a member of the Institute for Cell Engineering and
the department of Biomedical Engineering

The Cahan Lab is an interdisciplinary group that devises and tests computational tools to address fundamental questions in the fields of stem cell engineering, developmental biology, and cancer biology. We are a new lab and are always looking for new members. Graduate students in the JHU Biomedical Engineering or Biochemistry, Cellular, and Molecular Biology PhD programs who are interested in joining are encouraged to to discuss rotations.

We have opportunities for computationally-oriented postdoctoral fellows to work on problems in gene regulatory network reconstruction and single cell RNA-Seq in the contexts of cell fate engineering, development, and cancer. Candidates must have a PhD in Computational Biology, Computer Science, or a related field, proficiency in R, Python, or Julia, and excellent communication skills as demonstrated by first author publications. If you are interested, and include your CV.

Gene Regulatory Networks

Gene regulatory networks (GRNs), encoded in the genome of an organism, define the complete set of regulatory relationships among genes and gene products. GRNs govern the cell’s transcriptional output both at steady state and in response to perturbations, and thus act as major molecular determinants of cell-type identity. The study of GRNs is a central and unifying component of our research program. We are actively developing new algorithms to reconstruct GRNs, to measure their establishment, to infer their dynamics, and to model intercellular regulatory networks. We are especially interested in understanding how cell type specific GRNs are established during development and we use the articular chondrocyte and hematopoietic stem cell to explore this topic.

The assessment question

To what extent is a cell population, derived via directed differentiation of pluripotent stem cells or via direct conversion between somatic cells, equivalent to the desired cell type? We have developed a computational platform, CellNet, that uses transcriptional profiles and GRNs to address this question. The lab is now extending this platform to different data types (e.g. single cell RNA-Seq) and sources and enhancing it so that it can be applied to assess models of human cancers.

The improvement problem

Several lessons emerged from our application of CellNet to gene expression data of all compatible cell-engineering experiments in the public domain. First, we found that cells derived by directed differentiation approached their in vivo target cell types more closely than those derived through direct conversion. Second, GRNs of the starting cell type frequently were maintained in engineered cells. Third, there was substantial improvement of target cell type GRN status when cell fate engineering was practiced in situ, or after engineered cells were transplanted into their native niche. Finally, we documented the aberrant establishment of GRNs of other cell types (neither the starting or the target) in engineered cells. These insights are guiding our lab's efforts to develop generic systems to improve cell fate engineering protocols. Most of these efforts are based on GRNs and involve devising algorithms that predict the identity and timing of transcriptional regulator, microRNA, and signaling pathway modulations.

  • Dan's and Rachel's paper published!

    April 29th, 2021

    Dan's and Rachel's paper Evaluating the transcriptional fidelity of cancer models has been published. Use the web app to explore cancer models and analyze your own data, or go straight to the code.

  • New Member!

    April 7th, 2021

    Eric Kernfeld, a BME PhD student, has joined the lab! He will be co-advised by Alexis Battle.

  • Thesis defense

    February 15th, 2021

    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!

  • Grant

    January 13th, 2021

    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"!!!

  • Patrick's paper published!

    January 7th, 2021

    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.

  • Promotion

    Oct 1st, 2021

    Congratulations to Patrick for his promotion to Associate Professor!"

  • Qin Bian's paper published!

    June 24, 2020

    Qin Bian's paper A single cell transcriptional atlas of early synovial joint development has been published. See the web app to explore the data.

  • Graduation

    May 19th, 2020

    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"

  • New Member!

    January 27th, 2020

    Kathleen Noller, BME PhD student, has joined the lab! She earned her undergraduate degree in BME from Columbia University.

  • Bye Abby!

    January 17th, 2020

    Abby's last day in the Lab! Abby, you rock! We already miss you!

  • Yuqi Tan's paper published!

    July 31, 2019

    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.

  • Emily Lo's chapter published!

    May 17, 2019

    Emily Lo's chapter Cell Fate Engineering Tools for iPSC Disease Modeling has been published.

  • New Methods in Molecular Biology book

    May 16, 2019

    The book Computational Stem Cell Biology, which Patrick edited, has been published!

  • Emily Lo wins the ARCS/MWC Graduate Scholar award!

    April 2nd, 2019

    Emily Lo is a recipient of the ARCS/MWC Graduate Scholar Award! See ARCS for more information.

  • Yuqi is selected for an ISSCR talk!

