{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,10]],"date-time":"2026-03-10T08:13:59Z","timestamp":1773130439760,"version":"3.50.1"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2021,5,20]],"date-time":"2021-05-20T00:00:00Z","timestamp":1621468800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Tsinghua University-Peking University Jointed Center for Life Science","award":["61020100119"],"award-info":[{"award-number":["61020100119"]}]},{"name":"National Thousand Young Talents Program of China","award":["042021011"],"award-info":[{"award-number":["042021011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Hi-C is a genome-wide assay based on Chromosome Conformation Capture and high-throughput sequencing to decipher 3D chromatin organization in the nucleus. However, computational methods to detect functional interactions utilizing Hi-C data face challenges including the correction for various sources of biases and the identification of functional interactions with low counts of interacting fragments. We present Chrom-Lasso, a lasso linear regression model that removes complex biases assumption-free and identifies functional interacting loci with increased power by combining information of local reads distribution surrounding the area of interest. We showed that interacting regions identified by Chrom-Lasso are more enriched for 5C validated interactions and functional GWAS hits than that of GOTHiC and Fit-Hi-C. To further demonstrate the ability of Chrom-Lasso to detect interactions of functional importance, we performed time-series Hi-C and RNA-seq during T cell activation and exhaustion. We showed that the dynamic changes in gene expression and chromatin interactions identified by Chrom-Lasso were largely concordant with each other. Finally, we experimentally confirmed Chrom-Lasso\u2019s finding that Erbb3 was co-regulated with distinct neighboring genes at different states during T cell activation. Our results highlight Chrom-Lasso\u2019s utility in detecting weak functional interaction between cis-regulatory elements, such as promoters and enhancers.<\/jats:p>","DOI":"10.1093\/bib\/bbab181","type":"journal-article","created":{"date-parts":[[2021,4,22]],"date-time":"2021-04-22T13:01:58Z","timestamp":1619096518000},"source":"Crossref","is-referenced-by-count":21,"title":["Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data"],"prefix":"10.1093","volume":"22","author":[{"given":"Jingzhe","family":"Lu","sequence":"first","affiliation":[{"name":"School of Medicine, Tsinghua University, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Medicine and the Tsinghua-Peking Center for Life science, Tsinghua University, Beijing, 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