The paper "Genome-scale network reconstruction with transcript verification offers insight into Chlamydomonas reinhardtii metabolism and algal biotechnology" has been accepted for publication in Molecular Systems Biology.
The paper "Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii" has been published in BMC Genomics. See it here.
Matthew Oberhardt's recent paper in PLoS Computational Biology has been highlighted in the journal BioTechniques. See the article here.
Congratulations to Arvind Chavali who has won the grand prize at the Presidential Inauguration Poster Competition. His was selected as the best graduate poster among all disciplines. See pictures from the awards ceremony here!
Congratulations to Paul Jensen and Katie Estep, who have been awarded the Double-'Hoo research grant. This award supports joint research projects between undergraduate and graduate students.
Congratulations to our Annual 2v2 Lab Badminton Tournament winners, Sudhir and Charlie,
who beat out the competition during our end of the year lab party.
In collaboration with the Slingluff lab, Sudhir Chowbina recently published "Comprehensive analysis of RTK activation in human melanomas reveals novel autocrine signaling through IGF-1R." in Melanoma Research.
Congratulations to all involved in the Papin lab for the successful NIH R01 application
titled "Network analysis of pathogenicity in Pseudomonas aeruginosa"
Matthew Oberhardt,
Joanna
Goldberg,
Michael Hogardt, and Jason Papin have published
"Metabolic Network Analysis of Pseudomonas aeruginosa during Chronic
Cystic Fibrosis Lung Infection" in the Journal of Bacteriology.
Eytan Ruppin,
Jason Papin,
Luis de Figueiredo, and
Stefan Schuster's review, "Metabolic reconstruction,
constraint-based analysis and game theory to probe genome-scale metabolic
networks", was accepted for publication in
Current Opinion in Biotechnology.
Brian Schmidt, Xiefan Lin-Schmidt, Austin Chamberlin, Kourosh Salehi-Ashtiani, and
Jason Papin's review, "Metabolic systems analysis
to advance algal biotechnology," has been published in
Biotechnology Journal.
Congratulations to Dr. Matthew Oberhardt for defending his thesis and completing his PhD.
Congratulations to Tenzin Choden, Kristen Gruenther, and Jenny Lee for being selected as a finalists in this year's Undergraduate Research and Design Symposium for their project "Incorporating transcriptional regulation into the metabolic reconstruction of the Pseudomonas aeruginosa pathogen". (Picture)
Congratulations to Matthew Oberhardt for winning the
Whitaker
International Scholars Fellowship for post-doctoral work in Tel-Aviv.
Matthew is excited about this opportunity to continue cutting-edge
research abroad.
Congratulations to Matthew Oberhardt who was selected as the Dept. of
Biomedical Engineering's 2010 Biomedical Sciences (BIMS) Program
Outstanding Graduate Student nominee and nominee for the Michael J.
Peach and Jill E. Hungerford Awards.
Lauren Sefcik, Jennifer Wilson, Jason Papin, and Ed Botchwey recently published "Harnessing systems biology approaches to engineer functional microvascular networks" in Tissue Engineering Part B: Reviews.
Congratulations to Brian Schmidt, Jason Papin, and Michael Lawrence for their publication, "Nano-motion dynamics are determined by surface-tethered selectin mechanokinetics and bond formation," in PLOS Computational Biology.
Congratulations to the UVA iGEM team who won gold at the this year's iGEM competition. Jason Papin was one of the team's advisors.
Matthew Oberhardt recently published a review of genome scale metabolic reconstructions. We are excited for this review's potential impact in summarizing and crystallizing the directions in the field, and feel it will be a valuable resource for researchers interested in using these models.
George Glass, Jason Papin, and James Mandell's manuscript "Simple: A Sequential Immunoperoxidase Labeling and Erasing Method" was chosen as October's Article of the Month by the Journal of Histochemistry & Cytochemistry
Welcome to Kevin D'Auria, a new graduate student. Kevin completed his undergraduate studies in biomedical engineering at UNC.
A news story in Genetic Engineering & Biotechnology features the work of Arvind Chavali and Matthew Oberhardt on the reconstruction and analysis of the metabolic networks of human pathogens.