    March 28th, 2019

    Yuqi Tan was selected for a concurrent talk at ISSCR 2019 in Los Angeles for her SingleCellNet work! Her preprint is on BioRxiv.

  • Rachel wins AACR undergraduate award!

    February 11th, 2019

    Rachel Gleyzer has won the AACR undergraduate scholar award for her Cancer CellNet work!!

  • New grant!

    January 28th, 2019

    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.

  • Rising star

    January 2nd, 2019

    Patrick Cahan has received the BMES CMBE Rising Star award!

  • Congratulations to Ray Cheng!

    November 30th, 2018

    Ray Cheng passed his BCMB qualifying exam! Onward and upwards to bone marrow stem cell heterogeneity.

  • Publication!

    July 29th, 2018

  • New Member!

    June 18th, 2018

    Jordan Wilson from UC Davis program has joined the lab as a post-baccularate PREP scholar

  • New Member!

    June 18th, 2018

    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.

  • NSF GRFP

    April 3rd, 2018

    Congratulations to Emily Su for receiving an NSF Graduate Research Fellowship Program award, and to Emily Lo for receiving Honorable Mention!

  • Bye Remy!

    February 9th, 2018

    Remy's last day at the Cahan Lab! Thanks for all your hard work! We'll miss you!

  • Congratulations, Emily Su!

    January 31st, 2018

    Emily Su crushed it on her Doctoral Board Oral exam! Now back to trajectory inference.

  • Congratulations to Emily Lo!

    January 22th, 2018

    Emily Lo passed her Doctoral Board Oral exam with flying colors! Now it's time to make some organoids.

  • Publication!

    December 11th, 2017

    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

  • Grant

    September 1st, 2017

    Our JHU School of Medicine Innovation grant titled "Characterization of Novel Cell Populations in the Synovial Joint" has been awarded! See here.

  • Grant

    August 1st, 2017

    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.

  • New Member!

    June 1st, 2017

    Our rotation student Emily Su has officially joined the lab! She completed her undergrad here at Hopkins in Biomedical Engineering and Applied Math.

  • Graduation

    May 22nd, 2017

    Congratulations to Pavithra Kumar! She has earned her Masters in BME with her thesis titled "Comprehensive in silico assessment of cancer cell line fidelity."

  • Award!

    May 10th, 2017

    Congratulations to Qin Bian! She has been awarded a Maryland Stem Cell Foundation post-doctoral fellowship! See here for details.

  • Publication!

    April 27th, 2017

    RNA-seq CellNet paper officially published in Nature Protocols! Read it here or here.

  • Software

    March 24th, 2017

    RNA-seq CellNet R-Package available here.

  • Publication!

    January 3rd, 2017

    Pavithra's and Yuqi's review at Development, Understanding development and stem cells using single cell-based analyses of gene expression, is published!

  • Congrats Yuqi!

    December 12th, 2016

    Yuqi passes her PhD qualifying exam! Now get back to work.

  • New Website is live!

    September 8th, 2016

    Also check out our twitter page for the latest news from our lab.

  • New Member: Emily Lo

    August 22nd, 2016

    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.

  • New Member: Remy Schwab

    July 18th, 2016

    Remy Schwab joins us from McGill University in Montreal with undergraduate degrees in Chemistry and Economics.

  • New Member: Yuqi Tan

    May 27th, 2016

    Yuqi Tan joins us from the Chinese University of Hong Kong after completing her undergraduate degree in Cell and Molecular Biology.

  • Publication!

    May 5th, 2016

    Qin Bian's review, Computational Tools for Stem Cell Biology, is accepted to Trends in Biotechnology.

  • Laboratory Renovations Complete

    February 15th, 2016

    Fully equipped with a Cell Tissue Culture room, wetlab, and a beautiful office space for our computational biologists.

  • New Member: Abby Spangler

    February 2nd, 2016

    Abby Spangler joins us from Florida State University after completing her undergraduate degree in Marine Biology.

  • New Member: Qin Bian

    December 2nd, 2015

    Qin Bian joins us from the Shanghai University of Traditional Chinese Medicine.

  • New Member: Pavithra Kumar

    September 9th, 2015

    Our first member, Pavithra Kumar, joins us from SASTRA University in India with a degree in Bioengineering.

  • A Lab is Born

    September 1st, 2015

    Patrick Cahan's first day at JHMI!

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