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: cran: iCluster

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/iCluster

Integrative clustering of multiple genomic data types
2 versions
Latest release: over 12 years ago
1 dependent package
0 downloads

Papers Mentioning iCluster 134

10.3389/fonc.2020.00423
Computational Oncology in the Multi-Omics Era: State of the Art
Cited by: 55
Author(s): Guillermo de Anda-Jáuregui, Enrique Hernández‐Lemus
Software Mentions: 46
Published: over 4 years ago
10.3390/ijms21239157
NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC)
Cited by: 16
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Roberto Mantovani, Diletta Dolfini
Software Mentions: 15
Published: about 4 years ago
10.3389/fonc.2020.00973
Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data
Cited by: 8
Author(s): Lauren Hsu, Aedín C. Culhane
Software Mentions: 10
Published: over 4 years ago
10.1186/s13073-021-00930-x
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data
Cited by: 72
Author(s): Olivier Poirion, Jiangbin Zheng, Kumardeep Chaudhary, Sijia Huang, Lana X. Garmire
Software Mentions: 9
Published: over 3 years ago
10.1177/1177932219899051
Multi-omics Data Integration, Interpretation, and Its Application
Cited by: 527
Author(s): Indhupriya Subramanian, Srikant Verma, Sanjiv Kumar, Abhay Jere, Krishanpal Anamika
Software Mentions: 8
Published: almost 5 years ago
10.20892/j.issn.2095-3941.2020.0402
The m6A methylation landscape stratifies hepatocellular carcinoma into 3 subtypes with distinct metabolic characteristics
Cited by: 17
Author(s): Xiaotian Shen, Beiyuan Hu, Jing Xu, Wei Qin, Yan Fu, Shun Wang, Qiongzhu Dong, Lun–Xiu Qin
Software Mentions: 7
Published: almost 5 years ago
10.3390/genes10020087
Machine Learning and Integrative Analysis of Biomedical Big Data
Cited by: 185
Author(s): Bilal Mirza, Wei Wang, Jie Wang, Howard Choi, Neo Christopher Chung, Peipei Ping
Software Mentions: 7
Published: almost 6 years ago
10.1093/bfgp/elx018
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
Cited by: 91
Author(s): Luciane T. Kagohara, Genevieve Stein-O’Brien, Dylan Z. Kelley, Emily Flam, Heather C. Wick, Ludmila Danilova, Hariharan Easwaran, Alexander V. Favorov, Jiang Qian, Daria A. Gaykalova, Elana J. Fertig
Software Mentions: 7
Published: over 7 years ago
10.1093/gigascience/giaa064
Integrative computational epigenomics to build data-driven gene regulation hypotheses
Cited by: 10
Author(s): Tyrone Chen, Sonika Tyagi
Software Mentions: 6
Published: over 4 years ago
10.3389/fgene.2016.00002
Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges
Cited by: 16
Author(s): Louise B. Thingholm, Lars van Brakel Andersen, Enes Makalic, Melissa C. Southey, Mads Thomassen, Lise Lotte Hansen
Software Mentions: 6
Published: almost 9 years ago
10.1186/s40246-021-00323-6
An ensemble of the iCluster method to analyze longitudinal lncRNA expression data for psoriasis patients
Cited by: 2
Author(s): Suyan Tian, Chi Wang
Software Mentions: 6
Published: over 3 years ago
10.1186/s12918-015-0211-x
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential
Cited by: 41
Author(s): Claudia Cava, Gloria Bertoli, Isabella Castiglioni
Software Mentions: 6
Published: over 9 years ago
10.1186/s12967-021-02705-9
Eight-lncRNA signature of cervical cancer were identified by integrating DNA methylation, copy number variation and transcriptome data
Cited by: 23
Author(s): Qihang Zhong, Minzhen Lu, Wei Yuan, Yueyi Cui, Hanqiang Ouyang, Yong Fan, Zhaohui Wang, Congying Wu, Jie Qiao, Jing Hang
