Publications

• Li S, Zeng W, Ni X, Liu Q, Li W, Stackpole ML, Zhou Y, Gower A, Krysan K, Ahuja P, Lu DS, Raman SS, Hsu W, Aberle DR, Magyar CE, French S, Han SHB, Garon EB, Agopian VG, Wong WH^#, Dubinett SM^#, Zhou XJ^# (2023). #Joint corresponding author.
  Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.
  Proc Natl Acad Sci USA. 2023 Jul;120(28):e2305236120.
  News highlight by UCLA news, The Medical News, Drug Target Review, Medical Xpress, and Healthcare in Europe. Check out its media coverage summary.
• Yildirim A, Hua N, Boninsegna L, Polles G, Gong K, Hao S, Li W, Zhou XJ, Alber F (2023).
  Mapping the nuclear microenvironment of genes at a genome-wide scale.
  Nature Structural and Molecular Biology. In Press.
• Li S, Hu R, Small C, Kang TY, Liu CC, Zhou XJ^#, Li W^# (2023). #Joint corresponding author.
  cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA.
  Nature Protocol. 2023 Feb 27. doi: 10.1038/s41596-023-00807-w.
• Stackpole ML*, Zeng W*, Li S*, Liu CC, Zhou Y, He S, Yeh A, Wang Z, Sun F, Li Q, Yuan Z, Yildirim A, Chen PJ, Winograd P, Tran B, Lee YT, Li PS, Noor Z, Yokomizo M, Ahuja P, Zhu Y, Tseng HR, Tomlinson JS, Garon EB, French S, Magyar CE, Dry S, Lajonchere C, Geschwind D, Choi G, Saab S, Alber F, Wong WH, Dubinett SM, Aberle DR, Agopian VG^#, Han SHB^#, Ni X^#, Li W^#, Zhou XJ^# (2022). *Joint first author; #Joint corresponding author.
  Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.
  Nature Communication. 2022 Sep 29;13(1):5566. doi: 10.1038/s41467-022-32995-6.
  It has been recognized as one of the "Top 25 Health Sciences Articles of 2022" by Nature Communications
  News highlight by UCLA news, Genome Web, ScieneDaily, Biocompare, and HemOnc Today.
• Boninsegna L, Yildirim A, Polles G, Quinodoz SA, Finn E, Guttman M, Zhou XJ, Alber F (2022).
  Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations.
  Nature Methods. 2022 Aug;19(8):938-949. doi: 10.1038/s41592-022-01527-x.
• Sun N, Zhang C, Lee YT, ...., Li W, Zhou XJ, ..., Agopian V, Tseng HR, Zhu Y (2022).
  HCC EV ECG score: an extracellular vesicle-based protein assay for detection of early-stage hepatocellular carcinoma.
  Hepatology. 2022 Jul 31. doi: 10.1002/hep.32692.
• Hu R, Zhou XJ, Li W (2022).
  Computational analysis of high-dimensional DNA methylation data for cancer prognosis.
  Journal of Computational Biology. 2022 Jun 6. doi: 10.1089/cmb.2022.0002.
• Li S, Zeng W, Ni X, Zhou Y, Stackpole ML, Noor ZS, Yuan Z, Neal A, Memarzadeh S, Garon EB, Dubinett SM, Li W, Zhou XJ (2022).
  cfTrack: Exome-wide mutation analysis of cell-free DNA to simultaneously monitor the full spectrum of cancer treatment outcomes: MRD, recurrence, and evolution.
  Clinical Cancer Research. 2022 Feb 11; doi: 10.1158/1078-0432.CCR-21-1242.
• Wang Z, Li S, You R, Zhu S, Zhou XJ, Sun F (2021).
  ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network.
  NAR Genom Bioinform. 2021 Aug 5;3(3):lqab066. doi: 10.1093/nargab/lqab066.
