The Lab

We are part of Weill Cornell’s The Feil Family Brain and Mind Research Institute and are located in the Belfer research building on 413 E 69th St in Manhattan. In very general terms, we are interested in how the same, within an individual mostly invariant genome, can give rise to functionally extremely diverse cell types – such as the ones that are the building blocks of the human brain. Obviously this diversity is represented by very cell type specific proteomes and transcriptomes – and for the latter we have developed an array of methods providing an unprecedented full-length view of RNA molecules. We will leverage and further develop these methods to investigate the brain and its diseases. You can find more a bit more detail here.

Hagen Tilgner

PhD from The Universidad Pompeu Fabra (Barcelona) in Roderic Guigó’s lab
Postdoc with Michael Snyder at Stanford University
Assistant professor at the Brain and Mind Research Institute at Weill Cornell

I spent most of my childhood (with the exception of a year in the US) in Berlin, Germany and went on to study Computer Science about 50-50 in Germany (Karlsruhe Institute of Technology) and France (ENSIMAG and Université Joseph Fourrier).  After 8 months at the Sanger Institute in Cambridge, UK in the Choudhary and Durbin labs working on mapping protein mass spectra to the genome, I went to do my PhD with Roderic Guigó at the CRG in Barcelona. Initially I worked on splicing simulation (which you can read about in this chapter of my thesis). I then turned my attention to the relationship between chromatin on the one hand and splicing and transcription on the other hand (check out for example these papers here, here, here, and here) on splicing dynamics and co-transcriptional splicing (you can read this paper here) and also made contributions to work on RNA and lncRNAs (read here and here among others) within the ENCODE project.
With the state of the art being short-read RNA sequencing, it was impossible to observe entire RNA molecules and thus to get “the entire message”. Thus, in Mike Snyder’s lab at Stanford, I focused my postdoc on long read sequencing for transcriptomics (check out these papers here, here, here and here). 


Paul Collier

I am from New Zealand but worked the last five years in the UK and at the EMBL in Heidelberg, Germany. I have worked in the space of genetics in both the private sector and the academic sector with the motivation of understanding biology and improving human health. I am now applying my knowledge to oversee wet-lab experiments and to push frontiers in neurogenetics through tech development.


Ishaan Gupta

I am eternally motivated to understand molecular nature of biological complexity and how it is re-purposed in the context of Homeostasis and disrupted during Disease. I did my undergrad training as a computer engineer and biologist from BITS Pilani India from 2005-2010 ( Thereafter I did two internships one with Prof. Mark Isalan at the CRG Barcelona to study yeast promoter evolution another with Prof. Peter Stadler’s group at the University of Leipzig ( implementing an affine gap model to to discover ncRNA families based on multiple sequencing alignments of secondary structures. For graduate school I went to EMBL Heidelberg where I worked with Prof. Lars Steinmetz ( developing technologies to precisely measure quantity and boundaries of mRNAs, Antisense transcription and RNA-protein interactions in model organisms such as yeast, Drosophila and Humans. At the Tilgner lab, I hope to further develop RNA quantification technologies that enable single molecular resolution of gene expression in the mammalian brain.


Yen-Chu Lin 

Yen-Chu is a graduate student in Biophysics, Physiology and System Biology program at Weill Cornell Medical College. She was born and raised in Taiwan, where she received her master in Neuroscience studying brain circuits in healthy and disease models by slice recording and imaging. Her research interest is in finding the functional diversity in different cell types of the brain and understanding how they work synchronously at the circuit level.


Ahmed Mahfouz

Ahmed is a visiting member of Tilgner Lab where is working on analyzing single cell RNA-seq data to better understand brain function. Ahmed Mahfouz is a postdoc at the Computational Biology Center of Leiden University Medical Center in The Netherlands, where he focuses on the computational analysis of high dimensional single cell omics. Previously, he studied Systems and Biomedical Engineering (B.Sc.) and Communication and Information Technology (M.Sc.) in Cairo. In 2010, Ahmed moved to The Netherlands to start his PhD at the Technical University of Delft, where he worked on developing computational methods to mine transcriptome atlases of the brain. In 2014, Ahmed spent three months at the Department of Genome Sciences at the University of Washington (Seattle, USA) where he worked on identifying autism risk genes at Evan Eichler’s Lab. This research visit was supported by a fellowship from the European Molecular Biology Organization (EMBO). 

Paul Wolujewicz

APaul is a PhD student at Weill Cornell in the Physiology, Biophysics and Systems Biology program.  He holds an MPH in biostatistics and epidemiology and an MS concentrating in pharmacological sciences.  His research background involves studying RNA trafficking, localization and splicing dynamics to predict stem cell differentiation as well as developing encodable fluorescent probes for live-cell RNA imaging.  He is interested in biology at the single-cell level and unveiling transcriptional programs involved in neural differentiation.  

Chuying "Naomi" Xia

Naomi is a rotating graduate student from the Neuroscience program. She graduated from Brown University in 2013 with an Sc.B. in Neuroscience and worked in research for two years at Harvard Medical School before joining Weill Cornell. In the Tilgner lab, she is interested in understanding how cellular mRNA isoforms contribute to functional diversity and ultimately, partake in aging and neurodegenerative disorders. 

Xi-He Xie

Present: Neuroscience Ph.D student at Weill Cornell Graduate School of Medical Sciences
Undergraduate in Biomedical Engineering at The Honors College at The City College of New York (CCNY).
Undergraduate research assistant in the Neural Engineering Group with Marom Bikson, David Parra, and Jacek Dmochowski

I was raised in Beijing, China and moved to the U.S. to join my family after completing elementary school. The STEM field caught my attention during my secondary education and I chose to pursue biomedical engineering during my undergraduate career. Dr. Marom Bikson at CCNY was kind enough to allow me to work in the neural engineering lab as an undergraduate, where I found my interest in neuroscience and helped produce clinician accessible tools that used computational models to visualize transcranial direct current stimulation (tDCS) (you can read about them HERE). After spending two years in the medical industry, traveling around the world, and coaching volleyball (played competitively during high school and college), I am now a neuroscience Ph.D student at Weill Cornell and rotating with Dr. Tilgner. During my rotation, I Hope to utilize my math-heavy background to dig out fascinating findings on co-regulated exons from a conservation perspective.