LaBaer Lab | Publications

Publication Archive

Older publications in the LaBaer Lab.

1986 | 1989 | 1993 | 1994 | 1997 | 2001 | 2002 | 2003 | 2004 | 2005 | 2006 | 2007

2007

Hu Y, Rolfs A, Bhullar B, Murthy TV, Zhu C, Berger MF, Camargo AA, KelleyF, McCarron S, Jepson D, Richardson A, Raphael J, Moreira D, Taycher E, Zuo D, Mohr S, Kane MF, Williamson J, Simpson A, Bulyk ML, Harlow E, Marsischky G, Kolodner RD, LaBaer J. “Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae.” Genome Res. 2007 Apr;17(4):536-43. Epub 2007 Feb 23. PMID: 17322287

Taycher E, Rolfs A, Hu Y, Zuo D,Mohr SE, Williamson J, LaBaer J. “A novel approach to sequence validating protein expression clones with automated decision making.” BMC Bioinformatics. 2007 Jun 13;8:198. PMID: 17567908

Murthy T, Rolfs A, Hu Y, Shi Z, Raphael J, Moreira D, Kelley F, McCarron S, Jepson D, Taycher E, Zuo D, Mohr S E, Fernandez M, Brizuela L, LaBaer J, “A full-genomic sequence-verified protein-coding gene collection for Francisella tularensis.” PLoS ONE 2007;2:e577 PMID: 17593976

Langlais C, Guilleaume B, Wermke N, Scheuermann T, Ebert L, LaBaer J, Korn B. “A systematic approach for testing expression of human full-length proteins in cell-free expression systems.” BMC Biotechnol. 2007 Oct 3;7:64. PMID: 17915018

Xu L, Zhu J, Hu X, Zhu H, Kim HT, LaBaer J, Goldberg A, Yuan J. “c-IAP1 cooperates with Myc by acting as a ubiquitin ligase for Mad1.” Mol Cell. 2007 Dec 14;28(5):914-22. PMID: 18082613

2006

Ramachandran N, Hainsworth E, Demirkan G, LaBaer J.“On-chip protein synthesis for making microarrays.” Methods Mol Biol. 2006;328:1-14. PMID: 16785638

Braun P, LaBaer J. “High Throughput Purification of Proteins from Escherichia Coli.” Cell Biology: A Laboratory Handbook, 3rd Edition, Volume 4. Elsevier Academic Press: Burlington, MA (2006): 73- 77.

Butcher RA, Bhullar BS, Perlstein EO, Marsischky G, LaBaer J, Schreiber SL. “Microarray-based method for monitoring yeast overexpression strains reveals small-molecule targets in TOR pathway.” Nat Chem Biol. 2006 Feb;2(2):103-9. Epub 2006 Jan 15. PMID: 16415861

Witt AE, Hines LM, Collins NL, Hu Y, Gunawardane RN, Moreira D, Raphael J, Jepson D, Koundinya M, Rolfs A, Taron B, Isakoff SJ, Brugge JS, LaBaer J. “Functional proteomics approach to investigate the biological activities of cDNAs implicated in breast cancer.” J Proteome Res. 2006 Mar;5(3):599-610. PMID: 16512675

Park J, Labaer J. “Recombinational cloning.” Curr Protoc Mol Biol. 2006 May;Chapter 3:Unit 3.20. PMID: 18265386

Cooper AA, Gitler AD, Cashikar A, Haynes CM, Hill KJ, Bhullar B, Liu K, Xu K, Strathearn KE, Liu F, Cao S, Caldwell KA, Caldwell GA, Marsischky G, Kolodner RD, Labaer J, Rochet JC, Bonini NM, Lindquist S. “Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson's models.” Science. 2006 Jul 21;313(5785):324-8. Epub 2006 Jun 22.

Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M. “A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report.”Mol Cell Proteomics. 2006 Oct;5(10):1996-2007. Epub 2006 Jul 24. PMID: 16867976

Chatterjee DK, LaBaer J. “Protein Technologies.” Current Opinion in Biotechnology, 17 (August 2006): 334-336.

