Publications

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 …

Study characterizing motor neuron programming dynamics published in Cell Stem Cell Read More »

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 …

Collaborative paper on the pioneer transcription factor, Foxa2, published in Molecular Cell Read More »

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 …

Collaborative paper on stomach to beta cell reprogramming published in Cell Stem Cell Read More »

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 …

Group publication accepted to PSB 2016 Read More »

A manuscript on which Shaun collaborated with Garam (Celine) Han and other members of Frank Pugh’s and Ross Hardison’s labs has been published. “Genome-wide organization of Gata1 and Tal1 determined at high resolution” appears in Molecular and Cell Biology. In the paper, Garam has used ChIP-exo to determine the positional organization of Gata1 and Tal1 …

Co-authored paper published in Molecular and Cell Biology Read More »

Our review on high-resolution protein-DNA binding assays and associated computational analyses has been published. The article is entitled “Protein-DNA binding in high-resolution“, and appears in Critical Reviews in Biochemistry and Molecular Biology. 

A paper on which Shaun collaborated with Simona Lodato and colleagues in Paola Arlotta’s lab in Harvard University has been published in Nature Neuroscience. “Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons” finds that Fezf2 is a selector gene that regulates the expression of gene sets that collectively define mouse corticospinal motor …

Collaboration with Arlotta lab published in Nature Neuroscience Read More »

Our group manuscript, entitled “An integrated model of multiple-condition ChIP-seq data reveals predeterminants of Cdx2 binding”, has been accepted for publication. The manuscript will be presented at the RECOMB 2014 conference, which will be held in Pittsburgh this year from April 2nd – 5th. As part of the conference submission, the manuscript was also reviewed …

Group paper accepted for publication in PLoS Computational Biology and for presentation at RECOMB 2014 Read More »

A paper on which we collaborated with Elizabeth Paik and her colleagues in Len Zon’s lab at Harvard University has been published in Stem Cell Reports. The paper, entitled “A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis“, examined the functions of Cdx4 and Sall4 during the initiation of zebrafish hematopoiesis using ChIP-seq, …

Co-authored paper published in Stem Cell Reports Read More »

Two papers which Shaun jointly first-authored with Esteban Mazzoni have been published in the same issue of Nature Neuroscience. In “Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity“, we describe the mechanism behind the combinatorial action of transcription factors in motor neuron programming. Specifically, we found that Isl1 cooperates with Phox2a …

Two papers published in Nature Neuroscience Read More »