Johns Hopkins University
Johns Hopkins University
JiHye Yea's paper, Signaling and transcriptional networks governing late synovial joint development, has been published in Developmental Biology.
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 Protocols00055-9).
Eric Kernfeld's paper, A comparison of computational methods for expression forecasting, in collaboration with Alexis Battles' lab, has been published.
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.
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".
Dan Peng's paper, OneSC: A computational platform for recapitulating cell state transitions, has been published.
Kathleen Noller's paper, Cell cycle expression heterogeneity predicts degree of differentiation, which describes the stemFinder method, has been published.
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!
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.
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.
Congratulations to Sharon Onggo on winning her F31 grant "Novel transcriptional regulators of synovial joint and bone development"!!!
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.
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!
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!
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 published00237-0).
Dr. JiHye Yea has joined the lab as a Postdoctoral fellow!
Kathleen Noller defended her PhD thesis, Computational analysis of single-cell transcriptomic data for the identification and characterization of cell identity and fate potential!
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.
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!
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
Sharon passed her Doctoral Board Oral exam with flying colors!
Our R35 MIRA grant, From intra to intercellular regulatory networks that define cell type identity, has been renewed!
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.
Sharon Onggo, a Pathobiology PhD student, has joined the lab! She will be co-advised by Aaron James.
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.
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.
Qin's last day in the Lab! Qin, you are the Greatest Of All Time! Best of luck in your future endevors.
Eric dominated his Doctoral Board Oral exam! Now on to modeling the relationships between the transcriptome and other aspects of the cell.
Kathleen passed her Doctoral Board Oral exam with flying colors! Now on to computational method development for single cell multiomics.
Dan aced his Doctoral Board Oral exam! Now on to applying network analytics and machine learning to cancer.
Eric Kernfeld, a BME PhD student, has joined the lab! He will be co-advised by Alexis Battle.
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!
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 Perspective Computational Stem Cell Biology: Open Questions and Guiding Principles has been published30596-8). 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.
Congratulations to Patrick for his promotion to Associate Professor!
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"
Kathleen Noller, BME PhD student, has joined the lab! She earned her undergraduate degree in BME from Columbia University.
Abby's last day in the Lab! Abby, you rock! We already miss you!
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 Cell Fate Engineering Tools for iPSC Disease Modeling has been published.
The book Computational Stem Cell Biology, which Patrick edited, has been published!
Emily Lo is a recipient of the ARCS/MWC Graduate Scholar Award! See ARCS for more information.
Yuqi Tan was selected for a concurrent talk at ISSCR 2019 in Los Angeles for her SingleCellNet work! Her preprint is on BioRxiv.
Rachel Gleyzer has won the AACR undergraduate scholar award for her Cancer CellNet work!!
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.
Patrick Cahan has received the BMES CMBE Rising Star award!
Ray Cheng passed his BCMB qualifying exam! Onward and upwards to bone marrow stem cell heterogeneity.
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!
Jordan Wilson from UC Davis program has joined the lab as a post-baccularate PREP scholar
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.
Congratulations to Emily Su for receiving an NSF Graduate Research Fellowship Program award, and to Emily Lo for receiving Honorable Mention!
Remy's last day at the Cahan Lab! Thanks for all your hard work! We'll miss you!
Emily Su crushed it on her Doctoral Board Oral exam! Now back to trajectory inference.
Emily Lo passed her Doctoral Board Oral exam with flying colors! Now it's time to make some organoids.
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 Biology30301-3)
Our JHU School of Medicine Innovation grant titled "Characterization of Novel Cell Populations in the Synovial Joint" has been awarded! See here.
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.
Our rotation student Emily Su has officially joined the lab! She completed her undergrad here at Hopkins in Biomedical Engineering and Applied Math.
Congratulations to Pavithra Kumar! She has earned her Masters in BME with her thesis titled "Comprehensive in silico assessment of cancer cell line fidelity."
Congratulations to Qin Bian! She has been awarded a Maryland Stem Cell Foundation post-doctoral fellowship! See here for details.
RNA-seq CellNet R-Package available here.
Pavithra's and Yuqi's review at Development, Understanding development and stem cells using single cell-based analyses of gene expression, is published!
Yuqi passes her PhD qualifying exam! Now get back to work.
Also check out our twitter page for the latest news from our lab.
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.
Remy Schwab joins us from McGill University in Montreal with undergraduate degrees in Chemistry and Economics.
Yuqi Tan joins us from the Chinese University of Hong Kong after completing her undergraduate degree in Cell and Molecular Biology.
Qin Bian's review, Computational Tools for Stem Cell Biology, is accepted to Trends in Biotechnology.
Fully equipped with a Cell Tissue Culture room, wetlab, and a beautiful office space for our computational biologists.
Abby Spangler joins us from Florida State University after completing her undergraduate degree in Marine Biology.
Qin Bian joins us from the Shanghai University of Traditional Chinese Medicine.