PROBER: oligonucleotide FISH probe design software. - Nicholas Navin; Vladimir Grubor; Jim Hicks; Evan Leibu; Elizabeth Thomas; Jennifer Troge; Michael Riggs; Pär Lundin; Susanne Månér; Jonathan Sebat; Anders Zetterberg; Michael Wigler (Bioinform., 2006)

When loss-of-function is loss of function: assessing mutational signatures and impact of loss-of-function genetic variants. - Kymberleigh A. Pagel; Vikas Pejaver; Guan Ning Lin; Hyun-Jun Nam; Matthew E. Mort; David N. Cooper; Jonathan Sebat; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (Bioinform., 2017)

SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes. - Danny Antaki; William M. Brandler; Jonathan Sebat (Bioinform., 2018)

Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome. - Kymberleigh A. Pagel; Danny Antaki; Aojie Lian; Matthew E. Mort; David N. Cooper; Jonathan Sebat; Lilia M. Iakoucheva; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2019)

Customized de novo mutation detection for any variant calling pipeline: SynthDNM. - Aojie Lian; James Guevara; Kun Xia; Jonathan Sebat (Bioinform., 2021)