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Publications of Dr. Twigger


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  • Twigger SN, Pruitt KD, Fernández-Suárez XM, Karolchik D, Worley KC, Maglott DR, Brown G, Weinstock G, Gibbs RA, Kent J, Birney E, Jacob HJ. “What everybody should know about the rat genome and its online resources” (2008) Nat Genet. May;40(5):523-7.
  • Aitman TJ, Critser JK, Cuppen E, Dominiczak A, Fernandez-Suarez XM, Flint J, Gauguier D, Geurts AM, Gould M, Harris PC, Holmdahl R, Hubner N, Izsvák Z, Jacob HJ, Kuramoto T, Kwitek AE, Marrone A, Mashimo T, Moreno C, Mullins J, Mullins L, Olsson T, Pravenec M, Riley L, Saar K, Serikawa T, Shull JD, Szpirer C, Twigger SN, Voigt B, Worley K. (2008) “Progress and prospects in rat genetics: a community view.” Nat Genet. May;40(5):516-22.
  • BioMoby Consortium (2008 ) “Interoperability with Moby 1.0--it's better than sharing your toothbrush!” Brief Bioinform. May;9(3):220-31
  • Genome Information Integration Project and H-Invitational 2 (2008) “The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts” Nucleic Acids Res. Jan;36 (Database issue):D793-9
  • Sander TL, Ou JS, Densmore JC, Kaul S, Matus I, Twigger S, Halligan B, Greene AS, Pritchard KA Jr, Oldham KT. (2007) “Protein composition of Plasminogen Activator Inhibitor Type 1-derived endothelial microparticles”, Shock, Aug 16th
  • Phillips GN Jr, Fox BG, Markley JL, Volkman BF, Bae E, Bitto E, Bingman CA, Frederick RO, McCoy JG, Lytle BL, Pierce BS, Song J, Twigger SN. (2007) “Structures of proteins of biomedical interest from the Center for Eukaryotic Structural Genomics”, J. Struct Funct. Genomics.
  • Simon N. Twigger, Mary Shimoyama, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob (2007) “The Rat Genome Database, update 2007 – Easing the path from disease to data and back again”, Nucleic Acid Res. 35:D658-662
  • Weinshenker, D., Wilson, M.M., Williams, K.M., Weiss, J.M., Lamb, N.E. and Twigger, S.N. (2005) “Hummer - A new method for identifying informative genetic markers in selectively bred rats”, Mamm. Genome 16:784-791.
  • Twigger SN, Pasko D, Nie J, Shimoyama M, Bromberg S, Campbell D, Chen J, dela Cruz N, Fan C, Foote C, Harris G, Hickmann B, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nigam R, Petri V, Reilly D, Ruotti V, Schauberger E, Seiler K, Slyper R, Smith J, Wang W, Wu W, Zhao L, Zuniga-Meyer A, Tonellato PJ, Kwitek AE, Jacob HJ. (2005) “Tools and strategies for physiological genomics: the Rat Genome Database”, Physiological Genomics, 17:246-256
  • Halligan, B.D., Ruotti, V., Twigger, S.N. and Greene, A.S. (2005) DeNovoID: a web-based tool for identifying peptides from sequence and mass tags deduced from de novo peptide sequencing by mass spectroscopy. Nucleic Acids Res, 33, W376-381.
  • Halligan, B. D., Slyper, R. Y., Twigger, S. N., Hicks, W., Olivier, M. and Greene, A. S., (2005) “ZoomQuant: An Application for the Quantitation of Stable Isotope Labeled Peptides”, J. Amer. Soc. Mass Spectrometry, 16: 302-306
  • Hicks, W.A., Halligan, B.D., Slyper, R.Y., Twigger, S.N., Greene, A.S. and Olivier, M. (2005) Simultaneous quantification and identification using 18O labeling with an ion trap mass spectrometer and the analysis software application "ZoomQuant". J Am Soc Mass Spectrom, 16, 916-925.