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.607817
Multi-Omics Data Fusion for Cancer Molecular Subtyping Using Sparse Canonical Correlation Analysis
Cited by: 8
Author(s): Qi Lin, Wei Wang, Tan Wu, Lina Zhu, Lingli He, Xin Wang
Software Mentions: 5
Published: over 3 years ago
10.1016/j.xpro.2021.100483
Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer
Cited by: 2
Author(s): A. Gordon Robertson, Christina Yau, Jian Carrot‐Zhang, Jeffrey S. Damrauer, Theo Knijnenburg, Nyasha Chambwe, Katherine A. Hoadley, Anab Kemal, Jean C. Zenklusen, Andrew D. Cherniack, Rameen Beroukhim, Wanding Zhou
Software Mentions: 5
Published: over 3 years ago
10.3389/fonc.2020.01052
A Novel Method for Cancer Subtyping and Risk Prediction Using Consensus Factor Analysis
Cited by: 9
Author(s): Duc Tran, Hung Son Nguyen, Uyen Phuong Le, George Bebis, Hung N. Luu, Tin Nguyen
Software Mentions: 5
Published: over 4 years ago
10.1186/s12859-021-04215-3
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis
Cited by: 5
Author(s): Xiaomei Li, Buu Truong, Taosheng Xu, Lin Liu, Jiuyong Li, Thuc Duy Le
Software Mentions: 5
Published: over 3 years ago
10.1172/jci.insight.146196
Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis
Cited by: 9
Author(s): Carolin Czauderna, Alicia Poplawski, Colm J. O’Rourke, Darko Castven, Benjamín Pérez-Aguilar, Diana Becker, Markus M. Nöthen, Margarete Odenthal, W Amer, M Schmiel, Uta Drebber, Harald Binder, Dirk A. Ridder, Mario Schindeldecker, Beate K. Straub, Peter R. Galle, Jesper B. Andersen, Snorri S. Thorgeirsson, Young Nyun Park, Jens U. Marquardt
Software Mentions: 5
Published: over 3 years ago
10.1186/s12859-015-0857-9
Methods for the integration of multi-omics data: mathematical aspects
Cited by: 272
Author(s): Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone Castellani, Luciano Milanesi
Software Mentions: 4
Published: almost 9 years ago
10.3390/jpm11080686
JDSNMF: Joint Deep Semi-Non-Negative Matrix Factorization for Learning Integrative Representation of Molecular Signals in Alzheimer’s Disease
Cited by: 5
Author(s): Sehwan Moon, Hyunju Lee
Software Mentions: 4
Published: over 3 years ago
10.1016/j.ebiom.2015.07.017
Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study
Cited by: 217
Author(s): Helen Ross-Adams, Alastair Lamb, Mark J. Dunning, Silvia Halim, Johan Lindberg, Charles E. Massie, Lars Egevad, Roslin Russell, Antonio Ramos-Montoya, Sarah L. Vowler, Naomi L. Sharma, Jonathan Kay, Hayley C. Whitaker, Jeremy Clark, Rachel Hurst, Vincent Gnanapragasam, Nimish Shah, Anne Y. Warren, Christopher S. Cooper, Andy G. Lynch, Rory Stark, Ian G. Mills, Henrik Grönberg, David E. Neal
Software Mentions: 4
Published: over 9 years ago
10.1186/s13059-020-02230-w
Comprehensive integrative profiling of upper tract urothelial carcinomas
Cited by: 27
Author(s): Xiaoping Su, Xiaofan Lu, Sehrish K. Bazai, Éva Compérat, Roger Mouawad, Hui Yao, Morgan Rouprêt, Jean Philippe Spano, David Khayat, Irwin Davidson, Nizar Tannir, Fangrong Yan, Gabriel G. Malouf
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2020.578345
Integration of Online Omics-Data Resources for Cancer Research
Cited by: 43
Author(s): Tonmoy Das, Geoffroy Andrieux, Musaddeque Ahmed, Sajib Chakraborty
Software Mentions: 4
Published: about 4 years ago
10.3389/fmed.2021.654635
Multi-Omics Integrative Analysis Uncovers Molecular Subtypes and mRNAs as Therapeutic Targets for Liver Cancer
Cited by: 4
Author(s): Yi Shen, Wei Xiong, Qi Gu, Qin Zhang, Yue Jia, Changsong Liu, Duan Wang
