Nansheng J. Chen

Jack Chen, Associate Professor

Department of Molecular Biology and Biochemistry
Simon Fraser University

Office: SSB8111
Phone: (778)782-4823
Email: chenn(at)sfu.ca

 B.Sc., Fudan University, Shanghai
Ph.D., Chinese Academy of Sciences, Qingdao
Home | Teaching | Professional activities | Projects | Research Group | Publications

SELECTED PUBLICATIONS

    2011

  1. Frech C and Chen N. Genome comparison of human and non-human malaria parasites reveals parasites-specific genes potentially linked to human disease. PLoS Computational Biology, 2011.
    News coverage

  2. Chu JSC, Tarailo-Graovac M, Zhang D, Wang J, Uyar B, Tu D, Trinh J, Baillie DL, and Chen N. Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans. Nucleic Acids Research, 2011.

  3. She R*, Chu JSC*, Uyar B, Wang J, Wang K, and Chen N. genBlastG: using BLAST searches to build homologous gene models. Bioinformatics. 2011 (* Joint First Authors).

  4. Christians JK, Cheema MS, Vergara IA, Watt CA, Pinto LJ, Chen N, and Moore MM. Quantitative Trait Locus (QTL) Mapping Reveals a Role for Unstudied Genes in Aspergillus Virulence. PLoS ONE, 2011.

  5. Williams CL, Li C, Kida K, Inglis PN, Mohan S, Semenec L, Bialas NJ, Stupay RM, Chen N, Blacque OE, Yoder BK, Leroux MR. MKS and NPHP modules cooperate to establish basal body/transition zone membrane associations and ciliary gate function during ciliogenesis. J. Cell Biol, 2011.

    6. 2010

  6. Tarailo-Graovac M, Wang J, Tu D, Baillie DL, Rose A, Chen N. Duplication of cyb-3 (Cyclin B3) suppresses sterility in the absence of mdf-1/MAD1 spindle assembly checkpoint component in Caenorhabditis elegans, Cell Cycle, 2010. Cover

  7. Nesbitt MJ, Moerman DG, Chen N. Identifying novel genes in C. elegans using SAGE tags. BMC Molecular Biology, 2010.

  8. Miyata ST, Kitaoka M, Wieteska L, Frech C, Chen N, and Pukatzki S. The Vibrio cholerae Type VI Secretion System: evaluating its role in the human disease Cholera. Frontiers in Microbiology - Cellular and Infectious Microbiology, 2010.

  9. Frech C, Chen N. Evaluation of gene family classification programs and comparative gene family classification. PLoS ONE , 2010.

  10. Colak R, Moser F, Chu JSC, Schonhuth A*, Chen N*, Ester M*. Inferring functional modules by density constrained biclustering. PLoS ONE, 2010 (*Co-senior authorships).

  11. Vergara IA and Chen N. Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster. BMC Genomics, 2010.

  12. Tarailo-Graovac M, Wang J, Chu JSC, Tu DK, Baillie DL, Chen N. Spindle assembly checkpoint genes reveal distinct as well as overlapping expression that implicates MDF-2/Mad2 in postembryonic seam cell development in Caenorhabditis elegans. BMC Cell Biology, 2010. Image of the month

  13. Chu JSC, Baillie DL, Chen N. Convergent evolution of RFX transcription factors and ciliary genes predated the origin of metazoans. BMC Evolutionary Biology, 2010.

  14. Mah A, Tu KN, Johnsen RC, Chu JSC, Chen N, Baillie DL. Characterization of CEH-6-mediated transcriptional regulation in Caenorhabditis elegans. BMC Molecular Biology, 2010.

  15. She R, Chu JSC, Wang K, Chen N. Fast and accurate gene prediction by decision tree classification. SIAM International Conference on Data Mining, 2010.

    16. 2009

  16. Hutter H, Ng MP, Chen N. GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. BMC Genomics, 2009.

  17. Vergara IA, Mah AK, Huang JC, Tarailo-Graovac M, Johnsen RC, Baillie DL, Chen N. Polymorphic segmental duplication in the nematode Caenorhabditis elegans. BMC Genomics, 2009.