  • Norberto de la Cruz, Susan Bromberg, Dean Pasko, Mary Shimoyama, Simon Twigger, Jiali Chen, Chin-Fu Chen, Chunyu Fan, Cindy Foote, Gopal R Gopinath, Glenn Harris, Aubrey Hughes, Yuan Ji, Weihong Jin, Dawei Li, Jedidiah Mathis, Natalya Nenasheva, Jeff Nie, Rajni Nigam, Victoria Petri, Dorothy Reilly, Weiye Wang, Wenhua Wu, Angela Zuniga-Meyer, Lan Zhao, Anne Kwitek, Peter Tonellato, and Howard Jacob. (2005) “The Rat Genome Database (RGD): Developments towards a Phenome Database” Nucleic Acids Res. 33:D485-491.
  • Halligan, B.D., E.A. Dratz, X. Feng, S.N. Twigger, P.J. Tonellato, and A.S. Greene. (2004). “Peptide identification using peptide amino acid attribute vectors”. J Proteome Res 3: 813-820.
  • Halligan, B.D., V. Ruotti, W. Jin, S. Laffoon, S.N. Twigger, and E.A. Dratz. (2004). “ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels”. Nucleic Acids Res 32: W638-644.
  • Etim, A., G. Zhou, X. Wen, H. Liu, V. Ruotti, S. Twigger, W. Jin, B. Matysiak, J. Mathis, P.J. Tonellato, and M.W. Datta. 2004. “ChromSorter PC: a database of chromosomal regions associated with human prostate cancer”. BMC Genomics 5: 27.
  • Gibbs, R.A. (and 129 other authors). (2004). “Genome sequence of the Brown Norway rat yields insights into mammalian evolution”. Nature 428: 493-521.
  • Twigger, S.N. (2004). “Of rats and men”. Genome Biol 5: 314.
  • Simon N. Twigger, Jeff Nie, Victor Ruotti, Jiaming Yu, Dan Chen, Dawei Li, Jed Mathis, Vijay Narayanasamy, Gopal R. Gopinath, Dean Pasko, Mary Shimoyama, Norberto de la Cruz, Susan Bromberg, Anne E. Kwitek, Howard J. Jacob and Peter J, Tonellato (2004) “Integrative Genomics: In Silico coupling of Rat physiology and complex traits to Mouse and Human data”, Genome Research, 14:651-660
  • Michael A. Thomas, Chin-Fu Chen, Michael I. Jensen-Seaman, Peter J. Tonellato and Simon N. Twigger (2003) “Phylogenetics of Rat Inbred Strains”, Mammalian Genome, 14:1-4.
  • Simon Twigger, Jian Lu, Mary Shimoyama, Dan Chen, Dean Pasko, Hanping Long, Jessica Ginster, Chin-Fu Chen, Rajni Nigam, Anne Kwitek-Black, Janan Eppig, Lois Maltais, Donna Maglott, Greg Schuler, Howard Jacob and Peter Tonellato (2002) “Rat Genome Database (RGD) – mapping disease onto the genome”, Nucleic Acids Res. 30: 125-128
  • Anne E. Kwitek-Black, Peter J. Tonellato, Dan Chen, Jo Gullings-Handley, Yongjian Samuel Cheng, Simon Twigger, Todd E. Scheetz, Thomas L. Casavant, Monika Stoll, Marcelo A. Nobrega, Masahide Shiozawa, M. Bento Soares, Val C. Sheffield, Howard J. Jacob (2001) “Automated Construction of High-Density Comparative Maps Between Rat, Human, and Mouse” Genome Research 11: 1935-1943
  • S. Twigger, J. Lu, M. Shimoyama, D. Pasko, P. Long, J. Ginster, C.F. Chen, R. Nigam, D. Chen, Z. Wang, A. Kwitek-Black, J. Eppig, D. Maglott, G. Schuler, F. Stahl, G. Levan, H. Jacob and P.J. Tonellato. “Rat Genome Database: A comparative genomics platform for rat, mouse and human”, Journal of Molecular Medicine, 79(2-3):B30, 2001