Software Mentions: 4
Published: over 3 years ago
10.1186/s12920-020-0659-4
Impact of mutations in DNA methylation modification genes on genome-wide methylation landscapes and downstream gene activations in pan-cancer
Cited by: 16
Author(s): Chai-Jin Lee, Hongryul Ahn, Dabin Jeong, Minwoo Pak, Ji Hwan Moon, Sun Kim
Software Mentions: 4
Published: almost 5 years ago
10.3390/ijms221910891
A Survey of Autoencoder Algorithms to Pave the Diagnosis of Rare Diseases
Cited by: 6
Author(s): David Pratella, Samira Ait-El-Mkadem Saadi, Sylvie Bannwarth, Véronique Paquis‐Fluckinger, Silvia Bottini
Software Mentions: 4
Published: about 3 years ago
10.1038/s41416-020-0799-5
A novel stratification framework for predicting outcome in patients with prostate cancer
Cited by: 8
Author(s): Bogdan A. Luca, Vincent Moulton, Christopher Ellis, Dylan R. Edwards, Colin Campbell, Rosalin Cooper, Jeremy Clark, Daniel Brewer, Christopher S. Cooper
Software Mentions: 4
Published: almost 5 years ago
10.26508/lsa.201900517
Evaluation of colorectal cancer subtypes and cell lines using deep learning
Cited by: 59
Author(s): Jonathan Ronen, Sikander Hayat, Altuna Akalin
Software Mentions: 4
Published: about 5 years ago
10.1186/s12859-016-1184-5
Stepwise iterative maximum likelihood clustering approach
Cited by: 12
Author(s): Alok Sharma, Daichi Shigemizu, Keith A. Boroevich, Yosvany López, Yoichiro Kamatani, Michiaki Kubo, Tatsuhiko Tsunoda
Software Mentions: 4
Published: over 8 years ago
10.1111/jcmm.16444
Risk stratification by long non‐coding RNAs profiling in COVID‐19 patients
Cited by: 27
Author(s): Jie Cheng, Xiang Zhou, Weijun Feng, Min Jia, Xinlu Zhang, Tongqing An, Minyuan Luan, Yi Pan, Shu Zhang, Zhaoming Zhou, Lu Wen, Yun Sun, Cheng Zhou
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12859-020-3465-2
PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data
Cited by: 33
Author(s): Amina Lemsara, Salima Ouadfel, Holger Fröhlich
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pcbi.1006520
Molecular characterization of breast and lung tumors by integration of multiple data types with functional sparse-factor analysis
Cited by: 13
Author(s): Tycho Bismeijer, Sander Canisius, Lodewyk Wessels
Software Mentions: 4
Published: about 6 years ago
10.3390/ijms20184414
Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets
Cited by: 59
Author(s): Nicolas Sompairac, Petr V. Nazarov, Urszula Czerwińska, Laura Cantini, Anne Biton, Askhat Molkenov, Zhaxybay Zhumadilov, Emmanuel Barillot, François Radvanyi, Alexander N. Gorban, Ulykbek Kairov, Andreï Zinovyev
Software Mentions: 4
Published: over 5 years ago
10.3390/cancers13030430
Effective Prediction of Prostate Cancer Recurrence through the IQGAP1 Network
Cited by: 4
Author(s): Yan Gu, Xiaozeng Lin, Anil Kapoor, Taosha Li, Pierre Major, Damu Tang
Software Mentions: 4
Published: almost 4 years ago
10.3390/ht8010004
A Selective Review of Multi-Level Omics Data Integration Using Variable Selection
Cited by: 127
Author(s): Cen Wu, Fei Zhou, Jie Ren, Xiaoxi Li, Yu Jiang, Shuangge Ma
Software Mentions: 3
Published: almost 6 years ago
10.3390/genes12020257
Differential Expression of a Panel of Ten CNTN1-Associated Genes during Prostate Cancer Progression and the Predictive Properties of the Panel towards Prostate Cancer Relapse
Cited by: 2
Author(s): Yan Gu, Mathilda Jing Chow, Anil Kapoor, Xiaozeng Lin, Wenjuan Mei, Damu Tang
Software Mentions: 3
Published: almost 4 years ago
10.1186/s13059-018-1455-8
Tensorial blind source separation for improved analysis of multi-omic data
