News

July 11-15, 2014: Member of Program Committee of ISMB 2014 to be held on July 11-15, 2014 in Boston. July 11-15, 2014: Member of Program Committee of ISMB 2014 to be held on July 11-15, 2014 in Boston. Mar 19, 2014: Talk entitled "Recent RNA algorithms and their applications" in Bioengineering at the California Institute of Technology. Mar 13, 2014: Talk entitled "Overview of RNA Bioinformatics Tools developed by the Clote Lab" in Computer Science at University of California at Irvine. Nov 29, 2013: Talk entitled "Recent Clote Lab RNA Bioinformatics Tools" in Bioinformatics at Universität Leipzig. Feb, 2013: Talk entitled "Recent Clote Lab RNA Bioinformatics Tools" at Jackson Lab, Connecticut. July 21-23, 2013: Program Committee member for ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB) 2013 September 22-25, 2013 Washington D.C. July 21-23, 2013: Member of Program Committee for the 21st Annual International Conference on Intelligent Systems for Molecular Biology , (ISMB/EECB) Berlin, Germany.

Mar 22, 2013: Talk of P. Clote, entitled "RNA computational toolbox: Algorithms and web servers to solve problems related with RNA secondary structure", University of Rhode Island, Kingston RI.

Mar 11-12, 2013: Dr. Henri Orland of the Commission d'Energie Atomique (CEA), Saclay, speaks at annual biology-physics colloquium at Boston College.

Mar 4-6, 2013: Member of Program Committee of the 5th International Conference on Bioinformatics and Computational Biology (BICoB-2013) , to be held in Honolulu, Hawaii, USA.

Feb 27, 2013: Talk of P. Clote, entitled "RNA conformational switches and the Fast Fourier Transform", MIT Bioinformatics Seminar.

Feb 18, 2013: Talk of P. Clote, entitled "RNA computational toolbox: Algorithms and web servers to solve problems related with RNA secondary structure", Jackson Laboratory for Genomic Medicine, Farmington, CT.

Dec 2-4, 2012: Poster entitled "Prediction of IRES elements in eukaryotic genomes via Complete RNA inverse folding", by I. Dotu, P. Clote, G. Lozano, E. Martinez-Salas presented by I. Dotu at Cell Symposia: Functional RNAs in Melia, Sitges, Spain.

Oct 7, 2012: Program Committee for WRSBS 2012: 1st International Workshop on Robustness and Stability of Biological Systems and Computational Solutions, Orlando, FL, Oct 7, 2012.

July 15-17, 2012: ISMB.
Poster Z40 in Proceedings Track PT07, entitled {\em Fragmentation-free LC-MS can identify hundreds of proteins}, by Peter Clote, Boston College; Pascal Bochet (Institut Pasteur, Systems Biology); Frank Rügheimer (Institut Pasteur, Systems Biology); Tina Guina (Institut Pasteur, Systems Biology); David Goodlett (University of Washington, Medicinal Chemistry); Peter Brooks (Institut Pasteur, Systems Biology); Benno Schwikowski (Institut Pasteur, Systems Biology). Date: Tuesday, July 17, 12:40 p.m. - 2:30 p.m.

July 16, 2012: ISMB.
Jazz quartet for reception of ISMB: P. Clote (alto sax) with Ron Kobayashi trio. See also Ron's site at MySpace. Here is a photo of the quartet at the ISMB banquet at Long Beach Aquarium -- this photo and other photos linked here, were generously provided by Klaas Rodenburg.

July 2-27, 2012: 14 hour mini-course on RNA by P. Clote at the Université Paris-Est Créteil.

July 6-7, 2012: Talk entitled Integrating chemical footprinting data into RNA secondary structure prediction by P. Clote at the Université Paris-Sud XI (Orsay).

March 12-14, 2011: Member of Program Committeee, BICoB2012, 4th International Conference on Bioinformatics and Computational Biology, held at Las Vegas, Nevada.

Program Committee, Workshop on Robustness and Stability of Biological Systems and Computational Solutions (WRSBS'12), to be held in conjunction with the 3rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2012).

Dec 2, 2011: Talk entitled Thermodynamics and Kinetics of RNA Secondary Structure, by K. Zarringhalam and P. Clote in Physics Colloquium at Williams College.

July 17-19, 2011: ISMB.
P. Clote was principal co-organizer for the Special session on RNA, 18 July 2011. Additional co-organizers: I.L. Hofacker, D.H. Mathews, P. Schuster.

July 13, 2011: Talk of P. Clote at Université Paris-Sud XI (Orsay).

