Available Positions

Faculty Member Position Available

Center for RNA Biology

Posted on: 8/7/12


The Center for RNA Biology, directed by Lynne E. Maquat, Ph.D., and co-directed by David H. Mathews, M.D., Ph.D., is soliciting applications from outstanding individuals holding a PhD and/or an MD degree(s) and at least two years of post-doctoral training for a position at the ASSISTANT, ASSOCIATE or FULL PROFESSOR level. Emphasis is being placed on wet-bench and/or computational studies having disease relevance, including but not limited to the study of RNA metabolism or the use of RNA as a therapeutic tool or target. Successful applicants are expected to develop independent, externally funded research programs and to contribute toward graduate- and medical-school teaching. The University of Rochester Medical Center and the adjacent undergraduate College of Arts & Sciences offer an outstanding research environment with established strengths in RNA Biology and excellent opportunities to collaborate with basic scientists and clinicians.

Applicants should apply online (UR Job Number 176618)and send a complete C.V., descriptions of research accomplishments and future research plans, and letters from three references to Sharon Kubiak.

Post-Doctoral Fellow Positions Available

Mechanisms of nonsense-mediated mRNA decay (NMD), STAU-mediated mRNA decay (SMD), and how dsRNA-binding proteins in addition to STAU influence RNA metabolism

Maquat Lab (Normal & Disease-Associated RNA Decay)
Posted on: 8/15/13


Interested post-doctoral applicants should note that there are many ongoing projects in the lab, and we are open to new ideas. Current post-docs in the lab have backgrounds in diverse topics that include protein chemistry, small RNAs in Drosophila, pre-mRNA splicing in human disease, X-ray crystallography of bacterial macromolecular structures, bioinformatics of mammalian-cell lncRNAs, and metabolism of human tRNases and miRNAs. Thus, we make a great team for developing multi-pronged and innovative approaches to study mammalian-cell metabolic pathways. What is written under Projects in the Maquat-lab web site offers simply a taste of what we have done, and what is written below offers just the tip of the iceberg of what we are interested in doing.

Opportunities are available to research the function of new and already identified NMD factors (Lejeune et al., 2003, Mol. Cell 12:675-687), factor roles in NMD (Chiu et al., 2003, RNA 9:77-87; Brumbaugh et al., 2004, Mol. Cell 14:585-598; Matsuda et al., 2007, Nat. Struct. Mol. Biol. 14:974-979; Kurosaki and Maquat, 2013, Proc. Natl. Acad. Sci. USA 110:3357-3362) and, in collaboration with Rob Singer (Albert Einstein College of Medicine), the spatial difference in cells between nucleus-associated and cytoplasmic NMD (Sato et al., 2008, Mol Cell 29:255-262; Trcek et al., 2013, Genes Dev 27:541-551). We are also interested in how cells utilize NMD for new purposes, and how NMD interfaces with other pathways of RNA and protein metabolism.

Opportunities are additionally available to study a related mRNA decay pathway that we have named Staufen1(STAU)-mediated mRNA decay (SMD) (Kim et al., 2005, Cell 120:195-208; Kim et al., 2007, EMBO J. 26:2670-2681). We aim to determine what defines intramolecular and intermolecular STAU-binding sites (Gong and Maquat, 2011, Nature, 470:284-288; Wang et al., 2013, Genes Dev 27: 793-804; Gong et al., 2013, Nat. Struct. Mol. Biol, in press; Elbarbary et al., 2013, Genes Dev 27:1495-1510) and how SINEs have evolved to constructively influence RNA processes.

We are also interested in how different dsRNA-binding proteins work together and in competition with one another. As one example, we are pursuing our finding that STAU1 binding to 3'UTR inverted Alu elements competes with binding of the largely nuclear paraspeckle protein p54nrb and the largely cytoplasmic protein kinase R (PKR) to mediate, respectively, the nuclear export and cytoplasmic translation of a number of mRNAs that contain these elements (Elbarbary et al., 2013, Genes Dev 27:1495-1510). What other dsRNA-binding proteins compete with STAU to influence cellular RNA metabolism, and how do other classes of 3'UTR inverted Alu elements identified by Elbarbary et al. (2013) differentially affect mRNA metabolism? We are simultaneously investigating why 3'UTR inverted Alu elements fail to trigger SMD.

Successful post-doctoral applicants will join a well-equipped group of interactive lab members with diverse backgrounds and broad expertise in newly remodeled labs. The University of Rochester is unique for its sizeable community of RNA researchers, its Center for RNA Biology: From Genome to Therapeutics, and its RNA Structure and Function Cluster, all of which include members of the Medical Center, in which the Maquat lab resides, as well as the College of Arts, Sciences and Engineering across the street.