Cited by: 20
Author(s): Andrew E. Teschendorff, Junqiang Han, Dirk S. Paul, Joni Virta, Klaus Nordhausen
Software Mentions: 3
Published: over 6 years ago
10.1093/bioinformatics/btaa593
Multiple kernel learning for integrative consensus clustering of omic datasets
Cited by: 13
Author(s): Alessandra Cabassi, Paul Kirk
Software Mentions: 3
Published: over 4 years ago
10.1093/bioinformatics/btx322
Molecular heterogeneity at the network level: high-dimensional testing, clustering and a TCGA case study
Cited by: 18
Author(s): Nicolas Städler, Frank Dondelinger, Steven M. Hill, Rehan Akbani, Yiling Lu, Gordon B. Mills, Sach Mukherjee
Software Mentions: 3
Published: over 7 years ago
10.1093/bioinformatics/btz058
NEMO: cancer subtyping by integration of partial multi-omic data
Cited by: 115
Author(s): Nimrod Rappoport, Ron Shamir
Software Mentions: 3
Published: almost 6 years ago
10.1073/pnas.2023070118
BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
Cited by: 55
Author(s): Kevin Wu, Kathryn E. Yost, Howard Y. Chang, James Zou
Software Mentions: 3
Published: over 3 years ago
10.7150/jca.31435
Aberrant AFP expression characterizes a subset of hepatocellular carcinoma with distinct gene expression patterns and inferior prognosis
Cited by: 15
Author(s): Wei Chen, Jianjun Peng, Jinning Ye, Weigang Dai, Guanghua Li, Yulong He
Software Mentions: 3
Published: almost 5 years ago
10.1093/bib/bby051
Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: over 5 years ago
10.1016/j.csbj.2021.01.029
Integrative approaches for analysis of mRNA and microRNA high-throughput data
Cited by: 18
Author(s): Petr V. Nazarov, Stephanie Kreis
Software Mentions: 3
Published: almost 4 years ago
10.1002/ctm2.538
A multi‐omics study delineates new molecular features and therapeutic targets for esophageal squamous cell carcinoma
Cited by: 10
Author(s): Xing Jin, Lei Liu, Junbiao Wu, Xinqiao Jin, Guanzhen Yu, Lijun Jia, Fengying Wang, Minxin Shi, Haimin Lu, Ji‐Bin Liu, Dan Liŭ, Jing Yang, Hua Li, Yan Ni, Qin Luo, Jia Wang, Wei Wang, Wen-Lian Chen
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0176278
Integrative clustering of multi-level ‘omic data based on non-negative matrix factorization algorithm
Cited by: 105
Author(s): Prabhakar Chalise, Brooke L. Fridley
Software Mentions: 3
Published: over 7 years ago
10.1186/s12859-017-1970-8
2D–EM clustering approach for high-dimensional data through folding feature vectors
Cited by: 7
Author(s): Alok Sharma, Piotr J. Kamola, Tatsuhiko Tsunoda
Software Mentions: 3
Published: about 7 years ago
10.3390/metabo3030741
Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile
Cited by: 53
Author(s): Larissa Stanberry, George I. Mias, Winston Haynes, Roger Higdon, M Snyder, Eugene Kolker
Software Mentions: 3
Published: over 11 years ago
10.1038/onc.2015.499
Enhanced MAPK signaling drives ETS1-mediated induction of miR-29b leading to downregulation of TET1 and changes in epigenetic modifications in a subset of lung SCC
Cited by: 26
Author(s): Molly A. Taylor, Mark Wappett, Oona Delpuech, Helen Brown, Christine Chresta
Software Mentions: 3
Published: almost 9 years ago
10.1371/journal.pone.0234062
Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma
Cited by: 6
Author(s): Can Li, Shanghua Ge, Jie Zhou, Jie Peng, Jiayu Chen, Shu-Hui Dong, Xiaoran Feng, Ning Su, Lunli Zhang, Zhong Ye, Libin Deng, Xiaoli Tang
Software Mentions: 3
Published: over 4 years ago
10.15252/msb.20178124
Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets
Cited by: 571