August 1-3, 2011: Member of Program Committee of BCB, ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB) 2011 held in Chicago.

June 14-17, 2011: Member of Program Committee of , International Conference on Artificial Neural Networks, held in Espoo, Finland.

March 23 -25, 2011: Member of Program Committee, 3nd International Conference on Bioinformatics and Computational Biology (BICoB-2011) March 23 -25, 2011, New Orleans.

Jan 24-28, 2011: Tutorial of P. Clote at Workshop on Biological Networks and Systems Biology, organized by E. Kranakis within the context of MITACS focus year on networks.

Sep 15, 2011: Award of National Science Foundation grant DMS-1016618, entitled Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA .

July 11-13, 2010: ISMB.
Talk at ISMB: Proceedings Track PT07, "Thermodynamics of RNA structures by Wang-Landau sampling", Date: Sunday, July 11 - 12:15 p.m. - 12:40 p.m. Room: 302 Feng Lou and Peter Clote.

Posters at ISMB:

  1. "Reliable identification of hundreds of proteins without peptide fragmentation", W.A. Lorenz, P. Clote;
  2. "Parametric maximum expected accurate RNA structure", F. Lou, P. Clote;
  3. "RNA structural segmentation", P. Clote, I. Dotu, W.A. Lorenz, P. Van Hentenryck;
  4. "Novel thermodynamics-based algorithm for probe-speci?c position-dependent hybridization free energy", Hosna Jabbari, Peter Clote;
  5. "RNA structural segmentation", P. Clote, I. Dotu, W.A. Lorenz, P. Van Hentenryck;
Music at ISMB: Sharp Eleventh performed for the closing reception at the Sheraton Hotel, July 13, 2010, from 6:30-8:00 pm. Special thanks to Steven Leard.

March 15 - 17, 2010: Poster, entitled "Reliable identification of hundreds of proteins without peptide fragmentation", by Pascal F. Bochet, Frank Rügheimher, Guina Tina, David R. Goodlett, Peter Clote and Benno Schwikowski. presented at JOBIM (Journées Ouvertes de Biologie, Informatique et Mathématiques) in Montpellier, Sep 7-9, 2010.

March 15 - 17, 2010: Program Committee member for the Sixth IASTED International Conference on Advances in Computer Science and Engineering, ACSE 2010, Sharm El Sheikh, Egypt.

Mar 17, 2010: Talk entitled "New results on RNA" at MIT Bioinformatics Seminar.

Mar 1-2, 2010: Keynote speaker for meeting "Quantitative Biology and Bioinformatics in Modern Medicine", All Ireland Initiative in Cancer Bioinformatics, Queen's University, Belfast. Title of talk: "Thermodynamics and kinetics of RNA secondary structure".

2009-2010: Scientific Advisory Board member for "Biological Networks and Systems Biology", supported by MITACS (Canada). Conference is within context of special topic year FP-NETS, "Advances in Network Analysis and its Applications".

December 14-16, 2009: Program committee of the 20th International Conference on Genome Informatics GIW2009), at Pacifico Yokohama in Japan.

Dec 4-6, 2009: Posters presented at the RECOMB Regulatory Genomics 2009, RECOMB Systems Biology 2009 and DREAM4 Reverse Engineering Challenges. Posters: P. Clote, "RNA Structural Segmentation", Y. Ding, "A Novel Algorithm for the Exact Calculation of Partition Function with respect to an Abstract Shape", I. Dotú, "Computing folding pathways between RNA secondary structures", V. Ilyin, "Functional annotation with TOPOFIT-DB including non-sequential relations", H. Jabbari, "Novel thermodynamics-based algorithm for probe-specific position-dependent hybridization free energy", W.A. Lorenz, "Rapid Estimation of RNA Kinetics".

Dec 5, 2009: Sharp Eleventh jazz trio to perform at Museum of MIT for reception of RECOMB Regulatory Genomics 2009, RECOMB Systems Biology 2009 and DREAM4 Reverse Engineering Challenges on Saturday Dec 5 from 8pm to 11pm.

July 30, 2009: Talk of P. Clote entitled "Saturated secondary structures and parametric methods" at meeting Benasque RNA 2009, July 27-Aug 6, 2009.

July 1, 2009: ISMB 2009 jazz performance in Vasa Museum by Per Danielsson (piano), Tamara Danielsson (soprano, tenor sax), Hans Backenroth (contrebasse), Peter Clote (alto sax).
Photos, generously provided by Pat Rodenburg: ISMB 2009 banquet, Vasa Museum, Stockholm, setting up, sound check, discussing first chart, first tune.

