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News 571 Publications 15 Members

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

Subramanian, Amarendran R Kaufmann, Michael Morgenstern, Burkhard

Published in Algorithms for Molecular Biology

BackgroundDIALIGN-T is a reimplementation of the multiple-alignment program DIALIGN. Due to several algorithmic improvements, it produces significantly better alignments on locally and globally related sequence sets than previous versions of DIALIGN. However, like the original implementation of the program, DIALIGN-T uses a a straight-forward greed...

Carbohydrate-actuated nanofluidic diode: switchable current rectification in a nanopipette.

Vilozny, Boaz Wollenberg, Alexander L Actis, Paolo Hwang, Daniel Singaram, Bakthan Pourmand, Nader

Published in Nanoscale

Nanofluidic structures share many properties with ligand-gated ion channels. However, actuating ion conductance in artificial systems is a challenge. We have designed a system that uses a carbohydrate-responsive polymer to modulate ion conductance in a quartz nanopipette. The cationic polymer, a poly(vinylpyridine) quaternized with benzylboronic ac...

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana, Ekta Fu, Yao Colonna, Vincenza Mu, Xinmeng Jasmine Kang, Hyun Min Lappalainen, Tuuli Sboner, Andrea Lochovsky, Lucas Chen, Jieming Harmanci, Arif ...

Published in Science (New York, N.Y.)

Interpreting variants, especially noncoding ones, in the increasing number of personal genomes is challenging. We used patterns of polymorphisms in functionally annotated regions in 1092 humans to identify deleterious variants; then we experimentally validated candidates. We analyzed both coding and noncoding regions, with the former corroborating ...

The Cancer Genome Atlas Pan-Cancer analysis project.

Weinstein, John N Collisson, Eric A Mills, Gordon B Shaw, Kenna R Mills Ozenberger, Brad A Ellrott, Kyle Shmulevich, Ilya Sander, Chris Stuart, Joshua M

Published in Nature genetics

The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pa...

Distinctive microRNA expression signatures in proton-irradiated mice

Khan, Shahid Yar Tariq, Muhammad Akram Perrott, James Patrick Brumbaugh, Christopher Drew Kim, Hyunsung John Shabbir, Muhammad Imran Ramesh, Govindarajan T. Pourmand, Nader

Published in Molecular and Cellular Biochemistry

Proton particles comprise the most abundant ionizing radiation (IR) in outer space. These high energy particles are known to cause frequent double- and single-stranded DNA lesions that can lead to cancer and tumor formation. Understanding the mechanism of cellular response to proton-derived IR is vital for determining health risks to astronauts dur...

Crystal structure of the avian astrovirus capsid spike.

DuBois, Rebecca M Freiden, Pamela Marvin, Shauna Reddivari, Muralidhar Heath, Richard J White, Stephen W Schultz-Cherry, Stacey

Published in Journal of virology

Astroviruses are small, nonenveloped, single-stranded RNA viruses that cause diarrhea in a wide variety of mammals and birds. On the surface of the viral capsid are globular spikes that are thought to be involved in attachment to host cells. To understand the basis of species specificity, we investigated the structure of an avian astrovirus capsid ...

Integrated genomic characterization of endometrial carcinoma

Kandoth, Cyriac Schultz, Nikolaus Cherniack, Andrew D. Akbani, Rehan Liu, Yuexin Shen, Hui Gordon Robertson, A. Pashtan, Itai Shen, Ronglai Benz, Christopher C. ...

Published in Nature

This paper from The Cancer Genome Atlas Research Network presents an in-depth genome-wide analysis of endometrial (uterine) carcinomas from more than 350 patients. Based on a series of genomic features including newly identified hotspot mutations in the DNA polymerase gene POLE, and novel mutations in the ARID5B DNA-binding protein, the authors pro...

Restoration of retinal structure and function after selective photocoagulation.

Sher, Alexander Jones, Bryan W Huie, Philip Paulus, Yannis M Lavinsky, Daniel Leung, Loh-Shan S Nomoto, Hiroyuki Beier, Corinne Marc, Robert E Palanker, Daniel ...

Published in The Journal of neuroscience : the official journal of the Society for Neuroscience

CNS neurons change their connectivity to accommodate a changing environment, form memories, or respond to injury. Plasticity in the adult mammalian retina after injury or disease was thought to be limited to restructuring resulting in abnormal retinal anatomy and function. Here we report that neurons in the mammalian retina change their connectivit...

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

Ewing, Adam D Ballinger, Tracy J Earl, Dent Harris, Christopher C Ding, Li Wilson, Richard K Haussler, David

Published in Genome Biology

BackgroundRetroposed processed gene transcripts are an important source of material for new gene formation on evolutionary timescales. Most prior work on gene retrocopy discovery compared copies in reference genome assemblies to their source genes. Here, we explore gene retrocopy insertion polymorphisms (GRIPs) that are present in the germlines of ...

Functional and evolutionary insight from the crystal structure of rubella virus protein E1.

DuBois, Rebecca M Vaney, Marie-Christine Tortorici, M Alejandra Kurdi, Rana Al Barba-Spaeth, Giovanna Krey, Thomas Rey, Félix A

Published in Nature

Little is known about the three-dimensional organization of rubella virus, which causes a relatively mild measles-like disease in children but leads to serious congenital health problems when contracted in utero. Although rubella virus belongs to the same family as the mosquito-borne alphaviruses, in many respects it is more similar to other aeroso...

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