• Kadara H, Tran LM, Liu B, Vachani A, Li S, Sinjab A, Zhou XJ, Dubinett SM, Krysan K. (2021).
  Early Diagnosis and Screening for Lung Cancer.
  Cold Spring Harb Perspect Med. 2021 Sep 1;11(9):a037994. doi: 10.1101/cshperspect.a037994.
• Li S, Noor Z, Zeng W, Stackpole ML, Ni X, Zhou Y, Yuan Z, Wong WH, Agopian VG, Dubinett SM, Alber F, Li W^#, Garon EB^#, Zhou XJ^# (2021). #Joint corresponding author.
  Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.
  Nature Communication. 2021 Jul 7;12(1):4172. doi: 10.1038/s41467-021-24457-2.
• Del Vecchio G*, Li Q*, Li W*, Thamotharan S, Tosevska A, Morselli M, Sung K, Janzen C, Zhou X, Pellegrini M, Devaskar SU (2020). *Joint first author.
  Cell-free DNA methylation and transcriptomic signature prediction of pregnancies with adverse outcomes.
  Epigenetics. Oct 13:1-20; doi: 10.1080/15592294.2020.1816774.
• Li W and Zhou XJ (2020).
  Methylation extends the reach of liquid biopsy in cancer detection.
  Nature Reviews Clinical Oncology. 2020 Jul; doi: 10.1038/s41571-020-0420-0.
• Court CM, Hou S, Liu L, Winograd P, DiPardo BJ, Liu SX, Chen PJ, Zhu Y, Smalley M, Zhang R, Sadeghi S, Finn RS, Kaldas FM, Busuttil RW, Zhou XJ, Tseng HR, Tomlinson JS, Graeber TG, Agopian VG (2020).
  Somatic copy number profiling from hepatocellular carcinoma circulating tumor cells.
  NPJ Precis Oncol. 2020 Jul 2;4:16. doi: 10.1038/s41698-020-0123-0. eCollection 2020.
• Chen P^*, Li S^*, Li W, Ren J, Sun F, Liu R^#, Zhou XJ^# (2019). *Joint first author; #Joint corresponding author.
  Rapid diagnosis and comprehensive bacteria profiling of sepsis based on cell-free DNA.
  J Transl Med. 2019 18(1):5. doi: 10.1186/s12967-019-02186-x.
• An Q, Hu Y, Li Q, Chen X, Huang J, Pellegrini M, Zhou XJ, Rettig M, Fan G. (2019)
  The size of cell-free mitochondrial DNA in blood is inversely correlated with tumor burden in cancer patients.
  Precis Clin Med. 2019 Sep;2(3):131-139. doi: 10.1093/pcmedi/pbz014.
• Li W*, Li Q*, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F and Zhou XJ (2018). *Joint first author.
  CancerDetector: Ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data
  Nucleic Acid Research, 2018 Sep;46(15):e89.

  News highlight by GenomeWeb.

• Chen P, Chen E, Chen L, Zhou XJ, Liu R (2018)
  Detecting early-warning signals of influenza outbreak based on dynamic network marker
  J Cell Mol Med. 2018 Oct 19. doi: 10.1111/jcmm.13943. [Epub ahead of print]
• Hua N, Tjong H, Shin H, Ke G, Zhou XJ, Alber F (2018)
  Producing genome structure populations with the dynamic and automated PGS software
  Nature Protocol, 2018 May;13(5):915-926.
• Kang S, Li Q, Chen Q, Zhou Y, Park S, Lee G, Grimes, B, Krysan K, Yu M, Wang W, Alber F, Sun F, Dubinett SM^#, Li W^#, Zhou XJ^# (2017). #Joint corresponding author.
  CancerLocator: Non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
  Genome Biology, 2017 Mar 24;18(1):53.

  News highlight by Science Daily, FoxNews, World Breaking News, Yahoo!, GenomeWeb, PulseHeadlines, Huffingtonpost, UCLA News, Metro, Telegraph. The media coverage summary.