June 22-24, 2009: Talk at 9th IEEE Conference on Bioinformatics and Bioengineering (BIBE 2009). Taichung, Taiwan, entitled "Asymptotics of Canonical RNA Secondary Structures", by Peter Clote, Evangelos Kranakis, Danny Krizanc.

June 9-11, 2009: Poster paper entitled "Generalized Peptide Mass Fingerprinting on whole-cell HPLC-MS proteomics experiments", by Pascal F. Bochet, Frank Rügheimher, Guina Tina, David R. Goodlett, Peter Clote and Benno Schwikowski. Presented at JOBIM (Journées Ouvertes de Biologie, Informatique et Mathématiques) in Nantes.

May 19, 2009: Talk entitled "RNA Structural Bioinformatics Tools" by Peter Clote in Computer Science Colloquium at Brown University.

Apr 29, 2009: Talk by Ivan Dotu at MIT Bioinformatics Seminar, entitled "Combinatorial Optimization Applications in Computational Biology".

Nov 16-18, 2008: International Program Committee (IPC) of International Association of Science and Technology for Development (IASTED) International Conference on Computational Biology and Bioinformatics (CBB 2008), Orlando, Florida, November 16-18, 2008.

Dec 1-2, 2008: Program committee of the 19th International Conference on Genome Informatics (GIW2008), Surfers Paradise Marriot Resort and Spa Gold Coast, Queensland Australia.

Oct 29 - Nov 2, 2008: Poster "Calculating Local Optima in the Turner energy model for RNA secondary structure" presented by A. Lorenz at 5th Annual RECOMB Satellite on Regulatory Genomics, Broad Institute, MIT.

Nov 1, 2008: Sharp Eleventh jazz trio at the combined meeting 5th Annual RECOMB Satellite on Regulatory Genomics, 4th Annual RECOMB Satellite on Systems Biology, and 3rd Annual DREAM reverse engineering challenges, held at MIT. Tom Appleman (electric bass), Ned Rosen (piano), Peter Clote (flute, alto and soprano sax).
Pictures (courtesy of Manolis Kellis): soprano sax, soprano sax (close up), flute.

Oct 30, 2008: NIH study section ZRG1 BST-Q (01) on Continued Development and Maintenance of Biomedical Software in Wash. DC.

Oct 15-17, 2008: Program committee of Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008) at Novotel, St Kilda, Melbourne , Australia.

Oct 4, 2008: Invited talk of P. Clote at 1st Digiteo Annual Forum October 2, 08 - Supélec (Paris).

Aug 4, 2008: Invited talk of P. Clote at Max-Planck-Institut für molekulare Pflanzenphysiologie, Golm (Potsdam).

July 28-Aug 3, 2008: P. Clote and J. Waldispühl present papers at RNA 2008, annual meeting of the RNA Society, Berlin.

July 28, 2008: Jazz Quartet performance at Reception of RNA 2008 in Berlin. Peter Clote (alto sax and flute), Robin Draganic (contrebasse), Tony Hurdle (trombone), and Larry Porter (piano).
Some pictures of the quartet playing at the reception (photos courtesy of Sabrina Schmidt). 1, 2, 3, 4.

July 19-23, 2008: W.A. Lorenz presents 2 poster papers at ISMB 2008, Toronto.

July 7, 2008: P. Clote presents invited talk at Bionumero, Paris.

June 30 - July 2, 2008: Poster and demonstration of RNAmutants: Exploring RNA mutational landscape by P. Clote at JOBIM 2008 (Journées Ouvertes de Biologie, Informatique et Mathematique), Lille.

June 1, 2008: Peter Clote receives Digiteo Foundation Chair of Excellence for research in computer science at Ecole Polytechnique and Universite Paris-Sud (Orsay). In collaboration with J.-M Steyaert (LIX,Polytechnique) and A. Denise (LRI, Orsay), during the next four years, Dr. Clote will build a research group for work in computational biology on RNA structure, gene-finders, and molecular design.

May 20, 2008: Sharp Eleventh jazz trio at Annual Banquet of Carroll School of Management, Boston College. Tom Appleman (contrebass), Ned Rosen (piano), Peter Clote (alto and soprano sax).

May 4, 2008: Dr. Ivan Dotu, Computer Science, Brown University, joins our group as a Visiting Scientist, thus strenthening collaborations with the Brown University Computer Science group of Prof. Pascal van Hentenryck, including Dr. Ivan Dotu, Dr. Manuel Cebrian. Collaborations have generated two papers, concerning the application of local search (TABU) and constraint programming (COMET) to protein structure for HP-model on the face-centered cubic lattice.

