The JAVELIN Question-Answering System at TREC 2003: A Multi-Strategh Approach with Dynamic Planning. - Eric Nyberg; Teruko Mitamura; James P. Callan; Jaime G. Carbonell; Robert E. Frederking; Kevyn Collins-Thompson; Laurie Hiyakumoto; Yifen Huang; Curtis Huttenhower; Scott Judy; Jeongwoo Ko; Anna Kupsc; et al. (TREC, 2003)

A General Methodology for Integration of Microarray Data. - Curtis Huttenhower; Olga G. Troyanskaya (CSB Workshops, 2005)

A scalable method for integration and functional analysis of multiple microarray datasets. - Curtis Huttenhower; Matthew A. Hibbs; Chad L. Myers; Olga G. Troyanskaya (Bioinform., 2006)

GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. - Rachel S. G. Sealfon; Matthew A. Hibbs; Curtis Huttenhower; Chad L. Myers; Olga G. Troyanskaya (BMC Bioinform., 2006)

Exploring the functional landscape of gene expression: directed search of large microarray compendia. - Matthew A. Hibbs; David C. Hess; Chad L. Myers; Curtis Huttenhower; Kai Li 001; Olga G. Troyanskaya (Bioinform., 2007)

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods. - Curtis Huttenhower; Avi I. Flamholz; Jessica N. Landis; Sauhard Sahi; Chad L. Myers; Kellen L. Olszewski; Matthew A. Hibbs; Nathan O. Siemers; Olga G. Troyanskaya; Hilary A. Coller (BMC Bioinform., 2007)

Assessing the functional structure of genomic data. - Curtis Huttenhower; Olga G. Troyanskaya (ISMB, 2008)

The Sleipnir library for computational functional genomics. - Curtis Huttenhower; Mark Schroeder; Maria D. Chikina; Olga G. Troyanskaya (Bioinform., 2008)

The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. - Curtis Huttenhower; Matthew A. Hibbs; Chad L. Myers; Amy A. Caudy; David C. Hess; Olga G. Troyanskaya (Bioinform., 2009)

Detailing regulatory networks through large scale data integration. - Curtis Huttenhower; K. Tsheko Mutungu; Natasha Indik; Woongcheol Yang; Mark Schroeder; Joshua J. Forman; Olga G. Troyanskaya; Hilary A. Coller (Bioinform., 2009)

Graphle: Interactive exploration of large, dense graphs. - Curtis Huttenhower; Sajid O. Mehmood; Olga G. Troyanskaya (BMC Bioinform., 2009)

Predicting Cellular Growth from Gene Expression Signatures. - Edoardo M. Airoldi; Curtis Huttenhower; David Gresham; Charles Lu 004; Amy A. Caudy; Maitreya J. Dunham; James R. Broach; David Botstein; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans. - Maria D. Chikina; Curtis Huttenhower; Coleen T. Murphy; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis. - Matthew A. Hibbs; Chad L. Myers; Curtis Huttenhower; David C. Hess; Kai Li 001; Amy A. Caudy; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana. - Ana Pop; Curtis Huttenhower; Anjali Iyer-Pascuzzi; Philip N. Benfey; Olga G. Troyanskaya (BMC Syst. Biol., 2010)

A Quick Guide to Large-Scale Genomic Data Mining. - Curtis Huttenhower; Oliver Hofmann 001 (PLoS Comput. Biol., 2010)

Simultaneous Genome-Wide Inference of Physical, Genetic, Regulatory, and Functional Pathway Components. - Christopher Y. Park; David C. Hess; Curtis Huttenhower; Olga G. Troyanskaya (PLoS Comput. Biol., 2010)

Optimized application of penalized regression methods to diverse genomic data. - Levi Waldron; Melania Pintilie; Ming-Sound Tsao; Frances A. Shepherd; Curtis Huttenhower; Igor Jurisica (Bioinform., 2011)

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome. - Sahar Abubucker; Nicola Segata; Johannes Goll; Alyxandria M. Schubert; Jacques Izard; Brandi L. Cantarel; Beltran Rodriguez-Mueller; Jeremy Zucker; Mathangi Thiagarajan; Bernard Henrissat; Owen White; Scott T. Kelley; et al. (PLoS Comput. Biol., 2012)

Microbial Co-occurrence Relationships in the Human Microbiome. - Karoline Faust; Jarupon Fah Sathirapongsasuti; Jacques Izard; Nicola Segata; Dirk Gevers; Jeroen Raes; Curtis Huttenhower (PLoS Comput. Biol., 2012)

Bioinformatics for the Human Microbiome Project. - Dirk Gevers; Mihai Pop; Patrick D. Schloss; Curtis Huttenhower (PLoS Comput. Biol., 2012)

