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Simon Kasif
Boston University
162Publications
45H-index
27.3kCitations
Publications 162
Newest
Published on Apr 23, 2018in PLOS Genetics 5.54
Daniel Lancour1
Estimated H-index: 1
(Boston University),
Adam C. Naj25
Estimated H-index: 25
(University of Pennsylvania)
+ 6 AuthorsSimon Kasif45
Estimated H-index: 45
(Boston University)
Improving accuracy in genetic studies would greatly accelerate understanding the genetic basis of complex diseases. One approach to achieve such an improvement for risk variants identified by the genome wide association study (GWAS) approach is to incorporate previously known biology when screening variants across the genome. We developed a simple approach for improving the prioritization of candidate disease genes that incorporates a network diffusion of scores from known disease genes using a ...
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Published on May 1, 2018in Diabetes 7.27
Jonathan M. Dreyfuss21
Estimated H-index: 21
,
Yixing Yuchi + 8 AuthorsAllison B. Goldfine52
Estimated H-index: 52
Bariatric surgery has emerged as a potent approach to improve obesity-related metabolic comorbidities including type 2 diabetes (T2D). However, molecular mechanisms responsible for metabolic improvement after bariatric surgery remain incompletely understood. We profiled and integrated the fasting plasma proteome (aptamer-based Somalogic platform) and metabolome (MS, Metabolon) from patients with T2D at baseline and up to 3 years after randomization to either gastric bypass (GB) or nonsurgical di...
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Published on Dec 1, 2017in Cell Reports 8.03
Alfred K. Ramirez2
Estimated H-index: 2
(Boston University),
Matthew D. Lynes10
Estimated H-index: 10
(Harvard University)
+ 5 AuthorsJonathan M. Dreyfuss21
Estimated H-index: 21
(Boston University)
Summary White adipocytes are specialized for energy storage, whereas brown adipocytes are specialized for energy expenditure. Explicating this difference can help identify therapeutic targets for obesity. A common tool to assess metabolic differences between such cells is the Seahorse Extracellular Flux (XF) Analyzer, which measures oxygen consumption and media acidification in the presence of different substrates and perturbagens. Here, we integrate the Analyzer's metabolic profile from human w...
3 Citations Source Cite
Published on Jun 25, 2017in bioRxiv
Simon Kasif45
Estimated H-index: 45
(Boston University),
Stanley Letovsky2
Estimated H-index: 2
(Boston University)
+ 1 AuthorsMartin Steffen17
Estimated H-index: 17
(Boston University)
The fathers of Artificial Intelligence (AI) dreamt about the application of AI to Scientific Discovery. We propose a new twist on these early dreams and describe a novel approach aimed at remodeling of the biomedical research infrastructure and catalyze gene function determination. We aim to start a bold discussion of new ideas aimed towards increasing the efficiency of the allocation of research capacities, reproducibility, provenance tracking, removing redundancy and catalyzing knowledge gain ...
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Published on Jul 18, 2017in bioRxiv
Irina Glotova , Michael Molla3
Estimated H-index: 3
(Harvard University)
+ 1 AuthorsSimon Kasif45
Estimated H-index: 45
(Boston University)
Length polymorphisms in genomic short tandem repeats have been implicated in a variety of diseases, most notably human neurodegenerative disorders. Expansions of tandem repeats are also associated with genomic instability in cancer. Our previous study of length-3 tandem repeats uncovered a surprising pattern in the length distribution of certain such repeats in the non-coding regions of the human reference genome: a bias towards repeats of length 3n - 1, (n > 3). That is, the observed frequency ...
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Published on Jan 4, 2016in Nucleic Acids Research 11.56
Yi-Chien Chang6
Estimated H-index: 6
(Boston University),
Zhenjun Hu17
Estimated H-index: 17
(Boston University)
+ 4 AuthorsMartin Steffen17
Estimated H-index: 17
(Boston University)
The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function ...
12 Citations Source Cite
Published on Oct 1, 2016in Molecular metabolism 6.29
Carles Lerin10
Estimated H-index: 10
(Harvard University),
Allison B. Goldfine52
Estimated H-index: 52
(Harvard University)
+ 14 AuthorsJustin R. Sysol3
Estimated H-index: 3
(National Institutes of Health)
Abstract Objective Plasma levels of branched-chain amino acids (BCAA) are consistently elevated in obesity and type 2 diabetes (T2D) and can also prospectively predict T2D. However, the role of BCAA in the pathogenesis of insulin resistance and T2D remains unclear. Methods To identify pathways related to insulin resistance, we performed comprehensive gene expression and metabolomics analyses in skeletal muscle from 41 humans with normal glucose tolerance and 11 with T2D across a range of insulin...
28 Citations Source Cite
Published on Dec 1, 2015in Molecular Cancer 7.78
Richard Park9
Estimated H-index: 9
(Boston University),
Tae-Min Kim16
Estimated H-index: 16
(Catholic University of Korea)
+ 1 AuthorsPeter J. Park80
Estimated H-index: 80
(Massachusetts Institute of Technology)
Background Copy number variations (CNVs) are increasingly recognized as significant disease susceptibility markers in many complex disorders including cancer. The availability of a large number of chromosomal copy number profiles in both malignant and normal tissues in cancer patients presents an opportunity to characterize not only somatic alterations but also germline CNVs, which may confer increased risk for cancer.
14 Citations Source Cite
Published on Mar 1, 2015in Molecular metabolism 6.29
Christopher Nogiec2
Estimated H-index: 2
(Boston University),
Alison Burkart7
Estimated H-index: 7
(Harvard University)
+ 3 AuthorsMary-Elizabeth Patti47
Estimated H-index: 47
(Harvard University)
Abstract Objective Dysregulated muscle metabolism is a cardinal feature of human insulin resistance (IR) and associated diseases, including type 2 diabetes (T2D). However, specific reactions contributing to abnormal energetics and metabolic inflexibility in IR are unknown. Methods We utilize flux balance computational modeling to develop the first systems-level analysis of IR metabolism in fasted and fed states, and varying nutrient conditions. We systematically perturb the metabolic network to ...
13 Citations Source Cite
Published on Apr 1, 2014in Cell 31.40
Mario L. Suvà14
Estimated H-index: 14
(Broad Institute),
Esther Rheinbay14
Estimated H-index: 14
(Broad Institute)
+ 21 AuthorsBrian V. Nahed24
Estimated H-index: 24
(Harvard University)
Summary Developmental fate decisions are dictated by master transcription factors (TFs) that interact with cis -regulatory elements to direct transcriptional programs. Certain malignant tumors may also depend on cellular hierarchies reminiscent of normal development but superimposed on underlying genetic aberrations. In glioblastoma (GBM), a subset of stem-like tumor-propagating cells (TPCs) appears to drive tumor progression and underlie therapeutic resistance yet remain poorly understood. Here...
281 Citations Source Cite
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