Literature DB >> 30496480

Multi-omic and multi-view clustering algorithms: review and cancer benchmark.

Nimrod Rappoport1, Ron Shamir1.   

Abstract

Entities:  

Year:  2019        PMID: 30496480      PMCID: PMC6344869          DOI: 10.1093/nar/gky1226

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


× No keyword cloud information.
Nucleic Acids Research, 2018, Vol. 46, No. 20, Pages 10546–10562, https://doi.org/10.1093/nar/gky889 Our paper included a benchmark comparing nine methods for multi-omics clustering, including PINS (1). We reported that PINS crashed when run on a breast cancer dataset. We performed all the benchmarks on a 64-bit computer, using the 32-bit version of R. In later tests we observed that PINS did not crash on 64-bit R, and it only crashed on 32-bit R due to insufficient memory. The clustering that PINS obtained on the breast cancer dataset had 4 enriched clinical parameters, and the P-value for the logrank test on that clustering was 0.05.
  1 in total

1.  A novel approach for data integration and disease subtyping.

Authors:  Tin Nguyen; Rebecca Tagett; Diana Diaz; Sorin Draghici
Journal:  Genome Res       Date:  2017-10-24       Impact factor: 9.043

  1 in total
  12 in total

Review 1.  A guide to machine learning for biologists.

Authors:  Joe G Greener; Shaun M Kandathil; Lewis Moffat; David T Jones
Journal:  Nat Rev Mol Cell Biol       Date:  2021-09-13       Impact factor: 94.444

2.  DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA-miRNA-mRNA regulatory axes.

Authors:  Chen Shen; Huiyu Li; Miao Li; Yu Niu; Jing Liu; Li Zhu; Hongsheng Gui; Wei Han; Huiying Wang; Wenpei Zhang; Xiaochen Wang; Xiao Luo; Yu Sun; Jiangwei Yan; Fanglin Guan
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 11.622

Review 3.  Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.

Authors:  Zhiqiang Pang; Guangyan Zhou; Jessica Ewald; Le Chang; Orcun Hacariz; Niladri Basu; Jianguo Xia
Journal:  Nat Protoc       Date:  2022-06-17       Impact factor: 17.021

Review 4.  Harnessing Big Data to Advance Treatment and Understanding of Pulmonary Hypertension.

Authors:  Christopher J Rhodes; Andrew J Sweatt; Bradley A Maron
Journal:  Circ Res       Date:  2022-04-28       Impact factor: 23.213

5.  Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data.

Authors:  Chunman Zuo; Luonan Chen
Journal:  Brief Bioinform       Date:  2021-07-20       Impact factor: 11.622

6.  Integrative analysis of genomic, epigenomic and transcriptomic data identified molecular subtypes of esophageal carcinoma.

Authors:  Mingyang Ma; Yang Chen; Xiaoyi Chong; Fangli Jiang; Jing Gao; Lin Shen; Cheng Zhang
Journal:  Aging (Albany NY)       Date:  2021-02-26       Impact factor: 5.682

7.  Inaccuracy of the log-rank approximation in cancer data analysis.

Authors:  Nimrod Rappoport; Ron Shamir
Journal:  Mol Syst Biol       Date:  2019-08       Impact factor: 11.429

8.  Bayesian analysis of cytokines and chemokine identifies immune pathways of HBsAg loss during chronic hepatitis B treatment.

Authors:  Sriram Narayanan; Veonice Bijin Au; Atefeh Khakpoor; Cheng Yan; Patricia J Ahl; Nivashini Kaliaperumal; Bernett Lee; Wen Wei Xiang; Juling Wang; Chris Lee; Amy Tay; Seng Gee Lim; John E Connolly
Journal:  Sci Rep       Date:  2021-04-02       Impact factor: 4.379

Review 9.  State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing.

Authors:  Michal Krassowski; Vivek Das; Sangram K Sahu; Biswapriya B Misra
Journal:  Front Genet       Date:  2020-12-10       Impact factor: 4.599

Review 10.  A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research.

Authors:  Efstathios Iason Vlachavas; Jonas Bohn; Frank Ückert; Sylvia Nürnberg
Journal:  Int J Mol Sci       Date:  2021-03-10       Impact factor: 5.923

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.