{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T13:32:30Z","timestamp":1776519150630,"version":"3.51.2"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T00:00:00Z","timestamp":1689292800000},"content-version":"vor","delay-in-days":13,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS 2212511"],"award-info":[{"award-number":["IIS 2212511"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CNAsim is a software package for improved simulation of single-cell copy number alteration (CNA) data from tumors. CNAsim can be used to efficiently generate single-cell copy number profiles for thousands of simulated tumor cells under a more realistic error model and a broader range of possible CNA mechanisms compared with existing simulators. The error model implemented in CNAsim accounts for the specific biases of single-cell sequencing that leads to read count fluctuation and poor resolution of CNA detection. For improved realism over existing simulators, CNAsim can (i) generate WGD, whole-chromosomal CNAs, and chromosome-arm CNAs, (ii) simulate subclonal population structure defined by the accumulation of chromosomal CNAs, and (iii) dilute the sampled cell population with both normal diploid cells and pseudo-diploid cells. The software can also generate DNA-seq data for sampled cells.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CNAsim is written in Python and is freely available open-source from https:\/\/github.com\/samsonweiner\/CNAsim.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad434","type":"journal-article","created":{"date-parts":[[2023,7,14]],"date-time":"2023-07-14T13:37:47Z","timestamp":1689341867000},"source":"Crossref","is-referenced-by-count":10,"title":["CNAsim: improved simulation of single-cell copy number profiles and DNA-seq data from tumors"],"prefix":"10.1093","volume":"39","author":[{"given":"Samson","family":"Weiner","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut , Storrs, CT 06269, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0039-2596","authenticated-orcid":false,"given":"Mukul S","family":"Bansal","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, University of Connecticut , Storrs, CT 06269, United States"},{"name":"Institute for Systems Genomics, University of Connecticut , Storrs, CT 06269, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,7,14]]},"reference":[{"key":"2023072302340518300_btad434-B1","doi-asserted-by":"crossref","first-page":"e51480","DOI":"10.7554\/eLife.51480","article-title":"Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing","volume":"9","author":"Baslan","year":"2020","journal-title":"eLife"},{"key":"2023072302340518300_btad434-B2","doi-asserted-by":"crossref","first-page":"iyab229","DOI":"10.1093\/genetics\/iyab229","article-title":"Efficient ancestry and mutation simulation with msprime 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