bioconductor: GOSemSim | Projects

10.3389/fcell.2020.577125

Development of a Metastasis-Related Immune Prognostic Model of Metastatic Colorectal Cancer and Its Usefulness to Immunotherapy
Cited by: 11
Author(s): Zhiwen Luo, Xiao Chen, Yefan Zhang, Zhen Huang, Hong Zhao, Jianjun Zhao, Zhiyu Li, Jianguo Zhou, Jianmei Liu, Jianqiang Cai, Xinyu Bi
Software Mentions: 26
Published: almost 4 years ago

10.7554/eLife.63003

Short-term exposure to intermittent hypoxia leads to changes in gene expression seen in chronic pulmonary disease
Cited by: 17
Author(s): Gang Wu, Yin Yeng Lee, Evelyn M. Gulla, Andrew Potter, Joseph A. Kitzmiller, Marc D. Ruben, Nathan Salomonis, JA Whitsett, Lauren J. Francey, John B. Hogenesch, Smith Dl
Software Mentions: 12
Published: almost 4 years ago

10.1186/s13073-016-0384-y

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits
Cited by: 131
Author(s): Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C. Knight
Software Mentions: 12
Published: about 8 years ago

10.1371/journal.pcbi.1003929

dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations
Cited by: 18
Author(s): Hai Fang
Software Mentions: 11
Published: about 10 years ago

10.1371/journal.pgen.1008748

Polygenic adaptation of rosette growth in Arabidopsis thaliana
Cited by: 19
Author(s): Benedict Wieters, Kim A. Steige, Fei He, Evan Koch, Sebastián E. Ramos-Onsins, Hongya Gu, Ya‐Long Guo, Shamil Sunyaev, Juliette de Meaux
Software Mentions: 11
Published: almost 4 years ago

10.18632/aging.202957

Integrative analysis identifies key mRNA biomarkers for diagnosis, prognosis, and therapeutic targets of HCV-associated hepatocellular carcinoma
Cited by: 8
Author(s): Yongqiang Zhang, Yuqin Tang, Chengbin Guo, Gen Li
Software Mentions: 11
Published: over 3 years ago

10.1038/s42003-021-02009-0

Pests, diseases, and aridity have shaped the genome of Corymbia citriodora
Cited by: 15
Author(s): Adam Healey, Mervyn Shepherd, Graham J. King, Jakob B. Butler, Jules S. Freeman, David J Lee, Brad M. Potts, Orzenil B. Silva‐Junior, Abdul Baten, Jerry Jenkins, Shengqiang Shu, John T. Lovell, Avinash Sreedasyam, Jane Grimwood, Agnelo Furtado, Dário Grattapaglia, Kerrie Barry, Hope Hundley, Blake A. Simmons, Jeremy Schmutz, René E. Vaillancourt, Robert J. Henry
Software Mentions: 10
Published: over 3 years ago

10.3390/genes11060677

Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms
Cited by: 6
Author(s): Ekaterina V. Poverennaya, Olga I. Kiseleva, Anastasia Romanova, Mikhail A. Pyatnitskiy
Software Mentions: 10
Published: over 4 years ago

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

10.3390/cancers13081768

Systematic Analysis of the Transcriptome Profiles and Co-Expression Networks of Tumour Endothelial Cells Identifies Several Tumour-Associated Modules and Potential Therapeutic Targets in Hepatocellular Carcinoma
Cited by: 8
Author(s): Thomas Mohr, Sonja Katz, Verena Paulitschke, Nadim Aizarani, Alexander Tolios
Software Mentions: 9
Published: over 3 years ago

10.1186/s12920-021-01079-7

Lung disease network reveals impact of comorbidity on SARS-CoV-2 infection and opportunities of drug repurposing
Cited by: 4
Author(s): Asim Bikas Das
Software Mentions: 8
Published: over 3 years ago

10.15252/msb.20188503

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Cited by: 479
Author(s): Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn M. Hallström, Thomas A. Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Lihua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Fredrik Pontén, Mathias Uhlén, Julien Gagneur, Hannes Hahne, Bernhard Küster
Software Mentions: 8
Published: almost 6 years ago

