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What's New

10/17/2024.
Jian has become a member of the RECOMB Steering Committee.
10/09/2024.
We received a gift award from Google Research on genomic language model.
10/02/2024.
We launched the Center for AI-Driven Biomedical Research (AI4BIO) [CMU News].
08/30/2024.
We received an MPI NIH R21 with the labs of Guttman (Caltech) and Lomvardas (Columbia).
08/09/2024.
Interpretable ML Perspective article published in Nature Methods [CMU News].
08/07/2024.
News & Views article in Nature Genetics on our GAGE-seq paper.
06/05/2024.
Tianming defended his PhD dissertation.
06/01/2024.
Junjie Tang and Remy Liu recently joined our lab as postdoc.
05/14/2024.
GAGE-seq published in Nature Genetics.
04/20/2024.
Jian joins the External Advisory Board of the NIA ADSP AI/ML Consortium.
04/08/2024.
scGHOST published in Nature Methods [CMU News].

12/15/2023.
Xinyue, Nick, Xue Er, and Shike join our lab as new PhD students.
10/26/2023.
Shaoheng gave a talk on LLMs for comp bio in a Generative AI Workshop at C3.ai DTI.
09/08/2023.
Shahul selected as CPCB NIH T32 Trainee.
09/06/2023.
Our review on methods for 3D genome analysis published in Nature Reviews Genetics.
09/01/2023.
Tianming received the Outstanding Research Accomplishment Award from the department.
07/20/2023.
Jian gave a talk with the title "LLMs in Computational Biology: A Primer" at CGSI in UCLA.
07/11/2023.
Jian gave a talk at the Human Cell Atlas 2023 meeting.
06/13/2023.
Jian gave a talk at the Genome Architecture Gordon Research Conference.
06/01/2023.
Jian will serve as the Program Chair for RECOMB 2024.
05/15/2023.
Shaoheng Liang joins our lab as a Lane Fellow. He did PhD with Luay Nakhleh (Rice) and Ken Chen (MD Anderson).
04/13/2023.
In collab. w/ Su-In Lee at UW, we received a Single-cell Data Insights grant from CZI.
04/11/2023.
Wendy's UNADON paper accepted by ISMB 2023.
01/31/2023.
Jian is elected 2022 AAAS Fellow [CMU News].
01/19/2023.
Jian represented the 4DN Program and gave a presentation to the NIH Council of Councils.
01/13/2023.
SPICEMIX published in Nature Genetics as a Cover Story [CMU News].
01/01/2023.
New CBD PhD student Akanksha Sachan joins our lab as a PhD student.

12/12/2022.
Kyle defended his PhD dissertation.
12/01/2022.
We received an award from Google Research to work on ML methods for genomics.
11/10/2022.
Yang received a grant from CZI to develop multimodal visualization tools.
10/19/2022.
Fast-Higashi published in Cell Systems and featured on the Cover.
10/05/2022.
New MLD student Ellie Haber joins our lab as a PhD student.
08/29/2022.
CMU School of Computer Science celebrates three chair professorships, including the Ray and Stephanie Lane Professorship that Jian received. [Photo]
08/08/2022.
Ruochi defended his PhD dissertation and will join the Broad Institute as an Eric and Wendy Schmidt Center Fellow.
08/01/2022.
Spencer Krieger joins our lab as a Lane Fellow.
07/21/2022.
Nucleome Browser published in Nature Methods. Also see our Tweetorial.
07/05/2022.
Jian starts his one-month visit to the Simons Institute at UC Berkeley.
02/18/2022.
College of Fellows of the American Institute for Medical and Biological Engineering [CMU News].
02/11/2022.
We received an R01 to develop ML methods for single-cell 3D epigenomics from NHGRI/NIH.

12/21/2021.
Two papers accepted to RECOMB 2022.
11/30/2021.
Yuchuan defended his PhD dissertation and will join the Illumina AI Lab.
11/02/2021.
Yang Yang received CMU SCS Dissertation Award Honorable Mention.
10/20/2021.
We received a Multi-PI grant from the NIH SenNet Program [CMU News].
10/11/2021.
Higashi published in Nature Biotechnology [CMU News].
09/29/2021.
Jian is named the Ray and Stephanie Lane Professor of Computational Biology [CMU News].
09/23/2021.
Tianming received Honorable Mention for the CBD Outstanding Research Accomplishment Award.
09/09/2021.
We are part of a Data and Admin Coordinating Center of the NHGRI IGVF [WashU News].
01/27/2021.
Jian has been promoted to Full Professor, effective on July 1, 2021.
01/14/2021.
Yuchuan's SPIN paper published in Genome Biology.

