Congratulations to Nick Pabon, PhD, for his first author paper in PlosCompBio

Dr. Nick Pabon publishes first author paper in PlosCompBio titled: “Predicting protein targets for drug-like compounds using transcriptomics” with Profs. Carlos J. Camacho and Ziv Bar-Joseph.

The paper describes the first method capable of predicting novel drug-target interactions using gene expression profiles. Nick contribution was specially notable in highlighting correlations between profiles indirectly related to the target as the main determinant of physical interactions in the machine learning model.

Read the full paper here

Pittsburgh Chromatin Club Mini-Symposium: 12/14

Friday December 14, 2018  1:00 – 5:00 PM UPMC Hillman Cancer Center, Cooper Classroom B/C

5115 Centre Avenue, Pittsburgh


1:00   Roni Lahr, Berman Lab, University of Pittsburgh School of Art & Sciences “The mTORC1-LARP1 axis in gene expression: Elucidating the molecular mechanism of La-related protein 1 in TOP translation.”

1:30   Miguel Brieno-Enriquez, University of Pittsburgh School of Medicine

“TERRA transcription and interacting proteins during PGC development”

2:00    Yi Shi, University of Pittsburgh School of Medicine

“Integrative proteomics to producing a large versatile repertoire of therapeutic nanobodies”

2:30    Refreshment Break

3:00    Joel McManus, Carnegie Mellon University “Finding and Testing Hidden uORFs”

3:30    Robin Lee, University of Pittsburgh School of Medicine

“Taking advantage of cell-to-cell variability to learn how cells process information.”

4:00   Jacob Stewart-Ornstein, Department of Computational and Systems Biology Research, Genome Stability Program, UPMC-Hillman Cancer Center

“Transcriptional linearity and dynamic feedback are hallmarks of stress responses from budding yeast to cancer.






Funding generously provided by the University of Pittsburgh, the Genome Stability Program at UPMC-Hillman Cancer Center, and the Microbiology and Molecular Genetics Department, University of Pittsburgh School of Medicine.

Organizers: Karen Arndt, Sanford Leuba, Ben Van Houten, and Andy VanDemark

Dr. Jingyu Zhang from Xing’s lab presented at Multiscale Cell Fate Symposium at UC Irvine

Dr. Jingyu Zhang from Xing’s lab presented at Multiscale Cell Fate Symposium at UC Irvine. The NSF-Simons Center for Mulitscale Cell Fate Research (CMCF) held their 2018 Inaugural Symposium on October 1-2, 2018. The Symposium focused on emergent properties of cell fate, and provided several opportunities for initiating collaborations between young researchers across disciplines, including a competition of Interdisciplinary Opportunity Award for supporting collaborative projects.

Chikina Lab Publish in The Journal of Clinical Investigation

Dr. Maria Chikina and associates contributed to a publication regarding avenues for the treatment of autoimmunity based on selectively exploiting the exhausted phenotype of tissue-infiltrating T cells.


While T cells are important for the pathogenesis of systemic lupus erythematosus (SLE) and lupus nephritis, little is known about how T cells function after infiltrating the kidney. The current paradigm suggests that kidney-infiltrating T cells (KITs) are activated effector cells contributing to tissue damage and ultimately organ failure. Herein, we demonstrate that the majority of CD4+ and CD8+ KITs in 3 murine lupus models are not effector cells, as hypothesized, but rather express multiple inhibitory receptors and are highly dysfunctional, with reduced cytokine production and proliferative capacity. In other systems, this hypofunctional profile is linked directly to metabolic and specifically mitochondrial dysfunction, which we also observed in KITs. The T cell phenotype was driven by the expression of an “exhausted” transcriptional signature. Our data thus reveal that the tissue parenchyma has the capability of suppressing T cell responses and limiting damage to self. These findings suggest avenues for the treatment of autoimmunity based on selectively exploiting the exhausted phenotype of tissue-infiltrating T cells.

Click here to view the full publication

Healthcare Startup SpIntellx Officially Launches

SpIntellx has officially launched as a computational pathology company applying its proprietary AI technologies to analyze whole slide images based on spatial analytics. Their mission is to develop tools that will improve the accuracy and efficiency of pathologists and to generate predictive data to optimize patient outcomes.

D. Lansing Taylor, Ph.D.
Chairman, Co-Founder

Chakra Chennubhotla, Ph.D.
President, Co-Founder

Michael Becich, M.D., Ph.D.

Jeffrey Fine, M.D.

Visit the website for more information:

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