  18. Ng MP*, Vergara IA*, Frech, C, Chen Q, Zeng X, Pei J, and Chen N. OrthoClusterDB: a web server for synteny blocks. BMC Bioinformatics, 2009 (* Joint First Authors).

  19. She R*, Chu JSC*, Wang K, Pei J, Chen N. genBlastA: enabling BLAST to identify homologous gene sequences. Genome Research, 2009 (* Joint First Authors).

    20. 2008

  20. Aftab S, Semenec L, Chu JS, Chen N. Identification and characterization of novel human tissue-specific RFX transcription factors. BMC Evolutionary Biology, 2008

  21. On C, Marshall C, Chen N, Moyes CD, Tibbits GF. Gene structure evolution of the Na+-Ca2+ exchanger (NCX) family. BMC Evolutionary Biology, 2008

  22. Zeng X, Pei J, Vergara IA, Nesbitt MJ, Wang K, Chen N. OrthoCluster: a new tool for mining synteny blocks and applications in comparative genomics. EDBT'08, March 25-30, 2008, Nantes, France. PDF

    23. 2007

  23. Mah AK, Armstrong KR, Chew DS, Chu JS, Tu DK, Johnsen RC, Chen N, Chamberlin HM, Baillie DL. Transcriptional regulation of AQP-8, A Caenorhabditis elegans aquaporin exclusively expressed in the excretory system, by the POU homeobox transcription factor CEH-6. Journal of Biological Chemistry, 282(38):28074-28086.

  24. Zhao Z, Thomas JH, Chen N, Sheps JA, Baillie DL. Comparative Genomics and Adaptive Selection of the ATP-Binding Cassette (ABC) Transporter Family in Caenorhabditis Species. Genetics, 2007 (Epub ahead of time)

  25. Bieri T, Blasiar D, Ozersky P, Antoshechkin I, Bastiani C, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Han M, Harris TW, Kishore R, Lee R, McKay S, Muller HM, Nakamura C, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Spooner W, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Durbin R, Stein LD, Sternberg PW, Spieth J. Nucleic Acid Res. 2007 Jan;35(Database issue):D506-10.

    26. 2006

  26. Chen N, Mah A, Blacque OE, Chu J, Phgora K, Khattra J, Chan S, Go A, Efimenko E, Johnsen R, Phirke P, Swoboda P, Marra M, Moerman DG, Leroux MR, Baillie DL, and Stein LD, Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biology, 2006;7(12):R126.

  27. Sea Urchin Genome Sequencing Consortium; Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Belle R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Geneviere AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallbook F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Rottinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006, 314(5801)

  28. Tischler J, Lehner B, Chen N and Fraser AG. Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution. Genome Biology. 2006, 7:R69

  29. Burke RD, Angerer LM, Elphick MR, Humphrey GW, Yaguchi S, Kiyama T, Liang S, Mu X, Agca C, Lkein WH, Brandhorst BP, Rowe M, Wilson K, Churcher AM, Taylor JS, Chen N, Murray G, Wang D, Mellott D, Olinski R, Hallbook F, Thorndyke MC. A genomic view of the sea urchin nervous system. Developmental Biology. 2006

  30. Chen N, Stein LD. Conservation and Functional Significance of Gene Topology in the Genome of Caenorhabditis elegans. Genome Research. 2006 May: 16:606-617.

  31. Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW. WormBase: better software, richer content. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D475-8.

    32. 2005

  32. Zhao Z, Fang L, Chen N, Johnsen RC, Stein L, Baillie DL. Distinct regulatory elements mediate similar expression patterns in the excretory cell of Caenorhabditis elegans. J Biol Chem. 2005 Nov 18;280(46):38787-94. Epub 2005 Sep 13.

  33. Chen N, Pai S, Zhao Z, Mah A, Newbury R, Johnsen RC, Altun Z, Moerman DG, Baillie DL, Stein LD. Identification of a nematode chemosensory gene family. Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):146-51. Epub 2004 Dec 23.

  34. Chen N, Harris TW, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Canaran P, Chan J, Chen CK, Chen WJ, Cunningham F, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Pai S, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D383-9.

