CCRG featured in Genome Technology Magazine

The November issue of Genome Technology Magazine has an article featuring our work developing integrated semantic resources for drug discovery: http://www.genomeweb.com/pfizer-funds-chemogenomics-drug-discovery-web-resource-indiana-university

Press release – Pfizer grant for chemogenomics research


BLOOMINGTON, Ind. — An Indiana University data mining expert will use a grant from Pfizer to create a public resource exploring connections between chemical compounds and their biological activities.
IU Bloomington School of Informatics and Computing Professor David Wild will use large-scale semantic Web-based data mining and network methods to seek to uncover previously undiscovered historical links between chemical compounds, drugs, biological pathways, targets, genes and diseases.
Pfizer has awarded Wild $140,000 to conduct the chemogenomics study and to facilitate research relating to the discovery of new therapies and treatments.
“This research is significant because it will for the first time provide a large-scale public chemogenomics resource with integrated data mining tools,” Wild said. “Biomedical researchers will be able to use this to seek to find new important biological relationships and to help discover new drugs.”
The field of chemogenomics, often described in a wider sense as “systems chemical biology,” is rapidly emerging as a way of helping discover new disease therapies and uncovering new uses for existing drugs.
Wild’s lab has already created Chem2Bio2RDF, a prototype semantic resource Web-based program that integrates vast quantities of public chemical and biological data on compounds, drugs, genes, pathways, diseases, side-effects and scholarly publications, along with some initial tools for mining the data.
That resource and its associated tools already show promise for important potential biomedical applications, including predicting off-target and multi-target interactions of drugs and chemical compounds, finding potential applications of existing drugs to new therapeutic areas, and discovery of currently unknown desirable biological effects of existing chemical compounds.
“Professor Wild and his research team are developing innovative solutions to some very complex data mining problems in associating chemical structure to biological activities across numerous databases relevant to drug discovery,” said Jeff Howe, senior director in Pfizer’s Computational Sciences Center of Emphasis. “We are pleased to support his leading-edge research on semantic Web-based data mining for chemogenomics and systems chemical biology.”
Peter Luke, senior director of R&D Business Development at Pfizer, said the support was an example of a growing willingness to create opportunities for collaborations between industry and academia.
“As pre-competitive research through open innovation with academic institutions becomes even more important within the pharmaceutical Industry, we are pleased to fund this research, which is yet another example of partnering with institutions to facilitate novel science programs,” Luke said.
About the Indiana University School of Informatics
Founded in 2000 as the first school of its kind in the United States, the Indiana University School of Informatics is dedicated to research and teaching across a broad range of computing and information technology, with emphases on science, applications and societal implications. The school includes the School of Informatics at IUPUI and the School of Informatics and Computing at Bloomington, where programs include computer science and informatics. The school administers a variety of bachelor and masters degree programs in computer science and informatics, as well as Ph.D. programs in computer science, and the first-ever Ph.D. in informatics. The school is dedicated to excellence in education and research, to partnerships that bolster economic development and entrepreneurship, and to increasing opportunities for women and underrepresented minorities in computing and technology. For more information, visit http://www.soic.indiana.edu.

Cheminformatics Postdoc wins award for scientific excellence

Qian Zhu, a postdoctoral fellow working with David Wild, has been named a winner of the fall 2010 CINF Scholarship for Scientific Excellence (see http://acscinf.org/html/sciexcel.html). The scholarship, awarded by the Division of Chemical Information (CINF) of the American Chemical Society (ACS) was given at the 240th ACS National Meeting in Boston, based on a competitive poster presentation on Qian’s work in a Lilly-funded project to develop a tool called WENDI for finding non-obvious links between chemical structures and biological effects. This work was recently published in a Journal of Cheminformatics article (http://www.jcheminf.com/content/2/1/6)

Chem2Bio2RDF paper in top 10 for BMC Bioinformatics

The BMC bioinformatics paper is in the top 10 for BMC bioinformatics for the last 30 days, with over 1,000 reads. The paper details our innovative chemogenomics system called Chem2Bio2RDF. You can read the paper here.

