BOL: Related items

Eivind Hovig's Lab

Tue, 03 Sep 2013 19:06:29 -0500

Bioinformatics relevant research topics are:

genomic scale studies
endogenous mechanisms of mutations, germ line and somatic
computational aspects of immunology in cancer
signalling networks
three-dimensional organization of information in the nucleus
gene silencing
metastatic cross-talk
kinase signaling
personalized medicine
detection of biomarkers in cancer
historical DNA variation

From : http://www.ous-research.no/hovig/

Group address:
Eivind Hovig, The Norwegian Radium Hospital, Montebello, 0310 Oslo,Norway
Email: ehovig@radium.uio.no

GenXPro GmbH

Rahul Agarwal — Thu, 22 May 2014 07:18:35 -0500

GenXPro GMbH is service provider for entire spectrum of nucleotide-based information of any biological sample. By combining intelligent data reduction techniques and latest next generation sequencing technologies, our service portfolio provides most accurate and cost efficient solutions for transcriptomic-, genomic- or epigenomic research.

GENXPRO GMBH, ALTENHÖFERALLEE 3, 60438 FRANKFURT MAIN, GERMANY

Website: http://www.genxpro.info/products_and_services/

PHONE: +49 (0)69- 95 73 97 10, FAX: +49 (0)69- 95 73 97 06

EMAIL: info@genxpro.de

Encode sequencing data freely available to download and use for academic means

Rahul Agarwal — Thu, 13 Mar 2014 18:18:08 -0500

In Encode, regulatory elements investigated via DNA hypersensitivity assays, assays of DNA methylation, and chromatin immunoprecipitation (ChIP) of proteins that interact with DNA, including modified histones and transcription factors, followed by sequencing (ChIP-Seq).

More information:

https://genome.ucsc.edu/ENCODE/pilot.html

Address of the bookmark: https://genome.ucsc.edu/ENCODE/

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

Address of the bookmark: https://github.com/lh3/bfc

Precision Medicine

Rahul Agarwal — Sat, 24 Aug 2013 15:47:03 -0500

Coupling established clinical–pathological indexes with state-of-the-art molecular profiling to create diagnostic, prognostic, and therapeutic strategies precisely tailored to each patient's requirements — hence the term “Precision medicine”

Source:http://www.nejm.org/doi/full/10.1056/NEJMp1114866

Another video on precision medicine:

http://www.youtube.com/watch?v=Pi8W0yOXnzE

Precision Medicine basically intergrates bioinformatics, genomics , genetics, molecular biology and nanotechnology to deliver precise cure/diagnotics to a specific patient.

Examples:

The drug imatinib (Gleevec) designed to inhibit an altered enzyme produced by a fused version of two genes found in chronic myelogenous leukemia.
The breast cancer drug trastuzumab (Herceptin) works only for women whose tumors have a particular genetic profile called HER-2 positive.

E.g. source :

http://www.bionews-tx.com/news/2013/08/15/how-the-impact-of-cancer-genomics-on-precision-medicine-is-revolutionizing-cancer-treatment/

Address of the bookmark: http://www.cbsnews.com/video/watch/?id=50149783n

Prof. Dr. med. Andreas Ramming

Wed, 07 Aug 2019 03:25:48 -0500

In many autoimmune diseases, a misdirected immune response leads to chronic inflammation and subsequently to fibrotic and degenerative tissue remodeling. Therapeutic options are available for inflammatory joint diseases, but only about 40% of patients respond to these existing therapies on a permanent basis. In the remaining cases, these therapies miss their target from the beginning or later during the course of treatment failure. There are currently no causal therapies available for the treatment of fibrotic autoimmune diseases such as systemic sclerosis. Therefore, there is an urgent need to develop new therapeutic options for the treatment of fibrotic and synovitic autoimmune diseases. His group is therefore deal with the molecular mechanisms of these misdirected signaling pathways for the development of novel, targeted therapies

http://www.medizin3.uk-erlangen.de/forschung/arbeitsgruppen/matrixbiologie-entzuendliche-signalwege-in-arthritis-und-fibrose/

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

Jit — Mon, 28 May 2018 09:41:39 -0500

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

Address of the bookmark: https://github.com/Illumina/manta

Queensland Centre for Medical Genomics, Grimmond Lab

Sun, 14 Jul 2013 11:58:34 -0500

Queensland Centre for Medical Genomics

Research Area:
pancreatic cancer; ovarian cancer; prostate cancer; bowel cancer; brain cancer; endometrial cancer; breast cancer; personalised medicine; high-throughput genomics

Link @ http://www.imb.uq.edu.au/sean-grimmond

Lateral Gene Transfer Is Enriched in Cancer Samples

Jitendra Narayan — Mon, 22 Jul 2013 05:13:06 -0500

There has been always a confusion on cancer and bacteria relationship. This is the first paper which shows lateral gene transfer causes cancer.

Find more at http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003107

Cancer's origins revealed

Jitendra Narayan — Thu, 15 Aug 2013 13:06:56 -0500

Researchers have provided the first comprehensive compendium of mutational processes that drive tumour development. Together, these mutational processes explain most mutations found in 30 of the most common cancer types. This new understanding of cancer development could help to treat and prevent a wide-range of cancers.

More at >> http://www.sanger.ac.uk/about/press/2013/130814.html