Interested individuals should send a C.V., including a description of past and on-going research, and the names and contact information of three references to Dr. Maquat.

Mechanism of Bacterial and Eukaryotic Translation

Ermolenko Lab (Mechanism of Protein Synthesis)
Posted on: 8/16/11


We are seeking talented and motivated postdoctoral fellow to study mechanism of bacterial and eukaryotic translation. We use ensemble and single molecule fluorescence resonance energy transfer to study structural dynamics of the ribosome and translation factors. Applicants must have a recent Ph.D. and expertise in molecular biology with publications in international peer-reviewed journals. Applicants with experience in ribosome and RNA biochemistry and/or fluorescent spectroscopy are encouraged to apply

Please submit a statement of research interests and experience, and current curriculum vitae to Dr. Ermolenko.

Molecular Virology, DNA Mutagenesis and RNA Editing

Smith Lab (Messenger RNA Expression & Processing)
Posted on: 8/5/11


A funded postdoctoral position is available at the junior or senior level to study the role of cellular defense systems such as APOBEC3G and Activation Induced Deaminase in suppressing viral infectivity, regulating immune response and/or contributing to genomic mutagenic activity. Candidates are being sought who are technically skilled, creative and highly motivated.

The candidate will have the opportunity to further their career training in a highly supportive environment consisting of an interdisciplinary team of investigators with expertise in virology, biochemistry, molecular biology and structural biology and state-of-the-art laboratories and core facilities in the lab and the Biochemistry Ph.D. program at the University of Rochester, Rochester, NY.

Prior graduate or postdoctoral training virology, molecular biology are desirable and/or high throughput assay development are desirable.

Interested applicants should send an application package via email to Prof. Smith. The application package should contain:

  • Cover letter
  • Full CV
  • List of three references

Functional Genomics Screen of Glycosyltransferase

Hagen Lab (Comprehensive Functional Genomics Screen of Glycosyltransferases)
Posted on: 3/28/11


Our lab is recruiting Post-doctoral fellows for work on current research projects. Our research projects provide opportunities for extensive training in the areas of molecular biology, glycobiology, recombinant protein expression, protein purification, biochemical characterization of enzymes, transgenic techniques, microscopy, loss of function reverse genetic screens. Postdoctoral fellows should have training in C. elegans or Drosophila development or have a strong background in molecular biology, glycobiology or proteomics research.

For more information or to apply please contact Dr. Hagen.

Mechanism and Regulation of DNA Replication and Repair

Bambara Lab (Human Genome Stability, DNA Damage Response, HIV Replication & Evolution)
Posted on: 1/1/10


An important area of investigation relating to both aging and cancer is the study of mechansims by which mammalian cells coordinate DNA replication and repair, so that damage is repaired before it is passed on to progeny. We are reconstituting the reactions of mammalian Okazaki fragment processing and base excision repair. We recently found that replication protein A greatly stimulates base excision repair and hypothesize that it serves a factor that coordinates the actions of the proteins involved. We are trying to determine the complex function of this protein. The Dna2 protein is both a helicase and nuclease. It is essential for DNA replication but what it does is still unknown. Its biochemical properties are similar to those of FEN1, yet FEN1 cannot be its substitute. We are trying to understand the nature of its essential contribution. The signaling protein p21cip1 is thought to mediate a shift from DNA replication to repair during chromosomal damage. It might do so by binding PCNA. Yet PCNA is involved in both processes. We are trying to determine the mechanism of regulation by p21cip1. The project involves training in protein expression, reconstitution of replication and repair pathways, structural analysis and mutagenesis of proteins, cell culture, and mechanisms of catalysis, regulation and signaling.

Recombination in HIV. The two chromosomes in HIV frequently recombine during replication, a process that evolves viral fitness in a highly undesirable manner. We found that recombination is so efficient because the two chromosomes bind to each other. This binding is most favorable at hairpins, and is stabilized by a process called kissing. The geometry of the loops on some hairpins particularly favor the kissing interaction. The interaction has the ability to propagate along the genome stabilizing many binding sites. The DNA strand being copied from one genome transfers to the other at these sites. We are using genetic modification of the sequence and structure of the RNA to probe the recombination mechanism both in vitro and in vivo. Results will give us a lot of information about RNA-RNA interaction, the mechanism of recombination and the unique evolution of HIV. The project involves reconstitution of recombination in vitro, measurement of RNA-RNA folding and interaction, studies of reverse transcriptase reaction mechanisms and cell culture.

Applicants should send three letters of recommendation to Dr. Bambara and be prepared to speak on their thesis work.

Openings are anticipated in summer 2012

The University of Rochester is an equal opportunity/affirmative action employer.