Applied Bioinformatics Core

What We Do

The Applied Bioinformatics Core (ABC) is a central service group that specializes in providing data management and analysis support to large genomic centers and research groups. The objective of the core is to provide analytical capabilities to support and advance biomedical research.
We have ample expertise analyzing biological data from diverse types of experiments including, but not limited to, high-throughput genomic assays.
We have extensive experience in building standardized workflows as well as customized, in-depth analyses with emphasis on thorough quality control and statistical rigor.
We perform detailed computational analyses that are driven by specific biological questions defined by the investigators.
We provide extensive reports with publication-ready images as well as the analysis source code.
The example projects should give you an impression of the most commonly performed analyses - we are by no means limited to them and are happy to tackle new challenges. Please contact us at abc@med.cornell.edu for inquiries.

Transcriptomics

Single-cell RNA-seq | Spatial transcriptomics | CITE-seq | Differential gene expression analysis with bulk RNA-seq | General RNA biology assays such as CLIP-seq or PRO-seq

Example Projects:

Single-cell RNA-seq of in vitro differentiated embryonic stem cells
Transcriptome changes induced by deletion of a GTPase
Combined CITE-seq and TCR-seq for understanding T cell populations driving autoimmunity

Epigenetics

ChIP-seq | ATAC-seq | Reduced representation bisulfite sequencing (RRBS) or targeted methylation | Whole Genome Bisulfite sequencing

Example Projects:

Effects of cancer drugs on chromatin accessibility
Whole-genome bisulfite sequencing of neuronal cells
Identifying key genes of neuronal differentiation using CUT&TAG

Genomics

Variant calling and annotation | Evolution of viral sequences | Classifications of pathogens

Example Projects:

Identification & annotation of genomic variants in different mutants of a rodent parasite
Functional annotation of sequence variants in a gene possibly related to a bleeding phenotype

Functional Analyses

GO term enrichments | Gene set enrichments | Pathway Analyses | DNA motifs | Integration of diverse data sets

Example Projects:

Understanding cancer-induced transcriptome changes in blood cells
Characterizing the effects of inhibitors of chromatin-associated molecules for immune cell functions

Computational Pipelines

Large-scale automation of analysis pipeline | Distribution and management of large datasets | Shiny apps

Example Projects:

HIPAA-certified pipeline for the identification of genomic variants in tumor patient samples (for the Institute for Precision Medicine)
PubShare data portal for downloading and sharing genomic data
Interactive application for storing, visualizing, and analyzing proteomics data

Training and Consulting

Walk-in clinic | Hands-on workshops | Meetings for coding tips exchange

Learn More

Walk-in Bioinformatics Clinics

Consulting and hands-on help with questions relating to performing bioinformatics tasks
Tuesdays, 1-2pm in Room LC504 at 1300 York Avenue, NYC
Currently held in person and online (via Zoom). Please email abc@med.cornell.edu for details.

Hands-on Workshops

Regularly held, intensive 12-hours-long courses open to members of the Tri-Institutional network

Introduction to R
Introduction to UNIX
Differential gene expression analysis using RNA-seq

Please email abc@med.cornell.edu for details

Selected Publications

Nease LA, Church KP, Delclaux I, Murakami S, Astorkia M, Zerhouni M, Cascio G, Hughes RO, Aguirre KN, Zumbo P, Dow LE, Jaffrey S, Betel D, Piskounova E. (2024) Selenocysteine tRNA methylation promotes oxidative stress resistance in melanoma metastasis. Nat Cancer. Oct 22. Epub ahead of print.

Falvo DJ, Grimont A, Zumbo P, Fall WB, Yang JL, Osterhoudt A, Pan G, Rendeiro AF, Meng Y, Wilkinson JE, Dündar F, Elemento O, Yantiss RK, Hissong E, Koche R, Betel D, Chandwani R. (2023) A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas. Dev Cell. Dec 18;58(24):2959-2973.e7.

Copertino DC Jr, Holmberg CS, Weiler J, Ward AR, Howard JN, Levinger C, Pang AP, Corley MJ, Dündar F, Zumbo P, Betel D, Gandhi RT, McMahon DK, Bosch RJ, Linden N, Macatangay BJ, Cyktor JC, Eron JJ, Mellors JW, Kovacs C, Benko E, Bosque A, Jones RB; AIDS Clinical Trials Group (ACTG) A5321 Team. (2023) The latency-reversing agent HODHBt synergizes with IL-15 to enhance cytotoxic function of HIV-specific T cells. JCI Insight. Sep 22;8(18):e169028

Rudloff MW, Zumbo P, Favret NR, Roetman JJ, Detrés Román CR, Erwin MM, Murray KA, Jonnakuti ST, Dündar F, Betel D, Philip M. (2023) Hallmarks of CD8+ T cell dysfunction are established within hours of tumor antigen encounter before cell division. Nat Immunol. Sep;24(9):1527-1539.

