UC Santa Cruz Bioengineering Cluster
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News 571 Publications 15 Members

Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing.

Gharizadeh, B Herman, Zs Eason, Rg Jejelowo, O Nader Pourmand

Published in Electrophoresis

Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequen...

Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.

Karchin, R Cline, M Mandel-Gutfreund, Y Kevin Karplus

Published in Proteins Structure Function and Bioinformatics

An important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may hav...

Non-enzymatic transfer of sequence information under plausible prebiotic conditions.

Olasagasti, F Kim, Hj Nader Pourmand Deamer, Dw

Published in Biochimie

We simulated in our laboratory a prebiotic environment where dry and wet periods were cycled. Under anhydrous conditions, lipid molecules present in the medium could form fluid lamellar matrices and work as organizing agents for the condensation of nucleic acid monomers into polymers. We exposed a mixture of 2 -deoxyribonucleoside 5 -monophosphates...

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Margulies, Eh Cooper, Gm Asimenos, G Thomas, Dj Dewey, Cn Siepel, A Birney, E Keefe, D Schwartz, As Hou, M ...

Published in Genome Research

A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; com...

The UCSC Genome Browser Database.

Karolchik, D Baertsch, R Diekhans, M Furey, Ts Hinrichs, A Lu, Yt Roskin, Km Schwartz, M Sugnet, Cw Thomas, Dj ...

Published in Nucleic Acids Research

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and q...

Identification of a Retinal Circuit for Recurrent Suppression Using Indirect Electrical Imaging.

Greschner, M Heitman, Ak Field, Gd Li, Ph Ahn, D Alexander Sher Litke, Am Chichilnisky, Ej

Published in Current Biology

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Kevin Karplus Karchin, R Shackelford, G Richard Hughey

Published in Bioinformatics

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