Research

My research focuses on systems biology of bacterial pathogens, and the study of microbial communities through metagenomics and other meta-omics data. Systems biology attempts to achieve a whole-system understanding of an organism, rather than focusing on a single gene at a time. I enjoy highly interdisciplinary research, working closely with experimental biologists, and linking them to computational analyses. After hours, I am involved in the local citizen science and DIYbio community, acting as the community projects coordinator at BioCurious in Sunnyvale, and co-founder and chair of Counter Culture Labs in the East Bay.

Postdoctoral researcher, Harvard Medical School, 2001-2004

Ph.D. in Computer Science, University of New Mexico, 2000

M.S. in Computer Science, Stanford University, 1993

M.S. in Electrical Engineering, Ghent University, Belgium, 1991

M.E. in Electrical Engineering, KIHO, Belgium, 1988

Griesemer M, Kimbrel J, Zhou CE, Navid A, D'haeseleer P. (2018) Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics 19:948

Franco M, D'haeseleer PM, Branda SS, Liou MJ, Haider Y, Segelke BW, El-Etr SH. (2018) Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT). Front Cell Infect Microbiol. 8:370.

D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J. (2017) Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Stand Genomic Sci. 12:67.

D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S. (2016) Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6. Genome Announc. 4(3). pii: e00649-16.

Simmons CW, Reddy AP, D'haeseleer P, Khudyakov J, Billis K, Pati A, Simmons BA, Singer SW, Thelen MP, VanderGheynst JS. (2014) Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw. Biotechnol Biofuels 7(1):495.

Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D'haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. (2014) Phylogenomically guided identification of industrially relevant GH1 beta-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 9(9):2082-91.

Gladden JM, Park JI, Bergmann J, Reyes-Ortiz V, D'haeseleer P, Quirino BF, Sale KL, Simmons BA, Singer SW. (2014) Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. Biotechnol Biofuels 7(1):15.

Bergmann J, Costa OY, Gladden J, Singer S, Heins R, D´haeseleer P, Simmons B, Quirino B (2014) Discovery of two novel beta-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett. 351(2):147-55.

Reddy AP, Simmons CW, D'haeseleer P, Khudyakov J, Burd H, Hadi M, Simmons BA, Singer SW, Thelen MP, Vandergheynst JS. (2013) Discovery of microorganisms and enzymes involved in high-solids decomposition of rice straw using metagenomic analyses. PLoS One 8(10):e77985.

D'haeseleer P, Gladden JM, Allgaier M, Chain PS, Tringe SG, Malfatti SA, Aldrich JT, Nicora CD, Robinson EW, Pasa-Tolic L, Hugenholtz P, Simmons BA, Singer SW. (2013) Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass. PLoS One. 8(7):e68465.

McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. (2013) From soil to structure, a novel dimeric beta-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem. 288(21):14985-92.

Chaudhury S, Abdulhameed MD, Singh N, Tawa GJ, D'haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A. (2013) Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLoS One. 2013 May 21;8(5):e63369

Deangelis KM, D'Haeseleer P, Chivian D, Simmons B, Arkin AP, Mavromatis K, Malfatti S, Tringe S, Hazen TC. (2013) Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron. Stand Genomic Sci. 2013 Feb 25;7(3):382-98

Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP. (2012) Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Proc Natl Acad Sci U S A. 109(32):E2173-82.

Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ. (2012) Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization. BMC Biotechnol. 12:38.

Borglin S, Joyner D, DeAngelis KM, Khudyakov J, D'haeseleer P, Joachimiak MP, Hazen T. (2012) Application of phenotypic microarrays to environmental microbiology. Current opinion in biotechnology. 23(1):41-8

Lu Z, Deng Y, Van Nostrand JD, He Z, Voordeckers J, Zhou A, Lee YJ, Mason OU, Dubinsky EA, Chavarria KL, Tom LM, Fortney JL, Lamendella R, Jansson JK, D'haeseleer P, Hazen TC, Zhou J. (2012) Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume. ISME J. 6(2):451-60.

Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, Batth T, Benke PI, D'haeseleer P, Sun N, Sale KL, Keasling JD, Lee TS, Petzold CJ, Mukhopadhyay A, Singer SW, Simmons BA, Gladden JM. (2012) A thermophilic ionic liquid-tolerant cellulase cocktail for the production of cellulosic biofuels. PLoS One. 7(5):e37010.

Jiao Y, D'haeseleer P, Dill BD, Shah M, Verberkmoes NC, Hettich RL, Banfield JF, Thelen MP. (2011) Identification of biofilm matrix-associated proteins from an acid mine drainage microbial community. Appl Environ Microbiol. 77(15):5230-7.

Hazen TC, Dubinsky EA, DeSantis TZ, Andersen GL, Piceno YM, Singh N, Jansson JK, Probst A, Borglin SE, Fortney JL, Stringfellow WT, Bill M, Conrad ME, Tom LM, Chavarria KL, Alusi TR, Lamendella R, Joyner DC, Spier C, Baelum J, Auer M, Zemla ML, Chakraborty R, Sonnenthal EL, D'haeseleer P, Holman HY, Osman S, Lu Z, Van Nostrand JD, Deng Y, Zhou J, Mason OU. (2010) Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science. 330(6001):204-8.

Allgaier M, Reddy A, Park JI, Ivanova N, D'haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS, Hugenholtz P. (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One. 5(1):e8812

DeAngelis, KM, JG Gladden, M Allgaier, P D’haeseleer, JL Fortney, A Reddy, P Hugenholtz, S Singer, J Van Der Gheynst, WL Silver, B Simmons, and TC Hazen. (2010) Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities. BioEnergy Research 3:146-158.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 462(7276):1056-60.

Tamura, M. and D’haeseleer, P. (2008) Microbial genotype-phenotype mapping by class association rule mining. Bioinformatics. 24(13):1523-9.

D'haeseleer, P. (2006) How does DNA sequence motif discovery work? Nat Biotechnol. 24(8):959-61.

D'haeseleer P. (2006) What are DNA sequence motifs? Nat Biotechnol. 24(4):423-5.

Nguyen, D. and D'haeseleer, P. (2006) Deciphering Principles of Transcription Regulation in Eukaryotic Genomes. Mol Syst Biol. 2:2006.0012.

D'haeseleer, P. (2005) How does gene expression clustering work? Nature Biotechnology 23(12):1499-501.

D'haeseleer, P. (2005) Closing the circle of osmoregulation. Nature Biotechnology, 23(8):941-2.

Segrš D, Zucker J, Katz J, Lin X, D'haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA, Church GM. (2003) From annotated genomes to metabolic flux models and kinetic parameter fitting. Omics 7(3):301-16.

Steffen M, Petti A, Aach J, D'haeseleer P, Church G. (2002) Automated modelling of signal transduction networks. BMC Bioinformatics. 3:34.

D'haeseleer P, Liang S, Somogyi R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics. 16(8):707-26.