Akshay today successfully defended his Ph.D. thesis, entitled “Computational modeling of sequence features driving transcription factor binding in neuronal programming”. He’s the first student to defend from our lab! Akshay has been highly successful during his graduate studies, with a co-first author paper in Cell Stem Cell, contributions to two other published articles, a first…
Tim Kunz, an undergraduate researcher in our lab since 2014, has won the Fred Wedler award for Outstanding Undergraduate Dissertation in Biochemistry & Molecular Biology. Tim recently graduated with a B.Sc. in Biochemistry & Molecular Biology. His honors thesis is entitled “Visualizing and understanding chromatin organization using self-organizing maps”, and describes a new machine-learning approach to…
Dr. Guray Kuzu has joined our lab as a Postdoctoral Scholar. Guray was previously a Postdoctoral Fellow in a joint position with Michael Tolstorukov (Harvard Medical School) and Erica Larschan (Brown University). In this position he studied, amongst other things, chromatin accessibility and the function of the CLAMP proteins in Drosophila X chromosome dosage compensation.…
A pair of Penn State News articles have recently featured our collaboration with Dr. Frank Pugh’s lab to build an automated pipeline for processing ChIP-exo data. As described in a recent Huck Institutes News article, we have been working with the Pugh lab to build a system for processing and analyzing ChIP-exo sequencing datasets. This…
Our manuscript describing the dynamics of induced motor neuron programming has been published in Cell Stem Cell. The manuscript, “A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells“, results from a close collaboration between our lab, Esteban Mazzoni’s lab at NYU, and Uwe Ohler’s lab at the Max Delbrück…
Divyanshi Srivastava, a graduate student in the MCIBS Bioinformatics & Genomics program, has joined our lab. Divyanshi has a BE in Computer Science, with an integrated MS in Biological Sciences from the Birla Institute of Technology, India. Her Master’s thesis was titled: ” Chromatin Mediated Antigenic Variation in Plasmodium falciparum“, and was carried out at the…
Lila Rieber has been awarded a 2016 Graduate Research Fellowship from the National Science Foundation! This prestigiousfellowship will enable her to pursue thesis research that aims to characterize the three-dimensional organization of chromatin in high resolution. Congratulations, Lila!
Our collaborative study with Ken Zaret and colleagues at University of Pennsylvania has been published. The manuscript, entitled “The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation“, appears in Molecular Cell. While nucleosomes are often thought to block transcription factor binding at tissue-specific enhancers, lead author Maki Iwafuchi-Doi in…
A manuscript on which Shaun and group member Guanjue Xiang collaborated with Qiao (Joe) Zhou and colleagues at Harvard University has been published. “Reprogrammed Stomach Tissue as a Renewable Source of Functional β Cells for Blood Glucose Regulation” appears in Cell Stem Cell. In this study, the Zhou lab demonstrate that antral stomach cells can…
Shefali Verma in our lab (co-advised with Marylyn Ritchie) has had a manuscript accepted for presentation and publication at the Pacific Symposium on Biocomputing. The manuscript is titled “Phenome-wide interaction study (PheWIS) in AIDS clinical trials group data (ACTG)“. In this article, Shefali proposes a pipeline to identify interactions among genetic variants that are associated…