Principal Investigator: 

John Lis


Laboratory Manager:

Janis K. Werner


Postdocs:

Abdullah Ozer

photoI am a Research Associate and I have been in the Lis Lab since 2007. I got my Bachelors degree in Molecular Biology and Genetics from Bilkent University, Turkey, and my Ph.D. in Molecular Biophysics from UT Southwestern Medical Center at Dallas, Texas. In my graduate study working with Richard K. Bruick in Department of Biochemistry at UTSW, I characterized the function of ING4 protein in regulation of mammalian Hypoxia Response Pathway, the primary cellular response mechanism for oxygen deprivation. I have a general interest in developing novel high-throughput technologies that enable us, in ways that were not possible before, to disrupt, image, and characterize biological processes particularly in transcriptional regulation in live cells. Since I have joined the Lis Lab, I have been involved in many projects including the improvement of RNA Aptamer selection and characterization methods and their implamantaton for selection and characterization of RNA aptamers to a number of proteins including many transcription factors, and imaging of proteins and their post-translational modifications with RNA aptamers in living cells. Recently, I have been working on developing novel and improved methods for determination of 4D nuclear architecture and characterization of enhancers with high resolution and high sensitivity in mammalian cells. Also in the last three years I have been involved in a challenging project called “Raising Irem and Harun”, serving as the father (trying hard to be a good one).


 Judhajeet Ray

Judajheet Ray

jr839@cornell.edu

I am a postdoc in the Lis lab since early 2015. I received my Bachelors and Masters degrees from University of Calcutta, India and my Ph.D. in Biochemistry from Iowa State University under the guidance of Prof. Marit Nilsen-Hamilton. During my Ph.D. I have developed an imaging technique utilizing RNA aptamers to detect gene expression in living cells. I am very much interested in the application of aptamers to answer biological questions. Currently I am involved in characterizing RNA aptamers selected against factors that are known to be involved in regulation of transcriptional pausing. The aptamers will be very useful tools to perturb the molecular interactions of these proteins inside cells to analyze their roles in Pol II pausing.


Anniina Vihervaara

av494@cornell.edu

My focus is to understand the molecular mechanisms that underlie transcriptional decisions in the dynamic chromatin environment. Currently, I utilize heat stress to induce a rapid change in the transcriptional profile of human cells and analyse how gene expression is adjusted and coordinated across the genome.


Erin Wissink

erin.wissink@cornell.edu

My interest is understanding how cells use gene expression to respond to their changing environments. I completed my PhD at Cornell in Andrew Grimson’s lab, where I investigated post-transcriptional gene regulation. I had a short postdoc at UCLA where I worked with Tracy Johnson’s group to understand connections between chromatin and splicing.  I joined the Lis lab in 2017, and I am profiling nascent transcription during a variety of stresses to identify the enhancers and genes that are turned on and off, especially after undergoing acute extracellular stresses.  Outside of lab, I can be found baking and exploring Ithaca’s natural beauty with my dog.


Eric Strobel


Sagar Shah

Due to the diversity and complexity of signaling networks in both physiological and disease states, I am interested in understanding the mechanisms that drive transcriptional programs and its regulation. During my doctoral studies in Biomedical Engineering at Johns Hopkins University School of Medicine and subsequent work at the Mayo Clinic, my research focused on studying transcriptional dysregulation in cancer by delineating novel YAP-mediated signaling networks that drive aggressive behavior for prognostic and therapeutic purposes. Currently, as a joint postdoctoral fellow in the Lis and Yu labs, I am characterizing the active transcriptional regulatory element landscape of cancer and studying its regulation to understand fundamental mechanisms underlying gene expression.


 Graduate Students:


 Nathaniel Tippens (Tri-Institutional Training Program)

Nathaniel Tippens

Nate is a PhD student in the Computational Biology and Medicine program, and he is working on a new experimental technique to map all protein-DNA interactions in accessible regions of the genome. He is interested in applying this and other genomic techniques to study the transcriptional mechanisms that specify cellular identity.


Lina Bagepalli (BMCB)

pic

I am a graduate student part of the Biochemistry, Molecular and Cell Biology field at Cornell. I did my undergraduate at Rensselaer Polytechnic Institute and previously studied cancer and cell biology related research. My current research involves elucidating the functions of the particular domains of the protein Heat Shock Factor 1 using RNA aptamers. I have characterized the binding of many selected aptamers using UV crosslinking and EMSA based methodologies and have identified that a majority of our selected HSF1 aptamers bind to the DNA Binding domain and Trimerization domain. I am continuing this work and am currently focused on using HSF1 aptamers a tools to inhibit HSF1 function measured by genome wide assays. In my free time, I like to cook, dance, paint and play the piano and violin.


Kara Rode (BMCB)


Michael DeBerardine (GGD)

I received my bachelors degree in Biochemistry & Molecular Biology from Brown University in 2015, and I’m currently a graduate student in the field of Genetics, Genomics and Development. My work in the lab combines rapid in vivo perturbations with genome-wide measurements to study the mechanistic basis of transcription regulation in humans. Of particular interest are the molecular mechanisms by which promoter-proximal pausing is regulated in humans, and how this regulation varies across different genes and in perturbative cellular states. In my spare time, I enjoy the outdoors, playing guitar, and singing.


Jawaher Al Zahrani (GGD)


Julius Judd (BMCB)

jaj256@cornell.edu

I received my Bachelors in Biochemistry and Molecular Biology from SUNY Albany. Prior to coming to Cornell, I investigated the mechanism of distributive conjugal transfer in mycobacteria under the guidance of Todd Gray and Keith Derbyshire at the Wadsworth Center. I am now a PhD student in the field of Biochemistry and Molecular Cell Biology, where I am co-advised by Cédric Feschotte. I am working to develop new tools for measuring the nascent transcriptional impacts of a genetic perturbation, in a massively parallel manner, and will use them to investigate the contribution of species-specific transposable elements to regulatory networks. Outside of the lab, I enjoy exploring the great outdoors by skiing, mountain and rock climbing, and cycling.


Alexandra Chivu (GGD)

Alex worked at the Genome Institute of Singapore (GIS) & Medical Research Council (MRC), London studying transcription bursts and epigenetic regulation in cancer and immunity. Currently Alex is interested in understanding the impact of chromatin architecture on transcriptional regulation, as well as developing new RNA-based technologies.


Philip Versluis (BMCB)

I am from Grand Rapids, Michigan and did my undergrad at Hope College in Holland, Michigan. During my undergrad I studied protein trafficking with Dr. Leah Chase and later Chromatin Modifying Enzymes with Dr. Scott Rothbart at the Van Andel Research Institute. I am a PhD student in the field of Biochemistry, Molecular and Cell Biology. I am interested in the mechanisms of RNA Polymerase II pause release, particularly how, and when different factors work to aid pause release. When not in lab, I enjoy Ithaca’s natural surroundings; weather permitting I like paddle boarding on Cayuga Lake and hiking in the surrounding countryside.


Zhou Zhou (BMCB)