Rubio-Navarro A, Gómez-Banoy N, Stoll L, Dündar F, Mawla AM, Ma L, Cortada E, Zumbo P, Li A, Reiterer M, Montoya-Oviedo N, Homan EA, Imai N, Gilani A, Liu C, Naji A, Yang B, Chong ACN, Cohen DE, Chen S, Cao J, Pitt GS, Huising MO, Betel D, Lo JC. (2023) A beta cell subset with enhanced insulin secretion and glucose metabolism is reduced in type 2 diabetes. Nat Cell Biol. Mar 16.:Epub.

Xia Y, Duca S, Perder B, Dündar F, Zumbo P, Qiu M, Yao J, Cao Y, Harrison MRM, Zangi L, Betel D, Cao J. (2022) Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration. Nat Commun. Dec 13;13(1):7704.

Stevenson EM, Terry S, Copertino D, Leyre L, Danesh A, Weiler J, Ward AR, Khadka P, McNeil E, Bernard K, Miller IG, Ellsworth GB, Johnston CD, Finkelsztein EJ, Zumbo P, Betel D, Dündar F, Duncan MC, Lapointe HR, Speckmaier S, Moran-Garcia N, Papa MP, Nicholes S, Stover CJ, Lynch RM, Caskey M, Gaebler C, Chun TW, Bosque A, Wilkin TJ, Lee GQ, Brumme ZL, Jones RB. (2022) SARS CoV-2 mRNA vaccination exposes latent HIV to Nef-specific CD8+ T-cells. Nat Commun. Aug 19;13(1):4888.

Shakiba M, Zumbo P, Espinosa-Carrasco G, Menocal L, Dündar F, Carson SE, Bruno EM, Sanchez-Rivera FJ, Lowe SW, Camara S, Koche RP, Reuter VP, Socci ND, Whitlock B, Tamzalit F, Huse M, Hellmann MD, Wells DK, Defranoux NA, Betel D, Philip M, Schietinger A. (2022) TCR signal strength defines distinct mechanisms of T cell dysfunction and cancer evasion. J Exp Med. Feb 7;219(2):e20201966.

Gearty SV, Dündar F, Zumbo P, Espinosa-Carrasco G, Shakiba M, Sanchez-Rivera FJ, Socci ND, Trivedi P, Lowe SW, Lauer P, Mohibullah N, Viale A, DiLorenzo TP, Betel D, Schietinger A. (2021) An autoimmune stem-like CD8 T cell population drives type 1 diabetes. Nature. Nov 30.

Ren Y, Huang SH, Macedo AB, Ward AR, Conce Alberto WD, Klevorn T, Leyre L, Copertino DC, Mota TM, Chan D, Truong R, Rohwetter T, Zumbo P, Dündar F, Betel D, Kovacs C, Benko E, Bosque A, Jones RB. (2021) Selective BCL-XL Antagonists Eliminate Infected Cells from a Primary Cell Model of HIV Latency but not from Ex Vivo Reservoirs. J Virol. Jul 12;95(15):e0242520.

Guttikonda SR, Sikkema L, Tchieu J, Saurat N, Walsh RM, Harschnitz O, Ciceri G, Sneeboer M, Mazutis L, Setty M, Zumbo P, Betel D, de Witte LD, Pe'er D, Studer L. (2021) Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer's disease. Nat Neurosci. Mar;24(3):343-354. doi: 10.1038/s41593-020-00796-z. [Epub ahead of print]

Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S. (2020) Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Nature. Sep;585(7825):426-432.

Odell SC, Taki F, Klein SL, Chen RJ, Levine OB, Skelly MJ, Nabila A, Brindley E, Gal Toth J, Dündar F, Sheridan CK, Fetcho RN, Alonso A, Liston C, Landau DA, Pleil KE, Toth M. (2020) Epigenomically Bistable Regions across Neuron-Specific Genes Govern Neuron Eligibility to a Coding Ensemble in the Hippocampus. Cell Rep. Jun 23;31(12):107789.

Scott AC, Dündar F, Zumbo P, Chandran SS, Klebanoff CA, Shakiba M, Trivedi P, Menocal L, Appleby H, Camara S, Zamarin D, Walther T, Snyder A, Femia MR, Comen EA, Wen HY, Hellmann MD, Anandasabapathy N, Liu Y, Altorki NK, Lauer P, Levy O, Glickman MS, Kaye J, Betel D, Philip M, Schietinger A. (2019) TOX is a critical regulator of tumour-specific T cell differentiation. Nature. 571, 270–274.

The Team

Doron Betel
Core Director