533 citations · 647 across the 6 of their papers we have counts for
7 papers
Gene targeting in disease networks
Deborah Weighill, Marouen Ben Guebila, Kimberly Glass +3
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of dis…
The importance of transparency and reproducibility in artificial intelligence research
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny +17
In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines…
Network-based Distance Metric with Application to Discover Disease Subtypes in Cancer
Jipeng Qiang, Wei Ding, John Quackenbush +1
While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns o…
PyPanda: a Python Package for Gene Regulatory Network Reconstruction
David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush +1
PANDA (Passing Attributes between Networks for Data Assimilation) is a gene regulatory network inference method that uses message-passing to integrate multiple sources of 'omics da…
Bipartite Community Structure of eQTLs
John Platig, Peter Castaldi, Dawn DeMeo +1
Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, th…
High Performance Computing of Gene Regulatory Networks using a Message-Passing Model
Kimberly Glass, John Quackenbush, Jeremy Kepner
Gene regulatory network reconstruction is a fundamental problem in computational biology. We recently developed an algorithm, called PANDA (Passing Attributes Between Networks for…
Estimating sample-specific regulatory networks
Marieke Lydia Kuijjer, Matthew Tung, GuoCheng Yuan +2
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models…