Publications

Published or Accepted Peer-Reviewed Papers

2013

72. Jesse M. Platt, Paul Ryvkin, Jennifer J. Wanat, Greg Donahue, M. Dan Ricketts, Steven P. Barrett, Shufei Song, Alejandro Chavez, Khaled Omar Abdallah, Stephen R. Master, Li-San Wang, and F. Brad Johnson.
    Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence.
    Genes & Development, in press, 2013.
71. Yuk Yee Leung, Paul Ryvkin, Lyle Ungar, Brian Gregory*, Li-San Wang*.
    CoRAL: Predicting non-coding RNAs from small RNA-sequencing data.
    Nucleic Acids Research, in press.
70. Reitz C, Jun G, Naj A, Rajbhandary R, Vardarajan B N, Wang L-S, Valladares O, Lin C-F, Larson EB, Graff-Radford NR, Evans D, De Jager PL, Crane PK, Buxbaum JD, Murrell JR, Raj T, Ertekin-Taner N, Logue M, Baldwin CT, Green RC, Barnes LL, Cantwell LB, Fallin DM, Go RCP, Griffith P, Obisesan TO, Manly JJ, Lunetta KL, Kamboh IM, Lopez OL, Bennett DA, Hendrie H, Hall KS, Goate AM, Byrd GS, Kukull WA, Foroud TM, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Mayeux R, Alzheimer Disease Genetics Consortium.
    Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans.
    JAMA, 309(14):1483-92, 2013.
69. Miyashita A, Koike A, Jun G, Wang L-S, Takahashi S, Matsubara E, Kawarabayashi T, Shoji M, Tomita N, Arai H, Asada T, Harigaya Y, Ikeda M, Amari M, Hanyu H, Higuchi S, Ikeuchi T, Nishizawa M, Suga M, Kawase Y, Akatsu H, Kosaka K, Yamamoto T, Imagawa M, Hamaguchi T, Yamada M, Moriaha T, Takeda M, Takao T, Nakata K, Fujisawa Y, Sasaki K, Watanabe K, Nakashima K, Urakami K, Ooya T, Takahashi M, Yuzuriha T, Serikawa K, Yoshimoto S, Nakagawa R, Kim J-W, Ki C-S, Won H-H, Na DL, Seo SWon, Mook-Jung I, George-Hyslop PSt., Mayeux R, Haines JL, Pericak-Vance MA, Yoshida M, Nishida N, Tokunaga K, Yamamoto K, Tsuji S, Kanazawa I, Ihara Y, Schellenberg GD, Farrer LA, Kuwano R.
    SORL1 Is Genetically Associated with Late-Onset Alzheimer’s Disease in Japanese, Koreans and Caucasians.
    PLoS ONE, 8(4):e58618, 2013.
68. Yih-Chii Hwang, Qi Zheng, Brian Gregory*, Li-San Wang*.
    High-throughput identification of long-range regulatory elements and their target promoters in the human genome.
    Nucleic Acids Research, 10.1093/nar/gkt188, 2013.
67. Urtishak KA, Edwards AY, Wang LS, Hudome A, Robinson BW, Barrett JS, Cao K, Cory L, Moore JS, Bantly AD, Yu QC, Chen IM, Atlas SR, Willman CL, Kundu M, Carroll AJ, Heerema NA, Devidas M, Hilden JM, Dreyer ZE, Hunger SP, Reaman GH, Felix CA.
    Potent obatoclax cytotoxicity and activation of triple death mode killing across infant acute lymphoblastic leukemia (ALL).
    Blood, in press, 2013.
66. Holton P, Ryten M, Nalls M, Trabzuni D, Weale ME, Hernandez D, Crehan H, Gibbs JR, Mayeux R, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD; Alzheimer's Disease Genetics Consortium, Ramirez-Restrepo M, Engel A, Myers AJ, Corneveaux JJ, Huentelman MJ, Dillman A, Cookson MR, Reiman EM, Singleton A, Hardy J, Guerreiro R.
    Initial assessment of the pathogenic mechanisms of the recently identified Alzheimer risk Loci.
    Annals of Human Genetics, 77(2):85-105, 2013. (Consortium author)
65. Lim ET, Raychaudhuri S, Sanders SJ, Stevens C, Sabo A, Macarthur DG, Neale BM, Kirby A, Ruderfer DM, Fromer M, Lek M, Liu L, Flannick J, Ripke S, Nagaswamy U, Muzny D, Reid JG, Hawes A, Newsham I, Wu Y, Lewis L, Dinh H, Gross S, Wang LS, Lin CF, Valladares O, Gabriel SB, Depristo M, Altshuler DM, Purcell SM; NHLBI Exome Sequencing Project, State MW, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Daly MJ.
    Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders.
    Neuron, 77(2):235-42, 2013.
64. S.E. Arnold, I.E. Vega, J.H. Karlawish, D.A. Wolk, J. Nunez, M. Negron, S.X. Xie, L.S. Wang, E. McCarty-Wood, J.Q. Trojanowski, MD, V. Van Deerlin.
    Frequency and clinicopathological characteristics of presenilin 1 Gly206Ala mutation in Puerto Rican Hispanics with dementia.
    Journal of Alzheimer's Disease, 33(4):1089-95, 2013.

