Epigenomics of Development and Disease
Graduate position available
PhD position in mathematical modeling of gene regulatory networks
A PhD student position is available starting Spring, 2017 to study how gene regulatory networks process cytokine signals during mouse hematopoiesis. The student will work on a National Science Foundation funded project with the goals of 1) Identifying gene regulatory networks induced upon cytokine stimulation using gene expression time series data and 2) Developing predictive computational models to dissect the order and timing of regulatory events controlling cell-fate choice.
Our lab employs a variety of intertwined experimental and computational approaches to study cell-fate specification. See http://arts-sciences.und.edu/biology/faculty/manu.cfm for more information. The student will be joining an multidisciplinary team with expertise in developmental biology, computational biology, mathematical modeling, and high performance computing.
The student will be expected to perform computational analysis of RNA-seq data, formulate mathematical models of gene regulation, write software, and perform simulations. The opportunity to learn and perform experiments will also be available if the student is so inclined. The student will also be expected to collaborate with other members of the lab and interact with the larger integrative systems biology group comprised of faculty from the Departments of Biology, Mathematics, Physics, Chemistry, and Computer Science, and the Medical School.
Interested candidates should contact Dr. Manu by email or phone:
Assistant Professor of Biology
Starcher Hall 209
University of North Dakota
+1 631 885 3040
Postdoctoral positions available
Two postdoctoral positions are available: please see links below.
- The CoBRE Epigenetics Bioinformatics Core will be hosting a hands-on two-day workshop for next generation sequencing (NGS) data analysis, tools, and resources for wet-lab biologists without basic knowledge of the UNIX command line or R statistical package on Monday, June 8th, 2015 and Thursday, June 11th, 2015. Registration is now full.
- Call for 2015 New Project RFA and 2015-2016 Pilot Project Proposals! Visit the Epigenetics Current Funding Opportunities webpage for details!
- Congratulations to Dr. Sumali Pandey, a post-doctoral fellow/research specialist in the Ohm lab for receiving a $19,500 pilot grant from the Upper Midwest Agricultural Safety and Health Center (UMASH) to study epigenomic remodeling associated marks in bronchial epithelium upon exposure to Aspergillus fumigatus spores.
- Congratulations to Drs. Roxanne Vaughan, Joyce Ohm, Sergei Nechaev, Lucia Carvelli, Cindy Anderson and Archana Dhasarathy for their $10.5 million COBRE award!
- Congratulations to Dr. Joyce Ohm for receiving her first NIH R01 grant for a total of $1,552,500; titled "Environmental Toxins and Stem Cell Epigenetic Remodeling". Other UND investigators who will collaborate with Dr. Ohm on this grant are Drs. Kurt Zhang, Brij Singh and John Watt.
Our epigenetics research working group has been meeting regularly since 2010 and has grown to include approximately twenty laboratories from three departments in the School of Medicine and Health Sciences, as well as talented scientists from the College of Nursing, the College of Arts and Sciences, and the USDA Grand Forks Human Nutrition Research Center. Most of the epigenetics group members are early career investigators or those with established research programs in other fields whose research has led them to the exciting area of epigenetics/epigenomics research. In addition to the five junior investigators who would receive project support through our COBRE (Center of Biomedical Research Excellence in the Epigenomics of Development and Disease) grant, this working group includes several well-established federally-funded investigators with expertise in cancer, neurodegenerative diseases, auto-immune disorders, and aging. The more established members of the group will serve as collaborators, mentors, and on the Internal Advisory Board to support the Center generally, and more specifically to assist the junior investigators with all aspects of our mission.
Group Research Interests
Featured Epigenetics Articles
Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Ohm JE, Mali P, Van Neste L, Berman DM, Liang L, Pandiyan K, Briggs KJ, Zhang W, Argani P, Simons B, Yu W, Matsui W, Van Criekinge W, Rassool FV, Zambidis E, Schuebel KE, Cope L, Yen J, Mohammad HP, Cheng L, Baylin SB. Cancer Res. 2010 Oct 1;70(19):7662-73.
Shimbo T, Du Y, Grimm SA, Dhasarathy A, Mav D, Shah RR, Shi H, Wade PA (2013). MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes. PLoS Genet. 2013 Dec;9(12):e1004028. doi: 10.1371/journal.pgen.1004028. Epub 2013 Dec 26. PMID: 24385926
Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Henriques, Gilchrist DA, Nechaev S, Bern M, Muse GW, Burkholder A, Fargo DC, Adelman K. Mol Cell. 2013 Nov 21;52(4):517-28.
RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. Samarakkody A, Abbas A, Scheidegger A, Warns J, Nnoli O, Jokinen B, Zarns K, Kubat B, Dhasarathy A, Nechaev S. Nucleic Acids Res. 2015 Mar 27. pii: gkv263. [Epub ahead of print]
Featured UND Investigator
Sergei Nechaev, PhD was appointed as an Assistant Professor in the Department of Anatomy and Cell Biology in January 2012. UNDSMHS recruited Dr. Nechaev from the National Institute of Environmental Health Sciences at NIH in North Carolina, where he was a postdoctoral researcher for five years. Dr. Nechaev earned his doctorate from the State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia.
Dr. Nechaev is the Project Leader for Project 1 of our proposed COBRE Center investigating the roles of RNA polymerase II pausing as a dynamic epigenetic mark during neural stem cell differentiation.
His pioneering work on RNA polymerase II pausing has resulted in a 2010 Science publication: Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila.
In his spare time, Sergei enjoys mushroom hunting and cross country skiing, depending on the season.
Genome Data and Technical Links
NIH Epigenomics Roadmap Project - a public resource of human epigenomic data intended to catalyze basic biology and disease-oriented research.
Genecards - a searchable, integrated database of human genes
UCSC Genome Browser - reference sequence information and working draft assemblies for a large collection of genomes
Database for Annotation, Visualization and Integrated Discovery (DAVID) - a comprehensive set of functional annotation tools to help investigators understand the biological meaning behind large list of genes
UNC (Chapel Hill) Histone antibody page - A useful collection of histone antibodies and assay conditions
Methprimer - a program for designing bisulfite-conversion-based Methylation PCR Primers.
Bisulfite sequencing Data presentation and Compilation (BDPCC) - an online DNA methylation analysis platform for analysis of primary bisulfate sequencing experiments
NIH R01 Toolkit - A very complete resource for persons seeking and maintaining NIH funding