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High performance computing (HPC)

Scientific Staff

 

Leslie P. Michelson, Ph.D.

 

Jeffrey Rosenfeld, Ph.D.

rosenf1@ca.rutgers.edu

973.972.1004

 

Dr. Jeffrey Rosenfeld has extensive experience in the analysis of next-generation sequencing data. His doctoral research at the Cold Spring Harbor Laboratory was focused on the analysis of ChIP-seq data for histone modifications in human cells.  This work resulted in one of the earliest papers on ChIP-seq utilizing Illumina sequencing. He also performed an extensive analysis of the function of the H3K9me3 histone modification.

After completing his doctorate, Dr. Rosenfeld began working as a research scientist in the laboratory of Dr. Todd Lencz at Zucker Hillside Hospital.  He was in charge of all next-generation sequencing analysis at the hospital including family-based exome sequencing and RNA-seq of cerebrospinal fluid (CSF).  He was also extensively involved in the analysis of genome association data especially in regards to computationally intensive tasks. In addition to investigating disease associations, Dr. Rosenfeld has studied the occurrence of multiple nucleotide polymorphisms (MNP) in the human genome and is supervising the study of non-traditional human variants such as MNPs and polymorphic SNPs for the 1000 Genomes Project.  Recently, Dr. Rosenfeld joined the High Performance and Research Computing group at UMDNJ and he is playing a key role in assisting researchers across the university in processing their next-generation sequencing data.

Dr. Rosenfeld also has an appointment as a Research Associate at the American Museum of Natural History where he works on whole-genome phylogenetics.    Normally, when scientists want to build a tree representing the relationships between organisms, they utilize a few highly conserved genes such as 16S rRNA.  This approach was reasonable when sequencing was expensive and there were very few complete genomes available, but it is a bit outmoded in an era when there are thousands of complete genomes that have been sequenced.   The technique developed by Drs.  Rosenfeld and DeSalle is termed the Venninator, and it takes whole genomes of organisms and groups them based upon the genes that are present in each genome.  The Venninator has been applied to many different groups of taxa including bacteria, Drosophila, yeast and a large dataset consisting of organisms across the Tree of Life.  This work has resulted in numerous publications.  Additionally, Drs. Rosenfeld and DeSalle are co-authoring a graduate-level textbook entitled A Primer on Phylgenomics.

Recent Publications

Papers:
1.  Samoshkin A, Dulev S, Loukinov D, Rosenfeld JA, Strunnikov AV. (2011) Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions. Chromosoma. In Press

2.  Lazzarinia, L, Rosenfeld JA, Huard RC, Hill V, Lapa e Silva JR,
DeSalle R, Rastogi N, Ho JL. (2011) Mycobacterium tuberculosis
spoligotypes that may derive from mixed strain infections are revealed
by a novel computational approach.   Infection, Genetics and Evolution.  In Press
3.  Lienau EK, DeSalle R, Allard M, Brown EW, Swofford D, Rosenfeld JA,
Sarkar IN and Planet PJ. (2010) The mega-matrix tree of life: using
genome-scale horizontal gene transfer and sequence evolution data as
information about the vertical history of life. Cladistics. 26:1-11

4.  Rosenfeld JA, Malhotra AK, Lencz T. (2010) Novel multi-nucleotide
polymorphisms in the human genome characterized by whole genome and
exome sequencing. Nucleic Acids Research 38(18): 6102-6111
5.  Rosenfeld JA, Xuan Z, DeSalle R. (2009) Investigating repetitively
matching short sequencing reads: the enigmatic nature of H3K9me3.
Epigenetics 4(3): 476 - 486
6.  Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. (2009)
Determination of Enriched Histone Modifications in Non-Genic Portions of the Human Genome.   BMC Genomics 10:143
7. Wang Z, Zang C, Rosenfeld JA*, Schones DE, Barski A, Cuddapah S, Cui K, Roh T-Y, Peng W, Zhang MQ, Zhao K. (2008) Combinatorial Patterns of Histone Acetylation and Methylation in the Human Genome. Nature Genetics 40(7): 897-903 *Co-first author
8. Rosenfeld JA, DeSalle R, Lee E, O’Grady P (2008) Using whole genome
presence/absence data to untangle function in Drosophila. Fly 2(6) 291-299

10. Lienau EK, DeSalle R, Rosenfeld JA, Planet PJ.   (2006) Reciprocal Illumination in the Gene Content Tree of Life.
11. Systematic Biology 55(3):441-4539. Lemke MJ, LienauEK, Rothe J, Pagioro TA, Rosenfeld JA, Desalle R.  (2008) Description of Freshwater Bacterial Assemblages from the Upper  Paraná  River Floodpulse System, Brazil. Microbial Ecology June 28,2008

12. Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R (2004) ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms Bioinformatics 20(18): 3462-3465

Text Books

DeSalle R and Rosenfeld JA, 2011. A Primer of Phylogenomics. Francis and Taylor (Under Contract, June 2010).


Book Chapters

DeSalle, R, Lienau, EK, Rosenfeld, JA and Planet, PJ, 2009. The Twin
Phylogenomic Challenges.  pp 23-30 in Darwin Evolution and Life; NIBR
2009 Symposium.   NIBR Inchon, Korea

Blogs

Guest Blogger on genomesunzipped.com November 2, 2011


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