Parasites are GO

The Malaria Genome Sequencing Consortium Meeting was held on 5–6 June 2001 in Cambridge, UK, and was followed by a workshop discussing the generation of new parasite-specific gene ontology (GO) terms. Present at the meeting, which focused primarily on malaria, were representatives from the research community, the sequencing centres, including the Sanger Centre (Cambridge, UK) and The Institute for Genome Research (TIGR; Rockville, MD, USA), the European Bioinformatics Institute (EBI; Cambridge, UK), Plasmo DB and the GO consortium (Cambridge, UK).     

Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate students

Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington University Department of Biology Science Outreach to create a video tour depicting the processes involved in large-scale sequencing. "Sequencing a Genome: Inside the Washington University Genome Sequencing Center" is a tour of the laboratory that follows the steps in the sequencing pipeline, interspersed with animated explanations of the scientific procedures used at the facility. Accompanying interviews with the staff illustrate different entry levels for a career in genome science. This video project serves as an example of how research and academic institutions can provide teachers and students with access and exposure to innovative technologies at the forefront of biomedical research. Initial feedback on the video from undergraduate students, high school teachers, and high school students provides suggestions for use of this video in a classroom setting to supplement present curricula.     

Food for thought from plant and animal genomes

A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.

Meeting Report

On 12 January, on a morning full of blue sky and cold sunshine, the Plant and Animal Genome XXI meeting opened its doors for the 21st time at the Town and Country Hotel in San Diego. I arrived a couple of hours late, a newbie toting a roller suitcase, a little unprepared for the sheer scope of the meeting I was about to attend. The diversity of topics and attendees at the meeting, ''The Largest Ag-Genomics Meeting in the World'', was stunning. Within my first hour, I would wind up eating my boxed lunch with a member of the transitional government of Egypt, who moonlights as a grad student in Colorado; and within my first afternoon, I would hear talks about drought resistance in rice, marker-assisted breeding in sweet cherry and transgressive segregation in cotton, not to mention the 12 concurrent sessions on topics from citrus genomes to swine breeding. As a plant developmental biologist interested in international agriculture, I chose talks with an eye towards the border between basic and applied research, the brackish zone where molecular biological innovations find their way into research centers, field trials, and ultimately, farmers'' fields. In this report, I will present examples of the diverse and exciting work being done at this intersection, and will conclude by highlighting some emerging trends and challenges on the horizon.     

The non-coding genome: a universe in expansion for fine-tuning the coding world

A report on the EMBO/EMBL Symposium on The Non-Coding Genome, held in Heidelberg, Germany, 9-12 October, 2013.We share 98% coding genome similarity with mouse and have about the same number of protein coding genes as worms, yet the differences in complexity are obvious. Where is this complexity encoded? A huge change in our understanding of genome evolution and regulation of gene expression arrived with the development of high-throughput sequencing technologies. It turns out that most of our genome is transcribed, but only a small percentage has coding information imbedded. The rest of the genome, the non-coding genome, mistakenly labeled as ‘junk DNA’, is where evolutionary complexity resides. In The Non-Coding Genome meeting, several research studies delved deeper into the importance of the non-coding genome, identifying novel classes of non-coding RNAs (ncRNAs) and novel regulatory functions, and expanding our knowledge about this new world, opening more exciting questions to study and answer.     

Clinical applications of sequencing take center stage

A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013.This year''s Advances in Genome Biology and Technology (AGBT) meeting reflected the current state of ''next generation'' sequencing (NGS) technologies: significantly reduced competition and innovation, and a strong focus on standardization and application. Announcements of technological breakthroughs - a hallmark of previous AGBT meetings - were markedly absent, but existing technologies continued to improve following the now expected exponential curve. Although applications ranged widely, there was a strong emphasis on clinical diagnosis.     

