Jingyi Jessica Li






I'm an Assistant Professor in the Department of Statistics at University of California, Los Angeles. Prior to that, I obtained my Ph.D. degree from the Interdepartmental Group in Biostatistics at Univeristy of California, Berkeley. I work with Profs Peter J. Bickel and Haiyan Huang. I received my B.S. (summa cum laude) from Department of Biological Sciences and Technology at Tsinghua University, China in 2007.


Research Interests

My primary research interests include developing statistical methods for understanding scientific problems, especially biological questions related to genome-wide data. I'm also interested in developing new statistical methodologies that are motivated by specific scientific problems but have broad applications. I have developed a method called SLIDE (Sparse Linear modeling of RNA-Seq data for Isoform Discovery and Abundance Estimation) and completed several bioinformatic analyses on D. melanogaster CRM discovery from ChIP-chip data.  Currently I'm working on an extension of SLIDE to multiple RNA-Seq samples, and a modENCODE project on comparison of D. melanogaster and C. elegans developmental stages from RNA-Seq data.  I'm also working with Prof. Bickel on a theoretical project on developing a measure of non-functional relationships from pairwise data.


Publications

1. Li JJ, Bickel PB, Zhang S, Huang H (2012). Joint modeling of multiple samples for mRNA isoform discovery and abundance estimation from RNA-Seq data. In preparation.

2. Li JJ, Huang H, Bickel PB, Brenner SE (2012). Comparison of D. melanogaster and C. elegans developmental stages by modENCODE RNA-Seq data. In preparation.

3. Li JJ, Huang H, Qian M, Zhang X (2012). Transcriptome analysis using next-generation sequencing.  Book chapter, in press.

4. Li JJ, Bickel PB, Biggin MD (2012). System Wide Analyses have Underestimated Protein Abundances and Transcriptional Importance in Animals. Submitted to Integrative Biology. [ArXiv version]

5. Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer B, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PB, Biggin MD, Celniker SE (2012). DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proc Natl Acad Sci. USA, 109(52):21330–21335. [html]

6. The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74. [html]

7. Gao Q, Ho C, Jia Y, Li JJ, Huang H (2012). Biclustering of linear patterns in gene expression data (CLiP). Journal of Computational Biology 19(6): 619-631. [html]

8. Li JJ, Jiang C-R, Brown BJ, Huang H, Bickel PJ (2011). Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation. Proc Natl Acad Sci. USA, 108(50):19867-19872. [software(SLIDE)] [html]

9. MacArthur S*, Li XY*, Li J*, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keranen SV, Knowles DW, Stapleton M, Bickel P, Biggin MD, Eisen MB (2009). Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology 10, R80. [html]

* Joint first authors


Softwares

SLIDE(Sparse Linear modeling of RNA-Seq data for Isoform Discovery and Abundance Estimation)

(Updates on May 7th, 2012 -- A feature was added for estimating the annotated isoform abundance without doing isoform discovery.)

(Updates on Apr 18th, 2012 -- A feature was added for removing erroneously mapped reads; a bug of multiprocessing was fixed.)

(Updates on Apr 5th, 2012 -- A feature was added for handling single-end RNA-Seq reads or a mixture of single-end and paired-end reads.)

Any feedback or comments are highly welcome!


Conferences and Posters

1. UC Systemwide Bioengineering Symposium, Berkeley, June 2012.  Talk title: "Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation."

2. Joint mod/mouse/ENCODE AWG/PI meeting, MIT, May 2012. Talk title: "Developmental stage comparison of D. melanogaster and C. elegans and tissue and cell line comparison of D. melanogaster and H. sapiens with modENCODE/ENCODE RNA-Seq data."

3. Bay Area RNA Club, UCSF, Jan 2012.  Talk title: "Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation."

4. Cold Spring Harbor Asia Conferences: Bioinformatics of Human and Animal Genomics, Suzhou, China, Nov 2011. Talk title: "Sparse linear modeling of RNA-seq data for isoform discovery and abundance estimation". (selected as the Best Presentation Award -- CSHA Fellowship)

5. Joint mod/ENCODE Consortia Meeting, Washington DC, May 2011. Talk and poster title: "Comparison between Developmental Stages of D. melanogaster and C. elegans with RNA-Seq data".


Teaching

1. Graduate student instructor (GSI) of STAT 215A (PhD course of Statistical Models: Theory and Application), Fall 2012, Department of Statistics, UC Berkeley

2. Graduate student instructor (GSI) of STAT 210A (PhD course of Theoretical Statistics), Fall 2010, Department of Statistics, UC Berkeley

3. Graduate student instructor (GSI) of STAT 200B (MA course of Introduction to Probability and Statistics at an Advanced Level), Spring 2010, Department of Statistics, UC Berkeley

4. Graduate student instructor (GSI) of STAT 131A (Upper level undergraduate course of Statistical Inferences for Social and Life Scientists), Spring 2009, Department of Statistics, UC Berkeley


Selected Awards

1. International Dissertation Field Work Grant, UC Berkeley Institute of International Studies, 2012-2013

2. Outstanding Graduate Student Instructor Award, UC Berkeley, 2010-2011

3. Distinguished Graduate of Class 2007, Tsinghua University, 2007


CV

[pdf]


Contact

Please contact me at jli [at] stat.ucla.edu