(s): Chen Chen, Junfei Zhao, Qiang Huang, Rui-Sheng Wang, Yu Xia
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2164-9-465

Prediction of evolutionarily conserved interologs in Mus musculus
Cited by: 24
Author(s): Sailu Yellaboina, Dawood B. Dudekula, Minoru S.H. Ko
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0007342

An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications
Cited by: 1
Author(s): Deng Pan, Liqing Zhang
Software Mentions: 1
Published: about 15 years ago

10.1038/cddis.2017.362

Adropin deficiency worsens HFD-induced metabolic defects
Cited by: 39
Author(s): Shi Chen, Kai Zeng, Qicai Liu, Zheng Guo, Sheng Zhang, Xiaorong Chen, Jinkun Lin, Junping Wen, Chengfei Zhao, Xinhua Lin, Feng Gao
Software Mentions: 1
Published: about 7 years ago

10.1186/s12864-017-3512-1

HAPPI-2: a Comprehensive and High-quality Map of Human Annotated and Predicted Protein Interactions
Cited by: 34
Author(s): Jake Y. Chen, Ragini Pandey, Thanh Nguyen
Software Mentions: 1
Published: over 7 years ago

10.1038/cddis.2017.32

CALCB splice region pathogenic variants leading to plasma cell neurotropic enrichment in type 1 autoimmune pancreatitis
Cited by: 13
Author(s): Qicai Liu, Falin Chen, Chaoyang Wu, Feng Gao, Ze-Hao Zhuang, Jin-tong Chen, Bin Cai, Tianming Zhang, Ling Guo, Lishan Lin, Chengfei Zhao
Software Mentions: 1
Published: almost 8 years ago

10.1093/database/bay093

ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases
Cited by: 7
Author(s): Wenjing Wang, Peng Zhang, Leijie Li, Zhaobin Chen, Wenming Bai, Guiyou Liu, Liangcai Zhang, Haiyang Jia, Li Li, Yuanzheng Yang, Mingzhi Liao
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2148-10-125

Functional bias in molecular evolution rate of Arabidopsis thaliana
Cited by: 16
Author(s): Andrew S. Warren, Ramu Anandakrishnan, Liqing Zhang
Software Mentions: 1
Published: over 14 years ago

10.1093/bioinformatics/btx803

Co-complex protein membership evaluation using Maximum Entropy on GO ontology and InterPro annotation
Cited by: 15
Author(s): Irina M. Armean, Kathryn S. Lilley, Matthew Trotter, Nicholas Pilkington, Sean B. Holden
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12263-016-0543-1

Tocotrienols induce endoplasmic reticulum stress and apoptosis in cervical cancer cells
Cited by: 21
Author(s): Raffaella Comitato, Barbara Guantario, Guido Leoni, Kalanithi Nesaretnam, Maria Beatrice Ronci, Raffaella Canali, Fabio Virgili
Software Mentions: 1
Published: almost 8 years ago

Projects: bioconductor: GOSim

Papers Mentioning GOSim 41