10.1186/s12920-019-0562-z

Clustering analysis of microRNA and mRNA expression data from TCGA using maximum edge-weighted matching algorithms
Cited by: 9
Author(s): Lizhong Ding, Zheyun Feng, Yongsheng Bai
Software Mentions: 8
Published: over 5 years ago

10.1371/journal.pone.0249691

Profiling DNA break sites and transcriptional changes in response to contextual fear learning
Cited by: 25
Author(s): Ryan Stott, Oleg Kritsky, Li‐Huei Tsai
Software Mentions: 8
Published: over 3 years ago

10.1186/s12864-018-4649-2

Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation
Cited by: 15
Author(s): Zhisong He, Qianhui Yu
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pbio.3000797

An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability
Cited by: 15
Author(s): Corey E. Hayford, Darren R. Tyson, Charles J. Robbins, Peter L. Frick, Vito Quaranta, Leonard A. Harris
Software Mentions: 7
Published: over 3 years ago

10.1186/1756-0500-5-360

LXtoo: an integrated live Linux distribution for the bioinformatics community
Cited by: 5
Author(s): Guangchuang Yu, Li-Gen Wang, Xiaohong Meng, Qing-Yu He
Software Mentions: 7
Published: over 12 years ago

10.3389/fonc.2019.00523

Comprehensive Gene Expression Analysis in NMIBC Using RNA-seq Reveals New Therapy Strategies
Cited by: 11
Author(s): Xiaoliang Chen, Fuquan Jiang, Jia Chen, Ming Liu, Yong-Hao Nan, Licheng Qu, Qingkuo Kong, Fangfang Hou, Wenshan Luo, Wanli Na, Xin Jin, Jiufeng Tan
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-019-43758-7

In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival
Cited by: 2
Author(s): Danish Memon, Jing Bi, Crispin Miller
Software Mentions: 7
Published: over 5 years ago

10.1038/s41598-020-75573-w

Development of a novel immune-related genes prognostic signature for osteosarcoma
Cited by: 17
Author(s): Zhi-Xi Wu, Yajun Deng, Guangzhi Zhang, Enhui Ren, Wenhua Yuan, Qiqi Xie
Software Mentions: 7
Published: about 4 years ago

10.1186/1471-2105-14-S16-S14

RMaNI: Regulatory Module Network Inference framework
Cited by: 6
Author(s): Piyush B. Madhamshettiwar, Stefan Maetschke, Melissa J. Davis, Mark A. Ragan
Software Mentions: 7
Published: about 11 years ago

10.1186/1752-0509-8-17

Identification of core T cell network based on immunome interactome
Cited by: 4
Author(s): Gabriel Teku, Csaba Ortutay, Mauno Vihinen
Software Mentions: 6
Published: almost 11 years ago

10.1038/s41598-020-57716-1

Ontology-driven integrative analysis of omics data through Onassis
Cited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: almost 5 years ago

10.18632/aging.202478

Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature
Cited by: 7
Author(s): Yan Qin, Jiehua Deng, Lihua Zhang, Jiaxing Yuan, Huawei Yang, Qiuyun Li
Software Mentions: 6
Published: almost 4 years ago

10.1534/g3.120.401350

Phenotypic Associations Among Cell Cycle Genes in Saccharomyces cerevisiae
Cited by: 3
Author(s): Rosa M Bermudez, Peter I-Fan Wu, Deanna Callerame, Staci E Hammer, James C. Hu, Michael Polymenis
Software Mentions: 6
Published: over 4 years ago

10.1186/s12885-020-6702-1

Identification of immune cells and mRNA associated with prognosis of gastric cancer
Cited by: 35
Author(s): Mingming Wang, Zedong Li, Pei Yu, Jianyu Fang, Tao Fang, Jiajia Wu, Jun Zhou
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1006840

