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Publications

Disease variants in genomes of 44 centenarians

To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide...

Authors:  Avinash Abhyankar  

Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia

Fanconi anemia (FA) is a rare bone marrow failure and cancer predisposition syndrome resulting from pathogenic mutations in genes encoding proteins participating in the repair of DNA interstrand crosslinks (ICLs). Mutations in 17 genes (FANCA-FANCS) have been identified in FA...

Authors:  Avinash Abhyankar  

A novel mutation in the POLE2 gene causing combined immunodeficiency

Early lymphocyte development requires the orchestrated interplay of pathways to maintain genomic integrity and accurate DNA repair during the proliferative bursts associated with antigen receptor rearrangement (1). Inborn errors in replication control or DNA repair can lead to primary immunodeficiency...

Authors:  Avinash Abhyankar  

Massively Parallel Processing of Whole Genome Sequence Data: An In-Depth Performance Study

This paper presents a joint effort between a group of computer scientists and bioinformaticians to take an important step towards a general big data platform for genome analysis pipelines. The key goals of this study are to develop a thorough...

Authors:  Toby Bloom   Avinash Abhyankar   Uday Evani  

The cellular and molecular origin of tumor-associated macrophages

Long recognized as an evolutionarily ancient cell type involved in tissue homeostasis and immune defense against pathogens, macrophages are being rediscovered as regulators of several diseases, including cancer. Here we show that in mice, mammary tumor growth induces the accumulation...

Authors:  Will Liao  

Genome wide mapping of Foxo1 binding-sites in murine T lymphocytes

The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized....

Authors:  Will Liao  

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

Both conventional T (Tconv) cells and regulatory T (Treg) cells are activated through ligation of the T cell receptor (TCR) complex, leading to the induction of the transcription factor NF-κB. In Tconv cells, NF-κB regulates expression of genes essential for...

Authors:  Will Liao   Dillon Maloney  

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