• Li Q, Tjong H, Li X, Gong K, Zhou XJ, Chiolo I, Alber F. (2017)
  The three-dimensional genome organization of Drosophila melanogaster through data integration
  Genome Biology. 2017 Jul 31;18(1):145.

• Dai C*, Li W*, Tjong H*, Hao S, Zhou Y, Li Q, Chen L, Zhu B, Alber F^#, Zhou XJ^# (2016). *Joint first author; #Joint corresponding author.
  Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities.
  Nature Communications, 2016 May 31;7:11549. doi: 10.1038/ncomms11549.
• Tjong H*, Li W*, Kalhor R, Gong K, Dai C, Li H, Zhou XJ, Larabell C, Chen L, Alber F (2016). *Joint first author.
  Population-based genome structure modeling reveals driving forces in 3D genome organization in human cells.
  Proc Natl Acad Sci USA, 2016 Mar 22;113(12):E1663-72.
• Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T,Richardson S, Sun S, Yang F, Shen YA, Murray R, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner S, Zhong Q, Trigg S, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani S, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, and Vidal M (2016).
  Widespread expansion of protein interaction capabilities by alternative splicing.
  Cell, 2016 Feb 11;164(4):805-17.
• Tseng C, Ghsoh D, Zhou XJ (2015)
  Integrating Omics data.
  The Cambridge Press. ISBN-13: 978-1107069114, ISBN-10: 1107069114
• Shin H, Yi S, Dai C, Tjoing H, Gong K, Alber F, Zhou XJ (2015).
  TopDom: An efficient and deterministic method for identifying topological domains in genomes.
  Nucleic Acid Research, 2015 Dec 23. pii: gkv1505.
• Li JR, Sun CH, Li W, Chao RF, Huang CC, Zhou XJ, Liu CC.
  Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells.
  Nucleic Acid Research, 2015 Nov 23. pii: gkv1282.
• Li W*, Liu CC*, Kang S*, Li JR, Tseng YT, Zhou XJ (2015). *Joint first-author
  Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level.
  Methods, 2015 Jul; pii: S1046-2023(15)30037-2.
• Li W, Gong K, Li Q, Alber F and Zhou XJ (2015).
  Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.
  Bioinformatics, 2015 Mar; 31(6):960-2.
• Gong K, Tjong H, Zhou XJ, Alber F (2015).
  Comparative 3D genome structure analysis of the fission and the budding yeast.
  PLoS One, 2015 Mar; 10(3):e0119672.
• Chen Q, Zhou XJ, Sun F (2015).
  Finding genetic overlaps among diseases based on ranked gene lists.
  Journal of Computational Biology, 2015 Feb; 22(2):111-23.
• Chen Y, Chen C, Zhang Z, Liu CC, Johnson ME, Espinoza CA, Edsall LE, Ren B, Zhou XJ, Grant SF, Wells AD, Chen L (2015).
  DNA binding by FOXP3 domain-swapped dimer suggests mechanisms of long-range chromosomal interactions.
  Nucleic Acid Research, 2015 Jan 30; 43(2):1268-82.
• Tseng YT, Li W, Chen C, Zhang S, Chen JJW, Zhou XJ, and Liu CC (2015).
  IIIDB: a database for isoform-isoform interactions and isoform network modules.
  BMC Genomics, 2015; 16(Suppl 2):S10.
• Wang W, Zhou XJ, Liu Z, Sun F (2015).
  Network tuned multiple rank aggregation and applications to gene ranking.
  BMC Bioinformatics, 2015; 16(Suppl 1):S6.
• Jiang CR, Liu CC, Zhou XJ and Huang H (2014).
  Optimal ranking in multi-label classification using local precision rates.
  Statistica Sinica, 24:1547-1570.
• Zhang S and Zhou XJ (2014).
