A graph-theoretic approach to testing associations between disparate sources of functional genomics data. - Raji Balasubramanian; Thomas LaFramboise; Denise Scholtens; Robert Gentleman (Bioinform., 2004)

Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis. - Thomas LaFramboise; Barbara A. Weir; Xiaojun Zhao; Rameen Beroukhim; Cheng Li 016; David Harrington; William R. Sellers; Matthew Meyerson (PLoS Comput. Biol., 2005)

A flexible rank-based framework for detecting copy number aberrations from array data. - Thomas LaFramboise; Wendy Winckler; Roman K. Thomas (Bioinform., 2009)

Optimization Algorithms for Identification and Genotyping of Copy Number Polymorphisms in Human Populations. - Gökhan Yavas; Mehmet Koyutürk; Thomas LaFramboise (PRIB, 2010)

COKGEN: A Software for the Identification of Rare Copy Number Variation from SNP Microarrays. - Gökhan Yavas; Mehmet Koyutürk; Z. Meral Özsoyoglu; Meetha P. Gould; Thomas LaFramboise (Pacific Symposium on Biocomputing, 2010)

Power to detect selective allelic amplification in genome-wide scans of tumor data. - Ninad Dewal; Matthew L. Freedman; Thomas LaFramboise; Itsik Pe'er (Bioinform., 2010)

Comparative analysis of algorithms for next-generation sequencing read alignment. - Matthew Ruffalo; Thomas LaFramboise; Mehmet Koyutürk (Bioinform., 2011)

Accurate estimation of short read mapping quality for next-generation genome sequencing. - Matthew Ruffalo; Mehmet Koyutürk; Soumya Ray; Thomas LaFramboise (Bioinform., 2012)

Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error. - Daniel M. Savel; Thomas LaFramboise; Ananth Grama; Mehmet Koyutürk (BCB, 2013)

Session introduction. - Gürkan Bebek; Mehmet Koyutürk; Thomas LaFramboise; Benjamin J. Raphael; Mark R. Chance (Pacific Symposium on Biocomputing, 2013)

Whole-exome sequencing enhances prognostic classification of myeloid malignancies. - Matthew Ruffalo; Holleh Husseinzadeh; Hideki Makishima; Bartlomiej Przychodzen; Mohamed Ashkar; Mehmet Koyutürk; Jaroslaw P. Maciejewski; Thomas LaFramboise (J. Biomed. Informatics, 2015)

Detection and quantification of mitochondrial DNA deletions from next-generation sequence data. - Colleen M. Bosworth; Sneha Grandhi; Meetha P. Gould; Thomas LaFramboise (BMC Bioinform., 2017)

Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree. - Daniel M. Savel; Thomas LaFramboise; Ananth Grama; Mehmet Koyutürk (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. - M. Khalid Khan Niazi; Keluo Yao; Debra L. Zynger; Steven K. Clinton; James Chen; Mehmet Koyutürk; Thomas LaFramboise; Metin N. Gurcan (IEEE J. Biomed. Health Informatics, 2017)

CytoConverter: a web-based tool to convert karyotypes to genomic coordinates. - Janet Wang; Thomas LaFramboise (BMC Bioinform., 2019)

SYSMut: decoding the functional significance of rare somatic mutations in cancer. - Sirvan Khalighi; Peronne Joseph; Deepak Babu; Salendra Singh; Thomas LaFramboise; Kishore Guda; Vinay Varadan (Briefings Bioinform., 2022)

A double Pólya-Gamma data augmentation scheme for a hierarchical Negative Binomial - Binomial data model. - Xuan Ma; Jenný Brynjarsdóttir; Thomas LaFramboise (Comput. Stat. Data Anal., 2024)