Cahan Lab 
Johns Hopkins University
Lab Timeline
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June 4th, 2026Pub
JiHye Yea's paper, Signaling and transcriptional networks governing late synovial joint development, has been published in Developmental Biology.
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Feb 28th, 2026Pub
JiHye Yea's paper, Protocol to investigate the effects of localized gene expression disruption on mouse limb development via direct siRNA injection and explant culture, is available at STAR Protocols.
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Nov 17th, 2025Pub
Eric Kernfeld's paper, A comparison of computational methods for expression forecasting, in collaboration with Alexis Battles' lab, has been published.
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March 28th, 2025Pub
Emily Lo's paper, DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation, in collaboration with Andy Feinberg's lab, has been published.
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February 28th, 2025Level up
Congratulations to Dr. Eric Kernfeld on the defense of his thesis, Assessing reliability of causal models of transcription! We are going to miss you very much! You are going to do great in your next career move! "Eric Kernfeld, yeah remember the name".
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November 21st, 2024Pub
Dan Peng's paper, OneSC: A computational platform for recapitulating cell state transitions, has been published.
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October 24th, 2024Pub
Kathleen Noller's paper, Cell cycle expression heterogeneity predicts degree of differentiation, which describes the stemFinder method, has been published.
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September 27th, 2024Level up
Congratulations to Dr. Dan Peng on the defense of his thesis, Developing Computational Frameworks for Inferring and Modeling Gene Regulatory Networks! We are going to miss you very much! You are going to do great in your next career move!
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August 21st, 2024Pub
Eric Kernfeld's paper, Transcriptome data are insufficient to control false discoveries in regulatory network inference, in collaboration with Alexis Battle's lab here at Hopkins, has been published.
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May 30th, 2024Pub
Emily Su's paper, Direct comparison of mass cytometry and single-cell RNA sequencing of human peripheral blood mononuclear cells, in collaboration with Eli Zunder's lab at University of Virgina, has been published.
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April 1st, 2024Grant
Congratulations to Sharon Onggo on winning her F31 grant "Novel transcriptional regulators of synovial joint and bone development"!!!
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January 4th, 2024Pub
Dan Peng's paper, Organogenetic transcriptomes of the Drosophila embryo at single cell resolution, in collaboration with Debbie Andrew's lab here at Hopkins, has been published.
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November 14th, 2023Level up
Congratulations to Dr. Ray Cheng on the defense of his thesis, Gene regulatory networks governing multipotency of adult murine bone marrow stromal cells! We are going to miss you very much! You are going to do great in your next career move!
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July 31st, 2023Level up
Congratulations to Dr. Emily Lo on the defense of her thesis, The landscape of epigenetic and transcriptional memory in pancreatic cancer initiation and progression! We are going to miss you very much! You are going to do great in your next career move!
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July 20th, 2023Pub
Emily Lo's paper, Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols, in collaboration with Mo Ebrahimkhani's lab at Univ. of Pittsburg, has been published.
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July 17th, 2023+1
Dr. JiHye Yea has joined the lab as a Postdoctoral fellow!
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June 26th, 2023Level up
Kathleen Noller defended her PhD thesis, Computational analysis of single-cell transcriptomic data for the identification and characterization of cell identity and fate potential!
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May 19th, 2023Pub
Kathleen's paper, RANK+TLR2+ myeloid subpopulation converts autoimmune to joint destruction in rheumatoid arthritis, in collaboration with Dr. Xu Cao's lab, has been published.
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February 22nd, 2023Level up
Emily Su defended her PhD thesis, Computational tools to explore cell identity transitions with application to cell fate engineering. We are going to miss you very much! You are going to do great at Harvard!
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January 9th, 2023Level up
Tiffany Chu's last day in the lab! Tiffany wrote a masterful Master's thesis: Detection of non-transcriptionally mediated changes in transcription factor activity using multiomic single-cell data. You are going to do great
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Oct 13th, 2022Level up
Sharon passed her Doctoral Board Oral exam with flying colors!
