P. D’haeseleer

发表

Context preserving crossover in genetic programming

Patrik D'haeseleer, P. D’haeseleer, 1994, Proceedings of the First IEEE Conference on Evolutionary Computation. IEEE World Congress on Computational Intelligence.

Mining the gene expression matrix: inferring gene relationships from large scale gene expression data

P. D’haeseleer, R. Somogyi, X. Wen, 1998 .

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Natalia N. Ivanova, Lynne A. Goodwin, P. D’haeseleer, 2009, Nature.

Deciphering principles of transcription regulation in eukaryotic genomes

Dat H. Nguyen, P. D’haeseleer, 2006, Molecular systems biology.

Discovery of two novel β-glucosidases from an Amazon soil metagenomic library.

P. D’haeseleer, B. Simmons, S. Singer, 2014, FEMS microbiology letters.

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

Ye Deng, Zhili He, Janet K Jansson, 2011, The ISME Journal.

The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes

James G. Jeffryes, Michael B. Mundy, José P. Faria, 2020, bioRxiv.

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

P. D’haeseleer, Jizhong Zhou, J. Jansson, 2010, Science.

Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community

P. D’haeseleer, J. VanderGheynst, B. Simmons, 2010, PloS one.

Strategies for Enhancing the Effectiveness of Metagenomic-based Enzyme Discovery in Lignocellulolytic Microbial Communities

W. Silver, P. D’haeseleer, B. Simmons, 2010, BioEnergy Research.

Discovery of Microorganisms and Enzymes Involved in High-Solids Decomposition of Rice Straw Using Metagenomic Analyses

P. D’haeseleer, J. VanderGheynst, C. Simmons, 2013, PloS one.

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)

Lynne A. Goodwin, P. D’haeseleer, N. Kyrpides, 2009, Standards in genomic sciences.

What are DNA sequence motifs?

P. D’haeseleer, 2006, Nature Biotechnology.

How does DNA sequence motif discovery work?

P. D’haeseleer, 2006, Nature Biotechnology.

Proteomic Profiling of Burkholderia thailandensis During Host Infection Using Bio-Orthogonal Noncanonical Amino Acid Tagging (BONCAT)

P. D’haeseleer, S. Branda, B. Segelke, 2018, Front. Cell. Infect. Microbiol..

From annotated genomes to metabolic flux models and kinetic parameter fitting.

Daniel Segrè, Jeremy Zucker, George M Church, 2003, Omics : a journal of integrative biology.

A Distributed Approach to Anomaly Detection

S. Forrest, P. D’haeseleer, 1998 .

Data and text mining Microbial genotype – phenotype mapping by class association rule mining

P. D’haeseleer, L. Livermore, M. Tamura, 2008 .

Combining multiple functional annotation tools increases coverage of metabolic annotation

P. D’haeseleer, Jeffrey A. Kimbrel, A. Navid, 2017, bioRxiv.

Combining multiple functional annotation tools increases coverage of metabolic annotation

P. D’haeseleer, Jeffrey A. Kimbrel, A. Navid, 2017, BMC Genomics.

Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6

P. D’haeseleer, P. Chain, K. Williams, 2016, Genome Announcements.

Complete genome sequence of Saccharomonospora viridis type strain (P101T)

P. D’haeseleer, N. Kyrpides, H. Klenk, 2009, Standards in genomic sciences.

Encapsulin carrier proteins for enhanced expression of antimicrobial peptides

Timothy S. Carpenter, P. D’haeseleer, D. Savage, 2019, Biotechnology and bioengineering.

Complete genome sequence of Slackia heliotrinireducens type strain (RHS 1T)

Lynne A. Goodwin, P. D’haeseleer, N. Kyrpides, 2009, Standards in genomic sciences.

FY07 LDRD Final Report Comparative Analysis of Genome Composition with Respect to Genotype-to-Phenotype Mapping and Metabolic Capability

P. D’haeseleer, 2008 .

Application of phenotypic microarrays to environmental microbiology.

Terry Hazen, Sharon Borglin, Marcin P Joachimiak, 2012, Current opinion in biotechnology.

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei

P. D’haeseleer, S. Branda, B. Segelke, 2021, Frontiers in Immunology.

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

S. Tringe, P. D’haeseleer, B. Simmons, 2013, PloS one.

Sequence, Structure, and Epitope Analysis of the Polymorphic Membrane Protein Family in Chlamydia trachomatis

P. D’haeseleer, E. Lau, B. Segelke, 2022, bioRxiv.

Glycoside Hydrolases from a targeted Compost Metagenome, activity-screening and functional characterization

P. D’haeseleer, B. Simmons, P. Adams, 2012, BMC Biotechnology.

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community

P. D’haeseleer, B. Simmons, S. Singer, 2014, Biotechnology for Biofuels.

An immunological approach to change detection: algorithms, analysis and implications

S. Forrest, P. D’haeseleer, P. Helman, 1996, Proceedings 1996 IEEE Symposium on Security and Privacy.

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10 T )

Goodwin, Nolan, Lynne, 2009 .

Complete genome sequence of Cryptobacterium curtum type strain (12-3 T )

Bristow, Ivanova, P. D’haeseleer, 2009 .

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei

P. D’haeseleer, S. Branda, B. Segelke, 2021, bioRxiv.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

Jonathan A. Eisen, Natalia N. Ivanova, P. D’haeseleer, 2009, Nature.

