Mura Lab

at the University of Virginia

Stuff to write home 'bout...

2017 | 2016 | 2015 | 2014 | 2013
2012 | 2011 | 2010 | 2009 | 2008
[thumbnails can be clicked upon for larger images]

2016

  • September
  • August
  • July
    • meeting & awards: Grad student Kim Stanek attends the American Crystallographic Association Annual Meeting in Denver, CO this month (July 22-26). Congratulations to Kim on being invited to present a talk at this meeting, and on receiving two travel awards for this meeting—one from the ACA and one from the UVa Chemistry Dept. Kim will also co-chair, with Betsy Goldsmith, one of the sessions on exciting new structures ('Hot Structures, I').
  • June
  • May
    • graduations & farewells: Congratulations to grad student Peter Randolph and to undergraduate Berk Ekmekci on their graduations this month. Peter successfully defended his dissertation this April, and is graduating with a PhD in Biochemistry. Peter begins postdoctoral studies in cryoEM with Scott Stagg, at FSU's Institute for Molecular Biophysics, next month. Berk graduates with a thesis-based BSc in Computational & Statistical Biophysics—a custom degree that we devised, under the auspices of UVa's Echols Scholar program, during Berk's time at UVa. Berk will begin graduate school in Data Sciences at GWU in the Fall, after a working internship.
  • April
    • Congratulations to graduate student Charles McAnany on being chosen as a 2016-17 Jefferson Scholars Foundation Dissertation Year Fellow! More info on this prestigious, university-wide honor is at http://tinyurl.com/h2rmj22, as well as the departmental announcement.
    • Congratulations to 3rd-year undergraduate Sebastian Coupe on being awarded the UVa Chemistry Department's Long Summer Research Scholarship! This award will help fund Sebastian's work on Hfq this Summer.
  • Jeffress logo
  • March
    • funding: Our collaboration with Kyle Lampe's lab (UVa ChemE) has led to a joint funding award through the Jeffress Memorial Trust and Carman Trust Grant Program in Interdisciplinary Research. This grant (2016.Jeffress.Carman.7644) funds a project entitled "Computational Simulation and Experimental Synthesis of Engineered Extracellular Matrix Proteins for Neural Tissue Engineering".

2015

  • July
  • May
    • meeting: Grad student Peter Randolph attends the RNA Society's Annual Meeting in Madison, WI, and presents a poster on his biophysical and crystallographic work with Sm-like archaeal proteins. Congratulations to Peter on receiving a departmental travel award to help attend this meeting!
    • Congratulations to graduate student Thushani Nilaweera on receiving the "Best Graduate Poster Presentation" award in the Structural Biology, Biochemistry & Biophysics section at the Virginia Academy of Sciences 93rd Annual Meeting, held this month at James Madison University in Harrisonburg, VA.
  • April
    • Here is Thushani presenting her work on Hfq to UVa President Sullivan at this Spring's "Public Day" event...
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      Thushani presenting her Hfq work to President Sullivan!
  • March
    • Welcome to the newest lab affiliate!!!...
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      Mr Calvin Aubin Mura, welcome!!!...
    • Congratulations to grad student Thushani Nilaweera, whose poster presentation received a second-place award at this year's UVa Robert J. Huskey Research Exhibition.
  • February
    • meeting: Grad students Charles McAnany and Matt Cline attend the Biophysical Society's Annual Meeting in Baltimore, MD. Charles presents a poster on his simulation-based analyses of the C-terminal region of desmoplakin, with the aim of elucidating the dynamical roles of various post-translational modifications (PTMs) and point mutations in this large (≈3000-residue) human protein.