2012

63. Buxbaum JD, Daly MJ, Devlin B, Lehner T, Roeder K, State MW; Autism Sequencing Consortium.
    The autism sequencing consortium: large-scale, high-throughput sequencing in autism spectrum disorders.
    Neuron, 76(6):1052-6, 2012.
62. Whitcomb DC, Larusch J, Krasinskas AM, Klei L, Smith JP, Brand RE, Neoptolemos JP, Lerch MM, Tector M, Sandhu BS, Guda NM, Orlichenko L; Alzheimer’s Disease Genetics Consortium, (52 authors) , Devlin B.
    Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis.
    Nature Genetics, 44(12):1349-54, 2012. (Consortium author)
61. Jun G, Vardarajan BN, Buros J, Yu CE, Hawk MV, Dombroski BA, Crane PK, Larson EB; Alzheimer's Disease Genetics Consortium, Mayeux R, Haines JL, Lunetta KL, Pericak-Vance MA, Schellenberg GD, Farrer LA.
    Comprehensive search for Alzheimer disease susceptibility loci in the APOE region.
    Archives of Neurology, 69(10):1270-9, 2013. (Consortium author)
60. Turner PE, McBride RC, Duffy S, Montville R, Wang LS, Yang YW, Lee SJ, Kim J.
    Evolutionary genomics of host-use in bifurcating demes of RNA virus phi-6.
    BMC Evolutionary Biology, 12(1):153, 2012.
59. Coppola G, Chinnathambi S, Jiyong Lee J, Dombroski BA, Baker MC, Soto-Ortolaza AI, Lee SE, Klein E, Huang AY, Sears R, Lane JR, Karydas AM, Kenet RO, Biernat J, Wang LS, ... (59 other authors).
    Evidence for a Role of The Rare p.A152T Variant in MAPT in increasing the Risk for FTD-Spectrum and Alzheimer's Diseases.
    Human Molecular Genetics, doi: 10.1093/hmg/dds161, 2012.
58. Zou F, Chai HS, Younkin CS, Allen M, Crook J, Pankratz VS, Carrasquillo MM, Rowley CN, Nair AA, Middha S, Maharjan S, Nguyen T, Ma L, Malphrus KG, Palusak R, Lincoln S, Bisceglio G, Georgescu C, Kouri N, Kolbert CP, Jen J, Haines JL, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD; Alzheimer's Disease Genetics Consortium, Petersen RC, Graff-Radford NR, Dickson DW, Younkin SG, Ertekin-Taner N.
    Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants.
    PLoS Genetics, 8(6):e1002707, 2012.
57. Li-San Wang*, Yuk Yee Leung, Shu-Kai Chang, Susan Leight, Malgorzata Knapik-Czajka, Young Baek, Leslie M. Shaw, Virginia M.-Y. Lee, John Q. Trojanowski, Christopher M. Clark.
    Comparison of xMAP and ELISA assays for detecting CSF biomarkers of Alzheimer's Disease.
    Journal of Alzheimer's Disease, 2012, in press.
56. David J. Irwin, T. McMillan, Jon B. Toledo, Steven E. Arnold, Leslie M. Shaw, Li-San Wang, Vivianna Van Deerlin, Virginia M.-Y. Lee, John Q. Trojanowski, Murray Grossman.