Complete genome sequence of Halogeometricum borinquense type strain (PR3T)

Lynne A. Goodwin, P. D’haeseleer, N. Kyrpides, 2009, Standards in genomic sciences.

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus

Hannah L. Woo, P. D’haeseleer, B. Simmons, 2011, Proceedings of the National Academy of Sciences.

Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Simon Daefler, Ali Navid, Anders Wallqvist, 2013, PloS one.

From Soil to Structure, a Novel Dimeric β-Glucosidase Belonging to Glycoside Hydrolase Family 3 Isolated from Compost Using Metagenomic Analysis

Paul D Adams, Blake A Simmons, Trent Northen, 2013, The Journal of Biological Chemistry.

Genetic network inference: from co-expression clustering to reverse engineering

Patrik D'haeseleer, Shoudan Liang, Roland Somogyi, 2000, Bioinform..

Automated modelling of signal transduction networks

Martin Steffen, George M. Church, Patrik D'haeseleer, 2002, BMC Bioinformatics.

How does gene expression clustering work?

Patrik D'haeseleer, P. D’haeseleer, 2005, Nature Biotechnology.

Reconstructing gene networks from large scale gene expression data

Stephanie Forrest, Patrik D'haeseleer, S. Forrest, 2000 .

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Matthew DeJongh, Nicholas Chia, James G. Jeffryes, 2020, Nucleic Acids Res..

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Matthew DeJongh, Nicholas Chia, James G. Jeffryes, 2020, Nucleic Acids Res..

A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels

Blake A. Simmons, Jay D. Keasling, Steven W. Singer, 2012, PloS one.

Microbial genotype–phenotype mapping by class association rule mining

Patrik D'haeseleer, Makio Tamura, P. D’haeseleer, 2008, Bioinform..

Complete genome sequence of Thioalkalivibrio sp. K90mix

P. D’haeseleer, N. Kyrpides, A. Lapidus, 2011, Standards in genomic sciences.

Estimating and improving protein interaction error rates

George M. Church, Patrik D'haeseleer, G. Church, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw

Amrita Pati, Konstantinos Billis, Blake A Simmons, 2014, Biotechnology for Biofuels.

Identification of Biofilm Matrix-Associated Proteins from an Acid Mine Drainage Microbial Community

Jillian F. Banfield, Manesh Shah, Robert L. Hettich, 2011, Applied and Environmental Microbiology.

Linear Modeling of mRNA Expression Levels During CNS Development and Injury

Patrik D'haeseleer, Stefanie Fuhrman, X. Wen, 1998, Pacific Symposium on Biocomputing.

The Polymorphic Membrane Protein G Has a Neutral Effect and the Plasmid Glycoprotein 3 an Antagonistic Effect on the Ability of the Major Outer Membrane Protein to Elicit Protective Immune Responses against a Chlamydia muridarum Respiratory Challenge

P. D’haeseleer, M. Coleman, S. Pal, 2023, Vaccines.

Complete genome sequence of Kytococcus sedentarius type strain (541T)

Lynne A. Goodwin, P. D’haeseleer, N. Kyrpides, 2009, Standards in genomic sciences.

Complete genome sequence of “Enterobacter lignolyticus” SCF1

Natalia N. Ivanova, Hannah L. Woo, A. Arkin, 2011, Standards in genomic sciences.

Complete genome sequence of “ Enterobacter lignolyticus ” SCF 1

Natalia N. Ivanova, Jane, Hannah L. Woo, 2018 .

Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

S. Tringe, A. Arkin, P. D’haeseleer, 2013, Standards in genomic sciences.

Classification and general features of “ Enterobacter lignolyticus ” SCF 1 MIGS ID Property Term Evidence code Current classification Domain Bacteria

Natalia N. Ivanova, Hannah L. Woo, A. Arkin, 2011 .

Closing the circle of osmoregulation

P. D’haeseleer, 2005, Nature Biotechnology.

An immunological approach to change detection: algorithms, analysis and implications

Paul Helman, Stephanie Forrest, Patrik D'haeseleer, 1996, Proceedings 1996 IEEE Symposium on Security and Privacy.

An immunological approach to change detection: theoretical results

Patrik D'haeseleer, P. D’haeseleer, 1996, Proceedings 9th IEEE Computer Security Foundations Workshop.

Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate

Eoin L. Brodie, S. Tringe, P. D’haeseleer, 2017, Standards in genomic sciences.

Fungal Genome Sequencing and Bioenergy

J. Heitman, P. D’haeseleer, M. Himmel, 2008 .

Thioalkalivibrio sp. K90mix

Natalia N. Ivanova, Nikos, P. D’haeseleer, 2012 .

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry

M. Bendall, P. D’haeseleer, S. Deutsch, 2014, ACS chemical biology.

Complete genome sequence of Saccharomonospora viridis type strain ( P 101 T )

Manfred, P. D’haeseleer, N. Kyrpides, 2009 .

Complete genome sequence of Cryptobacterium curtum type strain (12-3T)

Victor Markowitz, Matt Nolan, Feng Chen, 2009, Standards in genomic sciences.

A Distributed Approach to Anomaly Detection

S. Forrest, P. D’haeseleer, 1998 .

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

P. D’haeseleer, Jizhong Zhou, J. Jansson, 2010, Science.

Phylogenomically Guided Identification of Industrially Relevant GH1 β-Glucosidases through DNA Synthesis and Nanostructure-Initiator Mass Spectrometry

M. Bendall, P. D’haeseleer, B. Simmons, 2014, ACS chemical biology.