Category Archives: Genome

Automation of osc shapes on Shruthi-1 from Genome
Fantastic automation possibilities.

By: Ashley Elsdon

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Automation of osc shapes on Shruthi-1 from Genome - Video

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

In the past 10 years, the ability to decode or sequence DNA has grown by a million-fold, a stunning rate of progress that is producing a flood of information about human biology and disease. Because of these advances, the scientific community and the world as a whole stands on the verge of a revolution in biology. In the coming decades scientists will be able to understand how cells are wired and how that wiring is disrupted in human diseases ranging from diabetes to cancer to schizophrenia. Now, with his free online course, 7.00x Introductory Biology: The Secret of Life, genome pioneer Eric Lander, the founding director of the Broad Institute and a professor at MIT and Harvard Medical School, will explain to students around the world the basics of biology the secret of life, so to speak so that they can understand todays revolution in biology.

EdX, the not-for-profit online learning initiative founded by Harvard University and the Massachusetts Institute of Technology (MIT), brings the best courses from the best faculty at the best institutions to anyone with an Internet connection. For the past 20 years, legendary teacher Lander has taught Introductory Biology to more than half of all MIT students. He has now adapted his course for online education, creating the newest course on the edX platform. The course, 7.00X, is now open for enrollment, with the first class slated for March 5th. This course will include innovative technology including a 3D molecule viewer and gene explorer tool to transform the learning experience. It is open to all levels and types of learners.

Introducing the freshman class of MIT to the basics of biology is exhilarating, said Lander. Now, with this edX course, I look forward to teaching people around the world. There are no prerequisites for this course other than curiosity and an interest in understanding some of the greatest scientific challenges of our time.

Those taking the course will learn the fundamental ideas that underlie modern biology and medicine, including genetics, biochemistry, molecular biology, recombinant DNA, genomics and genomic medicine. They will become familiar with the structure and function of macromolecules such as DNA, RNA and proteins and understand how information flows within cells. Students will explore how mutations affect biological function and cause human disease. They will learn about modern molecular biological techniques and their wide-ranging impact.

Eric Lander has created this remarkable digitally enhanced introduction to genetics and biology, said Anant Agarwal, President of edX. With this unique online version, he has brought the introductory biology course to a new level. It has been completely rethought and retooled, incorporating cutting-edge online interactive tools as well as community-building contests and milestone-based prizes.

With online courses through edX like 7.00x, what matters isnt what people have achieved or their transcripts, but their desire to learn. Students only need to come with a real interest in science and the desire to understand what's going on at the forefront of biology, and to learn the fundamental principles on which an amazing biomedical revolution is based from one of the top scientist in the world. 7.00x Introductory Biology: The Secret of Life is now available for enrollment. Classes will start on March 4,2013.

Dr. Eric Lander is President and Founding Director of the Broad Institute of Harvard and MIT, a new kind of collaborative biomedical research institution focused on genomic medicine. Dr. Lander is also Professor of Biology at MIT and Professor of Systems Biology at the Harvard Medical School. In addition, Dr. Lander serves as Co-Chair of the Presidents Council of Advisors on Science and Technology, which advises the White House on science and technology. A geneticist, molecular biologist and mathematician, Dr. Lander has played a pioneering role in all aspects of the reading, understanding and medical application of the human genome. He was a principal leader of the international Human Genome Project (HGP) from 1990-2003, with his group being the largest contributor to the mapping and sequencing of the human genetic blueprint. Dr. Lander was an early pioneer in the free availability of genomic tools and information. Finally, he has mentored an extraordinary cadre of young scientists who have become the next generation of leaders in medical genomics. The recipient of numerous awards and honorary degrees, Dr. Lander was elected a member of the U.S. National Academy of Sciences in 1997 and of the U.S. Institute of Medicine in 1999.

Previously announced new 2013 courses include: 8.02x Electricity and Magnetism from Walter Lewin; Justice from Michael Sandel; Introduction to Statistics from Ani Adhikari; The Challenges of Global Poverty from Esther Duflo; The Ancient Greek Hero from Gregory Nagy; Quantum Mechanics and Quantum Computation from Umesh Vazirani; Human Health and Global Environmental Change, from Aaron Bernstein and Jack Spengler.

In addition to these new courses, edX is bringing back several courses from the popular fall 2012 semester: Introduction to Computer Science and Programming; Introduction to Solid State Chemistry; Introduction to Artificial Intelligence; Software as a Service I; Software as a Service II; Foundations of Computer Graphics.