    35. 2004

  35. Chen N, Lawson D, Bradnam K, Harris TW, Stein LD. WormBase as an integrated platform for the C. elegans ORFeome.Genome Res. 2004 Oct;14(10B):2155-61.

  36. Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, Stein LD. WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D411-7.

  37. Chen N, Li B, Murphy TH, Raymond LA. Site within N-Methyl-D-aspartate receptor pore modulates channel gating. Mol Pharmacol. 2004 Jan;65(1):157-64.

    38. 2003

  38. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 2003 Nov;1(2):E45. Epub 2003 Nov 17.

  39. Li L, Fan M, Icton CD, Chen N, Leavitt BR, Hayden MR, Murphy TH, Raymond LA. Role of NR2B-type NMDA receptors in selective neurodegeneration in Huntington disease. Neurobiol Aging. 2003 Dec;24(8):1113-21.

    40. 2002

  40. Li B, Chen N, Luo T, Otsu Y, Murphy TH, Raymond LA. Differential regulation of synaptic and extra-synaptic NMDA receptors. Nat Neurosci. 2002 Sep;5(9):833-4.

  41. Zeron MM, Hansson O, Chen N, Wellington CL, Leavitt BR, Brundin P, Hayden MR, Raymond LA. Increased sensitivity to N-methyl-D-aspartate receptor-mediated excitotoxicity in a mouse model of Huntington's disease. Neuron. 2002 Mar 14;33(6):849-60.

    42. 2001

  42. Zeron MM, Chen N, Moshaver A, Lee AT, Wellington CL, Hayden MR, Raymond LA. Mutant huntingtin enhances excitotoxic cell death. Mol Cell Neurosci. 2001 Jan;17(1):41-53.

  43. Chen N, Ren J, Raymond LA, Murphy TH. Changes in agonist concentration dependence that are a function of duration of exposure suggest N-methyl-D-aspartate receptor nonsaturation during synaptic stimulation. Mol Pharmacol. 2001 Feb;59(2):212-9.

  44. Umemiya M, Chen N, Raymond LA, Murphy TH. A calcium-dependent feedback mechanism participates in shaping single NMDA miniature EPSCs. J Neurosci. 2001 Jan 1;21(1):1-9.

    45. 2000

  45. Hackam AS, Yassa AS, Singaraja R, Metzler M, Gutekunst CA, Gan L, Warby S, Wellington CL, Vaillancourt J, Chen N, Gervais FG, Raymond L, Nicholson DW, Hayden MR. Huntingtin interacting protein 1 induces apoptosis via a novel caspase-dependent death effector domain. J Biol Chem. 2000 Dec 29;275(52):41299-308.

  46. Chen N, Murphy TH, Raymond LA. Competitive inhibition of NMDA receptor-mediated currents by extracellular calcium chelators. J Neurophysiol. 2000 Aug;84(2):693-7.

    47. 1999

  47. Chen N, Luo T, Raymond LA. Subtype-dependence of NMDA receptor channel open probability. J Neurosci. 1999 Aug 15;19(16):6844-54.

  48. Chen N, Luo T, Wellington C, Metzler M, McCutcheon K, Hayden MR, Raymond LA. Subtype-specific enhancement of NMDA receptor currents by mutant huntingtin. J Neurochem. 1999 May;72(5):1890-8.

  49. Metzler M, Chen N, Helgason CD, Graham RK, Nichol K, McCutcheon K, Nasir J, Humphries RK, Raymond LA, Hayden MR. Life without huntingtin: normal differentiation into functional neurons. J Neurochem. 1999 Mar;72(3):1009-18.

  50. Chen N, Lucero MT. Transient and persistent tetrodotoxin-sensitive sodium currents in squid olfactory receptor neurons. J Comp Physiol [A]. 1999 Jan;184(1):63-72.

    51. 1997

  51. Chen N, Moshaver A, Raymond LA. Differential sensitivity of recombinant N-methyl-D-aspartate receptor subtypes to zinc inhibition. Mol Pharmacol. 1997 Jun;51(6):1015-23.

  52. Lucero MT, Chen N. Characterization of voltage- and Ca2+-activated K+ channels in squid olfactory receptor neurons. J Exp Biol. 1997 Jun;200(Pt 11):1571-86.

