Publications

1. Aach J, Bulyk ML, Church GM, Comander J, Derti A, and Shendure J. (2001) Computational comparison of two draft sequences of the human genome. Nature 409: 856-9.
2. Aach JA and Church GM. (2004) Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J Theor. Biol. in press.
3. Anderson LM, Choe SE, Yukhananov RY, Hopfner RL, Church GM, Pratt RE, and Dzau VJ. (2003) Identification of a novel set of genes regulated by a unique LXRalpha-mediated Transcription Mechanism. J Biol Chem 278:15252-152560.
4. Coleman FT, Mueschenborn S, Meluleni G, Ray C, Carey V, Vargas SO, Cannon CL, Ausubel FM, and Pier GB. (2003) Hypersusceptibility of cystic fibrosis mice to chronic Pseudomonas aeruginosa oropharyngeal colonization and lung infection. Proc. Natl. Acad. Sci. USA 100:1949-1954.
5. Déziel E, Lépine F, Milot S, Mindrinos MN, Tampakaki AP, He1 J, and Rahme LG. (2003) The Pseudomonas aeruginosa mvfR gene regulates the synthesis of 4-hydroxy-2-alkylquinolines, including the Pseudomonas quinolone signal (PQS) precursor and antibacterial compounds. Under review at Proc. Natl. Acad. Sci. USA.
6. Drenkard E and Ausubel FM. (2002) Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation. Nature 416:740-743.
7. Dudley AM, Aach J, Steffen MA, and Church GM. (2002) Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range. Proc. Nat. Acad. Sci. USA 99:7554-7559.
8. El Khoury JB, Moore KJ, Means TK, Leung J, Terada K, Toft M, Freeman MW, and Luster AD. (2003) CD36 mediates the innate host response to beta-amyloid. J Exp Med 197, 1657-1666
9. Fitzgerald ML, Mendez AJ, Moore KJ, Andersson LP, Panjeton HA and MW Freeman. (2001) ATP-binding Cassette Transporter A1 Contains an NH2-terminal Signal Anchor Sequence That Translocates the Protein's First Hydrophilic Domain to the Exoplasmic Space. J Biol Chem 276: 15137-45.
10. Freeman MW and KJ Moore. (2003) Elixirs for restraining inflammation. Nat Med 9:168-9.
11. Halfon MS, Grad Y, Church GM, and Michelson AM. (2002) Computation-based discovery of related transcriptional regulatory modules and motifs from a combinatorial model. Genome Research 12: 1019-1028.
12. He J, Baldini RL, Déziel E, Saucier M, Zhang Q, Liberati NT, Lee D, Urbach J, Goodman HM and Rahme LG. (2003) Two pathogenicity islands harboring novel plant and animal virulence genes are carried by the broad host range pathogen Pseudomonas aeruginosa strain PA14. Under review at Proc. Natl. Acad. Sci. USA
13. King OD, Lee JC, Dudley AM, Janse DM, Church GM, Roth FP. (2003) Predicting Phenotype from Patterns of Annotation. ISMB 2003; Bioinformatics. 2003 Jul;19 Suppl 1:I183-I189.
14. Kunjathoor VV, Febbraio M, Podrez EA, Moore KJ, Andersson L, Koehn S, Rhee JS, Silverstein R, Hoff HF, and Freeman MW. (2002) Scavenger receptors class A-I/II and CD36 are the principal receptors responsible for the uptake of modified low density lipoprotein leading to lipid loading in macrophages. J Biol Chem 277:49982-8.
15. Lee M-LT, Bulyk ML, Whitmore GA, Church GM. A statistical model for investigating binding probabilities of DNA nucleotide sequences using microarrays. Biometrics 58(4):981-8.
16. Mitra RD, Shendure J, Olejnik J, Olejnik EK, and Church GM. (2003) Fluorescent in situ Sequencing on Polymerase Colonies. Analyt. Biochem. 320:55-65
17. Mitra RD, Butty V, Shendure J, Williams BR, Housman DE, and Church GM. (2003) Digital Genotyping and Haplotyping with Polymerase Colonies. Proc. Natl. Acad. Sci. USA 100:5926-5931
18. Miyata S, Casey M, Frank DW, Ausubel FM and Drenkard E. (2003) Use of the Galleria mellonella caterpillar as a model host to study the role of the type III secretion system in Pseudomonas aeruginosa pathogenesis. Infection and Immunity 71:2404-13.
19. Moore KJ, Rosen ED, Fitzgerald ML, Randow F, Andersson LP, Altshuler D, Milstone DS, Mortensen RM, et al. (2001) The role of PPAR- gamma in macrophage differentiation and cholesterol uptake. Nat Med 7: 41-7.
20. Moore KJ, El Khoury J, Medeiros LA, Terada K, Geula C, Luster AD, and Freeman MW. (2002) A CD36-initiated signaling cascade mediates inflammatory effects of beta-amyloid. J Biol Chem 277:47373-9.
21. Shendure J and Church GM. (2002) Computational discovery of sense-antisense transcription in the mouse and human genomes. Genome Biology 3:1-14. Supplements: antisense &HumMus.
22. Steffen M, Petti A, D'haeseleer P, Aach J, and Church GM. (2002) Automated Modelling of Signal Transduction Networks. BMC Bioinformatics 3:34-44.
23. Steffen M, Jaffe JD, and Church GM. (2003) Analysis of DNA-Binding Proteins by Mass Spectrometry. Submitted to Nature Biotechnology.
24. Vitkup D, Sander C, Church GM. (2003) The Amino-acid Mutational Spectrum of Human Genetic Disease. Genome Biol. 4: R72.
25. Wang X and Seed B. (2003) A PCR Primer Bank For Quantitative Gene Expression Analysis. Nucleic Acids Research 31(24): e154; pp.1-8.
26. Wang X and Seed B. (2003) Selection of oligonucleotide probes to interrogate protein coding regions. Bioinformatics 19:796-802
27. Wright M and Church GM. (2002) An Open-source Oligonucleotide Microarray Probe Standard for Human and Mouse. Nat Biotechnol. 2002 Nov;20(11):1082-3. Supplement
28. Wilson DS, Keefe AD and Szostak JW. (2001) The use of mRNA display to select high-affinity protein-binding peptides. Proc Natl Acad Sci USA 98: 3750-5.
29. Yang Y and Seed B. (2003) BAC-Fishing: rapid site-specific gene targeting with intact bacterial artificial chromosomes, Nature Biotechnol 21:447-451
30. Zhu J, Shendure J, Mitra RD, and Church GM. (2003) Single molecule profiling of alternative pre-mRNA splicing. Science 301(5634):836-838