• 12/16. Our collaborative work on the role of UTX in reglating natural killer T cell epigenetic program has been accepted for publication in Nature Immunology. We thank the Stuart Orkin and Florian Winau labs for a rewarding collaboration.
  • 9/16. We welcome our new group members Qian Zhu and Isha Sethi.
  • 8/16. Our collaborative work on single cell transcript profiling of intestine stem cells has been accepted for publication in Cell Reports. We thank the Ramesh Shivdasani Lab for a rewarding collaboration.
  • 7/16. Our new software PySCUBA, a Python version of SCUBA for single-cell gene expression data analysis, is now available at GitHub.
  • 6/16. Lan Jiang's paper on detecting rare cell types from single-cell gene expression data has been accepted for publication in Genome Biology. The software, called GiniClust, is publicly accessible at here.
  • 6/16. Congratulations to Luca Pinello who will become an Assistant Professor at Mass General Hospital and Harvard Medical School starting in the fall.
  • 5/16. Gregory Giecold's ECLAIR paper has been accepted for publication in Nucleic Acids Reseach. We thank Lorenzo Trippa for a rewarding collaboration.
  • 4/16. We welcome our new group members Daphne Tsoucas, Sam Tracy, and Jiabei Yang.
  • 3/16. Luca Pinello's CRISPResso paper has been accepted for publication in Nature Biotechnology. We thank Dan Bauer's Lab for a rewarding collaboration.
  • 3/16. Our collaborative work on PRC2 function in adult somatic cells has been accepted for publication in Cell. We thank Ramesh Shivdasani's Lab for a rewarding collaboration.
  • 3/16. Our collaborative work on the effect of high-fat diet on enhancing stemness has been published in Nature. We thank the labs of Yilmaz, Sabatini, and Orkin's for a rewarding collaboration.
  • 2/16. We welcome our new group member Ruben Dries.
  • 2/16. Our CRISPResso software is upgraded and more powerful! The new version can support pooled, whole genome,and comparative analyses. The changes are also described in the updated manuscript.
  • 1/16. Our ECLAIR tool is published in bioRxiv.
  • 1/16. Our collaborative work on single cell analysis of mouse ESCs has been accepted for publication in Cell Reports. We thank the labs of Stuart Orkin and Guoji Guo for a rewarding collaboration.
  • 12/15. Jialiang Huang's paper on enhancer dynamics during hematopoiesis has been accepted for publication in Developmental Cell. We thank the labs of Stuart Orkin and Jian Xu for a rewarding collaboration.
  • 12/15. We welcome our new group member Xue (Scarlett) Zou.
  • 11/15. Our CRISPResso tool is published in bioRxiv.
  • 11/15. GC chaired the 2015 PQG conference on single-cell genomics.
  • 10/15. Assieh Saadatpour's review paper on single-cell analysis in cancer genomics has been published in Trends in Genetics. Click here for the link.
  • 09/15. Our collaborative work on usng CRISPR-cas9 saturating mutagenesis analysis of BCL11A enhancer has been published in Nature.
  • 07/15. Jialiang Huang's paper on prediction of chromatin interaction is accepted for publication in Genome Biology. The paper will appear in the special issue of 3D Organization of the Nucleus .
  • 06/15. Congratulations to Luca Pinello who has received an NHGRI K99 Award!
  • 06/15. Congratulations to Eugenio Marco who will leave our lab and become a computational biologist at Editas. Farewell. We will miss you!
  • 05/15. Congratulations to Yihao Li who has been accepted by UCLA as a master student.
  • 04/15. Kimbie Glass's paper on integrated network analysis of ovaraian cancer angiogenesis has been publish in BMC Bioinformatics. Click here for the paper.
  • 02/15. We welcome our new group member Sara Garcia.
  • 01/15. We welcome our new group member Lan Jiang.
  • 01/15. Our collaborative work on the non-canonical PRC2 complex has been published in Molecular Cell.
  • 12/14. Our SCUBA package for single-cell analysis is now publicly available. Click here for the link.
  • 11/15/14. Eugenio Marco's paper on bifurcation analysis of single-cell gene expression data is accepted for publication in PNAS. We sincerely thank the contributions from our collaborators on this project.
  • 11/06/14. our collaborative work on the effect of CDK7 inhibitor on MYC-driven cancer cells is published in today's online issue of Cell. This work was led by Edmond Chipumuro in Dr. Rani George's lab and Eugenio Marco led the bioinformatic analysis.
  • 11/14. We welcome our new group members Gregory Giecold, Yihao Li, and Li Min.