Author(s): Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C. Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle
Software Mentions: 3
Published: over 6 years ago
10.7717/peerj-cs.584
Machine learning analysis of TCGA cancer data
Cited by: 9
Author(s): José Liñares-Blanco, Alejandro Pazos, Carlos Fernández-Lozano
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pcbi.1009224
Evaluation and comparison of multi-omics data integration methods for cancer subtyping
Cited by: 43
Author(s): Ran Duan, Lin Gao, Yong Gao, Yuxuan Hu, Xu Han, Ming‐Feng Huang, Kuo Song, Hongda Wang, Yun Dong, Chaoqun Jiang, Chenxing Zhang, Songwei Jia
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0204186
EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma
Cited by: 6
Author(s): Borong Shao, Maria Moksnes Bjaanæs, Åslaug Helland, Christof Schütte, Tim Conrad
Software Mentions: 3
Published: almost 6 years ago
10.3389/fgene.2021.682841
MONTI: A Multi-Omics Non-negative Tensor Decomposition Framework for Gene-Level Integrative Analysis
Cited by: 6
Author(s): Il Bong Jung, Minsu Kim, Sungmin Rhee, Sangsoo Lim, Kai Sun
Software Mentions: 3
Published: over 3 years ago
10.1186/s12920-021-00876-4
Development and validation of prognostic markers in sarcomas base on a multi-omics analysis
Cited by: 4
Author(s): Yi Song, Kui Yang, Tuanhe Sun, Ruixiang Tang
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0216904
A multiobjective multi-view cluster ensemble technique: Application in patient subclassification
Cited by: 15
Author(s): Sayantan Mitra, Sriparna Saha
Software Mentions: 3
Published: over 5 years ago
10.18632/aging.102393
Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma
Cited by: 12
Author(s): Mingdong Li, Shengrong Long, Jinqu Hu, Zan Wang, Chao Geng, Shaowu Ou
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-021-91924-7
Mutant p53s and chromosome 19 microRNA cluster overexpression regulate cancer testis antigen expression and cellular transformation in hepatocellular carcinoma
Cited by: 4
Author(s): Goodwin G. Jinesh, Marco Napoli, Marian T. Smallin, Andrew John Davis, Hayley D. Ackerman, Payal Raulji, Nicole Montey, Elsa R. Flores, Andrew S. Brohl
Software Mentions: 3
Published: over 3 years ago
10.1186/s12911-020-1114-3
A multi-omics supervised autoencoder for pan-cancer clinical outcome endpoints prediction
Cited by: 7
Author(s): Kaiwen Tan, Weixian Huang, Jinlong Hu, Shen Dong
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-69179-5
Regulation of MYO18B mRNA by a network of C19MC miRNA-520G, IFN-γ, CEBPB, p53 and bFGF in hepatocellular carcinoma
Cited by: 9
Author(s): Goodwin G. Jinesh, Marco Napoli, Hayley D. Ackerman, Payal Raulji, Nicole Montey, Elsa R. Flores, Andrew S. Brohl
Software Mentions: 3
Published: over 4 years ago
10.1038/srep18517
Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer
Cited by: 134
Author(s): Magali Michaut, Suet-Feung Chin, Ian J. Majewski, Tesa Severson, Tycho Bismeijer, Leanne de Koning, Justine K. Peeters, Philip C. Schouten, Oscar M. Rueda, Astrid Bosma, Finbarr Tarrant, Yue Fan, Beilei He, Xue Zhou, Lorenza Mittempergher, Roelof J.C. Kluin, Jeroen Heijmans, Mireille H.J. Snel, Bernard Pereira, Andreas Schlicker, Elena Provenzano, H. Raza Ali, Alexander Gaber, Gillian O’Hurley, Sophie Lehn, Jettie J.F. Muris, Jelle Wesseling, Elaine W. Kay, Stephen‐John Sammut, Helen Bardwell, Aurélie Barbet, Floriane Bard, Caroline Lecerf, Darran P. O’Connor, Daniël J. Vis, Cyril H. Benes, Ultan McDermott, Mathew J. Garnett, Iris Simón, Karin Jirström, Thierry Dubois, Sabine C. Linn, William M. Gallagher, Lodewyk Wessels, Carlos Caldas, René Bernards
