Honors and awards


  1. ❖Recommended poster by Faculty of 1000, 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA, 2012.


  1. ❖Kentucky Opportunity Fellowship, University of Kentucky, 2011.


  1. ❖Huawei Scholarship, University of Science and Technology of China, 2007.

 

Yin Hu is currently a research scientist in the Computational Oncology division at Sage Bionetworks. He received his Ph.D. degree in Computer Science in year 2014 and his concurrent M.S. in Statistics in 2013, both from the University of Kentucky. Prior to his graduate studies, Yin finished a B.E. in Computer Science in the University of Science and Technology of China (USTC).


During his Ph.D., Yin focused on research topics in data mining and bioinformatics, under the supervision of Dr. Jinze Liu. The title of his Ph.D. dissertation was "A novel computational framework for transcriptome analysis with RNA-seq data." Now he is continuing on his work in algorithm development for high-throughput sequencing data, with a focus on cancer genomics.

 

Yin Hu, Ph.D.


Research Scientist

Sage Bionetworks

Contact: yin.hu AT sagebase.org

Publications


  1. ❖Adam Ewing*, Kathleen Houlahan*, Yin Hu*, Kyle Ellrott, Cristian Caloian, Takafumi Yamaguchi, J Bare, Christine P'ng, Daryl Waggott, Veronica Sabelnykova, Michael Kellen, Thea Norman, David Haussler, Gustavo Stolovitzky, Adam Margolin, Joshua Stuart, Stephen Friend. (2015) Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic single nucleotide variant detection. Nature Methods, accepted. (* co-first author)


  1. ❖Paul C. Boutros, Adam D. Ewing, Kyle Ellrott, Thea C. Norman, Kristen K. Dang, Yin Hu, Michael R. Kellen, Christine Suver, J. Christopher Bare, Lincoln D. Stein, Paul T. Spellman, Gustavo Stolovitzky, Stephen H. Friend, Adam A. Margolin, and Joshua M. Stuart. (2014) Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics, 46 (4), 318-319. [link]


  1. ❖Yan Huang, Yin Hu, and Jinze Liu. (2014) Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq. BMC Bioinformatics, 15 (Suppl 9), S3. (Also in 4th Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ), March 31 - April 1, 2014, Pittsburgh, USA.) [link]


  1. ❖Yin Hu, Yan Huang, Ying Du, Christian Orellana, Darshan Singh, Amy Johnson, Anais Monroy, Pei-Fen Kuan, Scott Hammond, Liza Makowski, Scott Randell, Derek Chiang, David Hayes, Corbin Jones, Yufeng Liu, Jan Prins, Jinze Liu. (2013) DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq. Nucleic Acids Research, 41 (2), e39. [link]


  1. ❖Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Chiang, Yufeng Liu, Jan F. Prins, and Jinze Liu. (2013) A Robust Method for Transcript Quantification with RNA-seq Data. Journal of Computational Biology, 20(3): 167-187. (Also in 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Apr 21 - Apr 24, 2012, Barcelona, Spain.) [link]


  1. ❖Darshan Singh, Christian F. Orellana, Yin Hu, Corbin D. Jones, Yufeng Liu, Derek Y. Chiang, Jinze Liu, and Jan F. Prins. (2011) FDM: a graph-based statistical method to detect differential transcription using RNA-seq data. Bioinformatics, 27(19): 2633-640. [link]


  1. ❖Yin Hu, Kai Wang, Xiaping He, Derek Y. Chiang, Jan F. Prins, and Jinze Liu. (2010) A Probabilistic Framework for Aligning Paired-end RNA-seq Data. Bioinformatics, 26(16):1950-1957. [link]


  1. ❖Jizhou Gao, Yin Hu, Jinze Liu, and Ruigang Yang. (2009) Unsupervised Learning of High-order Structural Semantics from Images. International Conference on Computer Vision (ICCV), Sept 26 - Oct 4, 2009, Kyoto, Japan, pp.2122-2129. [link]

