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2012

• March
  • Congratulations to grad student Jen Patterson — her oral presentation received a second-place award in UVa's 2012 Robert J. Huskey Research Exhibition.
• January
  • Congratulations to grad student Tomek Kabzinski on his MSc thesis defense.

2011

• December
  • Grad student Jen Patterson visited the Kelly Lab at NCSU for a couple days to learn a lot about culturing the Thermotogales...
• November
  • Grad student Peter Randolph attended Wyatt Instruments' Light Scattering University in Santa Barbara, CA.
• September
  • A sincere welcome to Eli Chen, who recently graduated from UVa with dual degrees in Music (DMP) and Chemistry/Biochemistry, and who'll begin a part-time research position in the lab this month.
  • Funding: Congratulations to all involved (Gunnoe, Mura, Sabat) for a successful NSF MRI grant proposal, funding the acquisition of new X-ray diffraction equipment in the Chemistry Department; of great relevance for StrucBio, this new instrumentation will enable us to screen the diffraction quality of macromolecular crystal specimens in the Department. Further information can be found at the departmental announcement.
• August
  • Grad student Jen Patterson visits the Lowe Lab at UCSC for a couple weeks of mini-sabbatical, where she learned a lot about experimental biochemistry with RNA...
  • Congratulations to co-advisee Chris Lee on receiving a travel scholarship to attend the NBCR's 2011 Summer Institute. Chris, who is working on the development of computational pipelines for automated annotation of biochemical function for structural genomics targets, was particularly interested in the computer-aided drug discovery (CADD) and virtual screening sessions.
• June
  • Congratulations to Peter Randolph on being one of four UVa grad students selected for the biophysics training grant.
  • Congratulations to Cameron Mura on receiving a $1100 travel grant from the UIUC/NSF Materials Computation Center, for attending the 2011 CECAM workshop on protein–nucleic acid interactions.
  • Grad students Tomek Kabzinski, Jen Patterson, and Peter Randolph present posters on their work at the 41^st Mid-Atlantic Macromolecular Crystallography Meeting at the NCI in Frederick, MD (June 2–4).
• May
  • Congratulations to second-year graduate student Jen Patterson on receiving the "Best Graduate Poster Presentation" award in the Structural Biology, Biochemistry & Biophysics section at the Virginia Academy of Sciences 89^th Annual Meeting, held 26-May in Richmond, VA.
  • Congratulations to undergraduate alumna Sarah Ebmeier on being admitted to graduate school; Sarah will begin PhD studies in the Molecular, Cell & Developmental Biology program at Yale University this Fall.
  • Workshop: Several UVaCompBio undergrads, accompanied by Cameron Mura, attended the BioTrac40 workshop on "Protein Bioinformatics" at the NIH campus in Bethesda, MD this 17-20 May.
• April
  • Congratulations to undergraduates Collin Conrad and Kanishk Jain, who have been awarded departmental Kenneth C. Bass Scholarships for Summer research.
• February
  • Funding: Congratulations to all involved (Columbus, Mura, Price) for a successful NSF 'TUES' grant proposal, funding the continued overhaul and redesign of the year-long undergraduate biochemistry labs. The course is being developed into a functional proteomics laboratory experience. Further information can be found at the departmental announcement.
  • Congratulations to second-year grad students Jen Patterson and Peter Randolph on passing their qualifying exams and successfully advancing to candidacy.
  • Publication: "A Lightweight, Flow-based Toolkit for Parallel and Distributed Bioinformatics Pipelines" was accepted on 18-Feb-2011 for publication in BMC Bioinformatics.
  • Publication: "Abstractions, Algorithms and Data Structures for Structural Bioinformatics in PyCogent" was accepted on 07-Feb-2011 for publication in the Journal of Applied Crystallography.
• January
  • Many thanks to the Jeffress Memorial Trust for renewal of our grant proposal (J-971) for an additional year.
  • On a related note, please see the new Philanthropic Contributions page to become a benefactor of the Mura Lab.