  • 11/14. Assieh Saadatpour's paper on single-cell analysis of leukemia is accepted for publication in Genome Biology. The paper will appear in the special issue of cancer progression and heterogeneity . We sincerely thank our collaborator Guoji Guo in Dr. Stuart Orkin's lab for a wonderful collaboration.
  • 9/14. We have received a new NIH R01 grant to study systems biology in erythpoiesis.
  • 7/14. Kimbie Glass will become an Assistant Professor at the Channing Lab of Harvard Medical School starting in the fall. Congratulations, Kimbie! Great to have you stay around!
  • 4/24/14. our collaborative work on induced hematopoietic stem cells is published in today's issue of Cell. This work was led by Jonah Riddell in Dr. Derrick Rossi's lab.
  • 4/15/14. Applications are invited to fill in one or two postdoc positions. Click here for details.
  • 1/21/14. Luca Pinello's paper on chromatin state plasticity is published in PNAS. Barvo! We thank our collaborator Jian Xu in Dr. Stuart Orkin's lab for a wonderful collaboration!
  • 11/22/13. We welcome our new member Jialiang Huang. Jialiang got his PhD degree in bioinformatics in CAS-MPG Partner Institute, Shanghai, and has become a postdoc fellow in our group.
  • 11/14/13. Eugenio Marco won a Stellar Poster Award at the PQG conference on Emerging Quantitative Issues in Disease Epigenetics.
  • 11/07/13. The Kimbie Glass/John Quackenbush team has been selected as one of the two winners of the Geoffrey Beene Global NeuroDiscovery Challenge and will receive a $50,000 award from Sanofi Pharmaceuticals! See the news release here .
  • 10/24/13. Epigenie publishes a headline article about our Epigenetics paper on eRNA analysis in collaboration with Sid Rao's group. The work was co-led by Kirthi Pulakanti and Luca Pinello.
  • 10/21/13. Welcome to our new member Assieh Saadatpour. Assieh got her PhD degree in mathematics from Penn State Univeristy and has become a postdoc fellow in our group.
  • 10/11/13. In today's issue of Science, the cover story reports our work on genetic variation in mediating BCL11A activity. The work was led by Dan Bauer in Dr. Stuart Orkin's lab.
  • 10/07/13. Kimbie Glass has just received a Geoffrey Beene Global NeuroDiscovery Challenge Award for proposing a novel approach to investigate gender differences of Alzheimer Disease progression. Congratulations, Kimble!
  • 9/12/13. Our work on single-cell analysis of hematopoietic cell lineages appeared online in the journal Cell Stem Cell. We thank our collaborator Guoji Guo and other people in Dr. Stuart Orkin's lab for a wonderful collaboration!
  • 08/29/13. Eugenio Marco's paper on chromosome biorientation is published in today's issue of Cell. Bravo!
  • 06/13. Kimbie Glass' PANDA software package is updated and posted here and at SourceForge.
  • 04/13. Kimbie Glass' paper on regulatory network inference using a message-passing strategy has been accepted by PLoS ONE.
  • 04/13. We have received a new grant from HSCI to work on single-cell gene expression analysis with application to cancer stem cells. One postdoc position is immediately available.
  • 03/13. GC Yuan has been promoted to associate professor.
  • 03/13. We are glad that the final chapter of Jessica Larson's PhD dissertation has just been accepted for publication in Genomics. Jessica graduated from our group last year and is now a computational biologist at Genetech.
  • 02/13. Our collaborative paper with Zhe Li and Stuart Orkin labs on the role of ETV1 in prostate cancer has been accepted by Genes & Development.
  • 10/16/12. Our paper on comparing fetal and adult erythroid transcriptional programs in human has been published in today's issue of Developmental Cell. This is a result of a fantastic collaboration with Dr. Jian Xu at Dr. Stuart Orkin's group.

  • 06/12. Welcome new members in our group! Dr. Eugenio Marco has joined our group as a postdoctoral fellow. Erdem Sanal has joined our group as a visiting undergraduate student.

  • 04/25/12. We have received a new NIH grant to study the chromatin states and long-range interactions. This is part of the ENCODE project. See here for the official announcement.

  • 04/13/12. Our ChIPseq analysis software MAnorm has been posted online.

  • 03/25/12. Our HMM chromatin domain detection software has been posted online.

  • 02/29/12. Jessica Larson successfully passed her Ph.D thesis defense. Her dissertation title is "Hidden Markov Models Predict Epigenetic Chromatin Domains". Part of her dissertation has resulted in two first-author publications. She is also the first student graduated from our group. Congratulations, Dr. Larson!