  Matrix factorization methods for integrative cancer genomics (2014).
  Methods in Molecular Biology, 1176:229-42.
• Liu CC*, Tseng YT*, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ (2014). *Joint first-author DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.
  Nucleic Acid Research, 2014 June; DOI: 10.1093/nar/gku412.
• Li W, Dai C, Kang S and Zhou XJ (2014).
  Integrative analysis of many RNA-seq datasets to study alternative splicing.
  Methods, 2014 Jun 1; 67(3):313-324.
• Li W*, Kang S*, Liu CC, Zhang S, Shi Y, Liu Y and Zhou XJ (2013). *Joint first-author
  High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method.
  Nucleic Acid Research, 2013 Dec; DOI: 10.1093/nar/gkt1362.
• You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G and Jones PA (2013).
  SNF5 is an essential executor of epigenetic regulation during differentiation.
  PLOS Genetics, 2013 Apr; 9(4):e1003459. DOI: 10.1371; p. 1-14.
• Pandiyan K, You JS, Dai C, Zhou XJ, Baylin SB, Jones PA, and Liang G (2013).
  Functional DNA demethylation is accompanied by chromatin accessibility.
  Nucleic Acid Research, 2013 Feb; DOI: 10.1093/nar/gkt077; p. 1-13.
• Zhou XJ and Alber F (2012).
  Zooming in on genome organization.
  Nature Methods, 2012 Oct; 9(10):961-963.
• Li W*, Zhang S*, Liu CC, and Zhou XJ (2012). *Joint first-author
  Identifying multi-layer gene regulatory modules from multi-dimensional genomic data.
  Bioinformatics, 2012 Oct; 28(19):2458-2466.
• Yuan W, Wu T, Fu H, Dai C, Wu H, Liu N, Li X, Xu M, Zhang Z, Niu T, Han Z, Chai J, Zhou XJ, Gao S, Zhu B (2012).
  Dense chromatin activates Polycomb repressive complex 2 to regulate H3 lysine 27 methylation.
  Science, 2012 Aug; 337(6097):971-975.
• Zhang S, Liu CC, Li W, Shen H, Laird P, Zhou XJ (2012).
  Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.
  Nucleic Acid Research, 2012 Oct; 40(19):9379-9391.
• Li W*, Dai C*, Liu CC, and Zhou XJ (2012). *Joint first-author
  Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling.
  Journal of Computational Biology, 2012 Jun; 19(6):710-730.
• Dai C*, Li W*, Liu J, and Zhou XJ (2012). *Joint first-author
  Integrating many co-splicing networks to reconstruct splicing regulatory modules.
  BMC Systems Biology, 2012 Jul; 6 Suppl 1:S17.
• Li W, Hu H, Huang Y, Li H, Mehan MR, Nunez-Iglesias J, Xu M, Yan X, and Zhou XJ (2012).
  Pattern mining across many massive biological networks.
  In Functional Coherence of Molecular Networks in Bioinformatics, Springer (M. Koyuturk, S. Subramaniam, and A. Grama eds., ISBN: 978-1-4614-0319-7). pages: 137-170.
• Taberlay PC, Kelly TK, Liu CC, You JS, de Carvalho DD, Miranda1 TB, Zhou XJ, Liang G, and Jones PA (2011).
  Polycomb repressed genes have permissive enhancers that initiate reprogramming.
  Cell, 147(6): 1283-1294.
• Dai C*, Li W*, Liu J, and Zhou XJ (2011). *Joint first-author
  Systematic reconstruction of splicing regulatory modules by integrating many RNA-seq datasets.
  IEEE International Conference on Systems Biology (ISB). Zhuhai, China. pp. 267-273.
• Li W, Hu H, Huang Y, Li H, Mehan MR, Nunez-Iglesias J, Xu M, Yan X, and Zhou XJ (2011).
  Frequent pattern discovery in multiple biological networks: algorithms and applications.
