☰

Chen-Shan Chin, Ph.D. - Publications

Affiliations: 
2002 University of Washington, Seattle, Seattle, WA 
Area:
Condensed Matter Physics
Tree Info Similar researchers PubMed Report error

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Majidian S, Agustinho DP, Chin CS, Sedlazeck FJ, Mahmoud M. Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biology. 24: 221. PMID 37798733 DOI: 10.1186/s13059-023-03061-1  0.487
2023 Hård J, Mold JE, Eisfeldt J, Tellgren-Roth C, Häggqvist S, Bunikis I, Contreras-Lopez O, Chin CS, Nordlund J, Rubin CJ, Feuk L, Michaëlsson J, Ameur A. Long-read whole-genome analysis of human single cells. Nature Communications. 14: 5164. PMID 37620373 DOI: 10.1038/s41467-023-40898-3  0.467
2023 Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y  0.405
2023 Chin CS, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, Zook JM. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nature Methods. PMID 37365340 DOI: 10.1038/s41592-023-01914-y  0.407
2022 Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, ... ... Chin CS, et al. Benchmarking challenging small variants with linked and long reads. Cell Genomics. 2. PMID 36452119 DOI: 10.1016/j.xgen.2022.100128  0.433
2022 Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, ... Chin CS, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5  0.492
2022 Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, ... ... Chin CS, et al. A complete reference genome improves analysis of human genetic variation. Science (New York, N.Y.). 376: eabl3533. PMID 35357935 DOI: 10.1126/science.abl3533  0.46
2022 Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, ... ... Chin CS, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987  0.491
2022 Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, ... ... Chin CS, et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology. PMID 35132260 DOI: 10.1038/s41587-021-01158-1  0.409
2021 McKernan K, Kane LT, Crawford S, Chin CS, Trippe A, McLaughlin S. A draft reference assembly of the genome. F1000research. 10: 281. PMID 34322225 DOI: 10.12688/f1000research.51613.2  0.482
2020 Garg S, Fungtammasan A, Carroll A, Chou M, Schmitt A, Zhou X, Mac S, Peluso P, Hatas E, Ghurye J, Maguire J, Mahmoud M, Cheng H, Heller D, Zook JM, ... ... Chin CS, et al. Chromosome-scale, haplotype-resolved assembly of human genomes. Nature Biotechnology. PMID 33288905 DOI: 10.1038/s41587-020-0711-0  0.405
2020 Höijer I, Johansson J, Gudmundsson S, Chin CS, Bunikis I, Häggqvist S, Emmanouilidou A, Wilbe M, den Hoed M, Bondeson ML, Feuk L, Gyllensten U, Ameur A. Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity. Genome Biology. 21: 290. PMID 33261648 DOI: 10.1186/s13059-020-02206-w  0.39
2020 Chin CS, Wagner J, Zeng Q, Garrison E, Garg S, Fungtammasan A, Rautiainen M, Aganezov S, Kirsche M, Zarate S, Schatz MC, Xiao C, Rowell WJ, Markello C, Farek J, et al. A diploid assembly-based benchmark for variants in the major histocompatibility complex. Nature Communications. 11: 4794. PMID 32963235 DOI: 10.1038/s41467-020-18564-9  0.464
2020 Nattestad M, Aboukhalil R, Chin CS, Schatz MC. Ribbon: Intuitive visualization for complex genomic variation. Bioinformatics (Oxford, England). PMID 32766814 DOI: 10.1093/Bioinformatics/Btaa680  0.459
2020 Ou S, Liu J, Chougule KM, Fungtammasan A, Seetharam AS, Stein JC, Llaca V, Manchanda N, Gilbert AM, Wei S, Chin CS, Hufnagel DE, Pedersen S, Snodgrass SJ, Fengler K, et al. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11: 2288. PMID 32385271 DOI: 10.1038/S41467-020-16037-7  0.476
2020 Mahmoud M, Gener AR, Khayat MM, English AC, Balaji A, Zhou A, Hehn A, Fungtammasan A, Chrisman BS, Chin C, Lin C, Lo C, Liao C, Carvalho CMB, Diesh C, et al. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine F1000research. 9: 1141. DOI: 10.12688/F1000Research.23773.1  0.502
2019 Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology. PMID 31406327 DOI: 10.1038/S41587-019-0217-9  0.547
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Chin CS, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.565
2019 Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin C, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, et al. A strategy for building and using a human reference pangenome F1000research. 8: 1751. DOI: 10.12688/F1000Research.19630.1  0.372
2018 Nguyen TT, Suryamohan K, Kuriakose B, Janakiraman V, Reichelt M, Chaudhuri S, Guillory J, Divakaran N, Rabins PE, Goel R, Deka B, Sarkar S, Ekka P, Tsai YC, Vargas D, ... ... Chin CS, et al. Author Correction: Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus. Scientific Reports. 8: 13274. PMID 30171192 DOI: 10.1038/S41598-018-31454-X  0.452
2018 Nguyen TT, Suryamohan K, Kuriakose B, Janakiraman V, Reichelt M, Chaudhuri S, Guillory J, Divakaran N, Rabins PE, Goel R, Deka B, Sarkar S, Ekka P, Tsai YC, Vargas D, ... ... Chin CS, et al. Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus. Scientific Reports. 8: 8924. PMID 29895987 DOI: 10.1038/S41598-018-27084-Y  0.53