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Sept 14th, 2022Grant
Our R35 MIRA grant, From intra to intercellular regulatory networks that define cell type identity, has been renewed!
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Sept 12th, 2022Pub
Ray's paper, Single-Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis, in collaboration with Maedeh Zamani in Ngan Huang's lab at Stanford, has been published.
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June 6th, 2022+1
Sharon Onggo, a Pathobiology PhD student, has joined the lab! She will be co-advised by Aaron James.
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May 16th, 2022Grant
The lab has received the Launch Award from the Maryland Stem Cell Research Foundation. The project title is Distilling Predictive Models of Human Stem Cell Fate Control from Single Cell Omics Data.
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May 4th, 2022Grant
The lab has received a Catalyst Award from Johns Hopkins University to explore the moleculary identity and origins of mouse skeletal stem cells using single cell multi-omics and lineage tracing.
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Februrary 22nd, 2022Level up
Qin's last day in the Lab! Qin, you are the Greatest Of All Time! Best of luck in your future endevors.
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Jan 27th, 2022
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July 27th, 2021Level up
Eric dominated his Doctoral Board Oral exam! Now on to modeling the relationships between the transcriptome and other aspects of the cell.
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July 13th, 2021Level up
Kathleen passed her Doctoral Board Oral exam with flying colors! Now on to computational method development for single cell multiomics.
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July 9th, 2021Level up
Dan aced his Doctoral Board Oral exam! Now on to applying network analytics and machine learning to cancer.
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April 29th, 2021
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April 7th, 2021+1
Eric Kernfeld, a BME PhD student, has joined the lab! He will be co-advised by Alexis Battle.
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February 15th, 2021Level up
Congratulations to Yuqi Tan, Ph.D on the defense of her thesis: Engineered cells: where they have been and what they have become. We are going to miss you very much! You are going to do great at Stanford!
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January 13th, 2021Grant
Congratulations to Emily Lo on winning her F31 grant "The transcriptional and epigenetic landscape of cell fate changes in murine pancreatic cancer initiation and metastasis"!!!
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January 7th, 2021Pub
Patrick's Perspective Computational Stem Cell Biology: Open Questions and Guiding Principles has been published. A team effort with Davide Cacchiarelli, Sara-Jane Dunn, Martin Hemberg, Susana de Sousa Lopes, Samantha Morris, Owen Rackham, Antonio del Sol, and Christin Wells.
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Oct 1st, 2020Level up
Congratulations to Patrick for his promotion to Associate Professor!
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June 24, 2020
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May 19th, 2020Level up
Congratulations to Da (Dan) Peng! He has earned his Masters in BME with his thesis titled "CancerCellNet: a computational platform to evaluate the transcriptional fidelity of cancer models"
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January 27th, 2020+1
Kathleen Noller, BME PhD student, has joined the lab! She earned her undergraduate degree in BME from Columbia University.
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January 17th, 2020Level up
Abby's last day in the Lab! Abby, you rock! We already miss you!
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July 31, 2019Pub
Yuqi Tan's paper SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species has been published. See the code and documentation on GitHub to use SingleCellNet to analyze your scRNA-Seq data.
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May 17, 2019Pub
Emily Lo's chapter Cell Fate Engineering Tools for iPSC Disease Modeling has been published.
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May 16, 2019Pub
The book Computational Stem Cell Biology, which Patrick edited, has been published!
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April 2nd, 2019Award
Emily Lo is a recipient of the ARCS/MWC Graduate Scholar Award! See ARCS for more information.
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March 28th, 2019Award
Yuqi Tan was selected for a concurrent talk at ISSCR 2019 in Los Angeles for her SingleCellNet work! Her preprint is on BioRxiv.
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February 11th, 2019Award
Rachel Gleyzer has won the AACR undergraduate scholar award for her Cancer CellNet work!!
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January 28th, 2019Grant
The lab has received a Development Research Program (DRP) Award through the Johns Hopkins Ovarian Cancer SPORE (NCI). The project title is Using gene regulatory networks to map cancer models to human tumors.
