Statistical Identification of Uniformly Mutated Segments within Repeats. - Süleyman Cenk Sahinalp; Evan E. Eichler; Paul W. Goldberg; Petra Berenbrink; Tom Friedetzky; Funda Ergün (CPM, 2002)

Recent duplication, evolution and assembly of the human genome. - Evan E. Eichler (RECOMB, 2002)

Identifying Uniformly Mutated Segments within Repeats. - Süleyman Cenk Sahinalp; Evan E. Eichler; Paul W. Goldberg; Petra Berenbrink; Tom Friedetzky; Funda Ergün (J. Bioinform. Comput. Biol., 2004)

The Role of Unequal Crossover in Alpha-Satellite DNA Evolution: A Computational Analysis. - Can Alkan; Evan E. Eichler; Jeffrey A. Bailey; Süleyman Cenk Sahinalp; Eray Tüzün (J. Comput. Biol., 2004)

Manipulating multiple sequence alignments via MaM and WebMaM. - Can Alkan; Eray Tüzün; Jerome Buard; Franck Lethiec; Evan E. Eichler; Jeffrey A. Bailey; Süleyman Cenk Sahinalp (Nucleic Acids Res., 2005)

Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data. - Can Alkan; Mario Ventura; Nicoletta Archidiacono; Mariano Rocchi; Süleyman Cenk Sahinalp; Evan E. Eichler (PLoS Comput. Biol., 2007)

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes. - Fereydoun Hormozdiari; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2009)

Session Introduction. - Can Alkan; Michael Brudno; Evan E. Eichler; Maricel G. Kann; Süleyman Cenk Sahinalp (Pacific Symposium on Biocomputing, 2010)

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing. - Iman Hajirasouliha; Fereydoun Hormozdiari; Can Alkan; Jeffrey M. Kidd; Inanç Birol; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. - Fereydoun Hormozdiari; Iman Hajirasouliha; Phuong Dao; Faraz Hach; Deniz Yörükoglu; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2010)

Targeted interrogation of copy number variation using SCIMMkit. - Troy Zerr; Gregory M. Cooper; Evan E. Eichler; Deborah A. Nickerson (Bioinform., 2010)

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes. - Fereydoun Hormozdiari; Iman Hajirasouliha; Andrew W. McPherson; Evan E. Eichler; Süleyman Cenk Sahinalp (RECOMB, 2011)

Sensitive and fast mapping of di-base encoded reads. - Farhad Hormozdiari; Faraz Hach; Süleyman Cenk Sahinalp; Evan E. Eichler; Can Alkan (Bioinform., 2011)

ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. - Phuong Dao; Ibrahim Numanagic; Yen-Yi Lin; Faraz Hach; Emre Karakoç; Nilgun Donmez; Colin C. Collins; Evan E. Eichler; Süleyman Cenk Sahinalp (Bioinform., 2014)

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications. - Faraz Hach; Iman Sarrafi; Farhad Hormozdiari; Can Alkan; Evan E. Eichler; Süleyman Cenk Sahinalp (Nucleic Acids Res., 2014)

The contribution of de novo coding mutations to autism spectrum disorder. - Ivan Iossifov; Brian J. O'Roak; Stephan J. Sanders; Michael Ronemus; Niklas Krumm; Dan Levy; Holly A. Stessman; Kali T. Witherspoon; Laura Vives; Karynne E. Patterson; Joshua D. Smith; Bryan Paeper; et al. (Nat., 2014)

Resolving Multicopy Duplications de novo Using Polyploid Phasing. - Mark J. P. Chaisson; Sudipto Mukherjee 001; Sreeram Kannan; Evan E. Eichler (RECOMB, 2017)

denovo-db: a compendium of human de novo variants. - Tychele Turner; Qian Yi; Niklas Krumm; John Huddleston; Kendra Hoekzema; Holly A. Stessman; Anna-Lisa Doebley; Raphael A. Bernier; Deborah A. Nickerson; Evan E. Eichler (Nucleic Acids Res., 2017)

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization. - Maryam Ghareghani; David Porubsky; Ashley D. Sanders; Sascha Meiers; Evan E. Eichler; Jan O. Korbel; Tobias Marschall (Bioinform., 2018)

StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps. - Mitchell R. Vollger; Peter Kerpedjiev; Adam M. Phillippy; Evan E. Eichler (Bioinform., 2022)

GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads. - Philip C. Dishuck; Allison N. Rozanski; Glennis Logsdon; David Porubsky; Evan E. Eichler (Bioinform., 2023)