Chapter 12: Human Microbiome Analysis. - Xochitl C. Morgan; Curtis Huttenhower (PLoS Comput. Biol., 2012)

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. - Benjamin Frederick Ganzfried; Markus Riester; Benjamin Haibe-Kains; Thomas Risch; Svitlana Tyekucheva; Ina Jazic; Xin Victoria Wang; Mahnaz Ahmadifar; Michael J. Birrer; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron (Database J. Biol. Databases Curation, 2013)

Inferring Developmental Stage Composition from Gene Expression in Human Malaria. - Regina Joice; Vagheesh Narasimhan; Jacqui Montgomery; Amar Bir Sidhu; Keunyoung Oh; Evan Meyer; Willythssa Pierre-Louis; Karl Seydel; Danny Milner; Kim Williamson; Roger Wiegand; Daouda Ndiaye; et al. (PLoS Comput. Biol., 2013)

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. - Omry Koren; Dan Knight; Antonio González; Levi Waldron; Nicola Segata; Rob Knight 001; Curtis Huttenhower; Ruth E. Ley (PLoS Comput. Biol., 2013)

Cross-study validation for the assessment of prediction algorithms. - Christoph Bernau; Markus Riester; Anne-Laure Boulesteix; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron; Lorenzo Trippa (Bioinform., 2014)

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. - Sihai Dave Zhao; Giovanni Parmigiani; Curtis Huttenhower; Levi Waldron (Bioinform., 2014)

MetaRef: a pan-genomic database for comparative and community microbial genomics. - Katherine Huang; Arthur Brady; Anup Mahurkar; Owen White; Dirk Gevers; Curtis Huttenhower; Nicola Segata (Nucleic Acids Res., 2014)

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. - James Kaminski; Molly K. Gibson; Eric A. Franzosa; Nicola Segata; Gautam Dantas; Curtis Huttenhower (PLoS Comput. Biol., 2015)

Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. - Daniela Börnigen; Svitlana Tyekucheva; Xiaodong Wang; Jennifer R. Rider; Gwo-Shu Lee; Lorelei A. Mucci; Christopher Sweeney; Curtis Huttenhower (PLoS Comput. Biol., 2016)

A Workshop on Microbiomics, Metagenomics, and Metabolomics. - Soha Hassoun; Curtis Huttenhower (BCB, 2017)

A Bayesian method for detecting pairwise associations in compositional data. - Emma H. Schwager; Himel Mallick; Steffen Ventz; Curtis Huttenhower (PLoS Comput. Biol., 2017)

bioBakery: a meta'omic analysis environment. - Lauren J. McIver; Galeb Abu-Ali; Eric A. Franzosa; Randall Schwager; Xochitl C. Morgan; Levi Waldron; Nicola Segata; Curtis Huttenhower (Bioinform., 2018)

Statistical approaches for differential expression analysis in metatranscriptomics. - Yancong Zhang; Kelsey N. Thompson; Curtis Huttenhower; Eric A. Franzosa (Bioinform., 2021)

A statistical model for describing and simulating microbial community profiles. - Siyuan Ma; Boyu Ren; Himel Mallick; Yo Sup Moon; Emma H. Schwager; Sagun Maharjan; Timothy L. Tickle; Yiren Lu 003; Rachel N. Carmody; Eric A. Franzosa; Lucas Janson; Curtis Huttenhower (PLoS Comput. Biol., 2021)

Multivariable association discovery in population-scale meta-omics studies. - Himel Mallick; Ali Rahnavard; Lauren J. McIver; Siyuan Ma; Yancong Zhang; Long H. Nguyen; Timothy L. Tickle; George Weingart; Boyu Ren; Emma H. Schwager; Suvo Chatterjee; Kelsey N. Thompson; et al. (PLoS Comput. Biol., 2021)

High-sensitivity pattern discovery in large, paired multiomic datasets. - Andrew R. Ghazi; Kathleen Sucipto; Ali Rahnavard; Eric A. Franzosa; Lauren J. McIver; Jason Lloyd-Price; Emma H. Schwager; George Weingart; Yo Sup Moon; Xochitl C. Morgan; Levi Waldron; Curtis Huttenhower (Bioinform., 2022)

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper. - Alexander G. McFarland; Nolan W. Kennedy; Carolyn E. Mills; Danielle Tullman-Ercek; Curtis Huttenhower; Erica M. Hartmann (Bioinform., 2022)

Discovering and exploring the hidden diversity of the human gut viruses using highly enriched virome samples. - Moreno Zolfo; Andrea Silverj; Aitor Blanco-Míguez; Paolo Manghi; Omar Rota Stabelli; Vitor Heidrich; Jordan Jensen; Sagun Maharjan; Eric A. Franzosa; Cristina Menni; Alessia Visconti; Federica Pinto; et al. (Zenodo, 2024)