12/18/2020.
Two papers accepted to RECOMB 2021.
11/19/2020.
Yang Yang defended her PhD dissertation and will join the lab of Dana Pe'er as a postdoc.
10/15/2020.
Our lab will lead a UM1 Center in the next phase of NIH 4D Nucleome [CMU News].
09/18/2020.
Ruochi received the Outstanding Research Accomplishment Award from the department.
06/25/2020.
Try our Nucleome Browser: a multimodal, interactive data visualization platform to integrate genomic, imaging, and 3D structure data to study 4D Nucleome. Watch an earlier talk.
06/25/2020.
Jian joined the Advisory Board of Cell Systems and the Editorial Board of Genome Biology.
05/20/2020.
MATCHA paper published in Cell Systems.
04/13/2020.
Yang Zhang's MutSpace paper accepted to ISMB 2020.
04/09/2020.
Jian Ma received Guggenheim Fellowship (in Computer Science) [CMU News].
02/20/2020.
MOCHI paper published in Genome Research as a Cover Article [CMU News].

12/23/2019.
Ruochi's paper accepted to RECOMB 2020.
12/20/2019.
Jian Ma promoted to Deputy Editor of PLOS Computational Biology.
12/19/2019.
Ruochi's Hyper-SAGNN paper accepted to ICLR 2020.
11/19/2019.
We received an ASPIRE Award from the Mark Foundation.
11/08/2019.
Yang Yang's Phylo-HMGP among the RECOMB/ISCB RSG Reading List 2018.
11/07/2019.
Kyle's SNIPER paper published by Nature Communications [CMU News].
08/15/2019.
Yang Yang will attend Women in Computational Biology conference at Janelia/HHMI.
08/07/2019.
Amazon AWS machine learning research award [News].
08/05/2019.
Jian gave a talk at the 2019 Gordon Conference on Genome Architecture in Cell Fate and Disease.
07/27/2019.
Yang Yang is selected to attend the EECS Rising Stars 2019 workshop.
07/18/2019.
Our lab received a 4DN OPAS grant from the NIH.
06/29/2019.
We will receive a Rhino-Bird Gift Award from Tencent AI Lab.
06/19/2019.
Phylo-HMRF published in Cell Systems.
06/18/2019.
We received renewal of our comparative genomics R01 (for 5 more years) from NHGRI/NIH.
04/09/2019.
Ben's paper accepted to ISMB 2019.
02/07/2019.
Preview article in Cell.
01/15/2019.
Jian is appointed as a Distinguished Speaker of the ACM.

12/19/2018.
Yang Yang's Phylo-HMRF paper accepted to RECOMB 2019.
12/07/2018.
Jian gave an invited talk at the 2018 4DN-ASCB Satellite Meeting.
10/04/2018.
NIH Director's Blog featured TSA-seq.
09/12/2018.
Our group is part of a new NIH Somatic Cell Genome Editing U01 (led by the Tsai lab).
08/28/2018.
TSA-seq (in collaboration with the Belmont lab) published in J Cell Biol.
08/26/2018.
Yang Yang received the Outstanding Research Accomplishment Award from the department.
07/01/2018.
Jian has been appointed as a regular member of the NIH GCAT study section.
06/20/2018.
CMU News Story on Phylo-HMGP.
05/29/2018.
Phylo-HMGP paper accepted by Cell Systems.
04/02/2018.
Ruochi's paper accepted to ISMB 2018.
01/22/2018.
Jian will serve as Associate Editor of PLOS Computational Biology.

