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2020 – today
- 2023
[j10]Monica T. Dayao, Alexandro Trevino
, Honesty Kim, Matthew Ruffalo, H. Blaize D'angio, Ryan Preska, Umamaheswar Duvvuri, Aaron T. Mayer, Ziv Bar-Joseph:
Deriving spatial features from in situ proteomics imaging to enhance cancer survival analysis. Bioinform. 39(Supplement-1): 140-148 (2023)- 2022
- [j9]Ye Yuan, Carlos Cosme, Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Jiachen Li, Naftali Kaminski, Ziv Bar-Joseph:
CINS: Cell Interaction Network inference from Single cell expression data. PLoS Comput. Biol. 18(9): 1010468 (2022)
2010 – 2019
- 2019
- [j8]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:
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nat. 574(7777): 187-192 (2019) - [j7]Matthew Ruffalo, Roby Thomas, Jian Chen, Adrian V. Lee, Steffi Oesterreich, Ziv Bar-Joseph:
Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS Comput. Biol. 15(2) (2019) - 2017
- [j6]Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma, Ziv Bar-Joseph:
Reconstructing cancer drug response networks using multitask learning. BMC Syst. Biol. 11(1): 96:1-96:15 (2017) - 2016
- [j5]Matthew Ruffalo, Ziv Bar-Joseph:
Genome wide predictions of miRNA regulation by transcription factors. Bioinform. 32(17): 746-754 (2016) - 2015
- [j4]Matthew Ruffalo, Holleh Husseinzadeh, Hideki Makishima, Bartlomiej Przychodzen, Mohamed Ashkar, Mehmet Koyutürk, Jaroslaw P. Maciejewski, Thomas LaFramboise:
Whole-exome sequencing enhances prognostic classification of myeloid malignancies. J. Biomed. Informatics 58: 104-113 (2015) - [j3]Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan:
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Comput. Biol. 11(12) (2015) - 2012
- [j2]Matthew Ruffalo, Mehmet Koyutürk, Soumya Ray, Thomas LaFramboise:
Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinform. 28(18): 349-355 (2012) - 2011
- [j1]Matthew Ruffalo, Thomas LaFramboise, Mehmet Koyutürk:
Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinform. 27(20): 2790-2796 (2011)
Coauthor Index
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