Li-San Wang

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 11

Top Topics

Sequence Alignment

Functional Genomics

High Throughput

Top Venues

Nucleic Acids Res.

J. Comput. Biol.

Publications

Jeffrey Cifello, Pavel P. Kuksa, Naveensri Saravanan, Otto Valladares, Li-San Wang, Yuk Yee Leung
hipFG: high-throughput harmonization and integration pipeline for functional genomics data. Bioinform. 39 (11) (2023)
Chixiang Chen, Yuk Yee Leung, Matei Ionita, Li-San Wang, Mingyao Li
Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge. Bioinform. 38 (19) (2022)
Pavel P. Kuksa, Chien-Yueh Lee, Alexandre Amlie-Wolf, Prabhakaran Gangadharan, Elizabeth E. Mlynarski, Yi-Fan Chou, Han-Jen Lin, Heather Issen, Emily Greenfest-Allen, Otto Valladares, Yuk Yee Leung, Li-San Wang
SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. Bioinform. 36 (12) (2020)
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. Bioinform. 35 (6) (2019)
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, William J. Salerno, Gerard D. Schellenberg, Li-San Wang
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinform. 35 (10) (2019)
Yuk Yee Leung, Otto Valladares, Yi-Fan Chou, Han-Jen Lin, Amanda Kuzma, Laura Cantwell, Liming Qu, Prabhakaran Gangadharan, William J. Salerno, Gerard D. Schellenberg, Li-San Wang
VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinform. 35 (11) (2019)
Mariusz Butkiewicz, Elizabeth E. Blue, Yuk Yee Leung, Xueqiu Jian, Edoardo Marcora, Alan E. Renton, Amanda Kuzma, Li-San Wang, Daniel C. Koboldt, Jonathan L. Haines, William S. Bush
Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. Bioinform. 34 (16) (2018)
Zilu Zhou, Weixin Wang, Li-San Wang, Nancy Ruonan Zhang
Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. Bioinform. 34 (14) (2018)
Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
SPAR: small RNA-seq portal for analysis of sequencing experiments. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Nathan D. Berkowitz, Ian M. Silverman, Daniel M. Childress, Hilal Kazan, Li-San Wang, Brian D. Gregory
A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). BMC Bioinform. 17 (2016)
Yuk Yee Leung, Pavel P. Kuksa, Alexandre Amlie-Wolf, Otto Valladares, Lyle H. Ungar, Sampath Kannan, Brian D. Gregory, Li-San Wang
DASHR: database of small human noncoding RNAs. Nucleic Acids Res. 44 (Database-Issue) (2016)
Yih-Chii Hwang, Chiao-Feng Lin, Otto Valladares, John Malamon, Pavel P. Kuksa, Qi Zheng, Brian D. Gregory, Li-San Wang
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. Bioinform. 31 (8) (2015)
Siavash Mirarab, Nam Nguyen, Sheng Guo, Li-San Wang, Junhyong Kim, Tandy J. Warnow
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. J. Comput. Biol. 22 (5) (2015)
Chiao-Feng Lin, Otto Valladares, Daniel M. Childress, Egor Klevak, Evan T. Geller, Yih-Chii Hwang, Ellen A. Tsai, Gerard D. Schellenberg, Li-San Wang
DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments. Bioinform. 29 (19) (2013)
Fan Li, Paul Ryvkin, Daniel M. Childress, Otto Valladares, Brian D. Gregory, Li-San Wang
SAVoR: a server for sequencing annotation and visualization of RNA structures. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Serita M. Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder, Tandy J. Warnow
DACTAL: divide-and-conquer trees (almost) without alignments. Bioinform. 28 (12) (2012)
Li-San Wang, James H. Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, Tandy J. Warnow
The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (4) (2011)
Paul Ryvkin, Yuk Yee Leung, Li-San Wang, Brian D. Gregory
Invited: Multiclass RNA function classification using next-generation sequencing. ICCABS (2011)
Mingyao Li, Muredach P. Reilly, Daniel J. Rader, Li-San Wang
Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinform. 26 (6) (2010)
Shane T. Jensen, Sameer Soi, Li-San Wang
A Bayesian approach to efficient differential allocation for resampling-based significance testing. BMC Bioinform. 10 (2009)
Stanislav Angelov, Boulos Harb, Sampath Kannan, Li-San Wang
norm. SODA (2006)
Li-San Wang, Tandy J. Warnow
Reconstructing Chromosomal Evolution. SIAM J. Comput. 36 (1) (2006)
Logan Everett, Li-San Wang, Sridhar Hannenhalli
Dense subgraph computation via stochastic search: application to detect transcriptional modules. ISMB (Supplement of Bioinformatics) (2006)
Li-San Wang, Doris Wagner, Chang Seob Kwon, Yanhui Su, Junhyong Kim
Transcriptional Target Prediction Using Qualitative Reasoning. EMBC (2006)
Jijun Tang, Li-San Wang
Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony. BIBE (2005)
Luay Nakhleh, Li-San Wang
Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) (2005)
Luay Nakhleh, Li-San Wang
Phylogenetic Networks: Properties and Relationship to Trees and Clusters. Trans. Comp. Sys. Biology 2 (2005)
Li-San Wang, Shane T. Jensen, Sridhar Hannenhalli
An Interaction-Dependent Model for Transcription Factor Binding. Systems Biology and Regulatory Genomics (2005)
Luay Nakhleh, Derek A. Ruths, Li-San Wang
RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON (2005)
Sridhar Hannenhalli, Li-San Wang
Enhanced position weight matrices using mixture models. ISMB (Supplement of Bioinformatics) (2005)
Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, Li-San Wang
Genome Identification and Classification by Short Oligo Arrays. WABI (2004)
Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy J. Warnow, Christopher J. Howe
. Comput. Humanit. 37 (1) (2003)
Li-San Wang
Genome Rearrangement Phylogeny Using Weighbor. WABI (2002)
Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow
Toward New Software for Computational Phylogenetics. Computer 35 (7) (2002)
Cara Stockham, Li-San Wang, Tandy J. Warnow
Statistically based postprocessing of phylogenetic analysis by clustering. ISMB (2002)
Bernard M. E. Moret, Jijun Tang, Li-San Wang, Tandy J. Warnow
Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65 (3) (2002)
Li-San Wang, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Tandy J. Warnow
Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. Pacific Symposium on Biocomputing (2002)
Li-San Wang, Tandy J. Warnow
Estimating true evolutionary distances between genomes. STOC (2001)
Li-San Wang
Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes. WABI (2001)
Bernard M. E. Moret, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman
New approaches for reconstructing phylogenies from gene order data. ISMB (Supplement of Bioinformatics) (2001)
Mary E. Cosner, Robert K. Jansen, Bernard M. E. Moret, Linda A. Raubeson, Li-San Wang, Tandy J. Warnow, Stacia K. Wyman
A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. ISMB (2000)