BOL: Related items

The Minerva Research Group for Bioinformatics

Tue, 27 May 2014 15:48:14 -0500

The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

Paper test for cancer !!!

Shruti Paniwala — Wed, 26 Feb 2014 00:20:30 -0600

The American Cancer Society projects the numbers of new cancer cases and deaths expected each year in order to estimate the contemporary cancer burden, because cancer incidence and mortality data lag three to four years behind the current year. In addition, the regularly updated Facts & Figures publications present the most current trends in cancer occurrence and survival, as well as information on symptoms, prevention, early detection, and treatment. Cancer rates in developing nations have climbed sharply in recent years, and now account for 70 percent of cancer mortality worldwide. Early detection has been proven to improve outcomes, but screening approaches such as mammograms and colonoscopy, used in the developed world, are too costly to be implemented in settings with little medical infrastructure.

The US born Sangeeta Bhatia at Massachusetts Institute of Technology (MIT) has developed a cheap, simple, paper test that can detect cancer. These diagnostic, which works much like a pregnancy test, could reveal within minutes, based on a urine sample, whether a person have cancer or not. The MIT media announce the major and amazing breakthrough in cancer diagonistics. These newly developed technology will allow non-communicable diseases to be detect at early stage, which will be cheap and easily accessible to the masses. For the developing world it would be exciting to adapt it instead to a paper test that could be performed on unprocessed samples in a rural setting, without the need for any specialized equipment. The simple readout could even be transmitted to a remote caregiver by a picture on a mobile phone.

The MIT professor and Howard Hughes Medical Institute investigator Sangeeta Bhatia, who is also the John and Dorothy Wilson Professor of Health Sciences and Technology and Electrical Engineering and Computer Science, invented a new class of synthetic biomarker, which is highly specialized instrument to do these kind of analysis. These paper test essentially relies on nanoparticles that interact with tumor proteins called proteases, each of which can trigger release of hundreds of biomarkers that are then easily detectable in a patient's urine. The MIT nanoparticles are coated with peptides (short protein fragments) targeted by different MMPs. These particles congregate at tumor sites, where MMPs cleave hundreds of peptides, which accumulate in the kidneys and are excreted in the urine.

To create the test strips, the researchers first coated nitrocellulose paper with antibodies that can capture the peptides. Once the peptides are captured, they flow along the strip and are exposed to several invisible test lines made of other antibodies specific to different tags attached to the peptides. If one of these lines becomes visible, it means the target peptide is present in the sample. The technology can also easily be modified to detect multiple types of peptides released by different types or stages of disease.

In tests in mice, the researchers were able to accurately identify colon tumors, as well as blood clots. Bhatia says these tests represent the first step toward a diagnostic device that could someday be useful in human patients. "This is a new idea — to create an excreted biomarker instead of relying on what the body gives you," she says. "To prove this approach is really going to be a useful diagnostic, the next step is to test it in patient populations."

Reference:

Image: jasongrowclients

Homepage: http://lmrt.mit.edu/about.html

http://web.mit.edu/newsoffice/2014/a-paper-diagnostic-for-cancer-0224.html

http://timesofindia.indiatimes.com/home/science/PIO-develops-cheap-paper-test-to-detect-cancer/articleshow/30963615.cms

Cancer Dependency Map

Jit — Thu, 13 Feb 2020 04:38:47 -0600

The consequences of alterations in the DNA of cancer cells and subsequent vulnerabilities are not fully understood. This project aims to assign a dependency to every cancer cell in a patient which could be exploited to develop new therapies. This knowledge is foundational for precision cancer medicine.

Address of the bookmark: https://depmap.sanger.ac.uk/

Genomics and sequencing approach for identification of biomarkers to assess the efficacy of TGF-βRI inhibitors (of liver cancer) in vivo

Rahul Agarwal — Tue, 05 Aug 2014 13:55:32 -0500

Liver cancer is third leading cause of deaths and fourth most frequent occuring cancer worldwide. There are multiple signaling pathways responsible for causing cancer amongst which TGFb is most important cytokine whose signaling pathway promote cancer. However, main problem is to cure this cancer at late stage where we still have no treatment strategy to tackle this deadly cancer. Hence we need to find out new therapeutic target. One way is to look the relationships between mRNA, methylation and miRNA data of patients with different pathological conditions (cancer vs control either with inhibitor/not). MiRNA is small RNA molecules known to inhibit mRNA expression of particular gene by binding improperly to 3'UTR region of a gene and hence block binding of TF /translation of gene. CpG regions is known to located at promoter region of gene (5' UTR) and usually hypomethylated which allow to gene to transcribe and translate however sometime this region become hyper-methylated thats prevent expression of host gene. Thus , integration of these three data reveal new targets and pathways important for causing or preventing cancer and also reveal biomarker thats check the effects of inhibitor on signaling pathway underlying liver cancer.