    53. 1996

  53. Corotto FS, Piper DR, Chen N, Michel WC. Voltage- and Ca2+-gated currents in zebrafish olfactory receptor neurons. J Exp Biol. 1996 May;199(Pt 5):1115-26.
    54.


ABSTRACTS
  1. Frech C and Chen N. Synteny analysis of malaria parasite genomes reveals species-specific genes and pathways possibly linked to human disease. CSHL Genome Informatics Meeting, November 2-5, 2011, Cold Spring Harbor, NY.

  2. Frech C and Chen N. Comparative gene family classification reveals rapid expansion and contraction of virulence gene families in malaria parasites. CSHL Genome Informatics Meeting, November 2-5, 2011, Cold Spring Harbor, NY.

  3. Tarailo-Graovac M, Vergara IA, Rose AM and Chen N. Identification and characterization of genomic lesions that suppress lethality in the absence of spindle assembly checkpoint component, MDF-1/Mad1, in Caenorhabditis elegans. The EMBO Meeting 2011, September 10-13, 2011, Vienna. (Supported by a DeLill Nasser Award to Maja Tarailo-Graovac)

  4. Vergara IA, Tarailo-Graovac M, Wang J and Chen N. Loss-of-Function genomic variations in wild Caenorhabditis elegans. 18th International C. elegans Meeting, June 22-26, 2011, UCLA, Los Angeles.

  5. Chu JSCC, Tarailo-Graovac M, Wang J, Uyar B, Tu D, Trinh J, Baillie D and Chen N. Comparative genomics reveals novel regulatory mechanism for the transcription factor RFX/DAF-19 in C. elegans. 18th International C. elegans Meeting, June 22-26, 2011, UCLA, Los Angeles.

  6. Hingwing K, Wong T, Chen N, and Hawkins N. Identification of genes that function with dsh-2 to regulate asymmetric cell division. 18th Internati onal C. elegans Meeting, June 22-26, 2011, UCLA, Los Angeles.

  7. Chen N. RFX transcription factors and ciliary genes in choanoflagellates: still dating or happily engaged? 2011 International Choanoflagellate Workshop, June 16-19, 2011, UC Berkeley, Berkeley. (Invited talk)

  8. Frech C and Chen N. Computational comparison of six Plasmodium genomes identifies putative human virulence genes. SFU Health Research Day, May 12, 2011, Burnaby, BC.

  9. Vergara IA, Tarailo-Graovac M, Wang J, and Chen N. Loss-of-Function genomic variations in wild Caenorhabditis elegans. The Biology of Genomes, May 10-14, 2011, Cold Spring Harbor, NY.

  10. Uyar B, Chu JSCC, Vergara IA, Chua SY, Baillie DL, and Chen N. C. briggsae transcriptome: a platform for quantitative comparative genomics. High-Throughput Biology, CSH Asia. April 19-23, 2011, Suzhou, China.

  11. Frech C and Chen N. Computational comparison of six Plasmodium genomes identifies putative human virulence genes. 2011 Genome Canada Research Exchange & Poster Competition, April 15, 2011, Vancouver, BC.

  12. Frech C and Chen N. Computational comparison of six Plasmodium genomes identifies putative human virulence genes. 2011 MBB Colloquium, April 12, 2011, Burnaby, BC. (Christian won the top prize for presentation)

  13. Frech C and Chen N. Computational comparison of six Plasmodium genomes identifies putative human virulence genes. RECOMB2011, March 28-31, 2011, Vancouver, BC.