    Comparison of Cerebrospinal Fluid Levels of Tau and Abeta 1-42 in Alzheimer Disease and Frontotemporal Degeneration Using 2 Analytical Platforms.
    Archives of Neurology, 2012, in press.
55. Benjamin M. Neale, Yan Kou, Li Liu, Avi Ma’ayan, Kaitlin E. Samocha, Aniko Sabo, Chiao-Feng Lin, Christine Stevens, Li-San Wang, Vladimir Makarov, Paz Polak, Seungtai Yoon, Jared Maguire, Emily L. Crawford, Nicholas G. Campbell, Evan T. Geller, Otto Valladares, Chad Schafer, Han Liu, Tuo Zhao, Guiqing Cai, Jayon Lihm, Ruth Dannenfelser, Omar Jabado, Zuleyma Peralta et al.
    Patterns and rates of exonic de novo mutations in autism spectrum disorders.
    Nature, 2012, doi:10.1038/nature11011.
54. Fan Li, Paul Ryvkin, Micah Childress, Otto Valladares, Brian Gregory*, Li-San Wang*.
    SAVoR: a server for sequencing annotation and visualization of RNA structures.
    Nucleic Acids Research (web server issue), 2012, 10.1093/nar/gks310. (Link to website)
53. Serita Nelesen, Kevin Liu, Li-San Wang, C. Randal Linder and Tandy Warnow.
    DACTAL: divide-and-conquer trees (almost) without alignments.
    Bioinformatics (supplement issue for ISMB 2012), accepted.
52. Steven E Arnold, Natalia Louneva, Kajia Cao, Li-San Wang, Li-Ying Han, David A Wolk, Selamawit Negash, Sue E Leurgans, Julie A Schneider, Aron S Buchman, Robert S Wilson, Robert S Wilson, David A Bennett.
    Cellular, synaptic and biochemical features of resilient cognition in Alzheimer's disease.
    Neurobiology of Aging, 2012, in press.
51. Nan Liu, Michael Landreh, Kajia Cao, Masashi Abe, Gert-Jan Hendriks, Jason R. Kennerdell, Yongqing Zhu, Li-San Wang, Nancy M. Bonini.
    The microRNA miR-34 modulates ageing and neurodegeneration in Drosophila.
    Nature, 2012, doi:10.1038/nature10810. (Also read this review and this review.).
50. Fan Li, Qi Zheng, Paul Ryvkin, Isabelle Dragomir, Yaanik Desai, Subhadra Aiyer, Otto Valladares, Jamie Yang, Shelly Bambina, Leah R. Sabin, John I. Murray, Todd Lamitina, Arjun Raj, Sara Cherry, Li-San Wang*, Brian D. Gregory*.
    Global Analysis of RNA Secondary Structure in Two Metazoans.
    Cell Reports, 2012, 1(1):69-82.
49. S E Arnold, S X Xie, Y-Y Leung, L-S Wang, M A Kling, X Han, E J Kim, D A Wolk, D A Bennett, A Chen-Plotkin, M Grossman, W Hu6, V M-Y Lee, R Scott Mackin, J Q Trojanowski, R S Wilson and L M Shaw for the Alzheimer's Disease Neuroimaging Initiative.
    Plasma biomarkers of depressive symptoms in older adults.
    Translational Psychiatry, 2012, 2:e65; doi:10.1038/tp.2011.63.

