Yin Lab @ UCLA | Publications

(Lab members in bold. ^*co-first authors, ^†co-corresponding authors.)

Preprints

Chovanec P, He S, Yin Y. Lesions initiating spontaneous mitotic crossover are minimally subject to non-homologous end joining. bioRxiv 2026; 2026.05.11.724412. PMID: 42182344 PMCID: PMC13192724. [full text] [doi]
Guo L, Boocock J, Tome J, Chandrasekaran S, Hilt EE, Zhang Y, Sathe L, Li X, Luo C, Kosuri S, Shendure J, Arboleda VA, Flint J, Eskin E, Garner OB, Yang S, Bloom JS^†, Kruglyak L^†, Yin Y^†. Rapid cost-effective viral genome sequencing by V-seq. bioRxiv 2020; 2020.08.15.252510. [pdf] [doi]

Chovanec P, He S, Yin Y. Genome-wide mapping of Cas9-induced sister chromatid exchange across single and over 200 genomic sites in human cells. eLife 2026; 15: e112073. PMID: 42861852 PMCID: PMC13657629. [full text] [doi]
He S^†, Chovanec P, Yin Y^†. Protocol for mapping sister chromatid exchanges and structural variations using sci-L3-strand-seq. STAR Protocols 2026; 7(4): 104892. PMID: 42848518 PMCID: PMC13676703. [full text] [doi]
Chovanec P, Ridgley T, Yin Y. High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq. Nucleic Acids Res. 2026; 54(4): gkag119. PMID: 41674384 PMCID: PMC12895072. [full text] [doi]

Chovanec P, Yin Y. Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility. Nucleic Acids Res. 2025; 53(4): gkaf101. PMID: 39997216 PMCID: PMC11851118. [full text] [doi]

Guo L, Boocock J, Hilt EE, Chandrasekaran S, Zhang Y, Munugala C, Sathe L, Alexander N, Arboleda VA, Flint J, Eskin E, Luo C, Yang S, Garner O, Yin Y^†, Bloom JS^†, Kruglyak L^†. Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA. BMC Genomics 2022; 23(1): 260. PMID: 35379194 PMCID: PMC8978495. [full text] [doi]
Hilt EE, Boocock J, Trejo M, Le CQ, Guo L, Zhang Y, Sathe L, Arboleda VA, Yin Y, Bloom JS, Wang J, Elmore JG, Kruglyak L, Shrestha L, Mohamed Bakhash SA, Lin M, Xie H, Huang M, Roychoudhury P, Greninger A, Chandrasekaran S, Yang S, Garner OB. Retrospective detection of SARS-CoV-2 in symptomatic patients prior to widespread diagnostic testing in Southern California. Clin. Infect. Dis. 2022; 74(2): 271-277. PMID: 33939799 PMCID: PMC8135745. [full text] [doi]

Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EE, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Booeshaghi AS, Brandenberg OF, Guo L, Boocock J, Hochman M, Simpkins SW, Lin I, LaPierre N, Hong D, Zhang Y, Oland G, Choe BJ, Chandrasekaran S, Hilt EE, Butte M, Damoiseaux R, Kravit C, Cooper AR, Yin Y, Pachter L, Garner OB, Flint J, Eskin E, Luo C, Kosuri S, Kruglyak L, Arboleda VA. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nat. Biomed. Eng. 2021; 5(7): 657-665. PMID: 34211145 PMCID: PMC10810734. [full text] [doi]
Chovanec P, Yin Y. A mapping platform for mitotic crossover by single-cell multi-omics. Methods Enzymol. 2021; 661: 183-204. [book chapter / review] PMID: 34776212 PMCID: PMC8944907. [full text] [doi]

Yin Y^†, Jiang Y, Lam KG, Berletch JB, Disteche CM, Noble WS, Steemers FJ, Camerini-Otero RD, Adey AC, Shendure JA^†. High-throughput single cell sequencing with linear amplification. Mol. Cell 2019; 76(4): 676-690.e10. PMID: 31495564 PMCID: PMC6874760. [pdf] [full text]
Featured in Chinese by BioArt [link]
Jay Shendure hosted on Nature Biotech webcasts [link]
Chen W, McKenna A, Schreiber J, Haeussler M, Yin Y, Agarwal V, Noble WS, Shendure JA. Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair. Nucleic Acids Res. 2019; 47(15): 7989-8003. PMID: 31165867 PMCID: PMC6735782. [pdf] [full text]
Klein HL^†, Bacinskaja G, Che J, Cheblal A, Elango R, Epshtein A, Fitzgerald DM, Gomez-Gonzalez B, Khan SR, Kumar S, Leland BA, Marie L, Mei Q, Miller KM, Mine-Hattab J, Piotrowska A, Polleys EJ, Putnam CD, Radchenko EA, Saada AA, Sakofsky CJ, Shim EY, Stracy M, Xia J, Yan Z, Yin Y, Aguilera A, Argueso JL, Freudenreich CM, Gasser SM, Gordenin DA, Haber JE, Ira G, Jinks-Robertson S, King MC, Kolodner RD, Kuzminov A, Lambert SAE, Lee SE, Mirkin SM, Petes TD, Rosenberg SM, Rothstein R, Symington LS, Zawadzki P, Kim N^†, Lisby M^†, Malkova A^†. Guidelines for DNA recombination and repair studies: cellular assays of DNA repair pathways. Microbial Cell 2019; 6(1): 1-64. [book chapter / review] PMID: 30652105 PMCID: PMC6334234. [pdf] [full text]

Guo X^*, Chavez A^*, Tung A^*, Chan Y, Kaas C, Yin Y, Cecchni R, Lopez-Garnier S, Kelsic E, Schubert M, DiCarlo J, Collins JJ, Church GM. High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast. Nat. Biotechnol. 2018; 36(6): 540-546. PMID: 29786095 PMCID: PMC5990468. [pdf] [full text]

Yin Y, Dominska M, Yim E, Petes T. High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. eLife 2017; 6: e28069. PMID: 28714850 PMCID: PMC5531827. [pdf] [full text]

Deng SK, Yin Y, Petes TD, Symington LS. Mre11-Sae2 and RPA collaborate to prevent palindromic gene amplification. Mol. Cell 2015; 60(3): 500-8. PMID: 26545079 PMCID: PMC4636734. [pdf] [full text]
Yin Y, Petes TD. Recombination between homologous chromosomes induced by unrepaired UV-generated DNA damage requires Mus81p and is suppressed by Mms2p. PLoS Genet. 2015; 11(3): e1005026. PMID: 25738287 PMCID: PMC4349867. [pdf] [full text]

Yin Y, Petes TD. The role of Exo1p exonuclease in DNA end resection to generate gene conversion tracts in Saccharomyces cerevisiae. Genetics 2014; 197(4): 1097-109. PMID: 24835424 PMCID: PMC4125386. [pdf] [full text]

Yin Y, Petes TD. Genome-wide high-resolution mapping of UV-induced mitotic recombination events in Saccharomyces cerevisiae. PLoS Genet. 2013; 9(10): e1003894. PMID: 24204306 PMCID: PMC3814309. [pdf] [full text]

St Charles J^*, Hazkani-Covo E^*, Yin Y, Andersen SL, Dietrich FS, Greenwell PW, Malc E, Mieczkowski P, Petes TD. High-resolution genome-wide analysis of irradiated (UV and gamma-rays) diploid yeast cells reveals a high frequency of genomic loss of heterozygosity (LOH) events. Genetics 2012; 190(4): 1267-84. PMID: 22267500 PMCID: PMC3316642. [pdf] [full text]