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.
Services
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
Consulting and hands-on help with questions relating to performing bioinformatics tasks
Currently held online. 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
Team
Dr. Doron Betel
Core Director
Dr. Maider Astorkia Amiama
Computational Genomic Scientist
Paul Zumbo
Senior Staff Associate of Computational Genomics
Selected Publications
- 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.
- Notaras M, Lodhi A, Dündar F, Collier P, Sayles NM, Tilgner H, Greening D, Colak D. (2021) Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids. Mol Psychiatry. Nov 17.
- 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]
- Fassel H, Chen H, Ruisi M, Kumar N, DeSancho MT, Hajjar KA. (2021) Reduced Expression of Annexin A2 is Associated with Impaired Cell Surface Fibrinolysis and Venous Thromboembolism. Blood. Apr 22;137(16):2221-2230.
- 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.
- Au CC, Furness JB, Britt K, Oshchepkova S, Ladumor H, Soo KY, Callaghan B, Gerard C, Inghirami G, Mittal V, Wang Y, Huang XY, Spector JA, Andreopoulou E, Zumbo P, Betel D, Dow L, Brown KA. (2020) Three-dimensional growth of breast cancer cells potentiates the anti-tumor effects of unacylated ghrelin and AZP-531. Elife. Jul 15;9:e56913.
- 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.
- Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh CL, Yang D, Crespo M, Shukla A, Xiang Q, Dündar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massagué J, Garippa R, Evans T, Beer MA, Huangfu D. (2019) Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nat Genet. [Epub ahead of print]
- Yamada M, Cai W, Martin LA, N'Tumba-Byn T, Seandel M. (2019) Functional robustness of adult spermatogonial stem cells after induction of hyperactive Hras. PLoS Genet. 3;15(5):e1008139.
- Dupnik KM, Bean JM, Lee MH, Jean Juste MA, Skrabanek L, Rivera V, Vorkas CK, Pape JW, Fitzgerald DW, Glickman M. (2018) Blood transcriptomic markers of Mycobacterium tuberculosis load in sputum. Int J Tuberc Lung Dis. 22(8):950-958.
- Wong KG, Ryan SD, Ramnarine K, Rosen SA, Mann SE, Kulick A, De Stanchina E, Müller FJ, Kacmarczyk TJ, Zhang C, Betel D, Tomishima MJ. (2017) CryoPause: A New Method to Immediately Initiate Experiments after Cryopreservation of Pluripotent Stem Cells. Stem Cell Reports., 9(1):355-365.
- Chaudhary, N, Gonzalez, E, Chang, SH, Geng, F, Rafii, S, Altorki, NK, & McGraw, TE. (2016) Adenovirus Protein E4-ORF1 Activation of PI3 Kinase Reveals Differential Regulation of Downstream Effector Pathways in Adipocytes. Cell Reports, 17(12).
- Oren, DA, Wei, Y, Skrabanek, L, Chow, BKC, Mommsen, T, & Mojsov, S. (2016) Structural mapping and functional characterization of zebrafish class B G-protein coupled receptor (GPCR) with dual ligand selectivity towards GLP-1 and glucagon. PLoS ONE, 11(12):e0167718.
- Bayliss J, Mukherjee P, Lu C, Jain SU, Chung C, Martinez D, Sabari B, Margol AS, Panwalkar P, Parolia A, Pekmezci M, McEachin RC, Cieslik M, Tamrazi B, Garcia BA, La Rocca G, Santi M, Lewis PW, Hawkins C, Melnick A, David Allis C, Thompson CB, Chinnaiyan AM, Judkins AR, Venneti S. (2016) Lowered H3K27me3 and DNA hypomethylation define poorly prognostic pediatric posterior fossa ependymomas. Sci Transl Med., 8(366):366ra161.
- Palermo LM, Uppal M, Skrabanek L, Zumbo P, Germer S, Toussaint NC, Rima BK, Huey D, Niewiesk S, Porotto M, Moscona A. (2016) Features of Circulating ParainfluenzaVirus Required for Growth in Human Airway. MBio. 7(2):e00235.
- Webster AF, Zumbo P, Fostel J, Gandara J, Hester SD, Recio L, Williams A, WoodCE, Yauk CL, Mason CE. (2015) Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in ArchivalFormalin-Fixed Paraffin-Embedded Tissues. Toxicol Sci. 148(2):460-72.
Get in touch
Email
abc@med.cornell.eduAddress
1300 York Avenue
LC-502
New York, NY 10065
USA