Integrative annotation of variants from 1092 humans: application to cancer genomics

…, F Cunningham, US Evani, P Flicek, R Fragoza… - Science, 2013 - science.org
Introduction Plummeting sequencing costs have led to a great increase in the number of
personal genomes. Interpreting the large number of variants in them, particularly in noncoding …

Interactome INSIDER: a structural interactome browser for genomic studies

MJ Meyer, JF Beltrán, S Liang, R Fragoza, A Rumack… - Nature …, 2018 - nature.com
We present Interactome INSIDER, a tool to link genomic variant information with structural
protein–protein interactomes. Underlying this tool is the application of machine learning to …

[PDF][PDF] A proteome-wide fission yeast interactome reveals network evolution principles from yeasts to human

…, N Akturk, X Wei, BJ Fair, AG Degatano, R Fragoza… - Cell, 2016 - cell.com
Here, we present FissionNet, a proteome-wide binary protein interactome for S. pombe,
comprising 2,278 high-quality interactions, of which ∼50% were previously not reported in any …

[HTML][HTML] SAAMBE-3D: predicting effect of mutations on protein–protein interactions

S Pahari, G Li, AK Murthy, S Liang, R Fragoza… - International journal of …, 2020 - mdpi.com
Maintaining wild type protein–protein interactions is essential for the normal function of cell
and any mutation that alter their characteristics can cause disease. Therefore, the ability to …

An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders

S Chen, R Fragoza, L Klei, Y Liu, J Wang, K Roeder… - Nature …, 2018 - nature.com
Identifying disease-associated missense mutations remains a challenge, especially in large-scale
sequencing studies. Here we establish an experimentally and computationally …

[HTML][HTML] Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations

R Fragoza, J Das, SD Wierbowski, J Liang… - Nature …, 2019 - nature.com
Each human genome carries tens of thousands of coding variants. The extent to which this
variation is functional and the mechanisms by which they exert their influence remains largely …

[HTML][HTML] A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations

X Wei, J Das, R Fragoza, J Liang… - PLoS …, 2014 - journals.plos.org
Understanding the functional relevance of DNA variants is essential for all exome and genome
sequencing projects. However, current mutagenesis cloning protocols require Sanger …

[HTML][HTML] Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging

P Singh, R Fragoza, CS Blengini, TN Tran… - Nature …, 2021 - nature.com
Embryonic aneuploidy from mis-segregation of chromosomes during meiosis causes
pregnancy loss. Proper disjunction of homologous chromosomes requires the mismatch repair (…

SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein–protein binding affinity

G Li, S Pahari, AK Murthy, S Liang, R Fragoza… - …, 2021 - academic.oup.com
Motivation Vast majority of human genetic disorders are associated with mutations that affect
protein–protein interactions by altering wild-type binding affinity. Therefore, it is extremely …

Exploring mechanisms of human disease through structurally resolved protein interactome networks

J Das, R Fragoza, HR Lee, NA Cordero, Y Guo… - Molecular …, 2014 - pubs.rsc.org
The study of the molecular basis of human disease has gained increasing attention over the
past decade. With significant improvements in sequencing efficiency and throughput, a …