2011

48. Yuk Yee Leung*, Li-San Wang*.
    Multi-class classification using covariance among binary classifiers and its application to the analysis of tumor microarrays
    Proceedings of 6th IASTED International Conference on Computational Intelligence and Bioinformatics (CiB), November 7-9, 2011, Pittsburgh, USA.
47. Meng W, Yunk L, Wang LS, Maganty A, Xue E, Cohen PL, Eisenberg RA, Weigert MG, Mancini SJ, Luning Prak ET.
    
    Selection of Individual VH Genes Occurs at the Pro-B to Pre-B Cell Transition.
    Journal of Immunology, 2011 Aug 15;187(4):1835-44. Epub 2011 Jul 11.
46. Günter U Höglinger, Nadine M Melhem, Dennis W Dickson, Patrick M A Sleiman, Li-San Wang, (35 authors), Gerard D. Schellenberg.
    Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy.
    Nature Genetics, 43:699-705, 2011, doi:10.1038/ng.859.
45. Adam C Naj, Gyungah Jun, Gary W Beecham, Li-San Wang, (150 authors), Gerard D. Schellenberg.
    Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease.
    Nature Genetics 2011, doi:10.1038/ng.801.

2010

44. Mi-Ryung Han, Gerard D Schellenberg, Li-San Wang*, Alzheimer's Disease Neuroimaging Initiative (ADNI).
    Genome-wide association reveals genetic effects on human Abeta42 and tau protein levels in cerebrospinal fluids: a case control study.
    BMC Neurology 2010, 10:90.
43. Paul Ryvkin and Li-San Wang*.
    Phylogenetic Trees from Sequences.
    Problem Solving Handbook in Computational Biology and Bioinformatics, Heath L.S. and N.Ramakrishnan, eds. in press, 2010.
42. Qi Zheng, Paul Ryvkin, Fan Li, Isabelle Dragomir, Otto Valldares, Jamie Yang, Kajia Cao, Li-San Wang* and Brian D. Gregory*.
    Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis.
    PLoS Genetics, 6(9):e1001141. doi:10.1371/journal.pgen.1001141, 2010.
41. Kajia Cao, Alice S. Chen-Plotkin, Joshua B. Plotkin, Li-San Wang*.
    Age-Correlated Gene Expression in Normal and Neurodegenerative Human Brain Tissues.
    PLoS ONE, 5(9): e13098. doi:10.1371/journal.pone.0013098, 2010.
40. Li-San Wang*, Dubravka Hranilovic, Kai Wang, Ingrid E Lindquist, Lindsay Yurcaba, Zorana-Bujas Petkovic, Nicole Gidaya, Branimir Jernej, Hakon Hakonarson and Maja Bucan*.
    Population-based study of genetic variation in individuals with autism spectrum disorders from Croatia.
    BMC Medical Genetics, 11:134, doi:10.1186/1471/2350-11-134, 2010.
39. Jun G, Naj AC, Beecham GW, Wang LS, (31 co-authors), Gerard D. Schellenberg, and Alzheimer's Disease Genetics Consortium (ADGC).
    Meta-analysis Confirms CR1, CLU, and PICALM as Alzheimer Disease Risk Loci and Reveals Interactions With APOE Genotypes.
    Archives of Neurology, August 9, 2010. doi:10.1001/archneurol.2010.201.
38. Lauren M.F. Merlo, Li-San Wang, John W. Pepper, Peter S. Rabinovitch and Carlo C. Maley.
    Polyploidy, Aneuploidy and the Evolution of Cancer.
    In Poon RYC, ed., Advances in Experimental Medicine and Biology: Polyploidization and Cancer, : pp.1-13, Austin/New York: Landes Bioscience, Inc. and Springer Science+Business Media, 2010, in press.
37. Vivianna M. Van Deerlin, Patrick M. A. Sleiman, Maria Martinez-Lage, Alice Chen-Plotkin, Li-San Wang, ..., Gerard D, Schellenberg, Hakon Hakonarson, John Q. Trojanowski and Virginia M-Y Lee.
    Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions.
    Nature Genetics, doi:10.1038/ng.536, 2010.
36. Mingyao Li*, Muredach P. Reilly, Daniel J. Rader, and Li-San Wang*.
    Correcting Population Stratification in Genetic Association Studies Using a Phylogenetic Approach.
    Bioinformatics, doi:10.1093/bioinformatics/btq025, 2010.
35. John Q. Trojanowski, Steven E. Arnold, ... (16 other authors), Li-San Wang, Rachel Werner, Sharon X. Xie, Virginia M.-Y. Lee
    Design of comprehensive Alzheimer’s disease centers to address unmet national needs
    Alzheimer’s & Dementia, 6:150-155, 2010.
34. Paul Ryvkin, Steven G. Hershman, Li-San Wang*, and F.B. Johnson*.
    Computational approaches to the detection and analysis of sequences with G-quadruplex forming potential.
    Methods in Molecular Biology: G-Quadruplex DNA. Peter Baumann eds. pp.39-50, Springer, 2010.