2017 Korlach J, Gedman G, Kingan SB, Chin CS, Howard JT, Audet JN, Cantin L, Jarvis ED. De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads. Gigascience. 6: 1-16. PMID 29020750 DOI: 10.1093/Gigascience/Gix085  0.565
2017 Ghurye J, Pop M, Koren S, Bickhart D, Chin CS. Scaffolding of long read assemblies using long range contact information. Bmc Genomics. 18: 527. PMID 28701198 DOI: 10.1186/S12864-017-3879-Z  0.408
2017 Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, et al. Improved maize reference genome with single-molecule technologies. Nature. PMID 28605751 DOI: 10.1038/Nature22971  0.564
2017 Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, ... ... Chin CS, et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Research. PMID 28396521 DOI: 10.1101/Gr.213611.116  0.571
2017 Ghurye J, Pop M, Koren S, Bickhart D, Chin C. Chromosome scale de novo assembly of genomes using chromatin interaction data F1000research. 6. DOI: 10.7490/F1000Research.1114160.1  0.423
2016 Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, ... ... Chin CS, et al. Correction: Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. Plos Genetics. 12: e1006500. PMID 27935956 DOI: 10.1371/journal.pgen.1006500  0.415
2016 Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nature Methods. PMID 27749838 DOI: 10.1038/Nmeth.4035  0.572
2016 Sevim V, Bashir A, Chin CS, Miga KH. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics (Oxford, England). PMID 27153570 DOI: 10.1093/Bioinformatics/Btw101  0.533
2016 Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, ... ... Chin CS, et al. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. Plos Genetics. 12: e1005954. PMID 27082250 DOI: 10.1371/Journal.Pgen.1005954  0.509
2016 Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, ... ... Chin CS, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  0.529
2015 Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 1109. PMID 26448093 DOI: 10.1038/Nbt1015-1109C  0.41
2015 Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, ... ... Chin CS, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods. PMID 26121404 DOI: 10.1038/Nmeth.3454  0.559
2015 Mayor NP, Robinson J, McWhinnie AJ, Ranade S, Eng K, Midwinter W, Bultitude WP, Chin CS, Bowman B, Marks P, Braund H, Madrigal JA, Latham K, Marsh SG. HLA Typing for the Next Generation. Plos One. 10: e0127153. PMID 26018555 DOI: 10.1371/Journal.Pone.0127153  0.43
2015 Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature Biotechnology. 33: 623-30. PMID 26006009 DOI: 10.1038/Nbt.3238  0.582
2015 Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P. Extending reference assembly models. Genome Biology. 16: 13. PMID 25651527 DOI: 10.1186/S13059-015-0587-3  0.48
2014 Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Scientific Data. 1: 140045. PMID 25977796 DOI: 10.1038/Sdata.2014.45  0.565
2014 Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, et al. Fully Assembled Genome Sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992. Genome Announcements. 2. PMID 24699966 DOI: 10.1128/genomeA.00293-14  0.506
2013 Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods. 10: 563-9. PMID 23644548 DOI: 10.1038/Nmeth.2474  0.524
2013 Allard MW, Muruvanda T, Strain E, Timme R, Luo Y, Wang C, Keys CE, Payne J, Cooper T, Luong K, Song Y, Chin CS, Korlach J, Roberts RJ, Evans P, et al. Fully assembled genome sequence for Salmonella enterica subsp. enterica Serovar Javiana CFSAN001992. Genome Announcements. 1: e0008113. PMID 23516208 DOI: 10.1128/Genomea.00081-13  0.526
2012 Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, et al. A hybrid approach for the automated finishing of bacterial genomes. Nature Biotechnology. 30: 701-7. PMID 22750883 DOI: 10.1038/Nbt.2288  0.5
2010 Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Research. 38: e159. PMID 20571086 DOI: 10.1093/Nar/Gkq543  0.443
2010 Mardis E, Maupin R, Travers K, Chin C, Eid J, Chau B, Londry J, Baybayan P, Magrini V, McLellan M, Wylie T. Abstract 1159: Single molecule sequencing to detect and characterize somatic mutations in cancer genomes Cancer Research. 70: 1159-1159. DOI: 10.1158/1538-7445.Am10-1159  0.446
2007 Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. Gene expression patterns during adaptation of a helminth parasite to different environmental niches. Genome Biology. 8: R65. PMID 17456242 DOI: 10.1186/Gb-2007-8-4-R65  0.332
2006 Samanta MP, Tongprasit W, Sethi H, Chin CS, Stolc V. Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proceedings of the National Academy of Sciences of the United States of America. 103: 4192-7. PMID 16537507 DOI: 10.1073/Pnas.0507669103  0.337
2005 Jolly ER, Chin CS, Herskowitz I, Li H. Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis. Bmc Bioinformatics. 6: 275. PMID 16297241 DOI: 10.1186/1471-2105-6-275  0.455
2005 Chin CS, Chuang JH, Li H. Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Research. 15: 205-13. PMID 15653830 DOI: 10.1101/Gr.3243305  0.394
Show low-probability matches.