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Molecular Biology of the Cell highlights paper by Morozov & collaborators |
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Molecular Biology of the Cell editors select paper by Alex Morozov and collaborators James R. Broach and Karl A. Zawadzki of Princeton University to be highlighted in the journal's “InCytes from MBC”. The paper is available online here and the print edition will appear along with the InCyte highlight in August .
Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae Karl A. Zawadzki, Alexandre V. Morozov, and James R. Broach Mol. Biol. Cell, online June 3, 2009 , print version in press 10.1091/mbc.E09-02-0111
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Summer 2009 BioMaPS Institute Undergraduate Students |
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Bernstein Award Winner:  | Name: Thomas Ehrlich
Rutgers – College of Engineering
Major: Chemical Engineering
Class: 2010
Advisor: Joseph Marcotrigiano, CABM & Chemistry/Chemical Biology
Project: Determining the structure and specific functionality of the protein RIG-I |
BioMaPS/Molecular Biophysics Summer Scholars:  | Name: Noam Fine
Rutgers – School of Arts & Sciences
Major: Chemistry
Class: 2010
Advisor: Eddy Arnold, CABM & Chemistry/Chemical Biology
Project: Drug design for RNA polymerase inhibition |
 | Name: Daniel Weingard
Rutgers – School of Arts & Sciences
Major: Mathematics & Biology
Class: 2011
Advisor: Wilma Olson, BioMaPS & Chemistry/Chemical Biology
Project: Determining the orientation of a protein with respect to the DNA to which it is bound | RISE Summer Undergraduate Student:  | Name: Emily Nowicki
The College of New Jersey
Major: Biology
Class: 2010
Advisor: Todd Michael, Waksman Institute & Plant Biology and Pathology
Project: Metagenomics project on the symbiotic relationship between bradyrhizobium and duckweed |
DIMACS REU Summer Undergraduate Students:  | Name: Richard Cimino
Rutgers – College of Engineering
Major: Chemical Engineering
Class: 2011
Advisor: Gyan Bhanot, BioMaPS, MB & Biochemistry, & CINJ
Project: Cell population dynamics and cancer modeling in the human colon: an extension of the Johnston Feedback Model |  | Name: Alexandria Volkening
University of Maryland, Baltimore County
Major: Mathematics
Class: 2011
Advisor: Wilma Olson, BioMaPS & Chemistry/Chemical Biology
Project: How nucleosomes affect the topology of DNA |
Summer Scholar Supported by NSF Grant:  | Name: Evelyn Strombom
Swarthmore College, PA
Major: Biology and Economics
Class: 2012
Advisor: Troy Shinbrot, Biomedical Engineering
Project: Exploring the use of polyaccylamide hydrogels to study ductal cancer growth geometries | |
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BioMaPS RISE Summer Undergraduate Works on Metagenomics Project. |
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Emily Nowicki, The College of New Jersey During this summer 2009 Emily Nowicki, a rising senior at The College of New Jersey, will join the Michael Lab at the Waksman Institute of Microbiology as an undergraduate BioMaPS RISE Summer undergrad. Emily will merge both bioinformatic tools with wet bench techniques in the Michael Lab to understand symbiotic relationships between plants and microbes. Emily will be working on a project to understand the microbial symbionts of the smallest, fastest growing flowering plant, Spirodela polyrhiza, which is commonly known as the Greater Duckweed. The Michael lab is currently studying duckweed as a potential biomas crop for marginal wastewater and a model non-grass monocot aquatic plant. The Michael lab has taken a metagenomics approach to understand the microbial communities associated with duckweeds with Next Generation high-throughput sequencing. Deep sequencing has revealed multiple microbes that are associated with duckweeds in sterile culture, one of which is a photosynthetic nitrogen fixing Bradyrhizobium. Emily will design experiments to further analyze the high-throughput sequencing, fully sequence isolated microbes, and confirm the relationship between the microbes and Spirodela polyrhiza. |
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NY Times, Feb. 17, 2009 Morozov Awarded Sloan Foundation Fellowship |
The New York Times, February 17, 2009, page A11
Alex Morozov has been awarded an Alfred P. Sloan Research Fellowship for 2009. Alex was awarded the fellowship in the category "Molecular Biology (Computational and Evolutionary)". This is apt as Alex is one of the new breed of biological physicists who are working at the frontier of this fast moving interdisciplinary field.
The Sloan Foundation cited Alex together with a group of "early career scientists and scholars who demonstrate outstanding promise and potential to contribute substantially to their fields. Many past recipients have gone on to win Nobel Prizes, Fields Medals, and numerous other distinguished awards."