Ani Manichaikul and Arvind Chavali, in collaboration with researchers at the Dana Farber Cancer Institute, recently published a network model of algal metabolism, along with experimental validation of its associated gene products. The work, to be published in Nature Methods, pioneers a systems-level methodology bridging gene prediction with metabolic network analysis and opens opportunities for systematic metabolic engineering of algal biofuel production.
Shokoufeh Dianat and Jenna Zhang were selected as winners of the team category at the 2009 Undergraduate Research Design Symposium for their presentation "Computational methods that reveal the selective pressures causing the influenza virus to mutate." [ UVA News Release]
Arvind Chavali and Jennifer Robichaux's manuscript "Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi" was accepted for publication in BMC Systems Biology
Erwin Gianchandani and Jason Papin's manuscript "Functional states of the genome-scale Escherichia coli transcriptional regulatory system" was accepted for publication by PLOS Computational Biology
George Glass, Jason Papin, and James Mandell's manuscript "Simple: A Sequential Immunoperoxidase Labeling and Erasing Method" was accepted for publication by the Journal of Histochemistry & Cytochemistry.
Joseph Klembczyk and Arvind Chavali received a Double Hoo Research Grant for their project "Evaluating regulatory network structure in i>Leishmania". [ UVA News Release]
Erwin Gianchandani's manuscript describing systems-based discovery of the mechanism of a novel synthetic small molecule inducer of angiogenesis was accepted by the journal Biotechnology & Bioengineering.
George Glass, Erwin Gianchandani, and Corinne Locke's manuscript describing beta-arrestin 1 as a prognostic marker for malignant gliomas was recently accepted by the Journal of Neuropathology and Experimental Neurology.
The Virginia Genetically Engineered Machine (VGEM) team, including UVa students Patrick Gildea, Eyad Lababidi, Dan Tarjan, George Washington, and Brandon Freschcorn, received the bronze medal at MIT's iGEM 2008 for its transcription attenuator. (Click here for the UVa press release.)
Arvind Chavali received the 2008-2009 Award for Excellence in Scholarship in the Sciences & Engineering from the University of Virginia.
Erwin Gianchandani successfully defended his dissertation titled "Toward integrated biochemical network modeling: reconstructing and analyzing whole-cell biology."
Arvind Chavali and Erwin Gianchandani's review on agent-based modeling of immunological systems is featured on the cover of the December 2008 issue of Trends in Immunology.
Congratulations to Arvind Chavali and Erwin Gianchandani whose review on agent-based modeling of immunological systems was accepted by Trends in Immunology In addition, Erwin's recent pathway compendium analysis, with BME collaborators Ed Botchwey and Kristen Wieghaus, has been accepted by Bioinformatics.
Congratulations also to Matthew Oberhardt for the acceptance of his metabolic network reconstruction of Pseudomonas putida in PLoS Computational Biology.
Congratulations to Arvind Chavali who passed his Ph.D. qualifying examination. Arvind's recent reconstruction of the metabolic network of Leishmania major was also featured in this month's issue of the School of Engineering and Applied Science's E-News Online (click here for the article).
Congratulations to Ani Manichaikul whose reconstruction of the metabolic network of the algae Chlamydomonas reinhardtii in collaboration with researchers at Harvard University's Dana-Farber Cancer Institute is being funded by the Department of Energy (click here for the UVa press release).
Congratulations to Arvind Chavali and Matthew Oberhardt whose recent metabolic network reconstructions of Leishmania major and Pseudomonas aeruginosa, respectively, were featured in the news media. Press releases were distributed by the UVa School of Medicine and the UVa News Office. In addition, the work has appeared on WVIR-TV (NBC) channel 29 and elsewhere.
Congratulations to Arvind Chavali and Erwin Gianchandani who each received Graduate Student Travel Awards sponsored by the University of Virginia's Graduate Biosciences Society (GBS) for conferences they attended last fall.
Congratulations to Erwin Gianchandani who was selected as the Dept. of Biomedical Engineering's 2008 Biomedical Sciences (BIMS) Program Outstanding Graduate Student and nominee for the Michael J. Peach and Jill E. Hungerford Awards.
Congratulations to Arvind Chavali and Erwin Gianchandani, who each received Graduate Student Travel Awards sponsored by Northrop Grumman Mission Systems for upcoming fall conferences.