Sidow Lab

Fri, 07 Dec 2018 09:06:30 -0600

We study mechanisms of cancer evolution by using state-of-the-art genomic approaches at the bench and in analysis. Accurate genome reconstruction is our other major area of interest. We also collaborate on important questions for which our expertise in genomics and computation is relevant. Arend's biosketch highlights some of our past contributions.

http://www.sidowlab.org/

Bioinformatics Codes Search

Jitendra Narayan — Thu, 15 Aug 2013 11:08:52 -0500

I bet, this website will be your best friend in near future. This helps us to explore the existing open source codes and learn from it.

You can find some useful open source bioinformatics codes for your analysis work. You can use the left bar options to filtere out or narrow down your search result. This webpage can be an useful resource for a beginners bioinformatician as it contain several bioinformatics basics script that are commonly used by biological programmers and biologist.

Stand on the slumped, dandruff-covered shoulders of millions of computer nerds. _/\_

Enjoy the code and research work.

http://code.ohloh.net/search?s=bioinformatics

Address of the bookmark: http://code.ohloh.net/search?s=bioinformatics

XAMPP: Starting Apache fail Ubuntu

Ram Yash Pal — Sat, 07 Jun 2014 05:52:35 -0500

Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php

Programming language to build synthetic DNA

Jit — Mon, 30 Sep 2013 16:37:24 -0500

A team led by Georg Seelig (http://homes.cs.washington.edu/~seelig/index.html) at University of Washington has developed a programming language for chemistry that it hopes will streamline efforts to design a network that can guide the behavior of chemical-reaction mixtures in the same way that embedded electronic controllers guide cars, robots and other devices. In medicine, such networks could serve as “smart” drug deliverers or disease detectors at the cellular level.

Reference & More @

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2013.189.html

http://www.washington.edu/news/2013/09/30/uw-engineers-invent-programming-language-to-build-synthetic-dna/

Image source: washington.edu

Research assistant in computational biology

Wed, 24 Jun 2015 07:55:16 -0500

http://www.au.dk/en/about/vacant-positions/scientific-positions/stillinger/Vacancy/show/743161/5283/

Qualifications:
MSc degree in computer science, engineering, genetics or similar field with a strong emphasis on computational methods.

Deadline
01.08.2015

Genetic Test in India

Rahul Agarwal — Sun, 11 Aug 2013 10:54:35 -0500

1.Xcode Life Sciences Pvt. Ltd.
6B, Eldorado,
112, Nungambakkam High Road,
Nungambakkam, Chennai 600034
Tamil Nadu, India

2.Mapmygenome™
Royal Demeure,HUDA Techno Enclave,
Plot No. 12/2, Sector-1 500 081
Madhapur,Hyderabad
AP, India

3. DNA Labs India

http://www.dnalabsindia.com/lab.php

4.MedGenome Labs Pvt Ltd
(Division of SciGenom Labs Pvt Ltd.)
Plot no: 43A,SDF, 3rd floor
A Block,CSEZ, Kakanad, Cochin
Kerala - 682037
Phone: 0484 - 2413399
Fax: 0484 - 2413398
Email: info@medgenome.com

5.Narayana Nethralaya

Narayana Hrudayalaya Campus
Narayana Health City
# 258/A, Bommasandra, Hosur Road,
Bangalore - 560 099 - INDIA.
TEL: +91-80-66660655-0658
FAX: +91-80-66660650
Mobile: 9902 821128 (Emergency Only)
e-mail: info@narayananethralaya.com

6.BioAxis DNA Research Centre Private Limited
13-51,Sri Lakshmi Nagar colony,
Besides Big Bazar, Near Kamineni Hospitals
GSI Post BandalGuda (L B Nagar) Hydeabad-500068
Andhra Pradesh (India).
Phone : +91-40-24034503/+91-9246338983

7.Gene Guiide

8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61
09167 117799
info@geneguiide.com

See more at: http://www.geneguiide.com

8.INDIAN BIOSCIENCES
Regd. Office:
G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.
Phone: +91 (0)11 29236088, Email: info@inbdna.com.

9.SRL Limited

GP-26, MARUTI INDUSTRIAL ESTATE,

UDYOG VIHAR,SECTOR-18,

GURGAON - 122015

Tel: 0124-3001243 / 0124-3001209

SRL Limited
VASANT VIHAR, 8, PALAM MARG,
NEW DELHI - 110057
Tel: 011 - 4229 5333

Website: http://www.srlworld.com
National Customer care number:
Call Toll Free : 1800-222-660/1800-102-8282
E-mail id: customercare@srl.in

10.Tata Memorial Centre,

Advanced Centre for Treatment, Research and Education in Cancer

Kharghar, Navi Mumbai - 410 210, INDIA.

Tel: +91-22-2740 5000

Fax: +91-22-2740 5085

E-mail: mail@actrec.gov.in