Matthew Ruffalo

According to our database, Matthew Ruffalo authored at least 10 papers between 2011 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Deriving spatial features from <i>in situ</i> 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

2022

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., September, 2022

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

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, Julia Laskin, Pehr Harbury, Nicholas A. Nystrom, Jonathan C. Silverstein, Ziv Bar-Joseph, Kun Zhang, Katy Börner, Yiing Lin, Richard Conroy, Dena Procaccini, Ananda L. Roy, Ajay Pillai, Marishka Brown, Zorina S. Galis, Long Cai, Cole Trapnell, Dana Jackson, Garry P. Nolan, William James Greenleaf, Sylvia K. Plevritis, Sara Ahadi, Stephanie A. Nevins, Hayan Lee, Christian Martijn Schuerch, Sarah Black, Vishal Gautham Venkataraaman, Ed Esplin, Aaron Horning, Amir Bahmani, Xin Sun, Sanjay Jain, James S. Hagood, Gloria Pryhuber, Peter V. Kharchenko, Bernd Bodenmiller, Todd Brusko, Michael Clare-Salzler, Harry Nick, Kevin Otto, Clive Wasserfall, Marda Jorgensen, Maigan Brusko, Sergio Maffioletti, Richard M. Caprioli, Jeffrey M. Spraggins, Danielle Gutierrez, Nathan Heath Patterson, Elizabeth K. Neumann, Raymond Harris, Mark P. de Caestecker, Agnes B. Fogo, Raf Van de Plas, Ken Lau, Guo-Cheng Yuan, Qian Zhu, Ruben Dries, Peng Yin, Sinem K. Saka, Jocelyn Y. Kishi, Yu Wang, Isabel Goldaracena, Dong Hye Ye, Kristin E. Burnum-Johnson, Paul D. Piehowski, Charles Ansong, Ying Zhu, Tushar Desai, Jay Mulye, Peter Chou, Monica Nagendran, Sarah A. Teichmann, Benedict Paten, Robert F. Murphy, Jian Ma, Vladimir Yu. Kiselev, Carl Kingsford, Allyson Ricarte, Maria Keays, Sushma Anand Akoju, Matthew Ruffalo, Margaret Vella, Chuck McCallum, Leonard E. Cross, Samuel H. Friedman, Randy W. Heiland, Bruce William Herr II, Paul Macklin, Ellen M. Quardokus, Lisel Record, James P. Sluka, Griffin M. Weber, Philip D. Blood, Alexander Ropelewski, William Shirey, Robin M. Scibek, Paula M. Mabee, W. Christopher Lenhardt, Kimberly Robasky, Stavros Michailidis, John C. Marioni, Andrew Butler, Tim Stuart, Eyal Fisher, Shila Ghazanfar, Gökcen Eraslan, Tommaso Biancalani, Eeshit D. Vaishnav, Pothur Srinivas, Aaron Pawlyk, Salvatore Sechi, Elizabeth L. Wilder, James Anderson

Nat., 2019

2017

Reconstructing cancer drug response networks using multitask learning.

Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph

BMC Syst. Biol., 2017

2016

Genome wide predictions of miRNA regulation by transcription factors.

Matthew Ruffalo, Ziv Bar-Joseph

Bioinform., 2016

2015

Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.

Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan

PLoS Comput. Biol., 2015

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

2012

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise

Bioinform., 2012

2011

Comparative analysis of algorithms for next-generation sequencing read alignment.

Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk

Bioinform., 2011