Press Release: IU Cheminformatics and Chemistry Department win funding for potentially high impact collaborative project

David Wild (as Director of the Chemical Informatics Center) and Amar Flood (Chemistry) have won an IU Collaborative Research and Creative Activity award to bring together some of the latest cheminformatics methods developed at IU with leading-edge chemistry research to potentially make a significant impact on our understanding of the mechanisms of action of drugs in the body. The award, which includes nearly $10,000 to fund a student and equipment, will be used to apply cheminformatics data mining methods recently developed in the cheminformatics group in the School of Informatics and Computing to vast amounts of known chemical structure to examine the nature of Carbon-Hydrogen bonds that may act as an unexpected source of hydrogen bond donors, and thus contribute to the biological activity of chemical compounds. These kinds of bonds are the subject of a research study in the Flood group in Chemistry. Here is a press release from IU about the awards, taken from http://newsinfo.iu.edu/news/page/normal/14099.html

BLOOMINGTON, Ind. — Ten Indiana University Bloomington faculty members have received 2010 Collaborative Research and Creative Activity Funding. The renamed award, formerly known as Summer Faculty Fellowships, is granted by the Office of the Vice Provost for Research to foster collaborations and jump-start projects during the summer that involve IU Bloomington faculty and IU centers, institutes, and museums.
“These awards provide crucial support for our faculty and research scientists to develop new collaborations,” says Sarita Soni, vice provost for research at IU Bloomington, whose office oversees a variety of research funding programs for faculty. “The goal for this funding is to encourage faculty on the Bloomington campus to identify collaborations with any center, institute, or museum at IU that will help to expand their work or stimulate new ideas. Center directors also are encouraged to identify IU Bloomington faculty outside of their centers who can collaborate to advance or generate new research or creative activity.”
Each award provides up to $10,000 over a one-year period for work done in collaboration with a center, institute, or museum. Among the units involved in this year’s awards are the Center for Archaeology in the Public Interest, the Chemical Informatics Center, and the Research Center for Chinese Politics and Business, which is one of the first American university-based research centers operating in China.
Faculty who have received funding will pursue a wide variety of projects, including an investigation into the culture of the Yankeetown people who existed in southern Indiana from AD 700 to AD 1200; working with elementary-age African American girls from the Gary, Ind., to develop their mathematical thinking and reasoning; and an ethnographic study exploring how MBA students learn the ins and outs of “the executive way.”
A complete list of faculty and the centers, institutes, and museums follows. To learn more about the CRCAF, visit the OVPR site here.
2010 Collaborative Research and Creative Activity Funding
  • Solving the Mystery of Yankeetown; Susan Alt, Anthropology, and the Center for Archaeology in the Public Interest
  • A Collaboration to Create an Online Oral History Training Workshop; John Bodnar, Institute for Advance Studies, and the Center for the Study of History and Memory
  • Success Made Probable: Nurturing Future Statisticians through Project-based Learning; Dionne Cross, Education, and Center for P-16 Research and Collaboration
  • Cheminformatics Approaches to the Discovery of New CH Hydrogen Bond Donors; Amar Flood, Chemistry, and Chemical Informatics Center
  • Exceptional Citizens: Chinese Marital Immigrants, Contested Borders, and National Anxieties Across the Taiwan Strait; Sarah Friedman, Anthropology, and Research Center for Chinese Politics and Business
  • Learning the Executive Way: Men and Women of the B-School; Timothy Hallett, Sociology, and Center for Evaluation and Educational Policy
  • The Magic Web; Joss Marsh, English, and Institute for Digital Arts and Humanities
  • Development of an Improved Land Cover Classification Scheme to Estimate Ecosystem Functioning in Southern Indiana Forests; Richard Phillips, Biology, and Center for the Study of Institutions, Population, and Environmental Change
  • Heritage in the Heart of Crow Country; Laura Scheiber, Anthropology, and American Indian Studies Research Institute
  • Comparative Analyses of Reforestation Trends in Sao Paulo & Indiana: Factors Influencing Landowner Decisions; Catherine Tucker, Anthropology, and Center for the Study of Institutions, Population, and Environmental Change

Cheminformatics student Bin Chen wins award for scientific excellence

Indiana Cheminformatics PhD student Bin Chen is a winner of the 2010 CINF Scholarship for Scientific Excellence. The scholarship, awarded by the Division of Chemical Information (CINF) of the American Chemical Society (ACS) was given at the 239th ACS National Meeting in San Francisco, based on a competitive poster presentation on Bin’s work developing Chem2Bio2RDF (http://chem2bio2rdf.org). Chem2Bio2RDF is a large scale resource that for the first time integrates chemical and biological information in an RDF / Semantic Web environment allowing dynamic cross-source querying. More information about the award can be found at http://acscinf.org/html/cinffiz.html

New portal makes cheminformatics educational materials freely available

For several years, Indiana University School of Informatics has been building a graduate curriculum in cheminformatics with an emphasis on distance education, and in particular making cheminformatics learning as accessible as possible for people in a wide variety of disciplines in academia, industry and government. It has now launched a site, the Indiana Cheminformatics Education Portal, where many of the educational materials used at Indiana are being made freely available in wiki format. The site currently contains an initial selection of introductory cheminformatics topics which will be built up during the remainder of the year. The site can be accessed at http://icep.wikispaces.com

IU Cheminformatics Web Services find use in Second Life!