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Human Genome Pioneer Eric Lander to reveal “the secret of life”

Jan. 31, 2013 University of Utah researchers decoded the genetic blueprint of the rock pigeon, unlocking secrets about pigeons' Middle East origins, feral pigeons' kinship with escaped racing birds, and how mutations give pigeons traits like a fancy feather hairdo known as a head crest.

"Birds are a huge part of life on Earth, and we know surprisingly little about their genetics," especially compared with mammals and fish, says Michael D. Shapiro, one of the study's two principal authors and an assistant professor of biology at the University of Utah. "There are more than 10,000 species of birds, yet we know very little about what makes them so diverse genetically and developmentally."

He adds that in the new study, "we've shown a way forward to find the genetic basis of traits -- the molecular mechanisms controlling animal diversity in pigeons. Using this approach, we expect to be able to do this for other traits in pigeons, and it can be applied to other birds and many other animals as well."

The study appears Jan. 31 on Science Express, the website of the journal Science. Shapiro led the research with Jun Wang of China's BGI-Shenzhen (formerly Beijing Genomics Institute) and other scientists from BGI, the University of Utah, Denmark's University of Copenhagen and the University of Texas M.D. Anderson Cancer Center in Houston.

Key findings of the study of pigeons, which first were domesticated some 5,000 years ago in the Mediterranean region:

"The researchers sequenced the genome, or genetic blueprint, of the rock pigeon, Columba livia, among the most common and varied bird species on Earth. There are some 350 breeds with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and head -- including head crests that come in shapes known as hoods, manes, shells and peaks.

"The pigeon is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and a common parakeet known as a budgerigar or budgie, so "this will give us new insights into bird evolution," Shapiro says.

Using innovative software developed by study co-author Mark Yandell, a University of Utah professor of human genetics, the scientists revealed that a single mutation in a gene named EphB2 causes head and neck feathers to grow upward instead of downward, creating head crests.

"This same gene in humans has been implicated as a contributor to Alzheimer's disease as well as prostate cancer and possibly other cancers," Shapiro says, noting that more than 80 of the 350 pigeon breeds have head crests, which play a role in attracting mates in many bird species.

The researchers compared the pigeon genome to those of chickens, turkeys and zebra finches. "Despite 100 million years of evolution since these bird species diverged, their genomes are very similar," Shapiro says.

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Genome shows mutant gene gives pigeons fancy hairdos

Public release date: 31-Jan-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

January 31, 2013, Shenzhen, China In a study published today in Science, researchers from University of Utah, BGI, and other institutes have completed the genome sequencing of rock pigeon, Columba livia, among the most common and varied bird species on Earth. The work reveals the evolutionary secrets of pigeons and opens a new way for researchers to study the genetic traits controlling pigeons' splendid diversity. The findings also help to fill the genetic gaps in exploiting pigeon as a model for the molecular genetic basis of avian variation.

People are quite familiar with the homing pigeon that carried vital messages back and forth in the war period. These "war pigeons" which have been trained to carry messages are domesticated rock pigeons. Pigeons are common birds found in many parts of the world and have more than 350 breeds with different sizes, shapes, colors, color patterns, beaks, bone structure, vocalizations and arrangements of feathers on the feet and headincluding head crests that come in shapes known as hoods, manes, shells and peaks.

To study the genetic basis of the diversity of pigeon, researchers sequenced a pigeon breed named Danish tumbler as the reference genome, and re-sequenced additional 36 domestic breeds and two feral pigeons by next-gen sequencing technology. It is learned that the pigeon is among the few bird genomes sequenced so far, along with those of the chicken, turkey, zebra finch and parrot, which will give researchers new insights into bird evolution.

Researchers could know more about the origin of pigeons with more available genomic resource. Previous studies provided limited evidence of pigeon's origin in the Middle East and some breeds' origin in India, and indicated kinship between common feral or free-living city pigeons and escaped racing pigeons. With additional genomic data in this study, the researchers found there are a lot of shared genetic heritage between the breeds from Iran and the breeds that are suspected from India, which is consistent with historical records of trade routes between those regions. These analyses indicate that major pigeon breed groups all originated in the Middle East.

They also analyzed partial genomes of two feral pigeons: one from a U.S. Interstate-15 overpass in the Salt Lake Valley, and the other from Lake Anna in Virginia. Despite being separated by 1,000 miles, the two pigeons are genetically very similar to each other and to the racing homer breed, supporting the idea that escaped racing homers are probably major contributors to feral populations.

