Xuebing Wu, PhD
- Assistant Professor of Medical Sciences (in Medicine and in Systems Biology) (in the Institute for Clinical and Translational Research)
Overview
Xuebing Wu, PhD is an Assistant Professor in the Department of Medicine/Cardiology and the Department of Systems Biology at Columbia University Irving Medical Center. Dr. Wu received a B.S. and M.S. in Control Science and Engineering from Tsinghua University, Beijing and a PhD in Computational and Systems Biology from MIT, working with Phillip Sharp and Christopher Burge. As a Helen Hay Whitney Fellow, he continued postdoctoral work on functional genomics of RNA structures with David Bartel at Whitehead Institute/MIT. Research in the Wu laboratory integrates CRISPR, genomics, and machine learning to decode and target RNA in human health and disease. Dr. Wu has received a number of other distinctions including The RNA Society/Scaringe Young Scientist Award, Pew-Stewart Scholars Award, and NIH Director’s New Innovator Award.
Academic Appointments
- Assistant Professor of Medical Sciences (in Medicine and in Systems Biology) (in the Institute for Clinical and Translational Research)
Gender
- Male
Credentials & Experience
Education & Training
- Fellowship: Whitehead Institute / MIT / HHMI
Honors & Awards
2021 Paul A. Marks Scholar, Columbia University
2021 Pershing Square Sohn Prize for Young Investigators in Cancer Research
2020 NIH Director’s New Innovator Award (DP2)
2020 Pew-Stewart Scholars for Cancer Research
2019 The RNA Society / Scaringe Young Scientist Award
2019 Highly Cited Researcher, Clarivate / Web of Science
2018 Finalist, The Regeneron Prize for Creative Innovation in a Postdoc
2017 Margaret and Herman Sokol Postdoctoral Award, Whitehead Institute
2017 Oral Presenter Award, RNA Symposium, University at Albany, SUNY
2016-2019 Helen Hay Whitney Postdoctoral Fellowship, Helen Hay Whitney Foundation
2014 Honorable Mention, The Regeneron Prize for Creative Innovation in a Graduate Student
2011-2014 International Student Research Fellow, Howard Hughes Medical Institute
2009 Rising Stars of Research, Tsinghua University, China
2008 Top–grade Scholarship (the highest honor), Tsinghua University, China
2021 Pershing Square Sohn Prize for Young Investigators in Cancer Research
2020 NIH Director’s New Innovator Award (DP2)
2020 Pew-Stewart Scholars for Cancer Research
2019 The RNA Society / Scaringe Young Scientist Award
2019 Highly Cited Researcher, Clarivate / Web of Science
2018 Finalist, The Regeneron Prize for Creative Innovation in a Postdoc
2017 Margaret and Herman Sokol Postdoctoral Award, Whitehead Institute
2017 Oral Presenter Award, RNA Symposium, University at Albany, SUNY
2016-2019 Helen Hay Whitney Postdoctoral Fellowship, Helen Hay Whitney Foundation
2014 Honorable Mention, The Regeneron Prize for Creative Innovation in a Graduate Student
2011-2014 International Student Research Fellow, Howard Hughes Medical Institute
2009 Rising Stars of Research, Tsinghua University, China
2008 Top–grade Scholarship (the highest honor), Tsinghua University, China
Research
Xuebing Wu, PhD is an Assistant Professor in the Department of Medicine/Cardiology and the Department of Systems Biology at Columbia University Irving Medical Center. Dr. Wu received a B.S. and M.S. in Control Science and Engineering from Tsinghua University, Beijing and a PhD in Computational and Systems Biology from MIT, working with Phillip Sharp and Christopher Burge. As a Helen Hay Whitney Fellow, he continued postdoctoral work on functional genomics of RNA structures with David Bartel at Whitehead Institute/MIT. Research in the Wu laboratory integrates CRISPR, genomics, and machine learning to decode and target RNA in human health and disease. Dr. Wu has received a number of other distinctions including The RNA Society/Scaringe Young Scientist Award, Pew-Stewart Scholars Award, and NIH Director’s New Innovator Award.