2009

33. Jay Johnson, Kajia Cao, Paul Ryvkin, Li-San Wang*, and F. Brad Johnson*.
    Altered gene expression in the Werner and Bloom syndromes is associated with sequences having G-quadruplex forming potential.
    Nucleic Acids Research, doi:10.1093/nar/gkp1103, 2009.
32. Li-San Wang*, Jim Leebens-Mack, P. Kerr Wall, Kevin Beckmann, Claude W. dePamphilis, and Tandy Warnow*.
    The impact of multiple protein sequence alignment on phylogenetic estimation.
    IEEE Transactions on Computational Biology and Bioinformatics (TCBB), epub 01 Sept. 2009.
31. Shane T. Jensen, Sameer Soi, and Li-San Wang*.
    A Bayesian approach to efficient differential allocation for resampling-based significance testing.
    BMC Bioinformatics, 2009, 10:198.
30. Erika L. Pearce, Matthew C. Walsh, Pedro J. Cejas, Gretchen M. Harms, Hao Shen, Li-San Wang, Russell G. Jones and Yongwon Choi.
    Enhancing CD8 T-cell memory by modulating fatty acid metabolism.
    Nature, 2009; DOI: 10.1038/nature08097.
29. Shuzhang Yang, Kai Wang, Brittany Gregory, Wade Berrettini, Li-San Wang, Hakon Hakonarson, and Maja Bucan.
    Genomic Landscape of a Three-generation Pedigree Segregating Affective Disorder.
    PLoS One, 2009; 4(2): e4474.

    2008

28. Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson.
    Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae.
    Nucleic Acids Research, 2008; 36(1):144-156.

    2007

27. Larry Singh, Li-San Wang, and Sridhar Hannenhalli.
    TREMOR -- a tool for retrieving transcriptional modules by incorporating motif covariance."
    Nucleic Acids Research, 2007; 35(21): 7360-7371.

    2006

26. Li-San Wang, Shane T. Jensen, and Sridhar Hannenhalli.
    "An Interaction-dependent model for transcription factor binding."
    LNCS: Second Annual RECOMB Satellite Workshop on Regulatory Genomics, Volume 4023, pp. 225-234, 2006.
25. Li-San Wang, Doris Wagner, Chang Seob Kwon, Yanhui Su, and Junhyong Kim.
    "Transcriptional Target Prediction Using Qualitative Reasoning."
    Proceedings of the 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'06), pp. 3138-3141, 2006.
24. Logan Everett, Li-San Wang, and Sridhar Hannenhalli.
    "Dense subgraph computation via stochastic search: application to detect transcriptional modules."
    Bioinformatics 2006 22(14): Proceedings of The Twelfth International Conference on Intelligent Systems and Molecular Biology (ISMB'06), pp. e117-e123. (PDF) (PubMed)
23. Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David Stern, and Claude W. dePamphilis.
    "Adaptive Evolution of Chloroplast Genome Structure Inferred Using a Parametric Bootstrap Approach."
    BMC Evolutionary Biology, 6:13, 2006. (PubMed)
22. Li-San Wang and Tandy Warnow.
    "Reconstructing Chromosomal Evolution."
    SIAM Journal on Computing, 36: 99-131, 2006.
21. Li-San Wang, Tandy Warnow, Bernard M.E. Moret, Robert K. Jansen, and Linda A. Raubeson.
    "Distance-based Genome Rearrangement Phylogeny."
    Journal of Molecular Evolution, 63(4):473-83, 2006. (PubMed)
20. Stanislav Angelov, Boulos Harb, Sampath Kannan, and Li-San Wang.
    "Weighted Isotonic Regression under L1 Norm."
    Proceedings of the Seventeenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA'06), pp. 783-791, 2006 (PDF)

    2005

19. Jijun Tang and Li-San Wang.
    "Improving Genome Rearrangement Phylogeny Using Sequence-Style Parsimony."
    Proceedings of the IEEE Fifth Symposium on Bioinformatics and Bioengineering (BIBE'05), pages 137--144. (PDF)
18. Fan Ge, Li-San Wang, and Junhyong Kim.
    "The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer.
    Public Library of Science (PLoS) Biology, 3(10):e316, 2005. (PubMed)
17. Luay Nakhleh and Li-San Wang.
    "Phylogenetic Networks: Properties and Relationship to Trees and Clusters."
    LNCS Transactions on Computational Systems Biology 3680, special issue for IWBRA'05 (special invitation), pp. 82-99, 2005 (PDF)
16. Luay Nakhleh, Derek Ruths, and Li-San Wang.
    "RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer."
    Lecture Notes of Computer Science No. 3595: The Eleventh International Computing and Combinatorics Conference (COCOON'05), pp. 84-93. (PDF)
15. Sridhar Hannenhalli and Li-San Wang.
    "Enhanced position weight matrices using mixture models."
    Bioinformatics 2005 21(suppl1): Proceedings of The Eleventh International Conference on Intelligent Systems and Molecular Biology (ISMB'05), pp. i204-i212. (PDF) (PubMed)
14. Luay Nakhleh and Li-San Wang.
    "Phylogenetic Networks, Trees, and Clusters."
    Lecture Notes in Computer Science No. 3515: 2005 International Workshop on Bioinformatics Research and Applications (IWBRA'05), pp. 919-926. (PDF)
13. Li-San Wang and Tandy Warnow.
    "Distance-Based Genome Rearrangement Phylogeny."
    In Mathematics of Evolution and Phylogeny,, O. Gascuel ed., pp. 353-380, Oxford Univ. Press, 2005. (PDF)