Congratulations to Alex! |
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Morozov Receives NIH Grant to Study Chromatin Structure |
February 13, 2009. Alex Morozov has received today a $1.07 Million NIH R01 grant to develop biophysical models for predicting nucleosome positioning within chromatin structure, discriminating between its intrinsic and extrinsic relationships to gene regulation, and determining its responses to environmental and genetic perturbations.
The NIH study section which reviewed Morozov's grant application, stated that:
"The subject is of very high relevance and potential impact to current thinking in molecular epigenetic research - with potentially wide-ranging implications for understanding bases of medical abnormalities and for the design of therapeutic strategies - and the approach is judged to be very innovative."
Professor Morozov is an Assistant Professor of Physics and a BioMaPS Institute faculty member. A description of his research can be found at: http://www.physics.rutgers.edu/~morozov/ |
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New Faculty Appointments in Computational Biology |
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We are very pleased to announce that two computational biologists will soon be joining us. Kevin Chen and Alexander Schliep are the first joint faculty hires of the BioMaPS Institute with the Genetics and Computer Science Departments, respectively.
Dr. Chen will join the faculty in September 2009. After receiving his PhD in computer science from the University of California, Berkeley, he went to New York University where he is currently a post-doctoral fellow. Dr. Chen was recently awarded a prestigious NIH K99/R00 grant from the National Human Genome Research Institute. A major goal of his research is to use computational methods for the study of post-transcriptional regulation, especially mechanisms mediated by microRNAs. As outlined in an article in Nature Reviews Genetics (2007) that he co-authored with Nikolaus Rajewsky, a complete understanding of gene regulation requires the integration of regulatory mechanisms at all levels. Dr. Chen’s current research efforts will complement ongoing Institute studies of transcriptional regulation.
In September 2009 Dr. Schliep will relocate to Rutgers from the Department of Computational Biology, Max Planck Institute for Molecular Genetics in Berlin where he is currently group leader of the Bioinformatics Algorithms Group. An important focus of Dr. Schliep’s research is the integration of heterogeneous data to enable detailed analysis and modeling of biological systems. New methods for combining different types of data, such as gene expression profiles, genomic sequences, and image analyses, to explain a biological function can be used, for example, to quantify complex phenotypes and diseases, improve identification of clusters of genes that are temporally and spatially co-expressed, and provide important insights into the development of a wide variety of immune cell types from pluripotent stem cells . |
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DIMACS Workshop on the Evolution of Complex Phenotypes |
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On June 11-12, 2009 DIMACS will present the workshop "Identifying Genetic Signatures for the Evolution of Complex Phenotypes" co-organized by BioMaPS Institute faculty member Gyan Bhanot. This workshop (described at: http://dimacs.rutgers.edu/Workshops/Phenotypes/) will focus on methods to understand the evolution of complex phenotypes in SNP, sequence and gene and protein expression data and on results obtained by applying such methods to private as well as public datasets. |
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The following courses are being offered by faculty of the BioMaPS Institute in the Spring 2009 semester: 16:118:507:01. Physics of Living Matter. Instructor: A. Morozov (3 credits) 16:118:617:02. Genetic Systems & Structures. Instructors: W. Olson, D. Case, K. Mischaikow (3 credits) 16:160:538:01. Methods in Molecular Biophysics. Instructors: D. Case, B. Kalodimos (3 credits) 16:696:602:01. Seminar in Molecular Biophysics. Instructor: W. Olson (1 credit)
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Graduate Program in Top Ten |
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A study of 375 American universities published in the Chronicle of Higher Education (November 16, 2007 issue) reported that the Rutgers Graduate Program in Computational Biology and Molecular Biophysics earned a top ten ranking nationally when compared with corresponding programs in the category of “Bioinformatics & Computational Biology.” The study was based on the Faculty Scholarly Productivity Index developed by Academic Analytics, LLC. |
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New Course on Bioinformatics and Evolutionary Modeling of Human Populations |
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The following new course is being offered by BioMaPS faculty member Gyan Bhanot in the Spring 2009 semester: 01:694:421. Special Topics in Molecular Biology: Introduction to bioinformatics and evolutionary modeling of human populations. Prerequisite: 694:408 or 447:385 or 146:478. The goals of this course are to explain fundamental principals of evolutionary population genetics using simple mathematical ideas and tools, understand the role of mutations, drift, selection, migration, segregation and recombination in determining population structure and dynamics, understand how to find disease associated mutations, perform phylogenetic analysis, create models of human migration and evolution, and perform Monte Carlo simulations to study evolution. We will develop all the necessary concepts required from first principles. |
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