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Wednesday, 29 July 2015

The Increasing Speed of Bioinformatics

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The speed of implementation for genetic engineering is faster than ever. As a result, implications are larger and the stakes are higher.

BIOGRAPHY OF Raymond McCauley:

Raymond McCauley is a scientist, engineer, and entrepreneur working at the forefront of biotechnology. Raymond explores how applying technology to life — biology, genetics, medicine, agriculture — is affecting every one of us.. He is known for using storytelling and down-to-earth examples to show how quickly these changes are happening, right now.Read More


Friday, 17 July 2015

Creating ‘genomic origami’

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In a triumph for cell biology, researchers have assembled the first high-resolution, 3-D maps of entire folded genomes and found a structural basis for gene regulation, a kind of “genomic origami” that allows the same genome to produce different types of cells. The research appears online Thursday in the journal Cell.
  • A central goal of the five-year project, a collaboration among researchers at Harvard University, Baylor College of Medicine, Rice University, and the Broad Institute of Harvard and MIT, was to identify the loops in the human genome. Loops form when two bits of DNA that are far apart in the genome sequence end up in close contact in the folded version of the genome in a cell’s nucleus.
  • Researchers used a technology called “in situ Hi-C” to collect billions of snippets of DNA that were later analyzed for signs of loops. The team found that loops and other genome folding patterns are an essential part of genetic regulation.

A 3D Map of the Human Genome

“More and more, we’re realizing that folding is regulation,” said study co-first author Suhas Rao, a researcher at Baylor’s Center for Genome Architecture and a 2012 graduate of Harvard College. “When you see genes turn on or off, what lies behind that is a change in folding. It’s a different way of thinking about how cells work.”

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Oldest Neanderthal DNA found in Italian skeleton

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The calcite-encrusted skeleton of an ancient human, still embedded in rock deep inside a cave in Italy, has yielded the oldest Neanderthal DNA ever found.

These molecules, which could be up to 170,000 years old, could one day help yield the most complete picture yet of help paint a more complete picture of Neanderthal life, researchers say.

  • Although modern humans are the only remaining human lineage, many others once lived on Earth. The closest extinct relatives of modern humans were the Neanderthals, who lived in Europe and Asia until they went extinct about 40,000 years ago. Recent findings revealed that Neanderthals interbred with ancestors of today's Europeans when modern humans began spreading out of Africa — 1.5 to 2.1 percent of the DNA of anyone living outside Africa today is Neanderthal in origin. [Image Gallery: Our Closest Human Ancestor]
  • In 1993, scientists found an extraordinarily intact skeleton of an ancient human amidst the stalactites and stalagmites of the limestone cave of Lamalunga, near Altamura in southern Italy — a discovery they said had the potential to reveal new clues about Neanderthals.

"The Altamura man represents the most complete skeleton of a single nonmodern human ever found," study co-author Fabio Di Vincenzo, a paleoanthropologist at Sapienza University of Rome, told Live Science. "Almost all the bony elements are preserved and undamaged."

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One cell is all you need

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The notion that police can identify a suspect based on the tiniest drop of blood or trace of tissue has long been a staple of TV dramas, but scientists at Harvard have taken the idea a step further. Using just a single human cell, they can reproduce an individual’s entire genome.

  • As described in a Dec. 21 paper in Science, a team of researchers, led by Xiaoliang Sunney Xie, the Mallinckrodt Professor of Chemistry and Chemical Biology, and made up of postdoctoral fellow Chenghang Zong, graduate student Alec Chapman, and former graduate student Sijia Lu, developed a method — dubbed MALBAC, short for Multiple Annealing and Looping-based Amplification Cycles — that requires just one cell to reproduce an entire DNA molecule.
  • More than three years in the making, the breakthrough technique offers the potential for early cancer treatment by allowing doctors to obtain a genetic “fingerprint” of a person’s cancer from circulating tumor cells. It also could lead to safer prenatal testing for a host of genetic diseases.

“If you give us a single human cell, we report to you 93 percent of the genome that contains three billion base pairs, and if there is a single base mutation, we can identify it with 70 percent detectability, with no false positives detected,” Xie said. “This is a major development.”

  • In a second paper, published simultaneously, researchers from Xie’s lab worked with scientists at Peking University in China to demonstrate MALBAC by sequencing 99 sperm cells from one individual and examining the paternal and maternal contribution to each cell’s genome.

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Supercomputing reveals genetic code of cancer

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Cancer researchers must use one of the world's fastest computers to detect which versions of genes are only found in cancer cells. Every form of cancer, even every tumour, has its own distinct variants.

"This charting may help tailor the treatment to each patient," says Associate Professor Rolf Skotheim, who is affiliated with the Centre for Cancer Biomedicine and the Research Group for Biomedical Informatics at the University of Oslo in Norway, as well as the Department of Molecular Oncology at Radiumhospitalet, Oslo University Hospital.

  • His research group is working to identify the genes that cause bowel and prostate cancer, which are both common diseases. There are 4,000 new cases of bowel cancer in Norway every year. Only six out of ten patients survive the first five years. Prostate cancer affects 5,000 Norwegians every year. Nine out of ten survive.

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Overlooked DNA shuffling drives deadly paediatric brain tumour

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One of the deadliest forms of paediatric brain tumour, Group 3 medulloblastoma, is linked to a variety of large-scale DNA rearrangements which all have the same overall effect on specific genes located on different chromosomes. The finding, by scientists at the European Molecular Biology Laboratory (EMBL), the German Cancer Research Centre (DKFZ), both in Heidelberg, Germany, and Sanford-Burnham Medical Research Institute in San Diego, USA, is published online today in Nature.

  • To date, the only gene known to play an important role in Group 3 medulloblastoma was a gene called MYC, but that gene alone couldn't explain some of the unique characteristics of this particular type of medulloblastoma, which has a higher metastasis rate and overall poorer prognosis than other types of this childhood brain tumour. To tackle the question, Jan Korbel's group at EMBL and collaborators at DKFZ tried to identify new genes involved, taking advantage of the large number of medulloblastoma genome sequences now known.

"We were surprised to see that in addition to MYC there are two other major drivers of Group 3 medulloblastoma – two sister genes called GFI1B and GFI1," says Korbel. "Our findings could be relevant for research on other cancers, as we discovered that those genes had been activated in a way that cancer researchers don't usually look for in solid tumours."

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Thursday, 16 July 2015

"Bioinformatics: genomes and algorithms" by François Rechenmann

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François Rechenmann is a researcher in bioinformatics. He was research director at INRIA for over 30 years and has worked in the team Ibis whose research projects focus on digital biology. It now focuses its activities CEO of bioinformatics company Genostar .
François Rechenmann, 56, graduated in computer science from ENSIMAG/INPG in 1973. He got his PhD thesis from INPG in 1976, with the support of a CNRS grant. From 1976 to 1977, he worked as a scientist in the european Joint Research Center at Ispra in Italy (JRC-EURATOM).Since 1978, he is a researcher (senior researcher, "directeur de recherche", since 1983) of the french national research institute in computer science (INRIA).He has contributed to the MODULECO projet (development of methods and software for large econometric models) and the EDORA project (dynamical systems in ecology), before creating the SHERPA research group on object-oriented knowledge modeling, in Grenoble in 1988. Read More
 
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