11/18. Shengbao's paper on prediction of essential regulators of cell identity in the mouse cell atlas has been published in Cell Reports. We thank Guoji Guo's lab for a rewarding collaboration. 10/18. Qian's paper on integrative analysis of seqFISH and scRNAseq data has been published in Nature Biotechnology. We thank Long Cai's lab for a rewarding collaboration. 9/18. We have received a new NIH HubMap grant (in collaboration with Long Cai's group at Caltech) to develop novel in situ transcriptomic profiling strategies in single cells. 8/18. Congratulations to Daphne Tsoucas who will become a data scientist at Foresite Capital, to Jialiang Huang who will become a Professor at Xiamen Univeristy, and to Assieh Saadatpour who will become an Associate Principal Scientist at Merck. 8/18. Welcome our new members Yan Kai, Yuheng Lu, and Rui Dong. 6/18. Daphne has successfully passed her dissertation defense. Congratulations, Dr. Tsoucas! 5/18. Congratulations to Yuxi Liu for successful Master thesis defense. Yuxi will enter the PhD program in Genetic Epidemiology at Harvard this Fall. 4/18. Our group has received a pilot award from Chan-Zuckerberg Initiative for developing collaborative computational tools for the Human Cell Atlas. Our project will focus on developing new tools for integration of sequencing- and imaging-based single-cell gene expression data. The full annoucement can be found here. 4/18. Daphne's paper on GiniClust 2 has been accepted for publication in Genome Biology. The software can be found at Github. 3/18. Our collaborative work on the impact of inhibition of MICA/MICB shedding on promoting tumor immunity has been published in Science. We thank the Kai Wucherfennig lab for a rewarding collaboration. 3/18. Our collaborative work on Cut&Run analysis of BCL11A has been accepted for publication in Cell. We thank the Stuart Orkin lab for a rewarding collaboration. 2/18. Our collaborative work on the mouse cell atlas has been published in Cell. We thank the Guoji Guo lab for a rewarding collaboration. 2/18. Jialiang's paper on super-enhancer hierarchy has been accepted for publication in Nature Communications. 1/18. Luca's paper on the updated Haystack software has been accepted for publication in Bioinformatics. 1/18. Our collaborative work on cancer immunotherapy resistance has been published in Science. We thank the Kai Wucherpfennig and Shirley Liu labs for a rewarding collaboration. 8/17. We have received a new NIH R01 grant to study organizational structure of enhancers. 7/17. Congratulations to Sara Garcia who will become a research staff scientist at Mass General Hospital and Harvard Medical School. 7/17. Welcome our MIT RSI summer intern Zoe Weiss and new postdoc fellow Shengbao Suo. 4/17. Our opinion paper on challenges and emerging directions in single-cell analysis has been accepted for publication in Genome Biology. We thank Radcliffe Institute for Advanced Study for their generous support and all the collaborators for their contributions. A preprint can be found here . 3/17. Our collaborative work on Bmi1/crypt stem cell has been accepted for publication in Cell Stem Cell. We thank the Ramesh Shivdasani lab for a rewarding collaboration. 3/17. Welcome our new group member Kamrine Poels. 3/17. Our collaborative work on variant-aware mutagenesis has been accepted for publication in Nature Genetics. We thank the Stuart Orkin and Dan Bauer labs for a rewarding collaboration. 2/17. Our paper on multi-level chromatin state annotation has been accepted for publication in Nature Communications. We thank Manolis Kellis' Lab for a rewarding collaboration. 1/17. Daphne's review paper on single-cell cancer genomics has been published in Current Opinion in Genetics and Development. 1/17. Sam has passed the qualifying exam. Congratulations! 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!