Zuo D, Mohr SE, Hu Y, Taycher E, Rolfs A, Kramer J, Williamson J, LaBaer J. “PlasmID: a centralized repository for plasmid clone information and distribution.” Nucleic Acids Res. 2007 Jan;35(Database issue):D680-4. Epub 2006 Nov 28. PMID: 17132831

2005

LaBaer J, Ramachandran N. “Protein microarrays as tools for functional proteomics.”Curr Opin Chem Biol. 2005 Feb;9(1):14-9. PMID: 15701447

Fan M, Tsai J, Chen B, Fan K, LaBaer J. “A central repository for published plasmids.” Science. 2005 Mar 25;307(5717):1877. PMID: 15790830

Chang CY, LaBaer J. “DNA polymorphism detector: an automated tool that searches for allelic matches in public databases for discrepancies found in clone or cDNA sequences.” Bioinformatics. 2005 May 1;21(9):2133-5. Epub 2005 Feb 2. PMID: 15695424

Collins NL, Reginato MJ, Paulus JK, Sgroi DC, Labaer J, Brugge JS. “G1/S cell cycle arrest provides anoikis resistance through Erk-mediated Bim suppression.” Mol Cell Biol. 2005 Jun;25(12):5282-91. PMID: 15923641

Park J, Hu Y, Murthy TV, Vannberg F, Shen B, Rolfs A, Hutti JE, Cantley LC, Labaer J, Harlow E, Brizuela L. “Building a human kinase gene repository: bioinformatics, molecular cloning, and functional validation.” Proc Natl Acad Sci U S A. 2005 Jun 7;102(23):8114-9. Epub 2005 May 31. PMID: 15928075

LaBaer J. “So, you want to look for biomarkers (introduction to the special biomarkers issue).” J Proteome Res. 2005 Jul-Aug;4(4):1053-9. PMID: 16083254

Anderson KS, LaBaer J. “The sentinel within: exploiting the immune system for cancer biomarkers.” J Proteome Res. 2005 Jul-Aug;4(4):1123-33. PMID: 16083262

Ramachandran N, Larson DN, Stark PR, Hainsworth E, LaBaer J. “Emerging tools for real-time label-free detection of interactions on functional protein microarrays.” FEBS J. 2005 Nov;272(21):5412-25. PMID: 16262683

Komaroff AL, Labaer J.“Health for life. Genomic medicine: the science speeds up.” Newsweek. 2005 Dec 12;146(24):57. PMID: 16375163

2004

LaBaer J. “Mining the literature and large datasets.” Nat Biotechnol. 2003 Sep;21(9):9767. PMID: 12949554

Pearlberg J, LaBaer J. “Protein expression clone repositories for functional proteomics.” Curr Opin Chem Biol. 2004 Feb;8(1):98-102. PMID: 15036163

Seton-Rogers SE, Lu Y, Hines LM, Koundinya M, LaBaer J, Muthuswamy SK, Brugge JS. “Cooperation of the ErbB2 receptor and transforming growth factor beta in induction of migration and invasion in mammary epithelial cells.” Proc Natl Acad Sci U S A. 2004 Feb 3;101(5):1257-62. Epub 2004 Jan 22. PMID: 14739340

Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau AY, Walter JC, LaBaer J.“Self-assembling protein microarrays.” Science. 2004 Jul 2;305(5680):86-90. PMID: 15232106

Murthy TV, Wu W, Qiu QQ, Shi Z, LaBaer J, Brizuela L. “Bacterial cell-free system for high-throughput protein expression and a comparative analysis of Escherichia coli cell-free and whole cell expression systems.” Protein Expr Purif. 2004 Aug;36(2):217-25. PMID: 15249043

Hu Y, Labaer J. “Tracking gene-disease relationships for high-throughput functional studies.” Surgery. 2004 Sep;136(3):504-10. ISSN 0039-6060. PMID: 15349093

Nakamura K, Aebersold R, Bairoch A, Dunn M, Celis J, Hanash S, Hochstrasser D, Humphrey-Smith I, James P, Klose J, LaBaer J, Langen H, Mann M, Parekh R, Patterson S, Pearce C, Poepstorff P, Simpson RJ, Tomlinson I, Tsugita A, Yates J.“From genome to proteome--aim of human proteomics” Seikagaku. 2004 Oct;76(10):1271-4. PMID: 15580857

Marsischky G, LaBaer J. “Many paths to many clones: a comparative look at high-throughput cloning methods.” Genome Res. 2004 Oct;14(10B):2020-8. PMID: 15489321

