Weill Cornell Medical College

Applied Bioinformatics Core

Next generation sequencing resources

This page contains pointers to local sequencing facilities and educational resources that may be helpful to WCMC researchers looking to use high-throughput sequencing methods.

Inclusion on this page does not constitute an endorsement by the ABC, and is purely for convenience.

Sequencing Facilities

  • WCMC Genomics Resources Core Facility
    The core services for the Genomics Resources Core Facility (GRCF) include experimental design, sample manipulation, instrumentation, data analysis, interpretation, and validation. Supported next gen sequence applications include: Whole genome sequencing, all exome sequencing, protein-DNA/RNA interactions (ChIP-Seq, CLIP, etc.), RNA sequencing for SNP detection, expression analysis, splice variant detection and targeted resequencing
    For more information, contact Jenny Xiang at
  • WCMC Epigenomics Core Facility
    The Epigenomics Core Facility of Weill Cornell Medical College provides an array of epigenomics and bioinformatics research resources and services that include: DNA methylation profiling, protein-nucleic acid association (ChIP-Seq), genome sequencing, exome capture, RNA-seq and bioinformatics analysis.
    For more information, contact Alicia Alonso at
  • WCMC SMRT Sequencing Service
    The SMRT Sequencing Lab offers sequencing services using the Pacific Biosciences RSII sequencer. The Single Molecule Real-Time (SMRT) sequencing platform is useful for population analysis, full-length cDNA sequencing and a host of other niche utilities. Applications of the PacBio RS include: hard-to-sequence PCR amplicon sequencing, heterogeneous amplicon sequencing, long-read sequencing used to bridge scaffolds and compensate for Illumina biases
    For more information, contact Noah Alexander at
  • RU Genomics Resource Center
    Services offered by the Genomics Resource Center at Rockefeller University include: whole genome sequencing, exome sequencing, targeted sequencing, transcriptome sequencing, small RNA sequencing and ChIP-sequencing.
    For more information, contact Connie Zhao at
  • MSKCC Integrated Genomics Operation
    The Integrated Genomics Operation (IGO) at Memorial Sloan Kettering is a collaborative core facility whose services range from pathological review of tissue samples to data generation. The IGO can help with the extraction of RNA and DNA from both standard and challenging sources and perform sample quality control assessment as well as performing a range of functional genomics applications including: gene expression analysis, array comparative genomic hybridization, microRNA, single-nucleotide polymorphism (SNP), and chromatin immunoprecipitation, and methylation analysis.
    For more information, contact Agnes Viale at
  • New York Genome Center
    Services offered by the New York Genome Center include experimental design assistance, sample quality control processes, library preparation, sequencing, extensive data quality control, bioinformatics, and data storage. Sequencing capabilities include: human whole genome sequencing, exome sequencing, RNA sequencing, ChIP-seq and small RNA-seq.
    For more information, contact the New York Genome Center at

Educational Resources

  • Tri-I Biomedical Workshops
    This is a series of hands-on workshops on bioinformatics-related topics, open to faculty, students and staff at Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering. Workshop topics include: sequence analysis, UNIX, python, and R.
    For more information, email
  • ABC Computational Workshops
    The Applied Bioinformatics Core hosts a series of workshops that promote the effective use of bioinformatics and computational methods in scientific research. These hands-on workshops focus on the practical application of contemporary bioinformatics and data analysis tools, demonstrating best practices for managing and analyzing scientific data, with a particular emphasis on the scalability needed to effectively deal with today’s large-scale datasets. Workshop topics include: Unix and R.
    For more information, contact the ABC
  • Quantitative Understanding in Biology (condensed)
    A condensed version of the qBio course described below is planned for September 2015. This semester-long course will focus on the statistical topics, and will include hands-on R training.
    For more information, contact Jason Banfelder
  • Quantitative Understanding in Biology
    The Quantitative Understanding in Biology course is a two-semester course that teaches students to apply quantitative techniques to the analysis of experimental data and the modeling of biological systems. Topics include: practical aspects of data formatting and management; graphical, mathematical and verbal communication of quantitative concepts (including videotaping of students’ lectures); a review of statistics, with emphasis on the selection of appropriate statistical tests, the use of modern software packages, the interpretation of results, and the design of experiments; the formulation, evaluation, and analysis of mathematical models of biological function, with an emphasis on linear and non-linear regression, determination of model parameters, and the critical comparison of alternative models with regard to over-parameterization.
    For more information, contact Jason Banfelder
  • Quantitative Genomics and Genetics
    A semester-long course which examines the analysis techniques used to understand the genetics of complex phenotypes when using genomic data. This course covers the fundamentals of statistical methodology with applications to the identification of genetic loci responsible for disease, agriculturally relevant, and evolutionarily important phenotypes. Analysis techniques will focus on the central importance of generalized linear models in quantitative genomics with an emphasis on both frequentist and Bayesian computational approaches to inference.
    For more information, contact Jason Mezey at
  • Clinical and Research Genomics
    In this 10-week course, students will be given a strong foundation of knowledge of NGS technologies (both existing and emerging), learn the applications of these technologies for basic and clinical research, and learn the essential tools for the analysis, integration, and application of these data relative to other public databases and phenotype repositories.
    For more information, contact Christopher Mason at
  • GobyWeb Training
    GobyWeb is a web application to aid with the analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses.
    For more information, contact Fabien Campagne at

Applied Bioinformatics Core