BIOBASE Biological Databases - BIOBASE Biological Databases

ISMB 2012

Nonna Druker — Tue, 08 May 2012 12:16:26 +0000

July 15-17
Long Beach, CA
Booth #34

>> more information

BIO-IT Asia

Nonna Druker — Tue, 08 May 2012 12:04:12 +0000

Next Generation Sequencing: Data Management & Interpretation
June 7-8, 2012, Singapore
Booth #7

>> more information

European Human Genetics Conference (ESHG) 2012

Nonna Druker — Sat, 05 May 2012 12:10:03 +0000

June 23 – 26
Nürnberg, Germany

Booth #450

Corporate Satellites
Saturday, June 23, 2012, 11.45 – 13.15
Calling Pathogenic Variants from Whole Exome Sequencing Data

>> more information

Medical Library Association – MLA 2012

Nonna Druker — Thu, 26 Apr 2012 17:32:34 +0000

MLA Annual Meeting & Exhibition
May 18 – 23
Seattle, WA
Booth #332

Join us for a workshop on Monday, May 21 at 3:30 pm, Room 617
*Refreshments will be served

>> more information

Identifying the Causes of Differential Gene Expression

Nonna Druker — Wed, 18 Apr 2012 14:02:19 +0000

Supplementing Downstream Analysis Approach with Upstream Analysis Can Bring Additional Value
By Philip Stegmaier, Product Manager at BIOBASE

GEN – Genetic Engineering & Biotechnlogy News, Apr. 15, Vol. 32, No. 8

Read article >>

Genome Informatics Alliance 2012

Nonna Druker — Fri, 06 Apr 2012 14:17:09 +0000

The Genome Informatics Alliance (GIA) includes thought leaders from diverse disciplines, focused on potential solutions to advance future genome analysis beyond the 1000 Genomes era. GIA hosts annual meetings to advance multiple genome analytics.

The earlier meetings focused more on how to handle the actual data, how to assemble the reads and control quality. Now the focus has slightly shifted to the interpretation of that data for clinical use, with pathologists like Dr. Jared Schwartz and Cornell’s Dr. Debra Leonard.

BIOBASE, the leader in data annotation and curation for genomics, took part in the Genome Informatics Alliance 2012: Logistics meeting in Oregon, and had an opportunity to present on trends in annotation of genomic data.

Trends in Annotation of Genomic Data Presentation

GIA 2012 meeting heavily focused on how to deal with potentially millions of genomes coming out of healthcare in the future. With many useful applications for whole genome sequencing, ranging from improving crop yield and making crops more resistant to drought or pests to screening the vast diversity of currently unknown microbial life. The “killer app” however is in human health: identifying genetic risk, and tailoring treatment for the individual, “personalized medicine”. And if this will become reality, it will mean that a few thousand or even hundred thousand genomes will soon be increased to millions of genomes.

ChIP-seq Analysis

Nonna Druker — Thu, 05 Apr 2012 13:17:50 +0000

ChIP-seq is an advanced next generation sequencing (NGS) method to identify global DNA binding sites for a transcription factor of interest which combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing experiments.

The high resolution of ChIP-seq results, compared to ChIP-chip, has great potential to improve our understanding of transcriptional regulation. In order to uncover gene regulatory mechanisms and further to discover its associated biological events, effective computational analysis will be critical. The process of systematic ChIP-seq data analysis follows a series of steps which includes:

Peak identification – taking sequence reads aligned to a reference genome
Annotation – finding the location of peaks on the reference genome and finding known features
Visualization – displaying the located peaks
Motif prediction – finding patterns of common bases within the peaks, comparing these patterns with known transcription factor binding sites

The ExPlain™ analysis system, and advanced bioinformatics system, has built in functions to annotate and visualize the input ChIP-seq data. Using the power of TRANSFAC®’s transcription factor binding site derived positional weight matrices; ExPlain™ makes it easy to identify the factor binding patterns in ChIP-seq fragment.

Are you interested to learn more?

Join our next FREE webinar where we discuss the advantages that ChIP-seq technologies offer over traditional binding site analysis and demonstrate a typical application of ChIP-seq through the analysis of TAL1 intervals in two haematopoietic lineages using the ExPlain™ analysis system.

A systems approach identifies HIPK2 as a key regulator of kidney fibrosis

Nonna Druker — Tue, 20 Mar 2012 12:10:51 +0000

Kidney fibrosis is a common process that leads to the progression of various types of kidney disease. An integrated computational and experimental systems biology approach was used to identify protein kinases that regulate gene expression changes in the kidneys of human immunodeficiency virus (HIV) transgenic mice (Tg26 mice), which have both tubulointerstitial fibrosis and glomerulosclerosis.

TRANSFAC was used for identification of key signaling pathways activated in Tg26 kidney.

>> read full article

Improved methods for identifying copy number variation – an update from the XGEN Congress meeting in San Diego

Nonna Druker — Fri, 09 Mar 2012 14:18:55 +0000

Studies of single nucleotide variation and its role in inherited disease and cancer abound, but through attendance at this week’s XGEN Congress meeting in San Diego we had the opportunity to take a deeper look into the often overlooked role of structural variation, and in particular copy number variation, in disease research. Talks given by a number of leading scientists in the field spanned a wide range of topics from the challenges of identifying and characterizing copy number variation to examples of insights gained from studying copy number variation which may ultimately lead to alternate treatment strategies.

One of the many points that we were struck by during the course of the talks was the assertion that there is a very high false negative rate associated with current standard methods for identifying copy number variation. We tend to focus on the challenges of assigning functional significance to identified variants in our work, but the value of mapping variants to annotated functional properties clearly requires that the variants be reliably identified in the first place. It was therefore very interesting to hear from featured speaker Jinghui Zhang about work done in her lab at St. Jude Children’s Research Hospital to develop two novel algorithms, CREST and CONSERTING, for detecting previously unidentified structural variations with high fidelity as confirmed by independent validation. More information about the algorithms, as well as direct download access to the source code, can be found at the Zhang Lab website.

HGMD® Contributes to Landmark Genome Analysis in Nature and Science

Nonna Druker — Thu, 08 Mar 2012 19:12:12 +0000

March 8, 2012 — Nature published a paper on Insights into hominid evolution from the gorilla genome sequence. This publication acknowledges the use of Human Gene Mutation Database (HGMD) Professional. Click here to read a full article.

In addition, Science Magazine released a paper on A systematic survey of loss-of-function variants in human protein-coding genes. HGMD was used in the identification of 2951 putative loss-of-function (LoF) variants in a screen of 185 human genomes. This allowed the authors to estimate that human genomes typically contain ~100 genuine LoF variants, with ~20 genes completely inactivated. Rare LoF alleles were identified that are highly likely to be deleterious, including 26 known and 21 predicted severe disease-causing variants, as well as a number of common LoF variants in nonessential genes. Click here to read a full article.