Aguiar JC, LaBaer J, Blair PL, Shamailova VY, Koundinya M, Russell JA, Huang F, Mar W, Anthony RM, Witney A, Caruana SR, Brizuela L, Sacci JB Jr, Hoffman SL, Carucci DJ. “High-throughput generation of P. falciparum functional molecules by recombinational cloning.” Genome Res. 2004 Oct;14(10B):2076-82. PMID: 15489329

Labaer J, Qiu Q, Anumanthan A, Mar W, Zuo D, Murthy TV, Taycher H, Halleck A, Hainsworth E, Lory S, Brizuela L. “The Pseudomonas aeruginosa PA01 gene collection.” Genome Res. 2004 Oct;14(10B):2190-200. PMID: 15489342

Pearlberg J, Degot S, Endege W, Park J, Davies J, Gelfand E, Sawyer J, Conery A, Doench J, Li W, Gonzalez L, Boyce FM, Brizuela L, Labaer J, Grueneberg D, Harlow E. “Screens using RNAi and cDNA expression as surrogates for genetics in mammalian tissue culture cells.” Cold Spring Harb Symp Quant Biol. 2005;70:449-59. PMID: 16869783

2003

Hu Y, Hines LM, Weng H, Zuo D, Rivera M, Richardson A, LaBaer J. “Analysis of genomic and proteomic data using advanced literature mining.” J Proteome Res. 2003 Jul-Aug;2(4):405-12. PMID: 12938930

Braun P, LaBaer J. “High throughput protein production for functional proteomics.” Trends Biotechnol. 2003 Sep;21(9):383-8.PMID: 12948670

2002

Braun P, Hu Y, Shen B, Halleck A, Koundinya M, Harlow E, LaBaer J.“Proteome-scale purification of human proteins from bacteria.” Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2654-9. PMID: 11880620

Brizuela L, Richardson A, Marsischky G, Labaer J. “The FLEXGene repository: exploiting the fruits of the genome projects by creating a needed resource to face the challenges of the post-genomic era.” Arch Med Res. 2002 Jul-Aug;33(4):318-24. PMID: 12234520

LaBaer J.“Genomics, proteomics, and the new paradigm in biomedical research.” Genet Med. 2002 Nov-Dec;4(6 Suppl):2S-9S. PMID: 12544480

2001

Brizuela L, Braun P, LaBaer J. “FLEXGene repository: from sequenced genomes to gene repositories for high-throughput functional biology and proteomics.” Mol Biochem Parasitol. 2001 Dec;118(2):155-65. PMID: 11738706

1997

LaBaer J, Garrett MD, Stevenson LF, Slingerland JM, Sandhu C, Chou HS, Fattaey A, Harlow E. “New functional activities for the p21 family of CDK inhibitors.” Genes Dev. 1997 Apr 1;11(7):847-62. PMID: 9106657

Hiyama H, Iavarone A, LaBaer J, Reeves SA. “Regulated ectopic expression of cyclin D1 induces transcriptional activation of the cdk inhibitor p21 gene without altering cell cycle progression.” Oncogene. 1997 May 29;14(21):2533-42. PMID: 9191053

Hu G, Zhang S, Vidal M, LaBaer J, Xu T, Fearon ER. “Mammalian homologs of seven in absentia regulate DCC via the ubiquitin-proteasome pathway.” Genes and Development, 11.20 (1997): 2701–2714. PMID: 933433

1994

LaBaer J, Yamamoto KR. “Analysis of the DNA-binding affinity, Sequence Specificity and Context Dependence of the Glucocorticoid Receptor Zinc Finger Region.” J Molecular Biology, 239.5 (1994): 664–688. PMID: 801498

1993

Garabedian MJ, LaBaer J, Liu W-H, Thomas J. “Analysis of protein – DNA Interactions.” Gene Transcription - A Practical Approach, Oxford: Oxford University Press, (1993): 243–295. ISBN 0199632928.

1989

LaBaer J. “Rapid sequencing of miniprep DNA using Sequenase and end-labeled sequencing primer.” US Biochemicals, (Comments) 15 (1989): 19–20.

1986

LaBaer J, Tsien RY, Fahey KA, DeFranco AL. “Stimulation of the antigen receptor on WEHI-231 B lymphoma cells results in a voltage-independent increase in cytoplasmic calcium.” J Immunol. 1986 Sep 15;137(6):1836-44. PMID: 2427581