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Author Details

Indika Rajapakse
University of Michigan ann arbor
2006
39
15
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37276238HAT: Hypergraph analysis toolbox.PLoS Comput Biol2023
37864007A unified approach of detecting phase transition in time-varying complex networks.Sci Rep2023
37651193A lipid-associated macrophage lineage rewires the spatial landscape of adipose tissue in early obesity.JCI Insight2023
34990410Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters.JCI Insight2022
36043052Rearrangement of T Cell genome architecture regulates GVHD.iScience2022
33422939TCF7L2 silencing results in altered gene expression patterns accompanied by local genomic reorganization.Neoplasia2021
33795520Network dynamics of hypothalamic feeding neurons.Proc Natl Acad Sci U S A2021
337947394DNvestigator: time series genomic data analysis toolbox.Nucleus2021
34543633Understanding memory B cell selection.J Theor Biol2021
33289324Cellular reprogramming: Mathematics meets medicine.Wiley Interdiscip Rev Syst Biol Med2020
30909073Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression.Neoplasia2019
30808673Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo.Cancer Res2019
289617564D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities.Bioinformatics2018
30240614Genome Architecture Mediates Transcriptional Control of Human Myogenic Reprogramming.iScience2018
28734317The 4D Nucleome.Methods2017
28258094Nucleome Analysis Reveals Structure-Function Relationships for Colon Cancer.Mol Cancer Res2017
28461134Insight into dynamic genome imaging: Canonical framework identification and high-throughput analysis.Methods2017
28137861Emergence of function from coordinated cells in a tissue.Proc Natl Acad Sci U S A2017
28079771Advanced Research and Data Methods in Women's Health: Big Data Analytics, Adaptive Studies, and the Road Ahead.Obstet Gynecol2017
28129029Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers.Nucleus2017
29078370Algorithm for cellular reprogramming.Proc Natl Acad Sci U S A2017
27153657Spectral identification of topological domains.Bioinformatics2016
25738643Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids.Nucleus2015
26734724Periodicity of nuclear morphology in human fibroblasts.Nucleus2015
26080430Functional organization of the human 4D Nucleome.Proc Natl Acad Sci U S A2015
25116795Transcripts involved in calcium signaling and telencephalic neuronal fate are altered in induced pluripotent stem cells from bipolar disorder patients.Transl Psychiatry2014
23177740Genome-wide methylation profiles reveal quantitative views of human aging rates.Mol Cell2013
22782518Multivariate detection of gene-gene interactions.Genet Epidemiol2012
22761554What can systems theory of networks offer to biology?PLoS Comput Biol2012
21383074On emerging nuclear order.J Cell Biol2011
21941112Losing control: cancer's catastrophic transition.Nucleus2011
21911407Dynamics and control of state-dependent networks for probing genomic organization.Proc Natl Acad Sci U S A2011
20664641Networking the nucleus.Mol Syst Biol2010
20693400SEWAL: an open-source platform for next-generation sequence analysis and visualization.Nucleic Acids Res2010
19276122The emergence of lineage-specific chromosomal topologies from coordinate gene regulation.Proc Natl Acad Sci U S A2009
20640184Structures and Assumptions: Strategies to Harness Gene ÿ Gene and Gene ÿ Environment Interactions in GWAS.Stat Sci2009
22228908Hardy's "Small" Discovery Remembered.Not Am Math Soc2008
16644804Functional consequence of mutation in rat cardiac troponin T is affected differently by myosin heavy chain isoforms.J Physiol2006
16443664Troponin T modulates sarcomere length-dependent recruitment of cross-bridges in cardiac muscle.Biophys J2006
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Collaborators

Thomas Ried
Center for Cancer Research, National Cancer Institute
Co-authored papers 7
Charles Kooperberg
Co-authored papers 3
Max S Wicha
Co-authored papers 2
Darawalee Wangsa
Center for Cancer Research, National Cancer Institute
Co-authored papers 2
Jian-Bing Fan
Nanfang Hospital and Basic Medical College, Southern Medical University
Co-authored papers 1
Mats Ljungman
Co-authored papers 1
Li Zhang
Institute for Genomic Medicine, University of California
Co-authored papers 1
Guy Hughes
Lancaster University
Co-authored papers 1
Jordi Camps
Universitat Autonoma de Barcelona
Co-authored papers 1
Ling Zhao
Sun Yat-sen University
Co-authored papers 1
Danny Wangsa
Center for Cancer Research, National Cancer Institute, National Institutes of Health
Co-authored papers 1
Stephen H Friend
University of Oxford
Co-authored papers 1
James Y Dai
Fred Hutchinson Cancer Center
Co-authored papers 1
Menzies Chen
University of California
Co-authored papers 1
Rob DeConde
university of california san diego Health
Co-authored papers 1
Yuan Gao
Johns Hopkins University
Co-authored papers 1
Melvin G McInnis
University of Michigan ann arbor
Co-authored papers 1
SriniVas R Sadda
Doheny Eye Institute, University of California Los Angeles
Co-authored papers 1
Marina Bibikova
Departments of Bioinformatics and Clinical Genomics, Illumina Inc.
Co-authored papers 1
Kang Zhang
College of Animal Science and Technology, Guangxi University
Co-authored papers 1
Gilbert S Omenn
and School of Public Health, University of Michigan ann arbor
Co-authored papers 1
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 1
Justin Guinney
University of Washington
Co-authored papers 1
Gregory Hannum
University of California
Co-authored papers 1
Brandy Klotzle
Departments of Bioinformatics and Clinical Genomics, Illumina Inc.
Co-authored papers 1
Release 1.2