Chaining Algorithms for Alignment of Draft Sequence. - Mukund Sundararajan; Michael Brudno; Kerrin S. Small; Arend Sidow; Serafim Batzoglou (WABI, 2004)

ABC: software for interactive browsing of genomic multiple sequence alignment data. - Gregory M. Cooper; Senthil A. G. Singaravelu; Arend Sidow (BMC Bioinform., 2004)

Constructing a meaningful evolutionary average at the phylogenetic center of mass. - Eric A. Stone; Arend Sidow (BMC Bioinform., 2007)

SHRiMP: Accurate Mapping of Short Color-space Reads. - Stephen M. Rumble; Phil Lacroute; Adrian V. Dalca; Marc Fiume; Arend Sidow; Michael Brudno (PLoS Comput. Biol., 2009)

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++. - Eugene Davydov; David L. Goode; Marina Sirota; Gregory M. Cooper; Arend Sidow; Serafim Batzoglou (PLoS Comput. Biol., 2010)

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery. - Raheleh Salari; Syed Shayon Saleh; Dorna Kashef Haghighi; David Khavari; Daniel E. Newburger; Robert B. West; Arend Sidow; Serafim Batzoglou (J. Comput. Biol., 2013)

Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements. - Anshul Kundaje; Sofia Kyriazopoulou-Panagiotopoulou; Max W. Libbrecht; Cheryl L. Smith; Debasish Raha; Elliott E. Winters; Steven M. Johnson; Michael P. Snyder; Serafim Batzoglou; Arend Sidow (Adv. Math. Commun., 2013)

Read Clouds Uncover Variation in Complex Regions of the Human Genome. - Alex Bishara; Yuling Liu; Dorna Kashef Haghighi; Ziming Weng; Daniel E. Newburger; Robert B. West; Arend Sidow; Serafim Batzoglou (RECOMB, 2015)

svviz: a read viewer for validating structural variants. - Noah Spies; Justin M. Zook; Marc Salit; Arend Sidow (Bioinform., 2015)

De novo mutational signature discovery in tumor genomes using SparseSignatures. - Avantika Lal; Keli Liu; Robert Tibshirani; Arend Sidow; Daniele Ramazzotti (PLoS Comput. Biol., 2021)

Example dataset of stLFR linked reads to run Aquila_stLFR. - Yichen Henry Liu; Griffin L. Grubbs; Lu Zhang; Xiaodong Fang; David L. Dill; Arend Sidow; Xin Zhou (Zenodo, 2021)