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks
Cited by: 54
Author(s): Syed Bukhari, Michael C. Saul, Christopher H. Seward, Huimin Zhang, Miles K. Bensky, Noelle James, Sihai Dave Zhao, Sriram Chandrasekaran, Lisa Stubbs, Alison M. Bell
Software Mentions: 6
Published: over 7 years ago

10.3390/genes12050665

Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
Cited by: 6
Author(s): Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Software Mentions: 6
Published: over 3 years ago

10.1111/jcmm.14991

Mutational landscape and genetic signatures of cell‐free DNA in tumour‐induced osteomalacia
Cited by: 2
Author(s): Nan Wu, Zhen Zhang, Xi Zhou, Hengqiang Zhao, Yue Ming, Xue Wu, Xian Zhang, Xinzhuang Yang, Meng Zhou, Hua Bao, Weisheng Chen, Yong Wu, Sen Liu, Huizi Wang, Yuchen Niu, Yalun Li, Yu Zheng, Yang Shao, Na Gao, Ying Yang, Ying Liu, Wenli Li, Jia Liu, Na Zhang, Yang Xu, Yuan Xu, Mei Li, Yingli Sun, Jianzhong Su, Jianguo Zhang, Weibo Xia, Guixing Qiu, Yong Liu, Jiaqi Liu, Zhihong Wu
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-021-86319-7

Screening of osteoarthritis diagnostic markers based on immune-related genes and immune infiltration
Cited by: 15
Author(s): Wenhua Yuan, Qiqi Xie, Ke-Ping Wang, Wei Shen, Xiaofei Feng, Zheng Liu, Jin-Tao Shi, Xiaobo Zhang, Kai Zhang, Yajun Deng, Hai-Yu Zhou
Software Mentions: 6
Published: over 3 years ago

10.1007/s13353-020-00569-1

Differential expression of lung adenocarcinoma transcriptome with signature of tobacco exposure
Cited by: 11
Author(s): Raneem Y Hammouz, Joanna Kostanek, Aleksandra Dudzisz, Piotr J Witas, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 5
Published: over 4 years ago

10.3389/fonc.2021.637911

Phenotypic Plasticity Conferred by the Metastatic Microenvironment of the Brain Strengthens the Intracranial Tumorigenicity of Lung Tumor Cells
Cited by: 0
Author(s): Xin Wei, Kewei Bi, Bo Li
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-020-03769-y

C3: connect separate connected components to form a succinct disease module
Cited by: 6
Author(s): Bingbo Wang, Jie Hu, Yajun Wang, Chenxing Zhang, Yuanjun Zhou, Liang Yu, Guo Xia-zhen, Lin Gao, Yunru Chen
Software Mentions: 5
Published: about 4 years ago

10.7717/peerj.7171

Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples
Cited by: 10
Author(s): Huimei Wang, Mingwei Zhang, Qiqi Xie, Yu Jin, Qi Yan, Qiuyuan Yue
Software Mentions: 5
Published: over 5 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: almost 10 years ago

10.1186/s13059-016-0902-7

Comparative transcriptomics reveals the conserved building blocks involved in parallel evolution of diverse phenotypic traits in ants
Cited by: 67
Author(s): Claire Morandin, Mandy M. Y. Tin, Sílvia Abril, Crisanto Gómez, Luigi Pontieri, Morten Schiøtt, Liselotte Sundström, Kazuki Tsuji, Jes S. Pedersen, Heikki Helanterä, Alexander S. Mikheyev
Software Mentions: 5
Published: almost 9 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

10.1038/s41392-020-00378-2

Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis
Cited by: 11
Author(s): Mingsen Li, Liqiong Zhu, Jiafeng Liu, Huaxing Huang, Huizhen Guo, Li Wang, Lingyu Li, Sijie Gu, Jieying Tan, Jing Zhong, Bowen Wang, Zhen Mao, Yong Fan, Chunqiao Liu, Jing Yuan, Hong Ouyang
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41419-021-03644-5