Congratulations to Matthew Oberhardt, whose recent publication in the Journal of Bacteriology was featured on the cover of the journal's April 2008 issue. Matthew also received a Transatlantic Biotechnology Fellowship from the US-European Union Taskforce on Biotechnology Research, for a one-month research trip to Braunschweig, Germany, later this spring.
Congratulations to Erwin Gianchandani and lab alumni Jong Min Lee and James Eddy on their recent publication in PLoS Computational Biology.
Congratulations to Erwin Gianchandani for his recent presentation on behalf of the University of Virginia at the 2008 Virginia Council of Graduate Studies (VCGS) Research Forum in Richmond (click here for the UVa news release).
Congratulations to Matthew Oberhardt who received the 2007-2008 Award for Excellence in Scholarship in the Sciences & Engineering from the University of Virginia (click here for the UVa news release).
Congratulations to Arvind Chavali on his recent publication in Nature/EMBO Molecular Systems Biology.
Congratulations to Erwin Gianchandani, whose research was featured in the Winter 2008 issue of the University of Virginia's research publication called Explorations. Click here for the online version of the article (or here for the PDF).
Congratulations to Erwin Gianchandani and Matthew Oberhardt on their recent publications.
Congratulations to Erwin Gianchandani for his recent publication in Tissue Engineering along with BME collaborators Kristen Wieghaus and Ed Botchwey. The paper was selected by the journal's editors as an " Editor's top pick - hot paper." Click here for the UVa press release.
Congratulations to Matthew Oberhardt on his recent publication.
Congratulations to Arvind Chavali, Erwin Gianchandani and Corinne Locke on their conference presentations this fall at BMES and ICSB.
See here for an opening of a DOE-funded post-doctoral fellowship.
Congratulations to Arvind Chavali who successfully defended for his Master of Engineering (M.E.) in Biomedical Engineering.
Congratulations to Matthew Oberhardt who passed his Ph.D. qualifying examination.
CSBL has received funding from a NSF CAREER Award for a project on interrogating pathogen-host relationships (click here for the UVa news release)!
Congratulations to Jeffrey Whittemore, James Eddy and Kyle Williams for being selected as finalists in the University of Virginia's Undergraduate Research and Design Symposium for their work on Leishmania major (click here for the UVa news release).
Congratulations to Erwin Gianchandani who successfully defended his master's thesis and received a Master of Science in Biomedical Engineering.
CSBL has received funding from the UVa-Cancer Center for a pilot project on applying a novel immunohistochemical signaling network analysis platform (I-SNAP) to multiple cancer types. Dr. James Mandell in the Department of Pathology is a co-principal investigator on the project.
Congratulations to Jeffrey Whittemore who successfully completed the prestigious 2006 Raven Society Fellowship for his work on Leishmania.
Congratulations to Erwin Gianchandani who received the 2006-2007 Award for Excellence in Scholarship in the Sciences & Engineering from the University of Virginia (click here for the UVa news release).
Congratulations to Arvind Chavali, Matthew Oberhardt, Erwin Gianchandani, and Jeffrey Whittemore on their conference presentations this fall. Arvind delivered a poster at BMES in Chicago and a talk at AIChE in San Francisco; Matthew and Erwin presented at BMES and AIChE, respectively; and Jeff attended ASCB in San Diego.
Congratulations to Erwin Gianchandani on the publication of his paper on matrix formalism for transcriptional regulatory networks, which is featured on the cover of the August 2006 issue of PLoS Computational Biology. [Abstract]
Congratulations to Erwin Gianchandani who passed his Ph.D. qualifying examination.
Congratulations to Jong Min Lee ( abstract) and Erwin Gianchandani ( abstract) on their recent publications.
CSBL has received funding from the UVa- Coulter Foundation Translational Research Award for a project on identifying and characterizing signaling networks in glioblastomas. Dr. James Mandell in the Department of Pathology is a co-principal investigator on the project.
Jeffrey Whittemore, a third-year undergraduate student doing research in the CSBL, has received a prestigious 2006 Raven Society Fellowship for his research project. The project involves constructing a life-cycle model of Leishmania, which may then be coupled with an intracellular network reconstruction to generate novel drug targets for the treatment of leishmaniasis.