  14. Chen N. Mariculture in the era of genomics. 2011 International Symposium of Mariculture and Disaster Response, March 18-20, 2011, Ningbo, China. (Invited talk)

  15. Vergara IA, Tarailo-Graovac M, Wang J, She R, Wang K, Chen N.Loss-of-function mutations in a natural isolate of Caenorhabditis elegans. Hinxton/CSHL Genome Informatics Meeting, September 15-19, 2010, Hinxton, UK. (Selected for Platform presentation)

  16. Vergara IA, Tarailo-Graovac M, She R, Wang K, Chen N. Identification and Functional Characterization of Genomic Variations: Lessons from C. elegans. Annual Seattle-Vancouver Worm Meeting, May 14, 2010, UBC. (Selected for Platform presentation)

  17. Vergara IA, Tarailo-Graovac M, She R, Wang K, Chen N. Identification and Functional Characterization of Genomic Variations: Lessons from C. elegans. Annual MBB Symposium 2010, April 15, 2010, SFU. (Platform presentation)

  18. Uyar B, Chu JSC, Vergara IA, Frech C, and Chen N. Genome Annotation Improvement of Four Caenorhabditis Species: C. briggsae, C. remanei, C. brenneri, and C. japonica. VanWorm Meeting, Feb 10, 2010, SFU. (Platform presentation)

  19. Vergara IA, Fong K, Schwartz EM, Baillie DL and Chen N. Annotation and analysis of repeats in five Caenorhabditis species. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles.

  20. Tarailo-Graovac M, Wang J, Chu JSC, Tu D, Baillie DL, and Chen N. Spatiotemporal analysis of promoter functions implicates spindle assembly checkpoint genes in polyploidization in Caenorhabditis elegans. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles. (Selected for platform presentation)

  21. Vergara IA, Mah AK, Huang JC, Tarailo-Graovac M, Johnsen RC, Baillie DL, and Chen N.Polymorphic segmental duplication in the nematode Caenorhabditis elegans. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles.

  22. Hutter H, Ng MP, and Chen N. GExplore: Multi-gene data mining for worm geneticists. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles.

  23. Chu JSC, She R, Wang K, and Chen N. Reannotating the C. briggsae genome using genBlastG, a new homology-based gene finder. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles.

  24. Vergara IA and Chen N. Characterization of synteny blocks and comparative analysis of operons in Caenorhabditis species. 17th International C. elegans meeting, June 24-28, 2009, UCLA, Los Angeles.

  25. Chu JSC and Chen N. OrthoCluster and GenBlastG. Genomics and Evolution Workshop. 17th International C. elegans Meeting, June 24-28, 2009, UCLA, Los Angeles. (Platform presentation)

  26. Chu JSC, Baillie DL, and Chen N. DAF-19 represses a Pellino-like gene in C. elegans via a divergent X-box motif. Seattle-Vancouver C. elegans Meeting. (Platform presentation)

  27. Chu JSC, Baillie DL, and Chen N. DAF-19 represses a Pellino-like gene in C. elegans via a divergent X-box motif. 2009 MBB Symposium, Simon Fraser University. (Jeff won the third prize for this presentation)

  28. Vergara IA, Ng P, Zeng X, Mah AK, Baillie DL, Pei J, and Chen N. Comparative analysis of genomic structural variations in multiple species. Genome Informatics. September 10 - 14, 2008, Joint Cold Spring Harbor Laboratory / Wellcome Trust Sanger Institute, Hinxton, UK. (Selected for platform presentation)

  29. Chu JSC, Wang J, Aftab S, Lee D, Tu D, Tarailo-Graovac M, Nesbitt M, Ng P, Johnsen R, Baillie DL, Chen N. Computational and molecular characterization of RFX transcription factor mediated transcription. Systems Biology: Global Regulation of Gene Expression. March 27-March 30, 2008, Cold Spring Harbor Laboratory, New York.

  30. Zeng X, Vergara I, Nesbitt M, Pei J, and Chen N. OrthoCluster: a depth-first search algorithm for identifying synteny blocks and genomic strucutral variants. Genome Informatics. November 1 - November 5, 2007, Cold Spring Harbor Laboratory, New York. (Selected for platform presentation)

  31. Zeng X, Nesbitt MJ, Pei J, Chen N. OrthoCluster: A depth-first search algorithm for identifying synteny blocks and genomic structural variants. Research Exchange 2007 - Genomics Forum, UBC, Vancouver, April 13, 2007.

  32. She R, Chu J, Pei J, Chen N, Wang K. genBLAST: a graph-simulation based fast searching algorithm for identifying homologous genes. Research Exchange 2007 - Genomics Forum, UBC, Vancouver, April 13, 2007.