Selected Publications
1. Haq I, Ngo JC, Roy N, Zhang Y, Fujita M, Soni RK, Bennett DA, Wu X, Menon V, Olah M, Sher F.
An integrated toolkit for microglia functional genomics.
Genome Medicine, under review
2. Zhang Y*, Zhang W*, Zhao J, Ito T, Jin J, Aparicio AO, Zhou J, Guichard VA, Fang Y, Que J, Urban JF Jr, Hanna JH, Ghosh S, Wu X, Ding L, Basu U, Huang Y
Lineage-specific requirement of m6A RNA methylation for innate lymphoid cell responses.
Nature Immunology, accepted in principle
3. Kesner JS*, Chen Z*, Shi P, Aparicio OA, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X.
Noncoding translation mitigation.
Nature, in press
Related preprint: bioRxiv, 2022.07.20.500724; doi: https://doi.org/10.1101/2022.07.20.500724
4. Shi P#, Murphy MR, Aparicio AO, Kesner JS, Fang Z, Chen Z, Trehan A, Guo Y, Wu X#.
Collateral activity of the CRISPR/RfxCas13d system in human cells.
Communications Biology, 2023, 6:334
Related preprint: bioRxiv, 2021, 2021.11.30.470032; doi: https://doi.org/10.1101/2021.11.30.470032
5. Zhang C*, Konermann S*, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D.
Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d.
Cell. 2018, 175:212-223
6. Tycko J, Barrera LA, Huston N, Friedland AE, Wu X, Gootenberg JS, Abudayyeh OO, Myer VE, Wilson CJ, Hsu PD.
Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells.
Nature Communications. 2018, 9:2962
7. Jiang W*, Wei Y*, Long Y*, Owen A, Wang B, Wu X, Luo S, Dang Y, Ma DK.
A genetic program mediates cold-warming response and promotes stress-induced phenoptosis in C. elegans.
eLife. 2018, 7:e35037
8. Liu XS, Wu H, Krzisch M, Wu X, Greaf J, Muffat J, Hnisz D, Li C, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R.
Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene.
Cell. 2018, 172:979–992
9. Chiu AC*, Suzuki HI*, Wu X, Mahat DB, Kriz AJ, Sharp PA.
Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP.
Molecular Cell. 2018, 69:648–663
10. Wu X, Bartel DP.
Widespread influence of 3′-end structures on mammalian mRNA processing and stability.
Cell. 2017, 169:905–917
11. Wu X#, Bartel DP#.
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences.
Nucleic Acids Research. 2017, W1:gkx323
12. Liu XS*, Wu H*, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Shivalila CS, Dadon D, Young RA, Jaenisch R.
Editing DNA methylation in the mammalian genome.
Cell. 2016, 167:233-247
13. Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter J, Black DL, Kharchenko PV, Sharp PA, Walsh CA.
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.
Cell. 2016, 166:1147-1162 (cover story)
14. Ran FA*, Cong L*, Yan WX*, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F.
In vivo genome editing using Staphylococcus aureus Cas9.
Nature. 2015, 520:186-191
15. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F#, Sharp PA#.
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
Nature Biotechnology. 2014, 32:670-676
16. Wu X, Kriz AJ, Sharp PA.
Target specificity of the CRISPR-Cas9 system.
Quantitative Biology. 2014, 2:59-70 (review & cover, peer reviewed)
17. Chen S*, Xue Y*, Wu X, Cong L, Bhutkar A, Bell E, Zhang F, Langer R, Sharp PA.
Global microRNA depletion suppresses tumor angiogenesis.
Genes & Development. 2014, 28:1054-1067
18. Wu X, Sharp PA.
Divergent transcription: a driving force for new gene origination?
Cell. 2013, 155:990-996 (perspective/theory, peer reviewed)
19. Almada AA*, Wu X*, Kriz AJ, Burge CB, Sharp PA.
Promoter directionality is controlled by U1 snRNP and polyadenylation signals.
Nature. 2013, 499:360-363
20. Cong L*, Ran FA*, Cox D, Lin S, Barretto R, Habib R, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F.
Multiplex genome engineering using CRISPR/Cas systems.