2014

  • November
  • October
    • Welcome to Sai Teja Bondalapati, a new undergraduate student who has joined the lab and who will begin working with Kim this Fall.
  • August
  • June
    • publication: Our article "An Introduction to Biomolecular Simulations and Docking" has been accepted for publication in a special issue of Molecular Simulation, focused on Recent Advances in Molecular Biology.
    • More crystallographic travels... Kim & Berk visit the Advanced Photon Source at Argonne National Lab to collect synchrotron X-ray diffraction data.
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      Berk Ekmekci in action at the beamline...
    • farewell: A StrucBio goodbye lunch for former graduate student Dr Jen Patterson, who successfully defended her PhD and who will begin postdoctoral studies on the biochemistry of RNAP at the NIH later this month.
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      Cam and Jen toasting, with the lab in the background (Peter, Matt, Charles, Berk) and foreground (Kim and Thushani).
  • May
    • meeting & awards: Grad students Peter Randolph and Kim Stanek attend the American Crystallographic Association Annual Meeting in Albuquerque, New Mexico (May 24-28). Congratulations to Peter on being invited to present a talk at this meeting. Congratulations to Kim on receiving the RCSB PDB Poster Prize, awarded for "the best student poster presentation".
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      Kim with her prize!
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      The 2014 ACA meeting was in Albuquerque, New Mexico.
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      Peter at the podium for his presentation!
  • April
    • graduating: Congratulations to grad student Jen Patterson on successfully defending her PhD dissertation this April 4! Jen, who is the first PhD graduate of our lab, files her dissertation this Spring and then begins postdoctoral work at the NIH in June. We had the good fortune of having Prof Andrew Feig present, as he was making a seminar visit to UVa.
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      Jen Patterson's thesis defense.
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      The audience at Jen's thesis defense.
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      Dr Patterson and Dr Mura, post-thesis defense...
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      The graduation/hooding ceremony.
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      The graduation/hooding ceremony.
  • February
    • award: Congratulations to undergraduate Berk Ekmekci on receiving a 2014–2015 Harrison Undergraduate Research Award from UVa.
    • meeting: Grad students Peter Randolph and Charles McAnany, along with Cam, attend the 58th Annual Meeting of the Biophysical Society in San Francisco, CA. Cam co-chaired a platform session on molecular dynamics simulations, and Charles and Peter presented their work on Sm proteins. Congratulations to Peter on being invited to present a talk at this meeting.
    • candidacy: Congratulations to second-year graduate students Charles McAnany and Kim Stanek on passing their qualifying exams and advancing to candidacy. Congratulations too to Kim on earning a "High Pass" commendation!
  • January
    • Welcome to two new graduate students who have joined the lab, Thushani Nilaweera and Matt Cline.

2013

  • December
    • More crystallographic travels... Peter, Kim, & Cam visit the Advanced Photon Source at Argonne National Lab, along with Ashton Brock and Ryan Oliver of the Columbus lab, to collect synchrotron diffraction data.
  • NSF logo
  • November
    • funding: Woohoo!!!!, we receive an NSF Career award for a proposal entitled "Experimental & Computational Studies of Ancient Sm–based RNA Assemblies." Further information can be found at the departmental announcement and at UVaToday.
    • Congratulations to grad student Peter Randolph on (i) having his abstract selected for an oral presentation at the Biophysical Society's 58th Annual Meeting in San Francisco this coming February, and also (ii) on receiving a Robert J. Huskey Travel Fellowship from UVa to aid his attendance of this meeting.
  • October
    • meeting: Grad students Jen Patterson and Peter Randolph, along with Cam, attend the Symposium on RNA X: RNA as Tool and Target. Jen and Peter present their work on Hfq and Sm proteins at this meeting, which is hosted at UNC Chapel Hill and organized by the RNA Society of North Carolina (Oct 18–19). Also, congratulations to Peter on being invited to deliver a talk at this meeting.
    • Congratulations to grad student Jen Patterson on receiving a Robert J. Huskey Travel Fellowship from UVa to aid her attendance of the Southeast Regional Meeting of the American Chemical Society (SERMACS) in Atlanta, GA this November.
  • July
    • Congratulations to grad student Jen Patterson on being selected for an all-expenses paid visit to attend and present her work at the National Institutes of Health's Eight Annual Graduate Student Research Conference.
  • June
    • Congratulations to grad student Charles McAnany on being one of only twenty-six individuals selected university-wide for the Tomorrow’s Professor Today program, offered by UVa's Teaching Resource Center. This program is "Designed to facilitate the transition from student to academic professional" and it "focuses on improving preparedness in three key areas – teaching, professional development, and adjustment to a university career".
    • Congratulations to grad student Charles McAnany on being accepted to, and attending, the TBCG's "Hands-On" Workshop on Computational Biophysics in Pittsburgh.
    • Congratulations to grad student Charles McAnany on being selected for a new 'TTSP' position in the coming academic year. The Teaching + Technology Support Partner (TTSP) position, funded by UVa's Teaching Resource Center, is a new departmental position wherein the selected graduate student provides entry- and mid-level support to faculty and other instructors who are pursuing the introduction of computational efforts into their pedagogy and curricula.
  • May
    • meeting: Grad students Peter Randolph and Kim Stanek, along with Cam, attend the Mid-Atlantic Macromolecular Crystallography Meeting, held at Duke University (May 30–June 1).
    • Congratulations to grad student Peter Randolph on being accepted to the 4th Workshop on Neutron Scattering Applications in Structural Biology, to be held at Oak Ridge National Lab this June.
    • Welcome to a new undergraduate student, Berk Ekmekci, who has joined the lab and who will begin pursuing computational research in late Summer.
    • Graduations & Farewells: Congratulations to grad student Chris Lee and to undergrad Kanishk Jain on their graduations this month. Chris successfully defended his thesis this March (see below) and is graduating with an MSc in Biochemistry. Chris will begin PhD studies in biochemistry this Fall at UCSD. Kanishk graduates with a BSc in Chemistry/Biochemistry this May and will begin graduate school at UCLA in July.
    • Congratulations to grad student Jen Patterson on being accepted to, and attending, the "Postdoctoral Prep" program at the Univ of Alabama, Birmingham.
  • April
    • Congratulations to undergraduate Ellen Schleckman, who has been awarded a Guerrant Scholarship for continuing her research in our lab this Summer.
    • publication: Our review "Archaeal and Eukaryotic Homologs of Hfq: A Structural and Evolutionary Perspective on Sm Function" was published in the April issue of RNA Biology.
    • More crystallographic travels... Peter, Kim & Cam visit the Advanced Photon Source at Argonne National Lab to collect synchrotron diffraction data.
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      Peter, Mike, Kim, Duilio
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      puck swap plate
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      "Bragg's favorite terminal at O'Hare..."
    • Peter & Cam visit UCLA for some crystallography...
      Royce Hall
      UCLA's Royce Hall
      Janss Steps
      UCLA's Janss Steps
      Jules Stein Eye Institute
      UCLA near Westwood, Jules Stein Eye Institute (center) and Doris Stein building (right)
      Young Hall
      Peter in front of Young Hall, home of the Department of Chemistry & Biochemistry
  • March
    • Congratulations to Chris Lee, a joint graduate student with the Columbus lab, on successfully defending his MSc thesis, entitled "Broad Specificity of a Zinc-dependent Small Alcohol Dehydrogenase from Thermotoga maritima Involved in the Glycerol Dismutation Pathway".
    • Congratulations to grad student Peter Randolph, whose poster presentation received a second-place award at UVa's 2013 Robert J. Huskey Research Exhibition.
    • Charles McAnany introducing his 'P4B' (Programming for Biochemistry) educational series on programming and algorithms (left), and Peter Randolph lecturing on the Laue equations in our X-ray Diffraction Series (right)...
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      Charles outlining the first of the 'P4B' (Programming for Biochemistry) educational series...
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      Peter lecturing on X-ray diffraction, deriving the Laue equations...
  • February
  • January
    • Welcome to two new graduate students, Charles McAnany and Kim Stanek, who have joined the lab, as well as undergraduate Katrina Nemri.

