Welcome to the Gordan Lab
We develop quantitative computational and experimental approaches to identify and characterize transcriptional regulatory regions in the human genome. We combine machine learning techniques and high-throughput assays. Focusing on transcription factors (TFs) that control cell proliferation and differentiation, our goals are to understand: (1) how these regulatory proteins interact with each other to select their unique targets across the genome, and (2) how this regulation is disrupted in diseased cells due to non-coding mutations and TF overexpression.
We are excited to share our paper on TF binding to DNA mismatches, now online at Nature. Awesome collaboration with the Al-Hashimi, Schumacher, Haran, Poon and Pufall labs. Many thanks to all the authors, and to our reviewers! Special thanks to James Fraser and Kale Kundert for the News and Views on our paper. Congratulations to all authors, and especially to Ariel for designing and leading this study!
Check out our new QBiC-Pred web server for quantitative predictions of the effect of variants on TF binding. Feedback is always welcome: email@example.com. Enjoy!
Check out our new iMADS web server. It includes quantitative models of specificity and differential specificity for human TFs, easy-to-access genome-wide predictions, and an online tool to make predictions for custom sequences. Feedback is always welcome: firstname.lastname@example.org. Enjoy!
- Sep 2021: Ariel will start his laboratory at the Weizmann Institute of Science! Congratulations and best of luck to Dr. Afek!
- Sep 2021: Zack will give a talk at the annual Environmental Mutagenesis and Genomics Society (EMGS) meeting
- July 2021: Yuning gives fantastic presentation at the 2021 ISMB/ECCB conference, on how “Combining in vitro quantification with in vivo detection of protein-DNA interactions reveals subtle signals in gene regulatory networks”
- July 2021: Zack is awarded the Duke SOM Precision Genomics Collaboratory-OBGE Graduate Student Pilot Research Grant Award to study the competitive binding of TFs and UV-DDB to DNA
- Spring 2021: Olivier Boivin, Shengyu Li, and Kyle Pinheiro de Oliveira join our lab. Welcome!
- May 2020: Yuning’s paper on competitive DNA binding by paralogous TFs was accepted at Genome Research. Congratulations!
- Oct 2020: Ariel’s paper on TF binding to mismatched DNA appeared online at Nature: “DNA mismatches reveal conformational penalties in protein–DNA recognition”. Congratulations to all the authors!
- Oct 2020: Wei successfully defends her preliminary exam. Congratulations!
- July 2020: Jingkang successfully defends his preliminary exam. Congratulations!
- Feb 2020: Harshit was awarded the Paul and Laurel Ghaffari Graduate Fellowship from the Duke University Graduate School
- Feb 2020: Our lab was awarded an NIH R01 grant to study “The role of transcription factor proteins in mutagenesis at regulatory sites”. Looking forward to all the exciting research proposed in the grant!
- Dec 2019: Yuze successfully defends his preliminary exam. Congratulations!
- Nov 2019: Harshit successfully defends his preliminary exam. Congratulations!
- Nov 2019: Our 2018 Cell Systems paper “Divergence in DNA specificity among paralogous transcription factors contributes to their differential in vivo binding” was selected for RSG Recommended Reading List 2018 by the ISCB Regulatory and Systems Genomics community. Congratulations to all authors!
- Nov 2019: Yuning will give an oral presentation at RECOMB Regulatory and Systems Genomics. Vincentius and Farica will give a poster presentation.
- July 2019: Harshit will give an oral presentation at ISMB (Regulatory and Systems Genomics COSI).
- June 2019: Ariel will give an oral presentation at the Albany meeting.
- May 2019: Vincentius and Jingkang’s QBiC paper is accepted at NAR. Congratulations!
- May 2019: This summer our lab will be hosting undergraduate student Ednan Ochieng from North Carolina A&T University, and PhD student Uma Kamaraj from Duke-NUS Medical School. Welcome!
- May 2019: Zack and Vincentius successfully defend their preliminary exams. Congratulations!
- Jan 2019: Wei Zhu joins our lab. Welcome!
- Oct 2018: Yuning successfully defends her preliminary exam. Congratulations!
- June 2018: Harshit Sahay joins our lab. Welcome!
- June 2018: Zack is accepted (with scholarship) to the CSHL course ‘Statistical Methods for Functional Genomics‘. Congratulations!
- May 2018: This summer our lab will be hosting three undergraduate students: Christina Magana-Ramirez (from Cal State Monterey Bay), Anna Darwish (Duke), and Ian Bunner (USC). Welcome!
- May 2018: Yuze Hou joins our lab. Welcome!
- May 2018: Ariel’s abstract on his latest mismatch results is accepted for oral presentation at Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes. Congratulations!
- May 2018: Our lab has 2 abstracts accepted for oral presentation at ISMB 2018! Congratulation to Ariel, Ning, Jingkang, and Yuning!
- May 2018: Yuning is accepted (with scholarship) to the CSHL course ‘Chromatin, Epigenetics & Gene Expression‘. Congratulations!
- Mar 2018: Our paper on divergence in specificity among paralogous TFs is official out: http://www.cell.com/cell-systems/fulltext/S2405-4712(18)30062-0 Congratulations!
- Mar 2018: Dinesh successful defends his PhD thesis. Congratulations, Dr. Manandhar!
- Feb 2018: Zack Mielko joins our lab. Welcome!
- Nov 2017: Jingkang and Dora’s paper on “Quantifying the impact of non-coding variants on transcription factor-DNA binding” was selected for the Top 10 Papers reading list at RECOMB Regulatory and Systems Genomics. Congratulations!
- April 2017: Yuning Zhang joins our lab. Welcome!
- Feb 2017: Anne Marie receives Foerster-Bernstein Postdoctoral Fellowship. Congratulations!
- Dec 2016: Jingkang and Dora’s paper on “Quantifying the impact of non-coding variants on transcription factor-DNA binding” was accepted for publication and oral presentation at RECOMB 2017
- Nov 2016: Jingkang gives oral presentation at RECOMB Regulatory and Systems Genomics 2016
- Oct 2016: Raluca receives Holland-Trice award for high risk/high impact discovery research in brain and disease (collaboration with Dr. Ornit Chiba-Falek, Department of Neurology, Duke University School of Medicine)
- Sep 2016: Jingkang gives oral presentation at AISC 2016
- Jul 2016: Ning gives oral and poster presentations, and wins Best Poster award at ISMB SIG Regulatory and Systems Genomics 2016. Congratulations!
- Jul 2016: Dinesh gives poster presentation at ISMB 2016
- Jul 2016: Raluca gives oral presentation at CSHL Banbury meeting “Measuring and modeling quantitative sequence-function relationships”
- Apr 2016: Ning successfully defends her PhD! Congratulations!
- Nov 2015: Ariel receives IDT postdoctoral fellowship! Congratulations!