Eradication of specific donor-dependent variations of mesenchymal stem cells in immunomodulation to enhance therapeutic values
Cited by: 19
Author(s): Chunxue Zhang, Liqiang Zhou, Zhen Wang, Wenxia Gao, Wei Chen, Huina Zhang, Bo Jing, Zhu Xu, Lei Chen, Changhong Zheng, Kaiyan Shi, Wu Li, Liming Cheng, Kunshan Zhang, Yi Sun
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-019-5779-x

Genome-wide enhancer annotations differ significantly in genomic distribution, evolution, and function
Cited by: 39
Author(s): Mary Lauren Benton, Sai Charan Talipineni, Dennis Kostka, John A. Capra
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0250660

System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study
Cited by: 3
Author(s): Utpala Nanda Chowdhury, Shamim Ahmad, M. Babul Islam, Salem A. Alyami, Julian M.W. Quinn, Valsamma Eapen, Mohammad Ali Moni
Software Mentions: 4
Published: over 3 years ago

10.3389/pore.2021.1609868

Screening and Validation of Independent Predictors of Poor Survival in Pancreatic Cancer
Cited by: 6
Author(s): Lingling Shui, Yan Cai, E Changyong, Jiyao Sheng, Xuewen Zhang
Software Mentions: 4
Published: over 3 years ago

10.3389/fcell.2015.00028

How to build personalized multi-omics comorbidity profiles
Cited by: 46
Author(s): Mohammad Ali Moni, Píetro Lió
Software Mentions: 4
Published: over 9 years ago

10.3389/fgene.2019.00600

Five-Feature Model for Developing the Classifier for Synergistic vs. Antagonistic Drug Combinations Built by XGBoost
Cited by: 38
Author(s): Xiangjun Ji, Weida Tong, Zhichao Liu, Tieliu Shi
Software Mentions: 4
Published: over 5 years ago

10.3389/fphar.2021.625543

The Synergistic Effects of 5-Aminosalicylic Acid and Vorinostat in the Treatment of Ulcerative Colitis
Cited by: 10
Author(s): Lina He, Shuting Wen, Zhuotai Zhong, Senhui Weng, Qilong Jiang, Hong Mi, Fengbin Liu
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.10933

Tissue-specific transcriptome analysis of drought stress and rehydration in Trachycarpus fortunei at seedling
Cited by: 2
Author(s): Xiaozhou Feng, Zhao Yang, Xiurong Wang
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2020.551065

Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
Cited by: 11
Author(s): Fang Cao, Yu Guo, Qiang Zhang, Yinchun Fan, Qian Liu, Jiancheng Song, Hua Zhong, Shengtao Yao
Software Mentions: 4
Published: about 4 years ago

10.1111/eva.12463

Plasticity in gene transcription explains the differential performance of two invasive fish species
Cited by: 47
Author(s): Kyle Wellband, Daniel D. Heath
Software Mentions: 4
Published: over 7 years ago

10.1098/rsob.160224

Interplay between RNA interference and heat shock response systems in Drosophila melanogaster
Cited by: 9
Author(s): S. Yu. Funikov, Sergei Ryazansky, Alexander Kanapin, Maria D. Logacheva, Aleksey A. Penin, А. В. Снежкина, Victoria Shilova, Д. Г. Гарбуз, Michael B. Evgen’ev, Olga G. Zatsepina
Software Mentions: 4
Published: about 8 years ago

10.1186/1752-0509-8-55

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level
Cited by: 29
Author(s): Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen K. Meurer, Kristin Seré, Qiong Lin, Boudewijn J. J. Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen, Holger Fröhlich
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0143742

Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine
Cited by: 11
Author(s): Zhonghua Sheng, Yi Sun, Ruixin Zhu, Na Jiao, Kailin Tang, Zhen Cao, Chao Ma
Software Mentions: 4
Published: about 9 years ago

10.1016/j.csbj.2020.07.010

MU-PseUDeep: A deep learning method for prediction of pseudouridine sites
Cited by: 8
Author(s): Saad Khan, Fei He, Duolin Wang, Yongbing Chen, Dong Xu
Software Mentions: 4
Published: almost 5 years ago

