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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

Conserved coexpression at single cell resolution across primate brains

22 Sep 2022 | bioRxiv
Suresh, Hamsini, Crow, Megan, Jorstad, Nikolas, Hodge, Rebecca, Lein, Ed, Dobin, Alexander, Bakken, Trygve, Gillis, Jesse

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

May 2022 | Nature | 605(7909):E3
ENCODE Project Consortium, Moore, Jill, Purcaro, Michael, Pratt, Henry, Epstein, Charles, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric, Freese, Peter, Gorkin, David, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian, Mortazavi, Ali, Keller, Cheryl, Zhang, Xiao-Ou, Elhajjajy, Shaimae, Huey, Jack, Dickel, Diane, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya, Zhang, Jialing, Victorsen, Alec, White, Kevin, Visel, Axel, Yeo, Gene, Burge, Christopher, Lécuyer, Eric, Gilbert, David, Dekker, Job, Rinn, John, Mendenhall, Eric, Ecker, Joseph, Kellis, Manolis, Klein, Robert, Noble, William, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy, Cherry, J, Myers, Richard, Ren, Bing, Graveley, Brenton, Gerstein, Mark, Pennacchio, Len, Snyder, Michael, Bernstein, Bradley, Wold, Barbara, Hardison, Ross, Gingeras, Thomas, Stamatoyannopoulos, John, Weng, Zhiping

Author Correction: Perspectives on ENCODE.

May 2022 | Nature | 605(7909):E4
ENCODE Project Consortium, Snyder, Michael, Gingeras, Thomas, Moore, Jill, Weng, Zhiping, Gerstein, Mark, Ren, Bing, Hardison, Ross, Stamatoyannopoulos, John, Graveley, Brenton, Feingold, Elise, Pazin, Michael, Pagan, Michael, Gilchrist, Daniel, Hitz, Benjamin, Cherry, J, Bernstein, Bradley, Mendenhall, Eric, Zerbino, Daniel, Frankish, Adam, Flicek, Paul, Myers, Richard

Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse.

Apr 2022 | Nature | 604(7904):E8
Bakken, Trygve, Jorstad, Nikolas, Hu, Qiwen, Lake, Blue, Tian, Wei, Kalmbach, Brian, Crow, Megan, Hodge, Rebecca, Krienen, Fenna, Sorensen, Staci, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian, Aldridge, Andrew, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa, Crichton, Kirsten, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas, Herb, Brian, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang, Liu, Christine, Liu, Hanqing, Lucero, Jacinta, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy, Moussa, Marmar, Nery, Joseph, Nicovich, Philip, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia, Owen, Scott, Palmer, Carter, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora, Rimorin, Christine, Rivkin, Angeline, Romanow, William, Sedeño-Cortés, Adriana, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna, Zhang, Renee, Ament, Seth, Behrens, M, Bravo, Hector, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick, Höllt, Thomas, Horwitz, Gregory, Keene, C, Kharchenko, Peter, Ko, Andrew, Lelieveldt, Boudewijn, Luo, Chongyuan, Mukamel, Eran, Pinto-Duarte, António, Preiss, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard, Smith, Kimberly, Spain, William, White, Owen, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan, McCarroll, Steven, Ting, Jonathan, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph, Linnarsson, Sten, Lein, Ed

Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

7 Mar 2022 | Genome Research | :gr.275613.121
Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander

Comparative cellular analysis of motor cortex in human, marmoset and mouse

6 Oct 2021 | Nature | 598(7879):111-119
Bakken, Trygve, Jorstad, Nikolas, Hu, Qiwen, Lake, Blue, Tian, Wei, Kalmbach, Brian, Crow, Megan, Hodge, Rebecca, Krienen, Fenna, Sorensen, Staci, Eggermont, Jeroen, Yao, Zizhen, Aevermann, Brian, Aldridge, Andrew, Bartlett, Anna, Bertagnolli, Darren, Casper, Tamara, Castanon, Rosa, Crichton, Kirsten, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Dembrow, Nikolai, Diep, Dinh, Ding, Song-Lin, Dong, Weixiu, Fang, Rongxin, Fischer, Stephan, Goldman, Melissa, Goldy, Jeff, Graybuck, Lucas, Herb, Brian, Hou, Xiaomeng, Kancherla, Jayaram, Kroll, Matthew, Lathia, Kanan, van Lew, Baldur, Li, Yang, Liu, Christine, Liu, Hanqing, Lucero, Jacinta, Mahurkar, Anup, McMillen, Delissa, Miller, Jeremy, Moussa, Marmar, Nery, Joseph, Nicovich, Philip, Niu, Sheng-Yong, Orvis, Joshua, Osteen, Julia, Owen, Scott, Palmer, Carter, Pham, Thanh, Plongthongkum, Nongluk, Poirion, Olivier, Reed, Nora, Rimorin, Christine, Rivkin, Angeline, Romanow, William, Sedeño-Cortés, Adriana, Siletti, Kimberly, Somasundaram, Saroja, Sulc, Josef, Tieu, Michael, Torkelson, Amy, Tung, Herman, Wang, Xinxin, Xie, Fangming, Yanny, Anna, Zhang, Renee, Ament, Seth, Behrens, M, Bravo, Hector, Chun, Jerold, Dobin, Alexander, Gillis, Jesse, Hertzano, Ronna, Hof, Patrick, Höllt, Thomas, Horwitz, Gregory, Keene, C, Kharchenko, Peter, Ko, Andrew, Lelieveldt, Boudewijn, Luo, Chongyuan, Mukamel, Eran, Pinto-Duarte, António, Preissl, Sebastian, Regev, Aviv, Ren, Bing, Scheuermann, Richard, Smith, Kimberly, Spain, William, White, Owen, Koch, Christof, Hawrylycz, Michael, Tasic, Bosiljka, Macosko, Evan, McCarroll, Steven, Ting, Jonathan, Zeng, Hongkui, Zhang, Kun, Feng, Guoping, Ecker, Joseph, Linnarsson, Sten, Lein, Ed

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

18 Aug 2021 | Cell Systems | 12(8):827-838.e5
Creason, Allison, Haan, David, Dang, Kristen, Chiotti, Kami, Inkman, Matthew, Lamb, Andrew, Yu, Thomas, Hu, Yin, Norman, Thea, Buchanan, Alex, van Baren, Marijke, Spangler, Ryan, Rollins, M, Spellman, Paul, Rozanov, Dmitri, Zhang, Jin, Maher, Christopher, Caloian, Cristian, Watson, John, Uhrig, Sebastian, Haas, Brian, Jain, Miten, Akeson, Mark, Ahsen, Mehmet, SMC-RNA Challenge Participants, Stolovitzky, Gustavo, Guinney, Justin, Boutros, Paul, Stuart, Joshua, Ellrott, Kyle

STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data

5 May 2021 | bioRxiv
Kaminow, Benjamin, Yunusov, Dinar, Dobin, Alexander

Multi-tissue integrative analysis of personal epigenomes

26 Apr 2021 | bioRxiv
Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, 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, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, 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, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark

Virtue as the mean: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses

22 Dec 2020 | bioRxiv
Kaminow, Benjamin, Ballouz, Sara, Gillis, Jesse, Dobin, Alexander

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