Science. 2013, 339 (6121):819-823
21. Hsu PD*, Scott DA*, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F.
DNA targeting specificity of RNA-guided Cas9 nucleases.
Nature Biotechnology. 2013, 31:827-832 (cover story)
22. Lyubimova A, Itzkovitz S, Junker JP, Fan ZP, Wu X, van Oudenaarden A.
Single-molecule mRNA detection and counting in mammalian tissue.
Nature Protocols. 2013, 8:1743–1758
23. Chen Y, Wu X, Jiang R.
Integrating human omics data to prioritize candidate genes.
BMC Medical Genomics. 2013, 6:57
24. Wu X, Li S.
Cancer gene prediction using a network approach.
Cancer Systems Biology (Edited by Wang E). CRC Press, 2010, Chapter 11:191-212 (book chapter)
25. Wu X, Liu Q, Jiang R.
Align human interactome with phenome to identify causative genes and networks underlying disease families.
Bioinformatics. 2009, 25:98-104
26. Tang W, Wu X, Jiang R, Li Y.
Epistatic module detection for case-control studies: A Bayesian model with a Gibbs sampling strategy.
PLOS Genetics. 2009, 5(5):e1000464
27. Jiang R, Tang W, Wu X, Fu W.
A random forest approach to the detection of epistatic interactions in case-control studies.
BMC Bioinformatics. 2009, 10(Suppl 1):S65
28. Zhang W, Zeng F, Wu X, Zhang X, Jiang R.
A comparative study of ensemble learning approaches in the classification of breast cancer metastasis.
International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. 2009, 242-245
29. Jiang R, Zeng F, Zhang W, Wu X, Yu Z.
Accelerating genome-wide association studies using CUDA compatible graphics processing units.
International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. 2009, 70-76
30. Wu X, Jiang R, Zhang MQ, Li S.
Network-based global inference of human disease genes.
Molecular Systems Biology. 2008, 4:189
An integrated toolkit for microglia functional genomics.
Genome Medicine, under review
2. Zhang Y*, Zhang W*, Zhao J, Ito T, Jin J, Aparicio AO, Zhou J, Guichard VA, Fang Y, Que J, Urban JF Jr, Hanna JH, Ghosh S, Wu X, Ding L, Basu U, Huang Y
Lineage-specific requirement of m6A RNA methylation for innate lymphoid cell responses.
Nature Immunology, accepted in principle
3. Kesner JS*, Chen Z*, Shi P, Aparicio OA, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X.
Noncoding translation mitigation.
Nature, in press
Related preprint: bioRxiv, 2022.07.20.500724; doi: https://doi.org/10.1101/2022.07.20.500724
4. Shi P#, Murphy MR, Aparicio AO, Kesner JS, Fang Z, Chen Z, Trehan A, Guo Y, Wu X#.
Collateral activity of the CRISPR/RfxCas13d system in human cells.
Communications Biology, 2023, 6:334
Related preprint: bioRxiv, 2021, 2021.11.30.470032; doi: https://doi.org/10.1101/2021.11.30.470032
5. Zhang C*, Konermann S*, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D.
Structural basis for the RNA-guided ribonuclease activity of CRISPR-Cas13d.
Cell. 2018, 175:212-223
6. Tycko J, Barrera LA, Huston N, Friedland AE, Wu X, Gootenberg JS, Abudayyeh OO, Myer VE, Wilson CJ, Hsu PD.
Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells.
Nature Communications. 2018, 9:2962
7. Jiang W*, Wei Y*, Long Y*, Owen A, Wang B, Wu X, Luo S, Dang Y, Ma DK.
A genetic program mediates cold-warming response and promotes stress-induced phenoptosis in C. elegans.
eLife. 2018, 7:e35037
8. Liu XS, Wu H, Krzisch M, Wu X, Greaf J, Muffat J, Hnisz D, Li C, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R.
Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene.
Cell. 2018, 172:979–992
9. Chiu AC*, Suzuki HI*, Wu X, Mahat DB, Kriz AJ, Sharp PA.
Transcriptional Pause Sites Delineate Stable Nucleosome-Associated Premature Polyadenylation Suppressed by U1 snRNP.
