bioinformatics_introbl2

Bioinformatics

Bioinformatics @ NYGC

Our team of bioinformaticians aims to develop, maintain and improve our analysis pipelines by leveraging the large amounts of sequencing data we produce. We work on estimating the sources of errors and variability in the data, defining methods to correct them, both computationally and on the lab side. We are also continually evaluating and benchmarking available tools, refining best practices to analyze and combine results, and are developing novel tools and methods.

We are also supporting our CLEP lab by providing the expertise in clinical interpretation of constitutional and cancer genomics.

Expertise

processOur diverse team of bioinformatics scientists has expertise in:

  • Statistical and population genetics
  • Cancer genomics
  • Expression analysis
  • Epigenomics and functional genomics
  • de novo genome assembly
  • Metagenomics
  • Clinical interpretation

Process

A typical project is initiated with one of the sequencing project managers. Our bioinformatics scientists are consulted to further refine the experimental design, analytic plan, and project deliverables.

The bioinformatics team performs standard and project-specific quality control, and analysis of sequencing data (e.g., differential expression and functional enrichment for RNA-Seq, variant annotation and interpretation for genome and exome sequencing, and somatic variant—both SNV and structural variant—for cancer). Results are delivered via our web interface or APIs and are stored and accessible for a period of time as part of NYGC’s Integrated Genomics.

Clinical Interpretation

As exome and genome sequencing data are processed and genomic variation between the sample and a reference are defined, annotated, and compared to existing databases, our bioinformatics scientists contribute to the last step of the analysis: clinical interpretation.

This usually requires ranking and filtering of putative candidates, manual curation, and functional validation (when possible) of our findings. NYGC’s analysis alleviates the need for the investigator to perform the standard computationally intensive analysis steps, thus freeing up time to focus on the biology.

Toby Bloom

Deputy Scientific Director, Informatics

Michael Zody

Research Director, Computational Biology

Belinda Cornes

Senior Bioinformatics Scientist

David Lin

Bioinformatics analyst

S. Ken Tian

Cancer Biologist & Assistant Lab Director, Molecular Diagnostics

Jimmy Liu

Bioinformatics Scientist, Complex Disease

Caitlin McHugh

Senior Bioinformatics Analyst, Statistical Genetics

Dayna Oschwald

Senior Director, Informatics Program Management

Sadia Rahman

Biocurator, Molecular Diagnostics

Rajeeva Musunuri

Bioinformatics Programmer

Alice Fang

Biocurator

Wayne Clarke

Senior Bioinformatics Analyst

Jennifer Shelton

Bioinformatics programmer

Kazimierz Wrzeszczynski

Bioinformatics Scientist

Bo-Juen Chen

Senior Bioinformatics Scientist

Will Liao

Senior Bioinformatics Scientist

Giuseppe Narzisi

Senior Bioinformatics Scientist

Andre Corvelo

Senior Bioinformatics Scientist

Heather Geiger

Bioinformatics Analyst

Kanika Arora

Senior Bioinformatics Analyst

Minita Shah

Senior Bioinformatics Analyst

Anne-Katrin Emde

Senior Bioinformatics Scientist

Phaedra Agius

Senior Bioinformatics Scientist

Nicolas Robine

Assistant Director, Computational Biology

Avinash Abhyankar

Manager, Clinical Informatics

Immunohistochemical analysis of T-type calcium channels in acquired melanocytic nevi and melanoma.

BACKGROUND AND OBJECTIVES: Cutaneous malignant melanoma arises from transformed melanocytes de novo or from congenital or acquired melanocytic nevi. We have recently reported that T-type Ca2+ channels (TTCs) are upregulated in human melanoma and play an important role on cell proliferation....

Authors:  Bo-Juen Chen  

Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors

Owing to its exquisite chemotherapy sensitivity, most patients with metastatic germ cell tumors (GCTs) are cured with cisplatin-based chemotherapy. However, up to 30% of patients with advanced GCT exhibit cisplatin resistance,...

Authors:  Dayna Oschwald   Kanika Arora  

Targeting renal cell carcinoma with a HIF-2 antagonist

Clear cell renal cell carcinoma (ccRCC) is characterized by inactivation of the von Hippel-Lindau tumour suppressor gene (VHL). Because no other gene is mutated as frequently in ccRCC and VHL mutations are truncal, VHL inactivation is regarded as the governing...

Authors:  Heather Geiger  

Structural insights into mis-regulation of protein kinase A in human tumors

The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of PKA signaling is implicated in tumorigenesis. Recent genomic studies have identified recurrent mutations...

Authors:  Nicolas Robine  

Prognostic value of miR-375 and miR-214-3p in early stage oral squamous cell carcinoma

MicroRNAs (miRs) control cell growth, apoptosis and differentiation, and thus play a key role in carcinogenesis. Identification of a set of miRs that demonstrate differential expression in oral squamous cell carcinoma (OSCC) patients with poor prognosis has potential for utility...

Authors:  Nicolas Robine  

Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.

Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops from a succession of key organisms. Disruption of the microbiota during maturation by low-dose antibiotic exposure can alter host metabolism and adiposity. We now show that...

Authors:  Nicolas Robine  

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