World's Best Scientists 2026 revealed!

D-Index & Metrics

Genetics

D-Index
56
Citations
51144
World Ranking
3441
National Ranking
1489

Research.com Recognitions

  • 2013 - Fellow of the Indian National Academy of Engineering (INAE)

Overview

Simon Kasif is affiliated with Boston University in the United States and has contributed extensively to the fields of Biochemistry, Genetics and Molecular Biology, and Medicine. Their research covers several subfields including Molecular Biology, Computational Theory and Mathematics, Physiology, Epidemiology, and Infectious Diseases.

The scientist's work focuses on topics such as Bioinformatics and Genomic Networks, Computational Drug Discovery Methods, RNA Research and Splicing, RNA modifications and cancer, Genomics and Phylogenetic Studies, Adipose Tissue and Metabolism, as well as Adipokines, Inflammation, and Metabolic Diseases.

Simon Kasif has coauthored papers with several frequent collaborators, including:

  • Mark Crovella
  • Nure Tasnina
  • Brian J. Haas
  • Alexander Dobin
  • Mahmoud Ghandi

The scientist has published in prominent venues, notably:

  • arXiv (Cornell University)
  • Nature Communications
  • bioRxiv (Cold Spring Harbor Laboratory)
  • Cell Reports Methods
  • Alzheimer's Research & Therapy

Recent published papers include:

  • Single-cell transcriptional networks in differentiating preadipocytes suggest drivers associated with tissue heterogeneity, 2020, Nature Communications
  • High-throughput mediation analysis of human proteome and metabolome identifies mediators of post-bariatric surgical diabetes control, 2021, Nature Communications
  • Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector, 2023, Cell Reports Methods
  • Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease, 2020, Alzheimer's Research & Therapy
  • We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data, 2020, PLoS Biology

Simon Kasif was awarded the title Fellow of the Indian National Academy of Engineering (INAE) in 2013.

Best Publications

  • Initial sequencing and analysis of the human genome.

    Eric S. Lander;Lauren M. Linton;Bruce Birren;Chad Nusbaum

  • Improved microbial gene identification with GLIMMER

    Arthur L. Delcher;Douglas Harmon;Simon Kasif;Owen White

  • Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.

    Jeremiah J Faith;Boris Hayete;Joshua T Thaden;Ilaria Mogno;Ilaria Mogno

  • Microbial gene identification using interpolated Markov models

    Steven L. Salzberg;Arthur L. Delcher;Simon Kasif;Owen White

  • Alignment of whole genomes

    Arthur L. Delcher;Simon Kasif;Robert D. Fleischmann;Jeremy Peterson

  • A system for induction of oblique decision trees

    Sreerama K. Murthy;Simon Kasif;Steven Salzberg

  • Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains

    Manching Ku;Richard P. Koche;Richard P. Koche;Richard P. Koche;Esther Rheinbay;Esther Rheinbay;Esther Rheinbay;Eric M. Mendenhall;Eric M. Mendenhall

  • Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

    Mario Luca Suva;Mario Luca Suva;Mario Luca Suva;Esther Rheinbay;Esther Rheinbay;Esther Rheinbay;Shawn M. Gillespie;Shawn M. Gillespie;Shawn M. Gillespie;Anoop Premswaroop Patel;Anoop Premswaroop Patel

  • Extracting conserved gene expression motifs from gene expression data.

    T. M. Murali;Simon Kasif

  • Predicting protein function from protein/protein interaction data: a probabilistic approach

    Stanley Letovsky;Simon Kasif

  • Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

    Bo Liu;Lina L. Faller;Niels Klitgord;Varun Mazumdar

  • Whole-genome annotation by using evidence integration in functional-linkage networks

    Ulas Karaoz;T. M. Murali;Stan Letovsky;Yu Zheng

  • An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma

    Esther Rheinbay;Mario L. Suvà;Mario L. Suvà;Mario L. Suvà;Shawn M. Gillespie;Shawn M. Gillespie;Shawn M. Gillespie;Hiroaki Wakimoto

  • OC1: randomized induction of oblique decision trees

    Sreerama Murthy;Simon Kasif;Steven Salzberg;Richard Beigel

  • RankGene: identification of diagnostic genes based on expression data.

    Yang Su;T. M. Murali;Vladimir Pavlovic;Michael Schaffer

  • Immediate-early and delayed primary response genes are distinct in function and genomic architecture

    John W. Tullai;Michael E. Schaffer;Steven Mullenbrock;Gabriel Sholder

  • Computational methods in molecular biology

    Steven L. Salzberg;David B. Searls;Simon Kasif

  • Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models

    Manway Liu;Arthur Liberzon;Sek Won Won Kong;Sek Won Won Kong;Weil R Lai

  • On the parallel complexity of discrete relaxation in constraint satisfaction networks

    Simon Kasif

  • Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

    Mario L. Suvà;Esther Rheinbay;Shawn M. Gillespie;Anoop P. Patel

Frequent Co-Authors

Arthur L. Delcher
Arthur L. Delcher University of Maryland, College Park
Steven L. Salzberg
Steven L. Salzberg Johns Hopkins University
Richard J. Roberts
Richard J. Roberts New England Biolabs
Charles R. Cantor
Charles R. Cantor Boston University
Bradley E. Bernstein
Bradley E. Bernstein Broad Institute
Richard Beigel
Richard Beigel Temple University
Isaac S. Kohane
Isaac S. Kohane Harvard University
Zhiping Weng
Zhiping Weng University of Massachusetts Chan Medical School
Peter J. Park
Peter J. Park Harvard University
Jill P. Mesirov
Jill P. Mesirov University of California, San Diego

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