10.1038/srep38046

THD-Module Extractor: An Application for CEN Module Extraction and Interesting Gene Identification for Alzheimer’s Disease
Cited by: 10
Author(s): Tulika Kakati, Hirak J. Kashyap, Dhruba K. Bhattacharyya
Software Mentions: 4
Published: about 8 years ago

10.3389/fgene.2020.563954

Identification of Critical Genes and Proteins for Stent Restenosis Induced by Esophageal Benign Hyperplasia in Esophageal Cancer
Cited by: 4
Author(s): Li Weng, Shanshan Shen, Shaoqiu Wu, Xiaoxing Yin, Bingyan Liu, Ming Shang, Xiaoping Zou, Aiwu Mao
Software Mentions: 4
Published: about 4 years ago

10.1186/s12870-020-2254-4

PlaPPISite: a comprehensive resource for plant protein-protein interaction sites
Cited by: 22
Author(s): Xiaodi Yang, Shiping Yang, Huan Qi, Tianpeng Wang, Hong Li, Ziding Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1186/1756-0500-5-617

Lung Cancer Signature Biomarkers: tissue specific semantic similarity based clustering of Digital Differential Display (DDD) data
Cited by: 33
Author(s): Mousami Srivastava, Pankaj Khurana, R. Sugadev
Software Mentions: 3
Published: about 12 years ago

10.1038/s41598-020-74100-1

Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta
Cited by: 9
Author(s): Aishwarya P. Yadama, Enrico Maiorino, Vincent J. Carey, Thomas F. McElrath, Augusto A. Litonjua, Joseph Loscalzo, Scott T. Weiss, Hooman Mirzakhani
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-021-07576-4

Long non-coding RNA pairs to assist in diagnosing sepsis
Cited by: 18
Author(s): Xubin Zheng, Kwong‐Sak Leung, Man‐Hon Wong, Lixin Cheng
Software Mentions: 3
Published: over 3 years ago

10.1186/s12863-014-0158-8

Identification of gene co-expression clusters in liver tissues from multiple porcine populations with high and low backfat androstenone phenotype
Cited by: 6
Author(s): Sudeep Sahadevan, Ernst Tholen, Christine Große‐Brinkhaus, K. Schellander, Dawit Tesfaye, Martin Hofmann‐Apitius, Mehmet Ulaş Çınar, Asep Gunawan, Michael Hölker, Christiane Neuhoff
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41398-020-0777-y

Further confirmation of netrin 1 receptor (DCC) as a depression risk gene via integrations of multi-omics data
Cited by: 23
Author(s): Huijuan Li, Na Qu, Hui Li, Xin Cai, Chuyi Zhang, Bao‐Liang Zhong, Shufang Zhang, Jing Chen, Bin Xia, Lu Wang, Qi Jia, Wei Li, Hong Chang, Xiao Xiao, Ming Li, Yi Li
Software Mentions: 3
Published: almost 5 years ago

10.1534/g3.116.031096

MeSH-Informed Enrichment Analysis and MeSH-Guided Semantic Similarity Among Functional Terms and Gene Products in Chicken
Cited by: 10
Author(s): Gota Morota, Timothy Beissinger, Francisco Peñagaricano
Software Mentions: 3
Published: over 8 years ago

10.1186/s13015-015-0035-7

An integrative approach for a network based meta-analysis of viral RNAi screens
Cited by: 6
Author(s): Sandeep Amberkar, Lars Kaderali
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0204426

Elucidation and analyses of the regulatory networks of upland and lowland ecotypes of switchgrass in response to drought and salt stresses
Cited by: 7
Author(s): Chunman Zuo, Yuhong Tang, Fang Hao, Yiming Liu, Xunzhong Zhang, Bingyu Zhao, Ying Xu
Software Mentions: 3
Published: about 6 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.0164295