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January 2nd, 2019Award
Patrick Cahan has received the BMES CMBE Rising Star award!
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November 30th, 2018Level up
Ray Cheng passed his BCMB qualifying exam! Onward and upwards to bone marrow stem cell heterogeneity.
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July 29th, 2018Pub
Abby Spangler's paper A single cell transcriptional portrait of embryoid body differentiation and comparison to progenitors of the developing embryo has been accepted and is online!
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June 18th, 2018+1
Jordan Wilson from UC Davis program has joined the lab as a post-baccularate PREP scholar
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June 18th, 2018+1
Ray Cheng from the BCMB program has officially joined the lab! He completed his medical degree at the National Yang-Ming University, in Taipei, Taiwan.
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April 3rd, 2018Award
Congratulations to Emily Su for receiving an NSF Graduate Research Fellowship Program award, and to Emily Lo for receiving Honorable Mention!
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February 9th, 2018Level up
Remy's last day at the Cahan Lab! Thanks for all your hard work! We'll miss you!
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January 31st, 2018Level up
Emily Su crushed it on her Doctoral Board Oral exam! Now back to trajectory inference.
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January 22th, 2018Level up
Emily Lo passed her Doctoral Board Oral exam with flying colors! Now it's time to make some organoids.
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December 11th, 2017Pub
Emily Su's review, in collaboration with Jeremy Velazquez from Mo Ebrahimkhani's lab, is online now at Trends in Biotechnology: Programming Morphogenesis through Systems and Synthetic Biology
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September 1st, 2017Grant
Our JHU School of Medicine Innovation grant titled "Characterization of Novel Cell Populations in the Synovial Joint" has been awarded! See here.
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August 1st, 2017Grant
Our ESI R35 grant titled "From intra to intercellular regulatory networks that define cell type identity" has been awarded by NIH/NIGMS! See RFA for more information about R35.
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June 1st, 2017+1
Our rotation student Emily Su has officially joined the lab! She completed her undergrad here at Hopkins in Biomedical Engineering and Applied Math.
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May 22nd, 2017Level up
Congratulations to Pavithra Kumar! She has earned her Masters in BME with her thesis titled "Comprehensive in silico assessment of cancer cell line fidelity."
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May 10th, 2017Award
Congratulations to Qin Bian! She has been awarded a Maryland Stem Cell Foundation post-doctoral fellowship! See here for details.
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April 27th, 2017
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March 24th, 2017Pub
RNA-seq CellNet R-Package available here.
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January 3rd, 2017Pub
Pavithra's and Yuqi's review at Development, Understanding development and stem cells using single cell-based analyses of gene expression, is published!
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December 12th, 2016Level up
Yuqi passes her PhD qualifying exam! Now get back to work.
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September 8th, 2016Pub
Also check out our twitter page for the latest news from our lab.
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August 22nd, 2016+1
Emily Lo joins us from the University of Washington in Seattle with her undergraduate degree in Molecular, Cellular, and Developmental Biology. She is co-advised by the Feinberg Lab.
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July 18th, 2016+1
Remy Schwab joins us from McGill University in Montreal with undergraduate degrees in Chemistry and Economics.
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May 27th, 2016+1
Yuqi Tan joins us from the Chinese University of Hong Kong after completing her undergraduate degree in Cell and Molecular Biology.
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May 5th, 2016Pub
Qin Bian's review, Computational Tools for Stem Cell Biology, is accepted to Trends in Biotechnology.
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February 15th, 2016+1
Fully equipped with a Cell Tissue Culture room, wetlab, and a beautiful office space for our computational biologists.
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February 2nd, 2016+1
Abby Spangler joins us from Florida State University after completing her undergraduate degree in Marine Biology.
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December 2nd, 2015+1
Qin Bian joins us from the Shanghai University of Traditional Chinese Medicine.
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September 9th, 2015+1
Our first member, Pavithra Kumar, joins us from SASTRA University in India with a degree in Bioengineering.
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September 1st, 2015+1
Patrick Cahan's first day at JHMI!