  Statistics in Biosciences, p. 1-20. DOI: 10.1007/s12561-011-9047-0.
• Li W, Liu CC, Zhang T, Li H, Waterman MS, Zhou XJ (2011).
  Integrative analysis of many weighted co-expression networks using tensor computation.
  PLoS Computational Biology, 7(6): e1001106.
• Zhang S, Li Q, Liu J, Zhou XJ (2011).
  A novel computational framework for simultaneous integration of multiple functional genomic datasets to identify microRNA-gene regulatory modules.
  Bioinformatics (ISMB 2011), 27(13):i401-i409.
• Xu B, Chen C, Chen H, Zheng SG, Bringas P, Xu M, Zhou X, Chen D, Umans L, Zwijsen A, and Shi W (2011).
  Smad1 and its target gene Wif1 coordinate BMP and Wnt signaling activities to regulate fetal lung development.
  Development, 2011 Mar;138(5):925-35.
• Huang H, Liu CC, Zhou XJ (2010).
  Bayesian approach to transforming public gene expression repositories into disease diagnosis databases.
  Proc Natl Acad Sci USA. 2010 Apr 13;107(15):6823-8. [pdf] #This paper was highlighted in PNAS, Nature SciBx, Facultyof1000, and GenomeWebNews.
• Mehan MR, Nunez-Iglesias J, Dai C, Waterman MS, Zhou XJ (2010).
  An integrative modular approach to systematically predict gene-phenotype associations.
  BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S62.
• Nunez-Iglesias J, Liu CC, Morgan TE, Finch CE, Zhou XJ (2010).
  Joint genome-wide profiling of miRNA and mRNA expression in Alzheimer's disease cortex reveals altered miRNA regulation.
  PLoS One. 2010 Feb 1;5(2):e8898.
• Li W, Xu M, Zhou XJ (2010).
  Unraveling complex temporal associations in cellular systems across multiple time-series microarray datasets.
  J Biomed Inform. 2010 Aug; 43(4):550-559.
• Xu M*, Li W*, James G, Mehan MR, Zhou XJ. (2009) *Joint first-author 
  Automated Multi-dimensional Phenotypic Profiling Using Large Public Microarray Repositories.
  Proc Natl Acad Sci USA. 106(30):12323-8. #This paper was highlighted in Nature Methods 6, 632 (2009), and selected by 2010 International Medical Informatics Association (IMIA) Yearbook of Medical Informatics.
• Friedman JM, Liang G, Liu CC, Wolff EM, Tsai YC, Ye W, Zhou X, Jones PA. (2009)
  The Putative Tumor Suppressor microRNA-101 Modulates the Cancer Epigenome by Repressing the Polycomb Group Protein EZH2.
  Cancer Res. 2009 Mar 3.
• Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ (2009)
  Integrative Disease Classification Based On Cross-Platform Microarray Data .
  BMC Bioinformatics. 10 Suppl 1:S25.
• Jin R, Macallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ (2009)
  Identifying Dynamic Network Modules with Temporal And Spatial Constraints.
  Pacific Symposium of Biocomputing. 2009:203-214.
• Mulkar-Mehta R, Hobbs J, Liu CC, Zhou XJ (2009)
  Discovering Causal and Temporal Relations in Biomedical Texts.
  AAAI Spring Symposium on Learning by Reading and Learning to Read. 2009:74-80.
• Mehan M, Nunez-Iglesias J, Kalakrishnan M, Waterman MS, Zhou XJ (2009)
  An Integrative network approach to map the transcriptome to the phenome.
  Journal of Computational Biology 2009 Aug; 16(8):1023-1034.
• Xu M, Kao MJ, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ (2008)
  Characterizing disease-specific pathways and their coordination by integrative microarray analysis with application to cancer.
  BMC Genomics. 2008;9 Suppl 1:S12.
• Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ (2007)
  Systematic discovery of functional modules and context-specific functional annotation of human genome.
  Bioinformatics (ISMB 2007), 23(13):i222-i229.
• Yan X, Mehan M, Huang Y, Waterman MS, Yu PS, Zhou XJ (2007)
  A graph-based approach to systematically reconstruct human transcriptional regulatory modules.
  Bioinformatics (ISMB 2007), 23(13):i577-i586.
• Pan F, Chiu CH, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Kamath K, Waterman MS, Finch CE, Zhou XJ. (2007)
  Gene Aging Nexus: A Web database and data mining platform for microarray data on aging.
  Nucleic Acids Res. 2007 Jan; 35(Database issue): D756-D759.
• Hu J, Li H, Waterman M, Zhou XJ (2006)
  Integrative missing value estimation for microarray data.
  BMC Bioinformatics. 2006 Oct 12; 7:449.
• Pan F, Kamath K, Zhang K, Pulapura S, Achar A, Nunez-Iglesias J, Huang Y, Yan X, Han J, Hu H, Xu M, Zhou XJ. (2006)
  Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.
  Bioinformatics. 22(13):1665-7.
• Tu Z, Wang L, Xu M, Zhou X, Chen T, Sun F (2006).
  Further understanding human disease genes by comparing with housekeeping genes and other genes.
  BMC Genomics 7:31.
• Hu H, Yan X, Huang Y, Han J, Zhou XJ (2005)
  Mining Closed Relational Graphs with Connectivity Constraints.
  Proceedings of the International Conference on Data Engineering (ICDE).Tokyo, Japan. pp. 357-358.
• Zhou XJ, Kao MJ, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH (2005)
  Functional annotation and network reconstruction through cross-platform integration of microarray data.
  Nature Biotechnology. 2005 Feb;23(2):238-43.
  *This paper was highlighted in Nature Review Genetics 6, 164(2005).
• Yan X, Zhou XJ, Han J (2005)
  Mining Closed Relational Graphs with Connectivity Constraints.
  Proceedings of the International Conference on Data Engineering (ICDE).Tokyo, Japan. pp. 357-358
• Zhou XJ, Gibson G. (2004)
  Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.
  Journal of Computational Biology 11(1):1-14.
• Zhou X, Krueger JG, Kao MJ, Lee E, Du F, Menter A, Wong WH, Bowcock AM (2003)
  Novel Mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array.
  Physiological Genomics 13:69-78.
• Zhou X, Kao MJ, Wong WH (2002)
  From the Cover: Transitive Functional Annotation By Shortest Path Analysis of Gene Expression Data.
  Proc Natl Acad Sci USA. 99(20):12783-12788.
  *This paper was highlighted in PNAS: 99(20):12509-12511| BioMedNet | The Faculty of 1000.
• Block-Alper L, Webster P, Zhou X, Supekov, Wong WH, Schultz P, and Meyer DI. (2002)
  IN02, a Positive Regulator of Lipid Biosynthesis, is Essential for the Formation of Inducible Membranes in Yeast.
  Molecular Biology of the Cell. (13) 40-51.
• Zhou X, Gonnet GH, Hallett M, Folkers G, James P. (2001)
  Cell Fingerprinting: An approach to classify cells using their protein extracts with mass spectrometric analysis.
  Proteomics. (1) 675-682.
• Zhou X, Gonnet GH, Hallett M, Chelvanayagam G. Folkers G. (2001)
  Identifying the most influential residues for alpha-helix formation: The subset selection problem using least squares optimization.
  Proceeding of the 16th ACM symposium on Applied Computing. 51-56. 2001.
• Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. (2000)
  An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins: Struc. Func. Gen. 2000 (41):248-256.
• Cannarozzi G, Hallett M, Norberg J, Zhou X. (2000)
  A Cross-Comparison of a Large Dataset of Genes.
  Bioinformatics 2000. 16(7):654-655.