Molecular Cell. 2018, 69:648–663
10. Wu X, Bartel DP.
Widespread influence of 3′-end structures on mammalian mRNA processing and stability.
Cell. 2017, 169:905–917
11. Wu X#, Bartel DP#.
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences.
Nucleic Acids Research. 2017, W1:gkx323
12. Liu XS*, Wu H*, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Shivalila CS, Dadon D, Young RA, Jaenisch R.
Editing DNA methylation in the mammalian genome.
Cell. 2016, 167:233-247
13. Zhang X, Chen MH, Wu X, Kodani A, Fan J, Doan R, Ozawa M, Ma J, Yoshida N, Reiter J, Black DL, Kharchenko PV, Sharp PA, Walsh CA.
Cell-Type-Specific Alternative Splicing Governs Cell Fate in the Developing Cerebral Cortex.
Cell. 2016, 166:1147-1162 (cover story)
14. Ran FA*, Cong L*, Yan WX*, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F.
In vivo genome editing using Staphylococcus aureus Cas9.
Nature. 2015, 520:186-191
15. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F#, Sharp PA#.
Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.
Nature Biotechnology. 2014, 32:670-676
16. Wu X, Kriz AJ, Sharp PA.
Target specificity of the CRISPR-Cas9 system.
Quantitative Biology. 2014, 2:59-70 (review & cover, peer reviewed)
17. Chen S*, Xue Y*, Wu X, Cong L, Bhutkar A, Bell E, Zhang F, Langer R, Sharp PA.
Global microRNA depletion suppresses tumor angiogenesis.
Genes & Development. 2014, 28:1054-1067
18. Wu X, Sharp PA.
Divergent transcription: a driving force for new gene origination?
Cell. 2013, 155:990-996 (perspective/theory, peer reviewed)
19. Almada AA*, Wu X*, Kriz AJ, Burge CB, Sharp PA.
Promoter directionality is controlled by U1 snRNP and polyadenylation signals.
Nature. 2013, 499:360-363
20. Cong L*, Ran FA*, Cox D, Lin S, Barretto R, Habib R, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F.
Multiplex genome engineering using CRISPR/Cas systems.
Science. 2013, 339 (6121):819-823
21. Hsu PD*, Scott DA*, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F.
DNA targeting specificity of RNA-guided Cas9 nucleases.
Nature Biotechnology. 2013, 31:827-832 (cover story)
22. Lyubimova A, Itzkovitz S, Junker JP, Fan ZP, Wu X, van Oudenaarden A.
Single-molecule mRNA detection and counting in mammalian tissue.
Nature Protocols. 2013, 8:1743–1758
23. Chen Y, Wu X, Jiang R.
Integrating human omics data to prioritize candidate genes.
BMC Medical Genomics. 2013, 6:57
24. Wu X, Li S.
Cancer gene prediction using a network approach.
Cancer Systems Biology (Edited by Wang E). CRC Press, 2010, Chapter 11:191-212 (book chapter)
25. Wu X, Liu Q, Jiang R.
Align human interactome with phenome to identify causative genes and networks underlying disease families.
Bioinformatics. 2009, 25:98-104
26. Tang W, Wu X, Jiang R, Li Y.
Epistatic module detection for case-control studies: A Bayesian model with a Gibbs sampling strategy.
PLOS Genetics. 2009, 5(5):e1000464
27. Jiang R, Tang W, Wu X, Fu W.
A random forest approach to the detection of epistatic interactions in case-control studies.
BMC Bioinformatics. 2009, 10(Suppl 1):S65
28. Zhang W, Zeng F, Wu X, Zhang X, Jiang R.
A comparative study of ensemble learning approaches in the classification of breast cancer metastasis.
International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. 2009, 242-245
29. Jiang R, Zeng F, Zhang W, Wu X, Yu Z.
Accelerating genome-wide association studies using CUDA compatible graphics processing units.
International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. 2009, 70-76
30. Wu X, Jiang R, Zhang MQ, Li S.
Network-based global inference of human disease genes.
Molecular Systems Biology. 2008, 4:189