2012

  • December
  • June
    • conference: Grad student Jen Patterson presents a poster on her work at the 42nd Mid-Atlantic Macromolecular Crystallography Meeting, held at UVA (May 31–June 2). Cameron Mura chairs a session on nucleic acids and nucleic acid–binding proteins at this meeting.
  • May
    • conference: Graduate student Jen Patterson presents her work at the Virginia Academy of Sciences 90th Annual Meeting, held May 23-24 in Norfolk, VA.
    • Congratulations to undergrad Kanishk Jain, who has been awarded a departmental Kenneth C. Bass Scholarships for research in our lab this Summer.
    • Graduations & Farewells: Congratulations to grad student Tomek Kabziński and to undergrad Collin Conrad on their graduations this month. Tomek successfully defended his thesis this past January and is graduating with an MSc in Biochemistry. Collin defended his undergrad thesis as part of the Distinguished Majors Program and will graduate with a BSc in Chemistry (Biochemistry focus).
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      Jen, Collin, Cam after Collin's successful defense
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      Collin at his DMP defense
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      Collin's DMP presentation
    • workshop: Grad student Peter Randolph attends the AUC workshop held at the NIH campus in Bethesda, MD.
  • April
    • Grad students Jen Patterson and Peter Randolph present their work at the Department's annual Third-year Poster Session.
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      Jen presenting her poster, 12apr2012, Chem Dept poster session
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      Peter presenting his poster, 12apr2012, Chem Dept poster session
  • March

2011

  • December
    • Grad student Jen Patterson visited the Kelly Lab at NCSU for a couple days to learn 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 should enable us to eventually 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
  • 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 89th 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.
  • NSF logo
  • February
  • Jeffress logo
  • 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
  • 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 ISMB-2010 bioinformatics meeting in Boston.
  • June
  • 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.
  • Jeffress logo
  • 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
  • July
  • 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
    • Welcome to the first two graduate students to join the lab, Marcin Cieślik and Tomek Kabziński.
    • Welcome to Sarah Ebmeier, a new undergraduate in the lab.

2008