iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes. - Jun Kong; Fei Zhu; Jim Stalker; David J. Adams (Bioinform., 2008)

Copy number variant detection in inbred strains from short read sequence data. - Jared T. Simpson; Rebecca E. McIntyre; David J. Adams; Richard Durbin (Bioinform., 2010)

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach. - Christiaan Klijn; Jan Bot; David J. Adams; Marcel J. T. Reinders; Lodewyk F. A. Wessels; Jos Jonkers (PLoS Comput. Biol., 2010)

Mutational Genomics for Cancer Pathway Discovery. - Jeroen de Ridder; Jaap Kool; Anthony Uren; Jan Bot; Johann de Jong; Alistair G. Rust; Anton Berns; Maarten van Lohuizen; David J. Adams; Lodewyk F. A. Wessels; Marcel J. T. Reinders (PRIB, 2013)

RetroSeq: transposable element discovery from next-generation sequencing data. - Thomas M. Keane; Kim Wong; David J. Adams (Bioinform., 2013)

Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes. - Mamunur Rashid; Carla Daniela Robles-Espinoza; Alistair G. Rust; David J. Adams (Bioinform., 2013)

A comprehensive engineering college-wide program for developing technical communication skills in students. - Ronald S. Harichandran; Jean Nocito-Gobel; Eric Brisart; Nadiye O. Erdil; Michael A. Collura; Samuel B. Daniels; W. David Harding; David J. Adams (FIE, 2014)

Genome-wide in vivo screen identifies novel host regulators of metastatic colonization. - Louise van der Weyden; Mark J. Arends; Andrew D. Campbell; Tobias Bald; Hannah Wardle-Jones; Nicola Griggs; Martin Del Castillo Velasco-Herrera; Thomas Tüting; Owen J. Sansom; Natasha A. Karp; Simon Clare; Diane Gleeson; et al. (Nat., 2017)

VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects. - Raul Ossio; O. Isaac Garcia-Salinas; Diego Said Anaya-Mancilla; Jair S. García-Sotelo; Luis A. Aguilar; David J. Adams; Carla Daniela Robles-Espinoza (Bioinform., 2019)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments. - Luca Barbon; Victoria Offord; Elizabeth J. Radford; Adam P. Butler; Sebastian S. Gerety; David J. Adams; Hong Kee Tan; Andrew J. Waters (Bioinform., 2022)

Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. - Albert Burger; Richard A. Baldock; David J. Adams; Shahida Din; Irene Papatheodorou; Michael Glinka; Bill Hill; Derek Houghton; Mehran Sharghi; Michael N. Wicks; Mark J. Arends (BMC Medical Informatics Decis. Mak., 2023)

CreoPep: A Universal Deep Learning Framework for Target-Specific Peptide Design and Optimization. - Cheng Ge; Han-Shen Tae; Zhenqiang Zhang; Lu Lu; Zhijie Huang; Yilin Wang; Tao Jiang; Wenqing Cai; Shan Chang; David J. Adams; Rilei Yu (CoRR, 2025)