12/22/2017.
Yang Yang's paper accepted to RECOMB 2018. Shashank's paper accepted to AISTATS 2018.
11/15/2017.
Jean Yang, Matt Fredrikson, and I received a grant from CMLH.
09/04/2017.
Collaborative paper w/ Quanquan Gu accepted to NIPS 2017.
08/25/2017.
Shashank Received Richard K. Mellon Foundation Presidential Fellowship.
08/25/2017.
We received support from the NIH BD2K Cloud Credits Model.
07/31/2017.
Jian gave a DragonStar course in computational biology sponsored by CCF.
07/22/2017.
We received an NSF grant to develop high-dimensional machine learning methods for genomics.
07/06/2017.
Jian gave a talk in Gordon Conference in Genome Architecture.
06/19/2017.
DESCHRAMBLER published in PNAS.
05/23/2017.
Yang Zhang has successfully defended his PhD dissertation.
04/07/2017.
Yang Yang's paper accepted by ISMB 2017.
03/24/2017.
Together with members from the Mirny lab (MIT) and the Gehlenborg lab (Harvard), we will offer a tutorial on 3D genome analysis at ISMB 2017.
02/28/2017.
Yuchuan gave a talk on nuclear compartmentalization at the CSHL Systems Biology meeting.

12/16/2016.
Ashok's cancer genome graph paper accepted by RECOMB 2017.
10/19/2016.
Jack Hou has successfully defended his PhD dissertation and will continue as an MD student.
08/30/2016.
With Russell Schwartz, we received a grant from the Center for Machine Learning and Health.
08/23/2016.
Lab research featured on Pittsburgh's NPR News Station WESA.
07/21/2016.
CMU News Story on Weaver.
05/19/2016.
Story from EECS at Penn State.
04/01/2016.
Yang Li's Weaver paper accepted by Cell Systems.
01/01/2016.
Our lab has moved from the University of Illinois at Urbana-Champaign to Carnegie Mellon.

12/04/2015.
New York Times featured our collaborative work on DNA storage (led by Olgica).
12/03/2015.
Olgica and Jian contributed a "Voices" piece in Cell.
11/04/2015.
Joint work with the Kemper lab accepted by Genome Biology
09/18/2015.
Together with Belmont (contact PI), van Steensel, Gilbert, and Zhao, we received a U54 center grant from the NIH 4D Nucleome program. Our lab will lead the computational development and modeling in the center. [IGB News]
07/15/2015.
Together with the Schwartz Lab, we received a multi-PI IMAT R33 grant from NIH/NCI.
07/03/2015.
Yang Li has successfully defended his PhD dissertation and is joining Invitae.
05/15/2015.
Jian is promoted to Associate Professor with tenure (effective 08/16/2015).
02/03/2015.
Yang Li received "Chinese Government Award for Outstanding Self-financed Students Abroad".

11/21/2014.
Jian was selected as a CAS Fellow.
08/18/2014.
We received an R01 grant from NIH/NHGRI.
06/27/2014.
Ken and Yang Zhang's TFBS evolution paper accepted by PLOS Computational Biology.
05/08/2014.
Jack has been selected as a CSE Fellow (2014-2015).
03/20/2014.
Yang Zhang received the Yee Memorial Fund Fellowship.
03/13/2014.
Jack was the runner-up in TBS reality show "King of the Nerds" (Season 2).

09/03/2013.
Led by Robinson and Stubbs, IGB GNDP received a $3M grant from the Simons Foundation.
07/30/2013.
Collaboration with Gene Robinson gets published as a cover story in PNAS.
05/24/2013.
We received a 3-year NSF ABI Innovation grant.
05/16/2013.
Collaboration with Olgica Milenkovic and Huimin Zhao received SRI funding.
01/10/2013.
RACA is published in PNAS [news] [software].

05/14/2012.
We received a 2-year grant from the Interdisciplinary Innovation Initiative (In3) program.
05/11/2012.
We received a Junior Cancer Investigator Pilot grant from UI Cancer Center.
02/21/2012.
We received an R21 grant from NIH/NHGRI to study conserved non-coding elements.
02/01/2012.
Jaebum joined Konkuk University (Seoul, Korea) as an Assistant Professor.

12/01/2011.
Jian is named one of "Tomorrow's PIs" by Genome Technology magazine [cover].
11/16/2010.
We received a 5-year NSF CAREER Award.
08/16/2009.
We received a faculty fellowship from NCSA.
08/16/2009.
Our lab started officially at the University of Illinois at Urbana-Champaign.