Software Mentions: 3
Published: almost 9 years ago
10.18632/aging.103202
Integrative analysis of genomic and epigenetic regulation of endometrial cancer
Cited by: 6
Author(s): Qihang Zhong, Junpeng Fan, Honglei Chu, Mujia Pang, Junsheng Li, Yong Fan, Ping Liu, Congying Wu, Jie Qiao, Rong Li, Jing Hang
Software Mentions: 3
Published: over 4 years ago
10.3389/fgene.2018.00477
Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma
Cited by: 122
Author(s): Li Zhang, Chenkai Lv, Yichen Jin, Ganqi Cheng, Yibao Fu, Dongsheng Yuan, Yiran Tao, Yongli Guo, Xin Ni, Tieliu Shi
Software Mentions: 3
Published: about 6 years ago
10.1186/s12864-018-4580-6
Clustering multilayer omics data using MuNCut
Cited by: 12
Author(s): Sebastian J. Teran Hidalgo, Shuangge Ma
Software Mentions: 3
Published: almost 7 years ago
10.1038/s41598-021-84514-0
Bayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data
Cited by: 2
Author(s): Yize Zhao, Changgee Chang, Margaret Hannum, Jasme Lee, Ronglai Shen
Software Mentions: 2
Published: almost 4 years ago
10.18632/aging.102047
Integrated multi-omics analysis of genomics, epigenomics, and transcriptomics in ovarian carcinoma
Cited by: 17
Author(s): Mingjun Zheng, Yuexin Hu, Rui Gou, Jing Wang, Xin Nie, Xiao Li, Qing Liu, Juanjuan Liu, Bei Lin
Software Mentions: 2
Published: over 5 years ago
10.18632/aging.103115
Epigenomic and genomic analysis of transcriptome modulation in skin cutaneous melanoma
Cited by: 12
Author(s): Wuzhen Chen, Pu Cheng, Jingxin Jiang, Yunqing Ren, Dang Wu, Dan Xue
Software Mentions: 2
Published: over 4 years ago
10.18632/aging.202556
Integrative analysis of genomic, epigenomic and transcriptomic data identified molecular subtypes of esophageal carcinoma
Cited by: 3
Author(s): Mingyang Ma, Yang Chen, Xiaoyi Chong, Fangli Jiang, Jing Gao, Lin Shen, Cheng Zhang
Software Mentions: 2
Published: almost 4 years ago
10.18632/aging.102168
Copy number variations primed lncRNAs deregulation contribute to poor prognosis in colorectal cancer
Cited by: 22
Author(s): Huimin Liu, Xiaoyu Gu, Guihua Wang, Ying Huang, Shaoqing Ju, Jianfei Huang, Xudong Wang
Software Mentions: 2
Published: over 5 years ago
10.1186/s12859-021-04029-3
Multi-dimensional data integration algorithm based on random walk with restart
Cited by: 14
Author(s): Yao Wen, Xinyu Song, Bowei Yan, Xisheng Yang, Lianlian Wu, Dongjin Leng, Song He, Xiaochen Bo
Software Mentions: 2
Published: almost 4 years ago
10.1186/1471-2105-9-81
Visualizing and clustering high throughput sub-cellular localization imaging
Cited by: 15
Author(s): Nicholas A. Hamilton, Rohan D. Teasdale
Software Mentions: 2
Published: almost 17 years ago
10.1186/s12885-021-07888-4
Multi-omics analysis of genomics, epigenomics and transcriptomics for molecular subtypes and core genes for lung adenocarcinoma
Cited by: 13
Author(s): Yue Zhao, Gao Yuan-fu, Xiaodong Xu, Ji-Wu Zhou, He Wang
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12864-015-2170-4
Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes
Cited by: 68
Author(s): Sunghwan Kim, José D. Herazo-Maya, Dongwan Kang, Brenda Juan-Guardela, John Tedrow, Fernando J. Martínez, Frank C. Sciurba, George C. Tseng, Naftali Kaminski
Software Mentions: 2
Published: about 9 years ago
10.1186/s12920-018-0435-x
Improvement of cancer subtype prediction by incorporating transcriptome expression data and heterogeneous biological networks
Cited by: 9
Author(s): Yang Guo, Qi Yang, Zhanhuai Li, Xuequn Shang
