{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T21:34:36Z","timestamp":1770932076004,"version":"3.50.1"},"reference-count":43,"publisher":"Institute of Electrical and Electronics Engineers (IEEE)","issue":"6","license":[{"start":{"date-parts":[[2025,11,1]],"date-time":"2025-11-01T00:00:00Z","timestamp":1761955200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/legalcode"}],"funder":[{"name":"NIH-NIA","award":["R01AG057896"],"award-info":[{"award-number":["R01AG057896"]}]},{"name":"NIH-NIA","award":["1RF1AG063507"],"award-info":[{"award-number":["1RF1AG063507"]}]},{"name":"NIH-NIA","award":["R01AG068293"],"award-info":[{"award-number":["R01AG068293"]}]},{"name":"NIH-NIA","award":["1R01AG066524"],"award-info":[{"award-number":["1R01AG066524"]}]},{"name":"NIH-NIA","award":["1R01AG065301"],"award-info":[{"award-number":["1R01AG065301"]}]},{"name":"NIH-NIA","award":["P30AG066546"],"award-info":[{"award-number":["P30AG066546"]}]},{"name":"NIH-NIA","award":["1R21AG087907"],"award-info":[{"award-number":["1R21AG087907"]}]},{"name":"NIH-NINDS","award":["RF1NS112391"],"award-info":[{"award-number":["RF1NS112391"]}]},{"name":"NIH-NINDS","award":["U19NS115388"],"award-info":[{"award-number":["U19NS115388"]}]},{"name":"NIH-NINDS","award":["5R01NS017950-39"],"award-info":[{"award-number":["5R01NS017950-39"]}]},{"name":"DHA","award":["HU00011920029"],"award-info":[{"award-number":["HU00011920029"]}]},{"name":"NIH-NIA","award":["P30AG066546-04"],"award-info":[{"award-number":["P30AG066546-04"]}]},{"name":"NIH-NIA","award":["R01AG082360-03"],"award-info":[{"award-number":["R01AG082360-03"]}]},{"name":"NIH-NIA","award":["R21AG087907"],"award-info":[{"award-number":["R21AG087907"]}]},{"name":"Rush Alzheimer&#x2019;s Disease Center, Rush University Medical Center"},{"name":"NIH-NIA","award":["RF1AG57473"],"award-info":[{"award-number":["RF1AG57473"]}]},{"name":"NIH-NIA","award":["P30AG010161"],"award-info":[{"award-number":["P30AG010161"]}]},{"name":"NIH-NIA","award":["R01AG015819"],"award-info":[{"award-number":["R01AG015819"]}]},{"name":"NIH-NIA","award":["R01AG017917"],"award-info":[{"award-number":["R01AG017917"]}]},{"name":"NIH-NIA","award":["U01AG46152"],"award-info":[{"award-number":["U01AG46152"]}]},{"name":"NIH-NIA","award":["U01AG61356"],"award-info":[{"award-number":["U01AG61356"]}]},{"name":"NIH-NIA","award":["RF1AG059082"],"award-info":[{"award-number":["RF1AG059082"]}]},{"name":"NIH-NIA","award":["P30AG072975"],"award-info":[{"award-number":["P30AG072975"]}]},{"name":"NIH-NIA","award":["R01AG036042"],"award-info":[{"award-number":["R01AG036042"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IEEE Trans. Comput. Biol. Bioinform."],"published-print":{"date-parts":[[2025,11]]},"DOI":"10.1109\/tcbbio.2025.3572783","type":"journal-article","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T13:03:42Z","timestamp":1748005422000},"page":"2341-2352","source":"Crossref","is-referenced-by-count":0,"title":["ZiPo: A Deep Neural Network to De-Noise Single-Cell RNA Sequencing Data"],"prefix":"10.1109","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2119-0769","authenticated-orcid":false,"given":"Mohsen","family":"Sharifitabar","sequence":"first","affiliation":[{"name":"Department of Cell Systems &amp; Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0349-4360","authenticated-orcid":false,"given":"Shiva","family":"Kazempour","sequence":"additional","affiliation":[{"name":"Department of Cell Systems &amp; Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0222-7570","authenticated-orcid":false,"given":"Javad","family":"Razavian","sequence":"additional","affiliation":[{"name":"Department of Cell Systems &amp; Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4157-5579","authenticated-orcid":false,"given":"Sogand","family":"Sajedi","sequence":"additional","affiliation":[{"name":"The University of Texas MD Anderson Cancer Center, Houston, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4908-2479","authenticated-orcid":false,"given":"Soroosh","family":"Solhjoo","sequence":"additional","affiliation":[{"name":"F. Edward H&#x00E9;bert School of Medicine, Bethesda, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5902-6238","authenticated-orcid":false,"given":"Habil","family":"Zare","sequence":"additional","affiliation":[{"name":"Department of Cell Systems &amp; Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"263","reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1214\/17-AOAS1110"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1188-0"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1093\/biostatistics\/kxx053"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02601-5"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2020.09.014"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2772"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02554-5"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-03405-7"},{"key":"ref9","article-title":"MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data","author":"Dijk","year":"2017","journal-title":"BioRxiv"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.9501.2"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.05.061"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0033-z"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2226-y"},{"key":"ref14","first-page":"281","article-title":"Some methods for classification and analysis of multivariate observations [C]","volume-title":"Proc Berkeley Symp. Math. Statist. Probability","author":"MacQueen"},{"issue":"804","key":"ref15","article-title":"Sur la division des corps matriels en parties","volume":"1","author":"Steinhaus","year":"1956","journal-title":"Bull. Acad. Polonaise Sci."},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbw068"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-019-0122-6"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1002\/pmic.202070155"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.5555\/3045118.3045167"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1109\/cvpr.2016.90"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1109\/72.279181"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07931-2"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4292"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1007\/3-540-59497-3_175"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1226"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2012.07.003"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1186\/s12920-017-0253-6"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-559"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-84858-7"},{"key":"ref30","first-page":"2488","article-title":"How does batch normalization help optimization?","volume-title":"Proc. Adv. Neural Inf. Process. Syst.","author":"Santurkar"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1162\/neco_a_01603"},{"key":"ref32","article-title":"Deep learning using rectified linear units (ReLU)","author":"Agarap","year":"2018"},{"key":"ref33","article-title":"Language modeling with gated convolutional networks","author":"Dauphin","year":"2016"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-019-1195-2"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1038\/s41421-020-0157-z"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-018-0269-2"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1145\/3292500.3330701"},{"key":"ref38","article-title":"Adam: A method for stochastic optimization","author":"Kingma","year":"2014"},{"key":"ref39","first-page":"8026","article-title":"PyTorch: An imperative style, high-performance deep learning library","volume-title":"Proc. Adv. Neural Inf. Process. Syst.","author":"Paszke"},{"key":"ref40","article-title":"High-level library to help with training neural networks in PyTorch","author":"Fomin","year":"2020"},{"issue":"11","key":"ref41","article-title":"Visualizing data using t-SNE","volume":"9","author":"Van der Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"ref42","article-title":"Pigengene: Computing and using eigengenes","author":"Zare","year":"2016"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1038\/s43587-021-00142-3"}],"container-title":["IEEE Transactions on Computational Biology and Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/xplorestaging.ieee.org\/ielx8\/10723156\/11296745\/11012744.pdf?arnumber=11012744","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T20:58:28Z","timestamp":1770929908000},"score":1,"resource":{"primary":{"URL":"https:\/\/ieeexplore.ieee.org\/document\/11012744\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11]]},"references-count":43,"journal-issue":{"issue":"6"},"URL":"https:\/\/doi.org\/10.1109\/tcbbio.2025.3572783","relation":{},"ISSN":["2998-4165"],"issn-type":[{"value":"2998-4165","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11]]}}}