Cross-Species Analysis of Gene Expression and Function in Prefrontal Cortex, Hippocampus and Striatum
Cited by: 12
Author(s): Wei Chen, Xiayu Xia, Nan Song, Ying Wang, Hua Zhu, Wei Deng, Qi Kong, Xianmin Pan, Chuan Qin
Software Mentions: 3
Published: about 8 years ago

10.3390/cells10020334

A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them
Cited by: 4
Author(s): Jaume Forés-Martos, Anabel Forte, José Garcı́a-Martı́nez, José E. Pérez-Ortín
Software Mentions: 3
Published: almost 4 years ago

10.1002/2211-5463.12948

Expression of genes involved in drug metabolism differs between perfusable 3D liver tissue and conventional 2D‐cultured hepatocellular carcinoma cells
Cited by: 5
Author(s): Nobuhito Mori, Yasuyuki S. Kida
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: about 6 years ago

10.1186/s13040-018-0178-4

A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategies
Cited by: 15
Author(s): Jorge Parraga-Alava, Márcio Dorn, Mario Inostroza-Ponta
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/bty545

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes
Cited by: 6
Author(s): Luca Parca, Bruno Ariano, Andrea Cabibbo, Martina Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich
Software Mentions: 3
Published: over 6 years ago

10.1186/s12967-019-2010-4

Identifying subpathway signatures for individualized anticancer drug response by integrating multi-omics data
Cited by: 11
Author(s): Yanjun Xu, Qun Dong, Feng Li, Yingqi Xu, Congxue Hu, Jingwen Wang, Desi Shang, Xuan Zheng, Haixiu Yang, Chunlong Zhang, Mengting Shao, Mohan Meng, Zhiying Xiong, Xia Li, Yunpeng Zhang
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-12-S5-S4

SNP and gene networks construction and analysis from classification of copy number variations data
Cited by: 11
Author(s): Yang Liu, Yiu Fai Lee, Michael K. Ng
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-018-2314-z

Clustering approaches for visual knowledge exploration in molecular interaction networks
Cited by: 3
Author(s): Marek Ostaszewski, Emmanuel Kieffer, Grégoire Danoy, Reinhard Schneider, Pascal Bouvry
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4993-2

Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development
Cited by: 38
Author(s): Xianwen Meng, Peijing Zhang, Qi Chen, Jingjing Wang, Ming Chen
Software Mentions: 2
Published: over 6 years ago

10.1186/s12918-017-0456-7

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis
Cited by: 1
Author(s): Duanchen Sun, Yinliang Liu, Yu Xia, Lingyun Wu
Software Mentions: 2
Published: over 7 years ago

10.1186/1752-0509-7-S6-S5

Prediction of protein interaction types based on sequence and network features
Cited by: 6
Author(s): Florian Goebels, Dmitrij Frishman
Software Mentions: 2
Published: almost 12 years ago

10.1186/1752-0509-4-S2-S5

Shrunken methodology to genome-wide SNPs selection and construction of SNPs networks
Cited by: 7
Author(s): Yang Liu, Michael K. Ng
Software Mentions: 2
Published: over 14 years ago

10.1186/s12918-017-0400-x

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare
Cited by: 5
Author(s): Thorsten Will, Volkhard Helms
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.11900

IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models
Cited by: 3
Author(s): Xinyi Liu, Yueyue Shen, Youhua Zhang, Fei Liu, Zhiyu Ma, Z.Q. Yue, Yi Yue
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1007343

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers
Cited by: 70
Author(s): David J. Wooten, Sarah M. Groves, Darren R. Tyson, Qi Liu, Jing Shan Lim, Réka Albert, Carlos F. López, Julien Sage, Vito Quaranta
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0208626

Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology
Cited by: 58
Author(s): Muhammad Asif, Hugo Martiniano, Astrid M. Vicente, Francisco M. Couto
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0096491

The Longissimus and Semimembranosus Muscles Display Marked Differences in Their Gene Expression Profiles in Pig
Cited by: 15
Author(s): Frédéric Herault, Annie Vincent, Olivier Dameron, Pascale Le Roy, Pierre Chérel, Marie Damon
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0014219

