UC Santa Cruz Bioengineering Cluster
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News 571 Publications 15 Members

Comparative assembly hubs: web-accessible browsers for comparative genomics.

N, Nguyen G, Hickey Bj, Raney J, Armstrong H, Clawson A, Zweig D, Karolchik Wj, Kent David Haussler B, Paten ...

Published in Bioinformatics

Motivation: Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful ...

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Hoadley, Katherine A Yau, Christina Wolf, Denise M Cherniack, Andrew D Tamborero, David Ng, Sam Leiserson, Max D M Niu, Beifang McLellan, Michael D Uzunangelov, Vladislav ...

Published in Cell

Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a u...

The mutagenic footprint of low-fidelity Pol I ColE1 plasmid replication in E. coli reveals an extensive interplay betwee...

Troll, Christopher Yoder, Jordan Alexander, David Hernández, Jaime Loh, Yueling Camps, Manel

Published in Current Genetics

ColE1 plasmid replication is unidirectional and requires two DNA polymerases: DNA polymerase I (Pol I) and DNA polymerase III (Pol III). Pol I initiates leading-strand synthesis by extending an RNA primer, allowing the Pol III holoenzyme to assemble and finish replication of both strands. The goal of the present work is to study the interplay betwe...

Comprehensive molecular profiling of lung adenocarcinoma.

Published in Nature

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen gene...

A unifying model of genome evolution under parsimony

Paten, Benedict Zerbino, Daniel R Hickey, Glenn Haussler, David

Published in BMC Bioinformatics

BackgroundParsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation.ResultsWe present a data structure called a history graph that offers a practical basis for the analysis of genome evo...

Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder canc...

Pinto-Leite, Rosário Carreira, Isabel Melo, Joana Ferreira, Susana Isabel Ribeiro, Ilda Ferreira, Jaqueline Filipe, Marco Bernardo, Carina Arantes-Rodrigues, Regina Oliveira, Paula ...

Published in Tumor Biology

Several genomic regions are frequently altered and associated with the type, stage and progression of urinary bladder cancer (UBC). We present the characterization of 5637, T24 and HT1376 UBC cell lines by karyotyping, fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe am...

Deep Brain Stimulation for Tourette Syndrome: Target Selection

Viswanathan, Ashwin Jimenez-Shahed, Joohi Baizabal Carvallo, José Fidel Jankovic, Joseph

Published in Stereotactic and Functional Neurosurgery

Background/Aims: Tourette syndrome (TS) is a complex neurological disorder manifested chiefly by motor and phonic tics and a variety of behavioral comorbidities, including attention disorder, obsessive-compulsive disorder and impulse control problems. Surgical treatment is increasingly considered when tics become troublesome or even disabling or se...

Spatially patterned electrical stimulation to enhance resolution of retinal prostheses.

Jepson, Lauren H Hottowy, Paweł Mathieson, Keith Gunning, Deborah E Dąbrowski, Władysław Litke, Alan M Chichilnisky, E J

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

Retinal prostheses electrically stimulate neurons to produce artificial vision in people blinded by photoreceptor degenerative diseases. The limited spatial resolution of current devices results in indiscriminate stimulation of interleaved cells of different types, precluding veridical reproduction of natural activity patterns in the retinal output...

Compartmental genomics in living cells revealed by single-cell nanobiopsy.

Actis, Paolo Maalouf, Michelle M Kim, Hyunsung John Lohith, Akshar Vilozny, Boaz Seger, R Adam Pourmand, Nader

Published in ACS nano

The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Here, we developed a single-cell nanobiopsy platform based on scanning ion conductance microscopy (SICM) for continuous sampling of intracellular content from individual ce...

The unfolded protein response is activated in disease-affected brain regions in progressive supranuclear palsy and Alzhe...

Stutzbach, Lauren D Xie, Sharon X Naj, Adam C Albin, Roger Gilman, Sid Lee, Virginia M Y Trojanowski, John Q Devlin, Bernie Schellenberg, Gerard D

Published in Acta Neuropathologica Communications

BackgroundProgressive supranuclear palsy (PSP) is a neurodegenerative disorder pathologically characterized by intracellular tangles of hyperphosphorylated tau protein distributed throughout the neocortex, basal ganglia, and brainstem. A genome-wide association study identified EIF2AK3 as a risk factor for PSP. EIF2AK3 encodes PERK, part of the end...

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