Software Mentions: 2
Published: about 6 years ago
10.1186/1752-0509-7-14
Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties
Cited by: 51
Author(s): Yuanhua Liu, Valentina Devescovi, Suning Chen, Christine Nardini
Software Mentions: 2
Published: almost 12 years ago
10.1186/s13040-020-00222-x
Deep learning-based ovarian cancer subtypes identification using multi-omics data
Cited by: 28
Author(s): Long-Yi Guo, Wu Ai, Yongxia Wang, Liping Zhang, Hua Chai, Xuefang Liang
Software Mentions: 2
Published: over 4 years ago
10.1093/bioinformatics/bts595
Bayesian correlated clustering to integrate multiple datasets
Cited by: 197
Author(s): Paul Kirk, Jim E. Griffin, Richard S. Savage, Zoubin Ghahramani, David L. Wild
Software Mentions: 2
Published: about 12 years ago
10.1002/med.21764
Artificial intelligence and machine learning‐aided drug discovery in central nervous system diseases: State‐of‐the‐arts and future directions
Cited by: 89
Author(s): Sezen Vatansever, Avner Schlessinger, Daniel Wacker, H. Ümit Kanıskan, Jian Jin, Ming‐Ming Zhou, Bin Zhang
Software Mentions: 2
Published: about 4 years ago
10.1186/s12943-017-0673-0
In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer
Cited by: 20
Author(s): Basel Abu‐Jamous, Francesca M. Buffa, Adrian L. Harris, Asoke K. Nandi
Software Mentions: 2
Published: over 7 years ago
10.1002/1878-0261.12873
Targeted inhibition of ERα signaling and PIP5K1α/Akt pathways in castration‐resistant prostate cancer
Cited by: 11
Author(s): Julius Semenas, Tianyan Wang, Azharuddin Sajid Syed Khaja, A. K. M. Firoj Mahmud, Athanasios Simoulis, Thomas Grundström, Maria Fällman, Jenny L. Persson
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pcbi.1005781
Clusternomics: Integrative context-dependent clustering for heterogeneous datasets
Cited by: 47
Author(s): Evelina Gabašová, John E. Reid, Lorenz Wernisch
Software Mentions: 2
Published: about 7 years ago
10.1371/journal.pcbi.1008405
Cancer classification based on chromatin accessibility profiles with deep adversarial learning model
Cited by: 5
Author(s): Hai Yang, Qiang Wei, Dongdong Li, Zhe Wang
Software Mentions: 2
Published: about 4 years ago
10.3390/cancers13174297
Relevant and Non-Redundant Feature Selection for Cancer Classification and Subtype Detection
Cited by: 7
Author(s): Pratip Rana, Phuc Thai, Thang N. Dinh, Preetam Ghosh
Software Mentions: 2
Published: over 3 years ago
10.3390/cancers12123562
Single-Cell Spatial Analysis of Tumor and Immune Microenvironment on Whole-Slide Image Reveals Hepatocellular Carcinoma Subtypes
Cited by: 14
Author(s): Haiyue Wang, Yuming Jiang, Bailiang Li, Yi Cui, Dengwang Li
Software Mentions: 2
Published: about 4 years ago
10.3390/cancers13133106
SurvCNN: A Discrete Time-to-Event Cancer Survival Estimation Framework Using Image Representations of Omics Data
Cited by: 1
Author(s): Yogesh Kalakoti, Shashank Yadav, Durai Sundar
Software Mentions: 2
Published: over 3 years ago
10.1186/s13148-015-0159-0
The integrative epigenomic-transcriptomic landscape of ER positive breast cancer
Cited by: 22
Author(s): Yang Gao, Allison Jones, Peter A. Fasching, Matthias Ruebner, Matthias W. Beckmann, Martin Widschwendter, Andrew E. Teschendorff
Software Mentions: 2
Published: about 9 years ago
10.3389/fcvm.2017.00008
Multidimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease
Cited by: 23
Author(s): Douglas Arneson, Le Shu, Brandon L. Tsai, Rio Barrere‐Cain, Christine Sun, Xia Yang
Software Mentions: 2
Published: almost 8 years ago
10.3389/fgene.2017.00084