    2004

12. Stanislav Angelov, Boulos Harb, Sampath Kannan, Sanjeev Khanna, Junhyong Kim, and Li-San Wang.
    "Genome Identification and Classification by Short Oligo Arrays."
    Lecture Notes for Computer Science No. 3240: Proc. 4th Workshop on Algorithms in Bioinformatics (WABI'04), pp. 400-411. (PDF)

    2003

11. Matthew Spencer, Barbara Bordalejo, Li-San Wang, Adrian C. Barbrook, Linne R. Mooney, Peter Robinson, Tandy Warnow, and Christopher J. Howe.
    "Analyzing the Order of Items in Manuscripts of The Canterbury Tales."
    Computers and the Humanities, 37(1):97-109, February 2003, Kluwer Academic Pub.

    2002

10. Li-San Wang.
    "Genome Rearrangement Phylogeny Using Weighbor."
    Lecture Notes for Computer Sciences No. 2452: Proceedings for the Second Workshop on Algorithms in BioInformatics (WABI'02), Rome, Italy, pp. 112-125, September, 2002. (PDF)
9. Bernard M.E. Moret, Li-San Wang, and Tandy Warnow.
   "New Software for Computational Phylogenetics."
   IEEE Computer: Special Issue on Bioinformatics, 35(7): 55-64, July 2002. (PS)
8. Cara Stockham, Li-San Wang, and Tandy Warnow.
   "Statistically Based Postprocessing of Phylogenetic Analysis by Clustering."
   Proceedings of 10th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'02), Edmonton, Canada, pp. 285--293, August 2002. (PS) (PubMed)
7. Bernard M.E. Moret, Jijun Tang, Li-San Wang, and Tandy Warnow.
   "Steps Toward Accurate Reconstructions of Phylogenies from Gene-Order Data."
   Journal of Computer and Systems Sciences: Special Issue of Computational Biology, 65(3):508-525, 2002 (Invited article). (PS)
6. Li-San Wang, Robert Jansen, Bernard Moret, Linda Raubeson, and Tandy Warnow.
   "Fast Phylogenetic Methods For Genome Rearrangement Evolution: An Empirical Study."
   Proceedings of Fifth Pacific Symp. of Biocomputing (PSB'02), Hawaii, USA, pp. 524-535, 2002. (PS) (PubMed)

   2001

5. Li-San Wang.
   "Exact-IEBP: A New Technique For Estimating Evolutionary Distances Between Whole Genomes."
   Lecture Notes for Computer Sciences No. 2149: Proceedings for the First Workshop on Algorithms in BioInformatics (WABI'01), BRICS, University of Aarhus, Denmark, pp. 175-188, 2001. (PS)
4. Li-San Wang and Tandy Warnow.
   "Estimating true evolutionary distances between genomes."
   Proceedings of the Thirty-Third Annual ACM Symposium on the Theory of Computing (STOC'01), Crete, Greece, pp. 637-646, 2001. (PS)
3. Bernard M.E. Moret, Li-San Wang, Tandy Warnow, and Stacia Wyman.
   "New approaches for reconstructing phylogenies based on gene order."
   Proceedings of 9th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'01), Copenhagen, Denmark, pp. 165-173, 2001. (This paper is elected by the conference as one of the five best papers in ISMB'01.) (PDF) (PubMed)

   2000

2. Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman.
   "An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae."
   Proc. Gene Order Dynamics, Comparative Maps, and Multigene Families," DCAF-2000, Montreal (2000) in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, D. Sankoff and J. Nadeau, eds., Kluwer Academic Pub., Dordrecht, pp. 99-121, 2000. (PDF)
1. Mary E. Cosner, Robert K. Jansen, Bernard M.E. Moret, Linda A. Raubeson, Li-San Wang, Tandy Warnow, and Stacia Wyman.
   "A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes."
   Proc. 8th Int'l Conf. on Intelligent Systems for Molecular Biology (ISMB'00), San Diego, pp. 104-115, 2000. (PDF) (PubMed)