Web Services and Second Life combine to make a powerful tool for virtual chemistry! Cheminformatics web services at Indiana University developed through the NIH-funded ChemBioGrid project (http://www.chembiogrid.org) are now being used to drive advanced chemistry in Second Life. Pioneering work by Jean-Claude Bradley at Drexel University and Andy Lang at Oral Roberts University is enabling an increasing amount of chemistry and molecular modeling to be carried out in Second Life. The latest project, Orac, allows three-dimensional molecular conformations to be generated on-the-fly. The molecules that Orac makes can be manipulated in many ways. You can easily change the position, size and orientation; you can save the molecules to your inventory for later retrieval, make multiple copies and even distribute them to other users. Also, with a little scripting, you can make the molecules interact with users and even each other. A key part of Orac is the creation of 3D conformers from 2D structures, and this is done using real-time calls to the smi23d web service at Indiana University. This is one of many computation services available through the ChemBioGrid infrastructure. More information about Orac can be found in a YouTube Video (http://www.youtube.com/watch?v=tOfhuoRbnCg) and in a paper recently submitted to the Chemistry Central Journal (http://usefulchem.wikispaces.com/SLchemPaper). More information on the ongoing research into Cheminformatics Cyberinfrastructures at Indiana University can be found at http://cheminfo.wikispaces.com.

Press Release: IU Informatics professor named editor-in-chief of new cheminformatics journal

Taken from http://newsinfo.iu.edu/news/page/normal/10759.html

IU Informatics professor named editor-in-chief of new cheminformatics journal

FOR IMMEDIATE RELEASE
May 4, 2009

BLOOMINGTON, Ind. — Indiana University School of Informatics professor David Wild has been named editor-in-chief of the recently launched Journal of Cheminformatics (http://www.jcheminf.com). The publication is a peer-reviewed journal launched by Chemistry Central and BioMed Central, leading publishers of open access journals in biology, chemistry and medicine. The journal premiered its first edition in mid-March with several articles including an introductory editorial by Wild (http://www.jcheminf.com/content/1/1/1).

Wild will lead the journal jointly with Christoph Steinbeck, director of cheminformatics at the European Bioinformatics Institute. The journal accepts high quality articles in all aspects of the emerging field of cheminformatics, with a particular emphasis on the application of modern informatics techniques on the boundaries of chemistry, biology and drug discovery. It will publish monthly and will consider articles that relate to research, databases, methodology, software and commentary. Every article will undergo an extensive peer-review process to be conducted by an international editorial board.

“With the vast expansion of publicly available chemical and biological information, cheminformatics is becoming an increasingly important area of research that will play an important role in 21st century biomedical science and drug discovery,” Wild said. “The Journal of Cheminformatics is an important part of the growth of this area, and being open access will foster strong interaction with our sister fields of bioinformatics and genomics.”

“David Wild, who has been instrumental in the development of the cheminformatics program within the School of Informatics, is an excellent choice to serve as editor-in-chief of this new publication,” said Geoffrey Fox, chair of informatics at IU. “He has vast knowledge in the field, extending over research, education and industry issues.”

Wild has been on faculty at IU since 2004. He leads the cheminformatics graduate program and is currently working on research into aggregative data mining of publicly available chemical and biological data, funded in part by a grant from Eli Lilly that began last fall and recently was extended for an additional year. He has a bachelor’s degree in computing science from Aston University, U.K., and a doctorate in cheminformatics from Sheffield University, U.K.

About the IU School of Informatics

Founded in 2000 as the first school of its kind in the United States, the IU School of Informatics is dedicated to research and teaching across a broad range of computing and information technology, with emphases on science, applications and societal implications. The school includes Computer Science and Informatics on the Bloomington campus and Informatics on the IUPUI campus. The school administers a variety of bachelor and master’s degree programs in computer science and informatics, as well as doctorate degree programs in computer science and the first-ever Ph.D. in informatics. The School of Informatics is dedicated to excellence in education and research, to partnerships that bolster economic development and entrepreneurship, and to increasing opportunities for women and underrepresented minorities in computing and technology. For more information, visit www.informatics.indiana.edu.

To speak with Wild, please contact Lisa Herrmann, School of Informatics communications manager, at 812-855-4125 or ljherrma@indiana.edu.

Cheminformatics Research and Teaching Wiki now available

The cheminformatics@iu wiki is now available at http://cheminfo.wikispaces.com that is constantly updated with the latest information on our research, including project details and presentations. It also includes links to teaching materials.