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)

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)

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. - Matthew Ruffalo; Mehmet Koyutürk; Roded Sharan (PLoS Comput. Biol., 2015)

Genome wide predictions of miRNA regulation by transcription factors. - Matthew Ruffalo; Ziv Bar-Joseph (Bioinform., 2016)

Reconstructing cancer drug response networks using multitask learning. - Matthew Ruffalo; Petar Stojanov; Venkata Krishna Pillutla; Rohan Varma; Ziv Bar-Joseph (BMC Syst. Biol., 2017)

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. - Michael P. Snyder; Shin Lin; Amanda Posgai; Mark Atkinson; Aviv Regev; Jennifer Rood; Orit Rozenblatt-Rosen; Leslie Gaffney; Anna Hupalowska; Rahul Satija; Nils Gehlenborg; Jay Shendure; et al. (Nat., 2019)

Network-guided prediction of aromatase inhibitor response in breast cancer. - Matthew Ruffalo; Roby Thomas; Jian Chen; Adrian V. Lee; Steffi Oesterreich; Ziv Bar-Joseph (PLoS Comput. Biol., 2019)

CINS: Cell Interaction Network inference from Single cell expression data. - Ye Yuan; Carlos Cosme; Taylor Sterling Adams; Jonas Schupp; Koji Sakamoto; Nikos Xylourgidis; Matthew Ruffalo; Jiachen Li; Naftali Kaminski; Ziv Bar-Joseph (PLoS Comput. Biol., 2022)

Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. - Monica T. Dayao; Alexandro Trevino; Honesty Kim; Matthew Ruffalo; H. Blaize D'angio; Ryan Preska; Umamaheswar Duvvuri; Aaron T. Mayer; Ziv Bar-Joseph (Bioinform., 2023)