2010

• December
  • Publication: "Molecular Dynamics of Potential rRNA Binders: Single-stranded Nucleic Acids and Some Analogues" appeared on 30-Dec-2010 in the Journal of Physical Chemistry B; this work was co-authored with collaborator Joanna Panecka in the Trylska group's Biomolecular Machines Laboratory.
• September
  • Congratulations to Cameron Mura on being chosen as a 2010–2011 UVa Mead Honored Faculty. The funds will be used to develop a semester-long 'UVaCompBio' series, aimed at introducing upper-level undergraduates from computer science and the biosciences (biochemistry, biology, etc.) to this relatively new multidisciplinary area. More information can be found at the departmental notice or the Cavalier Daily press release.
• August
  • Publication: "An Introduction to Biomolecular Graphics" appeared on 26-Aug-2010 in PLoS Computational Biology; authors of this work include Cameron Mura and former undergraduate Colin McCrimmon. An accompanying online resource has been setup at the PyMOL wiki — http://pymolwiki.org/PLoS.
  • Software: Check-out our Software section for releases and associated information for two projects:
    (i) 'PaPy' (Parallel Pipelines in Python) is a lightweight, Python-based library for creation and deployment of distributed bioinformatic workflows; source-code, usage examples, documentation, etc. are freely available for this toolkit at http://muralab.org/PaPy.
    (ii) 'ZenCogent' refers to our integration of abstracted tools and generalized data-structures for macromolecular 3D structural analysis (kD trees for nearest neighbors; surface calculations; contact patches; etc.) into the feature-rich PyCogent package for sequence-based bioinformatics and phylogenetic analyses.
• July
  • Congratulations to grad student Peter Randolph on being accepted to, and attending, the TBCG's "Hands-On" Workshop on Computational Biophysics in San Diego.
  • Congratulations to grad student Marcin Cieslik on having his work accepted for a presentation at the ISMB2010 bioinformatics meeting in Boston.
• June
  • New website is live for our Structural biology, Computational biology, & Molecular biophysics ('SbCbMb') supergroup; check it out at http://wiki.chem.virginia.edu/SbCbMb.
• May
  • Congratulations to grad student Tomek Kabzinski on completing his qualifying exams and advancing to candidacy.
  • Congratulations to undergraduate Colin McCrimmon on receiving the Department of Chemistry's Hugh Miller Spencer Scholarship Award. Colin, who graduates with dual majors in Chemistry and Biology this month, will begin MD/PhD studies at UC Irvine next Fall.
• April
  • Congratulations to undergraduate Colin McCrimmon for successfully defending, on 30-Apr-2010, his thesis as part of the University's Distinguished Majors Program — "Investigation into the Cause of Disparate Macromolecular Crystal Space-group Frequencies".
• March
  • Congratulations to group member Thien Nguyen on a successful graduate school application process — Admitted to a number of programs, Thien will begin her PhD studies in biochemistry at UC San Diego next Fall.
  • Tomasz Wituła, an experimental biochemist who is currently conducting postdoctoral work in our collaborators' Biomolecular Machines Laboratory (Univ of Warsaw) will visit us from 22–28 March.
• January
  • Welcome to two new graduate students, Jennifer Patterson and Peter Randolph, who have just joined the lab.
  • The Mura Lab receives, and gratefully acknowledges, a funding award from the Jeffress Memorial Trust (J-971).

2009

• August
  • Publication: "PaPy: Parallel and Distributed Data-processing Pipelines in Python" has completed peer-review and been accepted for publication in the Proceedings of SciPy2009: The 8^th Annual Conference on Python for Scientific Computing.
  • Congratulations to graduate student Marcin Cieślik on having his bioinformatics software engineering work invited for presentation at the Eight Annual Python in Science Conference (SciPy09) at CalTech.
• July
  • Publication: "RapA, the SWI/SNF Subunit of Escherichia coli RNA Polymerase, Promotes the Release of Nascent RNA from Transcription Complexes" appeared on 06-Jul-2009 in Biochemistry; this work was co-authored with the lab of collaborator Max Sukhodolets.
  • Congratulations to undergraduate Colin McCrimmon on receiving not one, but two, awards for his poster presentation "Investigation into the Cause of Disparate Macromolecular Space Group Frequencies" at the 2009 Annual Meeting of the American Crystallographic Association (ACA). Colin received the IUCr Poster Prize and the American Institute of Physics Undergraduate Research Prize; more about these is at CINS, an ACA site, and at UVa Today.
• June
  • A sincere welcome to Joanna Panecka, a biophysics PhD student who will be visiting us this Summer from the Biomolecular Machines Laboratory at the Univ of Warsaw.
  • A sincere welcome to Thien Nguyen, who just recently graduated from UVa with a BS in Chemistry/Biochemistry, and who will begin a research position in the lab this month.
• April
  • Congratulations to recent undergraduate Ravi Sood on being admitted to graduate school. Ravi will begin PhD studies in computer science and computational biology at Rensselaer Polytechnic Institute (RPI) in Fall 2009.
  • Congratulations to recent undergraduate Daryl Banton on being admitted to medical school at UVa, where he will begin his studies this Summer/Fall.
• March
  • Congratulations to undergraduate Colin McCrimmon on receiving a travel award for the 2009 American Crystallographic Association (ACA) Annual Meeting this Summer in Toronto, Canada. Colin will present his analyses of protein crystal space groups.
  • Congratulations to undergraduate Colin McCrimmon on receiving a 2009–2010 Harrison Undergraduate Research Award from UVa.
  • Congratulations to undergraduate Sarah Ebmeier on receiving the NIH's Postbaccalaureate Intramural Research Training Award (IRTA), funding a two-year research stint in Bethesda. Sarah graduates with a BS in Biochemistry this Spring and will begin at NIH in July.
• January
  • A warm welcome to the first two graduate students to join the lab – Marcin Cieślik and Tomek Kabziński.

2008

• Fall 2008: Mura Lab 0^th birthday
• Publication: "Molecular Dynamics of a κB DNA Element: Base Flipping via Cross-strand Intercalative Stacking in a Microsecond-scale Simulation", by Mura & McCammon, appeared in the 15-Sep-2008 issue of Nucleic Acids Research.
• May 2008: Congratulations to undergraduate Colin McCrimmon, who was awarded a Bass Scholarship from the UVa Department of Chemistry for Summer research, and to undergrad Arjun Dayal, who received a Departmental Fellowship for Summer research.