A New Fast Heuristic for Computing the Breakpoint Phylogeny and Experimental Phylogenetic Analyses of Real and Synthetic Data. - Mary E. Cosner; Robert K. Jansen; Bernard M. E. Moret; Linda A. Raubeson; Li-San Wang; Tandy J. Warnow; Stacia K. Wyman (ISMB, 2000)

New approaches for reconstructing phylogenies from gene order data. - Bernard M. E. Moret; Li-San Wang; Tandy J. Warnow; Stacia K. Wyman (ISMB (Supplement of Bioinformatics), 2001)

Estimating true evolutionary distances between genomes. - Li-San Wang; Tandy J. Warnow (STOC, 2001)

Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes. - Li-San Wang (WABI, 2001)

Statistically based postprocessing of phylogenetic analysis by clustering. - Cara Stockham; Li-San Wang; Tandy J. Warnow (ISMB, 2002)

Fast Phylogenetic Methods for the Analysis of Genome Rearrangement Data: An Empirical Study. - Li-San Wang; Robert K. Jansen; Bernard M. E. Moret; Linda A. Raubeson; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2002)

Genome Rearrangement Phylogeny Using Weighbor. - Li-San Wang (WABI, 2002)

Toward New Software for Computational Phylogenetics. - Bernard M. E. Moret; Li-San Wang; Tandy J. Warnow (Computer, 2002)

Steps toward accurate reconstructions of phylogenies from gene-order data. - Bernard M. E. Moret; Jijun Tang; Li-San Wang; Tandy J. Warnow (J. Comput. Syst. Sci., 2002)

Analyzing the Order of Items in Manuscripts of The Canterbury Tales. - Matthew Spencer; Barbara Bordalejo; Li-San Wang; Adrian C. Barbrook; Linne R. Mooney; Peter Robinson 003; Tandy J. Warnow; Christopher J. Howe (Comput. Humanit., 2003)

Genome Identification and Classification by Short Oligo Arrays. - Stanislav Angelov; Boulos Harb; Sampath Kannan; Sanjeev Khanna; Junhyong Kim; Li-San Wang (WABI, 2004)

Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony. - Jijun Tang; Li-San Wang (BIBE, 2005)

RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. - Luay Nakhleh; Derek A. Ruths; Li-San Wang (COCOON, 2005)

Phylogenetic Networks, Trees, and Clusters. - Luay Nakhleh; Li-San Wang (International Conference on Computational Science (2), 2005)

Enhanced position weight matrices using mixture models. - Sridhar Hannenhalli; Li-San Wang (ISMB (Supplement of Bioinformatics), 2005)

An Interaction-Dependent Model for Transcription Factor Binding. - Li-San Wang; Shane T. Jensen; Sridhar Hannenhalli (Systems Biology and Regulatory Genomics, 2005)

Phylogenetic Networks: Properties and Relationship to Trees and Clusters. - Luay Nakhleh; Li-San Wang (Trans. Comp. Sys. Biology, 2005)

Transcriptional Target Prediction Using Qualitative Reasoning. - Li-San Wang; Doris Wagner; Chang Seob Kwon; Yanhui Su; Junhyong Kim (EMBC, 2006)

Dense subgraph computation via stochastic search: application to detect transcriptional modules. - Logan Everett; Li-San Wang; Sridhar Hannenhalli (ISMB (Supplement of Bioinformatics), 2006)

Weighted isotonic regression under the L1 norm. - Stanislav Angelov; Boulos Harb; Sampath Kannan; Li-San Wang (SODA, 2006)

Reconstructing Chromosomal Evolution. - Li-San Wang; Tandy J. Warnow (SIAM J. Comput., 2006)

Distance-based genome rearrangement phylogeny. - Li-San Wang; Tandy J. Warnow (Mathematics of Evolution and Phylogeny, 2007)

A Bayesian approach to efficient differential allocation for resampling-based significance testing. - Shane T. Jensen; Sameer Soi; Li-San Wang (BMC Bioinform., 2009)

Correcting population stratification in genetic association studies using a phylogenetic approach. - Mingyao Li; Muredach P. Reilly; Daniel J. Rader; Li-San Wang (Bioinform., 2010)

Invited: Multiclass RNA function classification using next-generation sequencing. - Paul Ryvkin; Yuk Yee Leung; Li-San Wang; Brian D. Gregory (ICCABS, 2011)

The Impact of Multiple Protein Sequence Alignment on Phylogenetic Estimation. - Li-San Wang; James H. Leebens-Mack; P. Kerr Wall; Kevin Beckmann; Claude W. dePamphilis; Tandy J. Warnow (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

DACTAL: divide-and-conquer trees (almost) without alignments. - Serita M. Nelesen; Kevin Liu; Li-San Wang; C. Randal Linder; Tandy J. Warnow (Bioinform., 2012)

SAVoR: a server for sequencing annotation and visualization of RNA structures. - Fan Li 002; Paul Ryvkin; Daniel M. Childress; Otto Valladares; Brian D. Gregory; Li-San Wang (Nucleic Acids Res., 2012)

DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments. - 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 (Bioinform., 2013)

HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements. - Yih-Chii Hwang; Chiao-Feng Lin; Otto Valladares; John Malamon; Pavel P. Kuksa; Qi Zheng; Brian D. Gregory; Li-San Wang (Bioinform., 2015)

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences. - Siavash Mirarab; Nam Nguyen; Sheng Guo; Li-San Wang; Junhyong Kim; Tandy J. Warnow (J. Comput. Biol., 2015)

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer). - Nathan D. Berkowitz; Ian M. Silverman; Daniel M. Childress; Hilal Kazan; Li-San Wang; Brian D. Gregory (BMC Bioinform., 2016)

DASHR: database of small human noncoding RNAs. - Yuk Yee Leung; Pavel P. Kuksa; Alexandre Amlie-Wolf; Otto Valladares; Lyle H. Ungar; Sampath Kannan; Brian D. Gregory; Li-San Wang (Nucleic Acids Res., 2016)

Functional annotation of genomic variants in studies of late-onset Alzheimer's disease. - 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 (Bioinform., 2018)

Integrative DNA copy number detection and genotyping from sequencing and array-based platforms. - Zilu Zhou; Weixin Wang 004; Li-San Wang; Nancy Ruonan Zhang (Bioinform., 2018)

SPAR: small RNA-seq portal for analysis of sequencing experiments. - Pavel P. Kuksa; Alexandre Amlie-Wolf; Zivadin Katanic; Otto Valladares; Li-San Wang; Yuk Yee Leung (Nucleic Acids Res., 2018)

DASHR 2.0: integrated database of human small non-coding RNA genes and mature products. - Pavel P. Kuksa; Alexandre Amlie-Wolf; Zivadin Katanic; Otto Valladares; Li-San Wang; Yuk Yee Leung (Bioinform., 2019)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - 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 (Bioinform., 2019)

VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. - 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 (Bioinform., 2019)

SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants. - 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 (Bioinform., 2020)

Omnibus and robust deconvolution scheme for bulk RNA sequencing data integrating multiple single-cell reference sets and prior biological knowledge. - Chixiang Chen; Yuk Yee Leung; Matei Ionita; Li-San Wang; Mingyao Li (Bioinform., 2022)

hipFG: high-throughput harmonization and integration pipeline for functional genomics data. - Jeffrey Cifello; Pavel P. Kuksa; Naveensri Saravanan; Otto Valladares; Li-San Wang; Yuk Yee Leung (Bioinform., 2023)