More Is Better: Recent Progress in Multi-Omics Data Integration Methods
Cited by: 482
Author(s): Sijia Huang, Kumardeep Chaudhary, Lana X. Garmire
Software Mentions: 2
Published: over 7 years ago
10.3389/fgene.2021.718915
Multi-View Spectral Clustering Based on Multi-Smooth Representation Fusion for Cancer Subtype Prediction
Cited by: 6
Author(s): Jian Liu, Shuguang Ge, Yuhu Cheng, Xuesong Wang
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.647141
Multi-Omics Data Fusion via a Joint Kernel Learning Model for Cancer Subtype Discovery and Essential Gene Identification
Cited by: 10
Author(s): Jie Feng, Limin Jiang, Shuhao Li, Jijun Tang, Wen Li
Software Mentions: 2
Published: almost 4 years ago
10.3390/genes10030238
Challenges in the Integration of Omics and Non-Omics Data
Cited by: 74
Author(s): Evangelina López de Maturana, Lola Alonso, Pablo Alarcón, Isabel Adoración Martín-Antoniano, Sílvia Pineda, Lucas Piorno, M. Luz Calle, Núria Malats
Software Mentions: 2
Published: almost 6 years ago
10.3390/genes12040526
Cancer Subtype Recognition Based on Laplacian Rank Constrained Multiview Clustering
Cited by: 2
Author(s): Shuguang Ge, Xuesong Wang, Yuhu Cheng, Jian Liu
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-020-70229-1
Multi-view clustering for multi-omics data using unified embedding
Cited by: 15
Author(s): Sayantan Mitra, Sriparna Saha, Mohammed Hasanuzzaman
Software Mentions: 2
Published: over 4 years ago
10.1002/advs.202100311
Identification and Characterization of Robust Hepatocellular Carcinoma Prognostic Subtypes Based on an Integrative Metabolite‐Protein Interaction Network
Cited by: 23
Author(s): Di Chen, Yiran Zhang, Wen Wang, Huan Chen, Ting Ling, Renyu Yang, Yawei Wang, Chao Duan, Yu Liu, Xin Guo, Lei Fang, Wuguang Liu, Xiumei Liu, Jing Liu, Wuxiyar Otkur, Huan Qi, Xiaolong Liu, Tian Xia, Hong‐xu Liu, Hulin Piao
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms18081652
Transcriptome Profiling in Human Diseases: New Advances and Perspectives
Cited by: 150
Author(s): Amelia Casamassimi, Antonio Federico, Monica Rienzo, Sabrina Esposito, Alfredo Ciccodicola
Software Mentions: 2
Published: over 7 years ago
10.3390/ijms21218202
Integrative Analysis of Multi-Omics Data Based on Blockwise Sparse Principal Components
Cited by: 8
Author(s): Soo‐Jin Park, Doyoen Kim, Kwanyoung Moon, Taesung Park
Software Mentions: 2
Published: about 4 years ago
10.18632/oncotarget.6527
Metronomic topotecan impedes tumor growth of<i>MYCN</i>-amplified neuroblastoma cells<i>in vitro</i>and<i>in vivo</i>by therapy induced senescence
Cited by: 36
Author(s): Sabine Taschner‐Mandl, Magdalena Schwarz, Johanna Blaha, Maximilian Kauer, Florian Kromp, Nelli Frank, Fikret Rifatbegovic, Tamara Weiss, Ruth Ladenstein, M Hohenegger, Inge M. Ambros, Peter F. Ambros
Software Mentions: 2
Published: about 9 years ago
10.18632/oncotarget.13718
DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival
Cited by: 15
Author(s): Thomas Fleischer, Jovana Klajic, Miriam Ragle Aure, Riku Louhimo, Arne V. Pladsen, Lars Ottestad, Nizar Touleimat, Marko Laakso, Ann Rita Halvorsen, Grethe I.G. Alnæs, Margit Riis, Åslaug Helland, Sampsa Hautaniemi, Per Eystein Lønning, Bjørn Naume, Anne‐Lise Børresen‐Dale, Jörg Tost, Vessela N. Kristensen
Software Mentions: 2
Published: about 8 years ago
10.18632/oncotarget.21643
ndmaSNF: cancer subtype discovery based on integrative framework assisted by network diffusion model
Cited by: 13
Author(s): Chao Yang, Shuguang Ge, Chun-Hou Zheng
Software Mentions: 2
Published: about 7 years ago