Meeting reports

Meeting report: 48^th meeting of the ASCB Meeting highlight: Genome Informatics (GIW-2008); 19^th International Conference on Genome Informatics Darwin 200 years     

Genomic triumph meets clinical reality

A report on the ''Genomic Disorders 2013: from 60 years of DNA to human genomes in the clinic'' meeting, held at Homerton College, Cambridge, UK, April 10-12, 2013.A meeting about genetics held in April 2013 in Cambridge, UK, started laden with historical overtones: it was 60 years to the month since the structure of DNA was reported as a result of work carried out by Watson and Crick just a short walk away. This year''s Genomic Disorders 2013 meeting was thus subtitled ''From 60 years of DNA to human genomes in the clinic'' and reflected on both the spectacular progress that has been achieved in these six decades, and also on the barriers to further advances.It has indeed been a remarkable journey. Progress in sequencing technologies has led to near-complete genome sequences of thousands of humans at a fraction of the cost of the Human Genome Project and prompted the push into clinical medicine, always a goal of the project. Within a working lifetime, the field had made a dramatic transition, likened to that from medieval guild to modern factory (Richard Durbin, The Wellcome Trust Sanger Institute, UK) or from the first car (which had to be preceded by a man walking with a red flag) towards the modern automobile industry (Robert C Green, Brigham and Women''s Hospital and Harvard Medical School, USA).In addition to celebrating the past, the major stumbling blocks on the road to clinical medicine came up during several rounds of discussions and are a main focus of this report. The challenges can be grouped as technological, annotation-related, biological or ethical, and seem to increase in difficulty and complexity in that order.     

Brave new world of post-genomics!

The Royal Society Discussion Meeting on "Utilizing the Genome Sequence of Parasitic Protozoa" was held at the Royal Society in London, UK, 21-22 March 2001.     

A walk from the wild side: the genetics of domestication of livestock and crops

The phenotypic variation found in domesticated plants and animals is striking, so much so that Darwin used it to illustrate the power of selection to effect change. Recent developments in genomics technologies are leading to dramatic progress in elucidating the genetic changes that occur during domestication. The Genetics Society Autumn Meeting on the genetics of domestication took place in November 2004 at the Royal Society in London, and was organised by Helen Sang (Roslin Institute, UK) and Jonathan Jones (John Innes Centre, UK). The meeting brought together many of the leading researchers on livestock and crop domestication and provided a timely and exciting account of recent progress in the field.     

Antibody Engineering & Therapeutics 2015: The Antibody Society's annual meeting December 7–10, 2015, San Diego,CA

Antibody Engineering & Therapeutics, the annual meeting of The Antibody Society, will be held in San Diego, CA in early December 2015. In this meeting preview, the chairs provide their thoughts on the importance of their session topics, which include antibody effector functions, reproducibility of research and diagnostic antibodies, new developments in antibody-drug conjugates (ADCs), preclinical and clinical ADC data, new technologies and applications for bispecific antibodies, antibody therapeutics for non-cancer and orphan indications, antibodies to harness the cellular immune system, overcoming resistance to clinical immunotherapy, and building comprehensive IGVH-gene repertoires through discovering, confirming and cataloging new germline IGVH genes. The Antibody Society''s special session will focus on “Antibodies to watch” in 2016, which are a subset of the nearly 50 antibodies currently in Phase 3 clinical studies. Featuring over 100 speakers in total, the meeting will commence with keynote presentations by Erica Ollmann Saphire (The Scripps Research Institute), Wayne A. Marasco (Dana-Farber Cancer Institute/Harvard Medical School), Joe W. Gray (Oregon Health & Science University), and Anna M. Wu (University of California Los Angeles), and it will conclude with workshops on the promise and challenges of using next-generation sequencing for antibody discovery and engineering from synthetic and in vivo libraries and on computational antibody design.     

Meeting highlights: genome sequencing and biology 2001

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.     

The meso-genomic era

A report from HGM2001, the sixth annual International Human Genome Meeting organized by The Human Genome Organisation (HUGO), Edinburgh, UK, 19-22 April 2001.     

Cephalopod genomics: A plan of strategies and organization

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.     

What would you do if you could sequence everything?

It could be argued that the greatest transformative aspect of the Human Genome Project has been not the sequencing of the genome itself, but the resultant development of new technologies. A host of new approaches has fundamentally changed the way we approach problems in basic and translational research. Now, a new generation of high-throughput sequencing technologies promises to again transform the scientific enterprise, potentially supplanting array-based technologies and opening up many new possibilities. By allowing DNA/RNA to be assayed more rapidly than previously possible, these next-generation platforms promise a deeper understanding of genome regulation and biology. Significantly enhancing sequencing throughput will allow us to follow the evolution of viral and bacterial resistance in real time, to uncover the huge diversity of novel genes that are currently inaccessible, to understand nucleic acid therapeutics, to better integrate biological information for a complete picture of health and disease at a personalized level and to move to advances that we cannot yet imagine.     

