Photo of Honoratus Van Bakel

Honoratus Van Bakel

  • ASSISTANT PROFESSOR Genetics and Genomic Sciences
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Education

  • M.S., University of Utrecht
    Medical Biology

  • Ph.D., University of Utrecht
    Bioinformatics and Molecular Biology

Biography

    Harm van Bakel's research is focused on understanding genome architecture, transcription regulation and coding- and non-coding RNA biology, with an emphasis on their relationship to disease. He uses a combination of Molecular Biology and Bioinformatics approaches to tackle these questions.

Research

A complete overview of the work in the lab can be found on the van Bakel Lab website.

Publications

Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. Cell 2014 Apr; 157(3).

Bongers G, Pacer ME, Geraldino TH, Chen L, He Z, Hashimoto D, Furtado GC, Ochando J, Kelley KA, Clemente JC, Merad M, van Bakel H, Lira SA. Interplay of host microbiota, genetic perturbations, and inflammation promotes local development of intestinal neoplasms in mice. The Journal of experimental medicine 2014 Mar; 211(3).

Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH. Characterization of the human ESC transcriptome by hybrid sequencing. Proceedings of the National Academy of Sciences of the United States of America 2013 Dec; 110(50).

de Boer CG, van Bakel H, Tsui K, Li J, Morris QD, Nislow C, Greenblatt JF, Hughes TR. A unified model for yeast transcript definition. Genome research 2014 Jan; 24(1).

van Bakel H, Tsui K, Gebbia M, Mnaimneh S, Hughes TR, Nislow C. A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. PLoS genetics 2013 May; 9(5).

Drogat J, Migeot V, Mommaerts E, Mullier C, Dieu M, van Bakel H, Hermand D. Cdk11-CyclinL Controls the Assembly of the RNA Polymerase II Mediator Complex. Cell reports 2012 Oct;.

van Bakel H, Stout JM, Cote AG, Tallon CM, Sharpe AG, Hughes TR, Page JE. The draft genome and transcriptome of Cannabis sativa. Genome biology 2011; 12(10).

van Bakel H. Interactions of transcription factors with chromatin. Sub-cellular biochemistry 2011; 52.

Lam KN, van Bakel H, Cote AG, van der Ven A, Hughes TR. Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays. Nucleic acids research 2011 Jun; 39(11).

Coudreuse D, van Bakel H, Dewez M, Soutourina J, Parnell T, Vandenhaute J, Cairns B, Werner M, Hermand D. A gene-specific requirement of RNA polymerase II CTD phosphorylation for sexual differentiation in S. pombe. Current biology : CB 2010 Jun; 20(12).

van Bakel H, Nislow C, Blencowe BJ, Hughes TR. Most dark matter transcripts are associated with known genes.. PLoS biology 2010 May; 8(5).

van Bakel H, Hughes TR. Establishing legitimacy and function in the new transcriptome. Briefings in functional genomics & proteomics 2009 Nov; 8(6).

Khanna M, Van Bakel H, Tang X, Calarco JA, Babak T, Guo G, Emili A, Greenblatt JF, Hughes TR, Krogan NJ, Blencowe BJ. A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300. RNA (New York, N.Y.) 2009 Dec; 15(12).

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Molecular cell 2008 Dec; 32(6).

van Werven FJ, van Bakel H, van Teeffelen HA, Altelaar AF, Koerkamp MG, Heck AJ, Holstege FC, Timmers HT. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes & development 2008 Sep; 22(17).

Industry Relationships

Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device and biotechnology companies to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their relationships with such companies.

Dr. Van Bakel did not report having any of the following types of financial relationships with industry during 2012 and/or 2013: consulting, scientific advisory board, industry-sponsored lectures, service on Board of Directors, participation on industry-sponsored committees, equity ownership valued at greater than 5% of a publicly traded company or any value in a privately held company. Please note that this information may differ from information posted on corporate sites due to timing or classification differences.

Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website at http://icahn.mssm.edu/about-us/services-and-resources/faculty-resources/handbooks-and-policies/faculty-handbook. Patients may wish to ask their physician about the activities they perform for companies.

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