Chen-Shan Chin

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 15

Top Topics

Arabidopsis Thaliana

Single Molecule

Acute Myeloid Leukemia

High Throughput Sequencing

Top Venues

Nature biotechnology

Scientific reports

This page only lists publications with an associated author ORCID identifier.

Publications

Davide Bolognini, Alma S Halgren, Runyang Nicolas Lou, Alessandro Raveane, Joana L Rocha, Andrea Guarracino, Nicole Soranzo, Chen-Shan Chin, Erik P Garrison, Peter H Sudmant
Recurrent evolution and selection shape structural diversity at the amylase locus. Nature (2024)
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J Hoyt, Dylan J Taylor, Nicolas Altemose, Paul W Hook, Sergey Koren, Mikko Rautiainen, Ivan A Alexandrov, Jamie Allen, Mobin Asri, Andrey V Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark E Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik P Garrison, Ariel Gershman, Jennifer L Gerton, Patrick G S Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F Hansen, Robert Harris, Gabrielle A Hartley, William T Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M Hubley, Sarah E Hunt, Stephen Hwang, Miten Jain, Rupesh K Kesharwani, Alexandra P Lewis, Heng Li, Glennis A Logsdon, Julian K Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J Martin, Ann M Mc Cartney, Rajiv C McCoy, Jennifer McDaniel, Brandy M McNulty, Paul Medvedev, Alla Mikheenko, Katherine M Munson, Terence D Murphy, Hugh E Olsen, Nathan D Olson, Luis F Paulin, David Porubsky, Tamara A Potapova, Fedor D Ryabov, Steven L Salzberg, Michael E G Sauria, Fritz J Sedlazeck, Kishwar Shafin, Valery A Shepelev, Alaina Shumate, Jessica M Storer, Likhitha Surapaneni, Angela M Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R Vollger, Brian P Walenz, Allison C Watwood, Matthias H Weissensteiner, Aaron M Wenger, Melissa A Wilson, Samantha Zarate, Yiming Zhu, Justin M Zook, Evan E Eichler, Rachel J O'Neill, Michael C Schatz, Karen H Miga, Kateryna D Makova, Adam M Phillippy
The complete sequence of a human Y chromosome. Nature (2023)
Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz J Sedlazeck, Peter H Sudmant, Justin Wagner, Justin M Zook
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nature methods (2023)
Joanna Hård, Jeff E Mold, Jesper Eisfeldt, Christian Tellgren-Roth, Susana Häggqvist, Ignas Bunikis, Orlando Contreras-Lopez, Chen-Shan Chin, Jessica Nordlund, Carl-Johan Rubin, Lars Feuk, Jakob Michaëlsson, Adam Ameur
Long-read whole-genome analysis of human single cells. Nature communications 14 (1) (2023)
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev I Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark E Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo Gomes de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik P Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, May Christine V Malicdan, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara A Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica M Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James W Torrance, Justin Wagner, Brian P Walenz, Aaron M Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, Adam M Phillippy
The complete sequence of a human genome. Science (New York, N.Y.) 376 (6588) (2022)
Arkarachai Fungtammasan, Alexandra J Lee, Jaclyn N Taroni, Kurt Wheeler, Chen-Shan Chin, Sean Davis, Casey S Greene
Ten simple rules for large-scale data processing. PLoS computational biology 18 (2) (2022)
Sergey Aganezov, Stephanie M Yan, Daniela C Soto, Melanie Kirsche, Samantha Zarate, Pavel Avdeyev, Dylan J Taylor, Kishwar Shafin, Alaina Shumate, Chunlin Xiao, Justin Wagner, Jennifer McDaniel, Nathan D Olson, Michael E G Sauria, Mitchell R Vollger, Arang Rhie, Melissa Meredith, Skylar Martin, Joyce Lee, Sergey Koren, Jeffrey A Rosenfeld, Benedict Paten, Ryan Layer, Chen-Shan Chin, Fritz J Sedlazeck, Nancy F Hansen, Danny E Miller, Adam M Phillippy, Karen H Miga, Rajiv C McCoy, Megan Y Dennis, Justin M Zook, Michael C Schatz
A complete reference genome improves analysis of human genetic variation. Science (New York, N.Y.) 376 (6588) (2022)
Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M Wenger, William J Rowell, Ziad M Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E Miller, David Jáspez, Jose Miguel Lorenzo-Salazar, Adrián Muñoz-Barrera, Luis Alberto Rubio-Rodríguez, Carlos Flores, Giuseppe Narzisi, Uday Shanker Evani, Wayne E Clarke, Joyce Lee, Christopher E Mason, Stephen E Lincoln, Karen H Miga, Mark T W Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M Zook, Fritz J Sedlazeck
Curated variation benchmarks for challenging medically relevant autosomal genes. Nature biotechnology 40 (5) (2022)