DNA 测序技术领域的相关政府投入分析

DNA测序技术是遗传工程的核心技术之一,发展快速和低成本的基因测序技术成为研究焦点。美国、欧盟等发达国家和地区大力支持DNA测序技术的创新研究,并投入了大量的科研经费。在美国,国家卫生研究院(NIH)下属的国家人类基因组研究院(NHGRI)、美国能源部(DOE)以及美国科学基金委(NSF)等机构是进行DNA测序技术相关项目经费分配的主要政府部门。DNA测序作为生命科学研究的关键技术也是欧盟框架计划资助的重要内容之一,其以多个欧洲国家间合作以及产学研合作的形式开展。中国在DNA测序技术领域也开展了一些研究。     

The snail (Biomphalaria glabrata) genome project

In 2001, ideas for a snail genome project were discussed at the American Society of Parasitologists meeting (New Mexico) and a snail genome consortium was subsequently established (the first consortium meeting was held in 2005). A proposal for sequencing the snail genome was submitted to the National Human Genome Research Institute, and Biomphalaria glabrata was prioritized as a non-mammalian sequencing target in 2004. The sequencing of the genome of this medically important snail is now underway.     

9th transgenic technology meeting (TT2010) in Berlin,Germany: a meeting report

The first Transgenic Technology (TT) Meeting was organized in 1999 by Johannes Wilbertz, Karolinska Institute, Stockholm, Sweden as a regional meeting. The TT Meetings continued in this way, constantly gathering additional practitioners of transgenic methodologies until the breakthrough in 2005 when the 6th TT Meeting in Barcelona, Spain, hosted by Lluis Montoliu (Centro Nacional de Biotecnologia, Madrid, Spain), generated the momentum to establish the International Society for Transgenic Technologies (ISTT). Since 2006, the ISTT has continued to promote the TT Meetings and provide its membership with a forum to discuss best practices and new methods in the field. The TT2010 Meeting was held at the Max Delbrück Center for Molecular Medicine (Berlin, Germany). Participation at the TT2010 Meeting exceeded the registration capacity and set a new attendance record. Session topics included methods for the generation of rat and mouse models of human disease, fundamental and advanced topics in rodent embryonic stem cells, and the newest transgenic technologies. Short presentations from selected abstracts were of especial interest. Roundtable discussions on transgenic facility establishment and cryoarchiving of mouse lines were favorably received. Students, technical staff, and professors participated in numerous discussions and came away with practical methods and new ideas for research.     

From proteins to systems: the British Society for Proteomics Research (BSPR) meeting 2005

This report describes the highlights of the second scientific meeting of the British Society for Proteome Research (BSPR), jointly organised with the European Bioinformatics Institute (EBI), and held at The Genome Centre, Cambridge UK in July 2005. The theme of the meeting was "From Proteins to Systems" covering many diverse aspects of proteomics, bioinformatics and systems biology.     

Meeting report: Ocean ‘omics science,technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013)

The National Science Foundation’s EarthCube End User Workshop was held at USC Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterize the needs and tools available to the community that is focusing on microbial and physical oceanography research with a particular emphasis on ‘omic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analyzing the existing data, on the need for the construction and curation of diverse federated databases, as well as development of shared, interoperable, “big-data capable” analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyber infrastructure constraints, (ii) the current and future ocean ‘omics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the ‘omics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.     

Genome studies at the PAG 2011 conference

The contents of the plenary lectures presented at the Plant and Animal Genome (PAG) meeting in January 2011 are summarized in order to provide some insights into the advances in plant, animal and microbe genome studies as they impact on our understanding of complex biological systems. The areas of biology covered include the dynamics of genome change, biological recognition processes and the new processes that underpin investment in science. This overview does not attempt to summarize the diversity of activities that are covered during the PAG through workshops, posters and the suppliers of cutting-edge technologies, but reviews major advances in specific research areas.