  33. Chu J, Johnsen, R, Baillie D, Chen N. Genes in a genome: randomly distributed or clustered? Research Exchange 2007 - Genomics Forum, UBC, Vancouver, April 13, 2007.

  34. Chu J, Hunt Newbury R, Moerman DG, Baillie DL, Chen N. Chromosomal clustering of tissue-specific genes in the nematode Caenorhabditis elegans genome. Systems Biology: global regulation of gene expression. Cold Spring Harbor Laboratory, New York. March 29-April 1, 2007.

  35. Chen N and Stein LD. Conservation and functional significance of overlapping genes in Caenorhabditis elegans. 15th International C. elegans Meeting, June 25-29, 2005, UCLA, Los Angeles. (Selected for platform presentation)

  36. Chen N and Stein LD. Systematic annotation of chemosensory genes in Caenorhabditis briggsae. 15th International C. elegans Meeting, June 25-29, 2005, UCLA, Los Angeles.

  37. Zhao Z, Fang L, Chen N, Johnsen R, Stein LD, Baillie DL. Independent cis-elements mediate same expression patterns in Caenorhabditis elegans. 15th International C. elegans Meeting, June 25-29, 2005, UCLA, Los Angeles.

  38. Chen N, Pai S, Zhao Z, Mah A, Newbury R, Johnsen RC, Altun Z, Moerman DG, Baillie DL, Stein LD. Identification of a novel nematode chemosensory gene family. Joint CSHL/Sanger Genome Informatics Meeting, Hinxton, UK, October, 2005. (Selected for platform presentation)

  39. Chen N and Stein LD. WormBase: what's new and what's next? East Coast Worm Meeting. New Haven. June 2005. (Selected for platform presentation)

  40. Chen N and Stein LD. WormBase as a platform for ORFeome and C. briggsae genome sequences. 3rd Annual ORFeome Symposium. Boston. December 2003. (Invited platform presentation)

  41. Chen N and Stein LD. Wormbase as a data mining resource. 14th International C. elegans Meeting, July, 2003, UCLA, Los Angeles. (Selected for platform presentation)

  42. Chen N and Raymond LA. Subtype-dependent interactions between NMDA receptors and huntingtin. Huntington's Disease: New Progress. Cape Cod, August, 1998. (Selected for platform presentation)

  43. Chen N, Wellington C, Metzler M, Hayden MR, Raymond LA. NMDA-mediated currents are increased in the presence of mutant huntingtin or absence of normal huntingtin. 17th International Meeting of the World Federation of Neurology, Research Group on Huntington's Disease, Sydney, Australia, September, 1997. (Selected for platform presentation)

  44. Chen N and Raymond LA. The role of glutamate receptor-HD proteion interactions in the pathogenesis of Huntington's Disease. 12th Annual Research Day, Department of Psychiatry, University of British columbia, March, 1997. (Won the McGeer and McGeer Award for best platform presentation)

  45. Chen N and Sun HB. Study of feeding sensitivity in the prawn Penaeus chinensis Osbeck. 11th International Symposium on Olfaction and Taste. Sappro, Japan. May 1993. (Selected for platform presentation)



BOOK CHAPTERS
  1. Vergara IA and Chen N. Using OrthoCluster to Identify Synteny Blocks and Genome Rearrangement Events. Current Protocols in Bioinformatics. John Willey & Sons. 2009.

  2. Tarailo-Graovac M and Chen N. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Current Protocols in Bioinformatics. John Wiley & Sons. 2009.

  3. Gupta B, Johnsen, R and N Chen. The genome and biology of the nematode Caenorhabditis briggsae. WormBook 2007.

  4. Chen N. Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences. Current Protocols in Bioinformatics. John Wiley & Sons. 2004.

  5. Chen N, Lee RY, Altun ZF, Boulin T, Sternberg PW and Stein LD. In Kotter,R. Neuroinformatics for C. elegans: Relating Mind and Body in Wormbase. (ed.), Neuroscience Databases: A Practical Guide. Kluwer Academic Publishers, Boston, MA, pp. 1-17. 2002.


INVITED REVIEWS
  1. Chen N. Bioinformatics in the era of genomics. Biotechnology Focus, November, 2008.