Discovering Cooperative Relationships of Chromatin Modifications in Human T Cells Based on a Proposed Closeness Measure
Cited by: 7
Author(s): Jie Lv, Hong Qiao, Hongbo Liu, Xueting Wu, Jiang Zhu, Jianzhong Su, Fang Wang, Ying Cui, Yan Zhang
Software Mentions: 2
Published: about 14 years ago

10.1186/2047-783X-19-31

RETRACTED ARTICLE: Reanalysis of the gene expression profile in chronic pancreatitis via bioinformatics methods
Cited by: 4
Author(s): Hang Yuan, Bin Wu, Shumei Ma, Xiaoyu Yang, Yin Li, Aijun Li
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2020.617136

Revealing the Interactions Between Diabetes, Diabetes-Related Diseases, and Cancers Based on the Network Connectivity of Their Related Genes
Cited by: 1
Author(s): Lijuan Zhu, Xu Ju, Qiuling Wang, Ailan Wang, Chao Li, Geng Tian, Huajun Zhang, Size Chen
Software Mentions: 2
Published: about 4 years ago

10.1534/g3.115.018127

Gene Network Reconstruction by Integration of Prior Biological Knowledge
Cited by: 39
Author(s): Yupeng Li, Scott A. Jackson
Software Mentions: 2
Published: over 9 years ago

10.1093/g3journal/jkaa035

Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12
Cited by: 1
Author(s): Peter I-Fan Wu, Curtis Ross, Deborah A. Siegele, James C. Hu
Software Mentions: 2
Published: almost 4 years ago

10.1186/s41065-021-00177-x

Identification of metabolism genes related to hepatocarcinogenesis and progression in type 2 diabetes mellitus via co-expression networks analysis
Cited by: 2
Author(s): Ye Bi, Bei Yin, Guo-Chang Fan
Software Mentions: 2
Published: over 3 years ago

10.1038/s41597-021-00944-5

High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production
Cited by: 8
Author(s): Mattia Müller, Lucas Pelkmans, Scott Berry
Software Mentions: 2
Published: over 3 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

10.1021/acs.jproteome.1c00150

Using Multilayer Heterogeneous Networks to Infer Functions of Phosphorylated Sites
Cited by: 3
Author(s): Joanne Watson, Jean-Marc Schwartz, Chiara Francavilla
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0165001

Dissecting the Origin of Breast Cancer Subtype Stem Cell and the Potential Mechanism of Malignant Transformation
Cited by: 11
Author(s): Xinyi Liu, Dongfei Feng, Dianming Liu, Shuyuan Wang, Xuexin Yu, Erfu Dai, Jing Wang, Lihong Wang, Wei Jiang
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0078896

Functional Networking of Human Divergently Paired Genes (DPGs)
Cited by: 3
Author(s): Bin Xie, Dapeng Wang, Yong Duan, Jun Yu, Hongxing Lei
Software Mentions: 1
Published: about 11 years ago

10.1186/s12859-015-0789-4

Inferring plant microRNA functional similarity using a weighted protein-protein interaction network
Cited by: 12
Author(s): Jun Meng, Dong Liu, Yushi Luan
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0033947

Spatial Proximity and Similarity of the Epigenetic State of Genome Domains
Cited by: 16
Author(s): Ekaterina E. Khrameeva, Andrey A. Mironov, Gennady Fedonin, Philipp Khaitovich, Mikhail S. Gelfand
Software Mentions: 1
Published: over 12 years ago

10.1111/jcmm.13873

C5aR1 interacts with <scp>TLR</scp>2 in osteoblasts and stimulates the osteoclast‐inducing chemokine <scp>CXCL</scp>10
Cited by: 24
Author(s): Yvonne Mödinger, Anna E. Rapp, Júlia Pázmándi, Anna Vikman, Karlheinz Holzmann, Melanie Haffner‐Luntzer, Markus Huber‐Lang, Anita Ignatius
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pcbi.1004892

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
Cited by: 33
Author(s): Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: GOSemSim

Papers Mentioning GOSemSim 118