Head crest is a common ornament and an important trait in mate selection in many bird species. With genome-wide population analysis, they found that the EphB2 (Ephrin receptor B2) gene acted like an on-off switch to create a head crest when mutated, and no head crest when normal.

In addition to obtain evidences from whole genome resequencing, they also confirmed the discovery by investigating the EphB2 locus in additional 61 crested birds from 22 breeds, and 69 uncrested birds from 57 breeds. Moreover, the researchers observed that the mutation and related changes in nearby DNA of EphB2 are shared by all crested pigeons, indicating the trait evolved just once and was spread to numerous pigeon breeds by breeders, but not evolved multiple times independently in different breeds.

Dr. Guojie Zhang, a major contributor from BGI, said, "I am so pleased to see this collaboration yields a significant achievement in tracking the origin of pigeons. This study provides new insights for researchers to better understand this lovely bird from the whole-genome level. Moreover, the pigeon genome will accelerate the studies of pigeons and other avian research, and provide a promising model for identifying the genetic basis of variation in traits of general interest."

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The genome of rock pigeon reveals the origin of pigeons and the molecular traits

Whole Genome Re-sequencing part.1
Resequencing process by Woori Kwak.

By: cnkgenomics

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Whole Genome Re-sequencing part.1 - Video

Global research team decodes chick pea genome

By: DoordarshanNational

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Global research team decodes chick pea genome - Video

Whole Genome Re-sequencing part.3
Resequencing procress by Woori Kwak.

By: cnkgenomics

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Whole Genome Re-sequencing part.3 - Video

Whole Genome Re-sequencing part 2
Resequencing process by Woori Kwak

By: cnkgenomics

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Whole Genome Re-sequencing part 2 - Video

MENLO PARK, Calif., Jan. 29, 2013 (GLOBE NEWSWIRE) -- Pacific Biosciences of California, Inc. (PACB) provider of the PacBio(R)RS High Resolution Genetic Analyzer, today announced it is releasing a new software upgrade that provides higher quality genome assemblies with near perfect base level accuracy in addition to other key features. The software upgrade extends the range of projects that uniquely benefit from the company's Single Molecule, Real-Time (SMRT(R)) DNA Sequencing method, and will be available to customers for download on January 31st.

SMRT Analysis 1.4 includes a new hierarchical de novo genome assembly process (HGAP), which allows researchers to assemble entire microbial and fungal genomes solely using PacBio long reads. As a result, users can generate better assemblies with a single library preparation and fewer SMRT(R) Cells than previous approaches that also required short-read sequencing technologies or circular consensus sequencing.

SMRT Analysis 1.4 also incorporates a new multi-read consensus algorithm called Quiver to determine the finished genome sequence with exceptional accuracy. Quiver can provide greater than 99.999% consensus accuracy for both resequencing and de novo assembly applications.

"The extra-long sequence reads and the subsequent highly accurate de novo assemblies produced by the PacBio RS through the latest software enhancements have immensely improved our ability to discover and understand novel genomes cost-effectively," said J. Craig Venter, Ph.D., Founder, Chairman, and Chief Executive Officer at The J. Craig Venter Institute and CEO of Synthetic Genomics.

The software upgrade also includes support for analyzing full-length cDNA transcripts, facilitating understanding of transcription, gene structure and alternative splicing. Unlike any other sequencing technology, SMRT Sequencing can span entire cDNA transcripts with a single read, revealing the complete exonic structure of transcripts.

Additional features of the new SMRT Analysis 1.4 upgrade include:

"We are committed to continually improving the performance of the PacBio RS, in part through developing software enhancements designed to leverage the unique characteristics of our system," said Kevin Corcoran, Senior Vice President of Market Development at Pacific Biosciences. "With long sequence reads, gold standard accuracy and higher quality assemblies, the genomics community can enjoy the benefits of truly finished genomes through SMRT Sequencing."

The new SMRT Analysis software upgrade is available for download from Pacific Biosciences' community website, along with sample data and protocols for cDNA sample preparation and barcoding. To access the software, data, and documentation, visit http://www.smrtcommunity.com.

For more information on the new SMRT Analysis software and the PacBio RS High Resolution Genetic Analyzer, please visit http://www.pacificbiosciences.com.

About Pacific Biosciences

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Pacific Biosciences' Software Upgrade Enhances De Novo Genome Assembly, Variant Calling and cDNA Transcript Analysis

Todd Hazelrigg w/ Genome-Superstition
Todd Hazelrigg and Genome jamming Stevie Wonder #39;s Superstition at The Spot on Broadway

By: THaze87

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Todd Hazelrigg w/ Genome-Superstition - Video