Education


  1. ❖Ph.D. in Computer Science, University of Kentucky, Lexington, KY, USA 2014


  1. ❖M.Sc. in Statistics (Mathematical Track), University of Kentucky, Lexington, KY, USA 2013


  1. ❖B.Eng. in Computer Science, University of Science and Technology of China, Hefei, China 2008     

Conference talks


  1. ❖DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (ACMBCB), highlights track, Washington DC, USA, 2013


  1. ❖Detection and quantification of differentially expressed genes using RNA-seq. The 2011 Southeast Regional IDeA Meeting, New Orleans, USA, 2011


  1. ❖A probabilistic framework for accurate detection of gene fusion events with paired-end RNA-seq reads. ISMB Special Interest Group on High Throughput Sequencing Analysis and Algorithms (HiTSeq), Boston, USA, 2010     


  1. ❖Detecting gene fusion with paired-end reads. The Annual Conference of Midsouth Computational Biology & Bioinformatics Society (MCBIOS), Jonesboro, USA, 2010     

Professional activities


  1. ❖Reviewer: Bioinformatics, PLoS Computational Biology, RECOMB


  1. ❖Program Committee member: ACM-BCB 2015, BIBM 2015

Published abstracts and poster presentations


  1. ❖Yin Hu,Rodrigo Dienstmann, and Justin Guinney. RNA-seq differential transcription analysis of TCGA colorectal cancer (CRC) transcriptomes reveals subtype-specific isoform usage. AACR Annual Meeting 2015, Philadelphia, USA, April, 2015.


  1. ❖Yin Hu,Rodrigo Dienstmann, and Justin Guinney. RNA-seq differential splicing analysis of over six hundred colorectal cancer transcriptomes reveals subtype-specific isoform usage. AACR Special Conference on Computational and Systems Biology of Cancer, San Francisco, USA, February, 2015.


  1. ❖                                Yin Hu, Yan Huang, Ying Du, Christian F. Orellana, Darshan Singh, Amy Johnson, Anais Monroy, Pei-Fen Kuan, Scott Hammond, Liza Makowski, Scott Randell, Derek Y. Chiang, D. Neil Hayes, Corbin D. Jones, Yufeng Liu, Jan F. Prins, and Jinze Liu. DiffSplice: the genome-wide detection of differential splicing events with RNA-seq. 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, USA, July, 2012.


  1. ❖Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, and Jinze Liu. A robust linear framework for transcript quantification using Multi-Splice features. 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long Beach, USA, July, 2012.


  1. ❖Yin Hu, Yan Huang, Derek Y. Chiang, Corbin D. Jones, Jan F. Prins, and Jinze Liu. An Ab Initio Method for Differential Transcriptome Analysis. UT-ORNL-KBRIN Bioinformatics Summit 2012, Louisville, USA, March, 2012.


  1. ❖Yan Huang, Yin Hu, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, and Jinze Liu. A linear framework for transcript quantification from RNA-seq data. UT-ORNL-KBRIN Bioinformatics Summit 2012, Louisville, USA, March, 2012. (Oral presentation)


  1. ❖Yan Huang, Yin Hu, Matthew S. Hestand, Corbin D. Jones, James N. MacLeod, Derek Y. Chiang, Yufeng Liu, Jan F. Prins, and Jinze Liu. A robust method for transcript quantification with RNA-seq data. ISMB Special Interest Group on High Throughput Sequencing Analysis and Algorithms (HiTSeq), Vienna, Austria, July, 2011.

Software


  1. ❖DiffSplice: detection and quantification of differential transcriptome expression using RNA-seq data.

            http://www.netlab.uky.edu/p/bioinfo/DiffSplice


  1. ❖MapPER: probabilistic alignment and full fragment reconstruction of paired-end RNA-seq data.

            http://www.netlab.uky.edu/p/bioinfo/MapPER