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Alexander Dobin

Alexander Dobin

Assistant Professor
Cancer Center Member

Ph.D., University of Minnesota, 2003

dobin@cshl.edu | 516-422-4123

Faculty Profile

Next generation sequencing technologies revolutionized many areas of genetics and molecular biology, enabling quantitative analyses of the entire genomes and paving the way for Personalized Medicine. We develop novel statistical methods and computational algorithms for multi-omics processing and integration, and leverage Big Genomic Data to elucidate various problems in precision health, such as genetic and epigenetic mechanisms of cancer development and progression, and clinical impact of functional variants.

Advancements in high-throughput sequencing technologies resulted in an explosive growth of multi-omics data. While presenting a tremendous opportunity for quantitative studies of numerous biological processes, crucial for both fundamental research and clinical applications, it also created a set of unique bioinformatics challenges for processing, integrating and interpreting of the vast amounts of data.

Dr. Alexander Dobin and colleagues are biological data scientists working to resolve these challenging via developing of highly efficient and accurate algorithms, such as STAR, the popular RNA-seq analysis software used by thousands of researchers worldwide. We are conceiving novel computational approaches to process data from emerging sequencing technologies, such as single-cell RNA-seq and long read nanopore sequencing, with a special emphasis on detecting RNA and DNA aberrations in tumors.

Another exciting research area in our group is functional annotation of the non-coding genome via integration of multi-omics data generated by ENCODE, Roadmap Epigenomics and GTeX consortia, essential for deciphering of gene regulation mechanisms, interpretation of disease associated variants in GWAS studies, and understanding epigenetic effects in cancer biology.

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All Publications

STAR+WASP reduces reference bias in the allele-specific mapping of RNA-seq reads

5 Feb 2024 | bioRxiv
Asiimwe, Rebecca, Alexander, Dobin

A mucus production programme promotes classical pancreatic ductal adenocarcinoma

23 Jan 2024 | Gut
Tonelli, Claudia, Yordanov, Georgi, Hao, Yuan, Deschênes, Astrid, Hinds, Juliene, Belleau, Pascal, Klingbeil, Olaf, Brosnan, Erin, Doshi, Abhishek, Park, Youngkyu, Hruban, Ralph, Vakoc, Christopher, Dobin, Alexander, Preall, Jonathan, Tuveson, David

Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets

20 Oct 2023 | Stem Cell Reports
Hazra, Rasmani, Utama, Raditya, Naik, Payal, Dobin, Alexander, Spector, David

Comparative transcriptomics reveals human-specific cortical features

13 Oct 2023 | Science | 382(6667):eade9516
Jorstad, Nikolas, Song, Janet, Exposito-Alonso, David, Suresh, Hamsini, Castro-Pacheco, Nathan, Krienen, Fenna, Yanny, Anna, Close, Jennie, Gelfand, Emily, Long, Brian, Seeman, Stephanie, Travaglini, Kyle, Basu, Soumyadeep, Beaudin, Marc, Bertagnolli, Darren, Crow, Megan, Ding, Song-Lin, Eggermont, Jeroen, Glandon, Alexandra, Goldy, Jeff, Kiick, Katelyn, Kroes, Thomas, McMillen, Delissa, Pham, Trangthanh, Rimorin, Christine, Siletti, Kimberly, Somasundaram, Saroja, Tieu, Michael, Torkelson, Amy, Feng, Guoping, Hopkins, William, Höllt, Thomas, Keene, C, Linnarsson, Sten, McCarroll, Steven, Lelieveldt, Boudewijn, Sherwood, Chet, Smith, Kimberly, Walsh, Christopher, Dobin, Alexander, Gillis, Jesse, Lein, Ed, Hodge, Rebecca, Bakken, Trygve

Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma

5 Sep 2023 | Proceedings of the National Academy of Sciences of the United States of America | 120(36):e2303859120
Sroka, Martyna, Skopelitis, Damianos, Vermunt, Marit, Preall, Jonathan, El Demerdash, Osama, de Almeida, Larissa, Chang, Kenneth, Utama, Raditya, Gryder, Berkley, Caligiuri, Giuseppina, Ren, Diqiu, Nalbant, Benan, Milazzo, Joseph, Tuveson, David, Dobin, Alexander, Hiebert, Scott, Stengel, Kristy, Mantovani, Roberto, Khan, Javed, Kohli, Rahul, Shi, Junwei, Blobel, Gerd, Vakoc, Christopher

Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

4 Sep 2023 | Nature Ecology and Evolution
Suresh, Hamsini, Crow, Megan, Jorstad, Nikolas, Hodge, Rebecca, Lein, Ed, Dobin, Alexander, Bakken, Trygve, Gillis, Jesse

The ENCODE Uniform Analysis Pipelines

19 Jul 2023
Hitz, Benjamin, Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi, Graham, Keenan, Sud, Paul, Gabdank, Idan, Strattan, J, Sloan, Cricket, Dreszer, Timothy, Rowe, Laurence, Podduturi, Nikhil, Malladi, Venkat, Chan, Esther, Davidson, Jean, Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Wahling, Ian, Lin, Khine, Jou, Jennifer, Hong, Eurie, Lee, Brian, Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel, Boley, Nathan, Trout, Diane, Dobin, Alexander, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva, Dudchenko, Olga, Weisz, David, Rao, Suhas, Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad, Mahajan, Ragini, Aiden, Erez, Gingeras, Thomas, Heath, Simon, Hirst, Martin, Kent, W, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J

Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector

22 May 2023 | Cell Reports Methods | 3(5):100467
Haas, Brian, Dobin, Alexander, Ghandi, Mahmoud, Van Arsdale, Anne, Tickle, Timothy, Robinson, James, Gillani, Riaz, Kasif, Simon, Regev, Aviv

The ENCODE Uniform Analysis Pipelines.

6 Apr 2023 | bioRxiv
Hitz, Benjamin, Lee, Jin-Wook, Jolanki, Otto, Kagda, Meenakshi, Graham, Keenan, Sud, Paul, Gabdank, Idan, Seth Strattan, J, Sloan, Cricket, Dreszer, Timothy, Rowe, Laurence, Podduturi, Nikhil, Malladi, Venkat, Chan, Esther, Davidson, Jean, Ho, Marcus, Miyasato, Stuart, Simison, Matt, Tanaka, Forrest, Luo, Yunhai, Whaling, Ian, Hong, Eurie, Lee, Brian, Sandstrom, Richard, Rynes, Eric, Nelson, Jemma, Nishida, Andrew, Ingersoll, Alyssa, Buckley, Michael, Frerker, Mark, Kim, Daniel, Boley, Nathan, Trout, Diane, Dobin, Alex, Rahmanian, Sorena, Wyman, Dana, Balderrama-Gutierrez, Gabriela, Reese, Fairlie, Durand, Neva, Dudchenko, Olga, Weisz, David, Rao, Suhas, Blackburn, Alyssa, Gkountaroulis, Dimos, Sadr, Mahdi, Olshansky, Moshe, Eliaz, Yossi, Nguyen, Dat, Bochkov, Ivan, Shamim, Muhammad, Mahajan, Ragini, Aiden, Erez, Gingeras, Tom, Heath, Simon, Hirst, Martin, James Kent, W, Kundaje, Anshul, Mortazavi, Ali, Wold, Barbara, Cherry, J

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

30 Mar 2023 | Cell | 186(7):1493-1511.e40
Rozowsky, Joel, Gao, Jiahao, Borsari, Beatrice, Yang, Yucheng, Galeev, Timur, Gürsoy, Gamze, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Li, Tianxiao, Liu, Jason, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Drenkow, Jorg, Adrian, Jessika, Aganezov, Sergey, Aguet, François, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Cortez Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Jiang, Yunzhe, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Meng, Ran, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, J, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Ardlie, Kristin, Cherry, J, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Bernstein, Bradley, Guigó, Roderic, Gingeras, Thomas, Gerstein, Mark

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