Shilpa Garg, Arkarachai Fungtammasan, Andrew Carroll, Mike Chou, Anthony Schmitt, Xiang Zhou, Stephen Mac, Paul Peluso, Emily Hatas, Jay Ghurye, Jared Maguire, Medhat Mahmoud, Haoyu Cheng, David Heller, Justin M Zook, Tobias Moemke, Tobias Marschall, Fritz J Sedlazeck, John Aach, Chen-Shan Chin, George M Church, Heng Li
Chromosome-scale, haplotype-resolved assembly of human genomes. Nature biotechnology 39 (3) (2020)
Aaron M Wenger, Paul Peluso, William J Rowell, Pi-Chuan Chang, Richard J Hall, Gregory T Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M Phillippy, Michael C Schatz, Gene Myers, Mark A DePristo, Jue Ruan, Tobias Marschall, Fritz J Sedlazeck, Justin M Zook, Heng Li, Sergey Koren, Andrew Carroll, David R Rank, Michael W Hunkapiller
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature biotechnology 37 (10) (2019)
Mark J P Chaisson, Ashley D Sanders, Xuefang Zhao, Ankit Malhotra, David Porubsky, Tobias Rausch, Eugene J Gardner, Oscar L Rodriguez, Li Guo, Ryan L Collins, Xian Fan, Jia Wen, Robert E Handsaker, Susan Fairley, Zev N Kronenberg, Xiangmeng Kong, Fereydoun Hormozdiari, Dillon Lee, Aaron M Wenger, Alex R Hastie, Danny Antaki, Thomas Anantharaman, Peter A Audano, Harrison Brand, Stuart Cantsilieris, Han Cao, Eliza Cerveira, Chong Chen, Xintong Chen, Chen-Shan Chin, Zechen Chong, Nelson T Chuang, Christine C Lambert, Deanna M Church, Laura Clarke, Andrew Farrell, Joey Flores, Timur Galeev, David U Gorkin, Madhusudan Gujral, Victor Guryev, William Haynes Heaton, Jonas Korlach, Sushant Kumar, Jee Young Kwon, Ernest T Lam, Jong Eun Lee, Joyce Lee, Wan-Ping Lee, Sau Peng Lee, Shantao Li, Patrick Marks, Karine Viaud-Martinez, Sascha Meiers, Katherine M Munson, Fábio C P Navarro, Bradley J Nelson, Conor Nodzak, Amina Noor, Sofia Kyriazopoulou-Panagiotopoulou, Andy W C Pang, Yunjiang Qiu, Gabriel Rosanio, Mallory Ryan, Adrian Stütz, Diana C J Spierings, Alistair Ward, AnneMarie E Welch, Ming Xiao, Wei Xu, Chengsheng Zhang, Qihui Zhu, Xiangqun Zheng-Bradley, Ernesto Lowy-Gallego, Sergei Yakneen, Steven McCarroll, Goo Jun, Li Ding, Chong Lek Koh, Bing Ren, Paul Flicek, Ken Chen, Mark B Gerstein, Pui-Yan Kwok, Peter M Lansdorp, Gabor T Marth, Jonathan Sebat, Xing-Hua Shi, Ali Bashir, Kai Ye, Scott E Devine, Michael E Talkowski, Ryan E Mills, Tobias Marschall, Jan O Korbel, Evan E Eichler, Charles Lee
Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature communications 10 (1) (2019)
Thong T Nguyen, Kushal Suryamohan, Boney Kuriakose, Vasantharajan Janakiraman, Mike Reichelt, Subhra Chaudhuri, Joseph Guillory, Neethu Divakaran, P E Rabins, Ridhi Goel, Bhabesh Deka, Suman Sarkar, Preety Ekka, Yu-Chih Tsai, Derek Vargas, Sam Santhosh, Sangeetha Mohan, Chen-Shan Chin, Jonas Korlach, George Thomas, Azariah Babu, Somasekar Seshagiri
Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus. Scientific reports 8 (1) (2018)
Thong T Nguyen, Kushal Suryamohan, Boney Kuriakose, Vasantharajan Janakiraman, Mike Reichelt, Subhra Chaudhuri, Joseph Guillory, Neethu Divakaran, P E Rabins, Ridhi Goel, Bhabesh Deka, Suman Sarkar, Preety Ekka, Yu-Chih Tsai, Derek Vargas, Sam Santhosh, Sangeetha Mohan, Chen-Shan Chin, Jonas Korlach, George Thomas, Azariah Babu, Somasekar Seshagiri
Author Correction: Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus. Scientific reports 8 (1) (2018)
Catherine C Smith, Amy Paguirigan, Grace R Jeschke, Kimberly C Lin, Evan Massi, Theodore C Tarver, Chen-Shan Chin, Saurabh Asthana, Adam Olshen, Kevin J Travers, Susana Wang, Mark J Levis, Alexander E Perl, Jerald P Radich, Neil P Shah
Heterogeneous resistance to quizartinib in acute myeloid leukemia revealed by single-cell analysis. Blood 130 (1) (2017)
Chen-Shan Chin, Paul Peluso, Fritz J Sedlazeck, Maria Nattestad, Gregory T Concepcion, Alicia Clum, Christopher Dunn, Ronan O'Malley, Rosa Figueroa-Balderas, Abraham Morales-Cruz, Grant R Cramer, Massimo Delledonne, Chongyuan Luo, Joseph R Ecker, Dario Cantu, David R Rank, Michael C Schatz
Phased diploid genome assembly with single-molecule real-time sequencing. Nature methods 13 (12) (2016)
Matthew Pendleton, Robert Sebra, Andy Wing Chun Pang, Ajay Ummat, Oscar Franzen, Tobias Rausch, Adrian M Stütz, William Stedman, Thomas Anantharaman, Alex Hastie, Heng Dai, Markus Hsi-Yang Fritz, Han Cao, Ariella Cohain, Gintaras Deikus, Russell E Durrett, Scott C Blanchard, Roger Altman, Chen-Shan Chin, Yan Guo, Ellen E Paxinos, Jan O Korbel, Robert B Darnell, W Richard McCombie, Pui-Yan Kwok, Christopher E Mason, Eric E Schadt, Ali Bashir
Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature methods 12 (8) (2015)
Konstantin Berlin, Sergey Koren, Chen-Shan Chin, James P Drake, Jane M Landolin, Adam M Phillippy
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nature biotechnology 33 (6) (2015)