Apr 3, 2008: Sharp Eleventh jazz performance for 50th anniversary of Carroll School of Management, BC Club, 100 Federal St., Boston. Ned Rosen (piano), Peter Clote (alto and soprano sax).

Apr 2, 2008: "Statistical sampling of RNA structures: Analysis and algorithmic improvements", Talk of Yann Ponty at MIT Bioinformatics Seminar.

Mar 15, 2008: Yann Ponty leaves Clote Lab to join Lab of Alessandra Carbone, at l'Universite Pierre et Marie Curie (Paris 6) for work on genomic analysis.

Mar 12, 2008: "Algorithms for exploring the mutation landscape of RNA molecules", Talk of Jerome Waldispühl at MIT Bioinformatics Seminar.

NSF Biological Informatics Postdoctoral Panel, Feb 21-Feb 22, 2008 at National Science Foundation , 4201 Wilson Boulevard, Arlington, VA 22230

Feb 13, 2008: "Riboswitches, RNA conformational switches and prokaryotic gene regulation", Talk of Peter Clote at MIT Bioinformatics Seminar.

Oct 29 - Nov 2, 2007: IMA Annual Program Year Workshop on RNA in Biology, Bioengineering and Nanotechnology, Institute for Mathematics and its Applications, University of Minnesota, 2 poster papers: i J. Waldispuhl, P. Clote, "Riboswitches, RNA conformational switches and prokaryotic gene regulation", ii Y. Ponty, P. Clote, "LocalMove: A web server to compute best on-lattice fits for biopolymers".

Oct 11-13, 2007: Recomb Satellite on Regulatory Genetics, Broad Institute of MIT, 4 poster papers: i Y. Ponty, P. Clote, "LocalMove: A web server to compute best on-lattice fits for biopolymers", ii F. Ferre, Y. Ponty, W.A. Lorenz, P. Clote, "DIAL: Dihedral alignment of RNA structures', iii J. Waldispuhl, P. Clote, "Riboswitches, RNA conformational switches and prokaryotic gene regulation", iv J. v. Eichborn, J Duarte, H. Stehr, M. Lappe "A network approach to literature management".

Oct 11, 2007: Sharp Eleventh jazz trio at the 4th Annual RECOMB Satellite on Regulatory Genomics, held at Broad Institute, MIT. Tom Appleman (electric bass), Ned Rosen (piano), Peter Clote (alto and soprano sax).

July 23-24, 2007: Two tutorials on RNA biology, structure and algorithms, at Institute of Mathematical Sciences, National University of Singapore. Tutorial I: "RNA: biology and secondary structure", Tutorial II: "RNA: algorithms".

June 28, 2007: Talk of P. Clote in Vingron Group, Max Planck Institute for Molecular Genetics. Talk entitled "Structural Bioinformatics: Recent tools for protein and RNA".

May 24, 2007: Talk of P. Clote in the Department of Mathematics of Ludwig-Maximilians Universitaet Muenchen Talk entitled "RNA: Asymptotics of minimum free energy and number of shapes".

May 23, 2007: Talk of P. Clote at Lehrstuhl fuer Genomorientierte Bioinformatik of the Technische Universitaet Muenchen. Talk entitled "Structural Bioinformatics: Recent tools for protein and RNA".

Apr 11, 2007: Talk of P. Clote at the Lehrstuhl fuer Bioinformatik of the Universitaet Leipzig. Talk entitled "Exploring RNA secondary structure landscape". Apr 3, 2007: Talk of P. Clote at Institut Pasteur. Talk entitled "Structural Bioinformatics Tools".

Apr 2, 2007: Talk of P. Clote at the Laboratoire d'Informatique (LIX) of Ecole Polytechnique. Talk entitled "New structural algorithms for proteins and RNA".

Mar 30, 2007: Talk of P. Clote in the Steyaert Bioinformatics Lab at the Laboratoire d'Informatique (LIX) of Ecole Polytechnique. Talk entitled "RNA: asymptotics and algorithms".

Mar 27, 2007: Talk of P. Clote at RNA meeting ARENA , organized by Helene Touzet. Talk entitled "Des algorithmes parametrises de l'ARN".

Mar 26, 2007: Talk of Y. Ponty at RNA meeting ARENA , organized by Helene Touzet. Talk entitled "Generation aleatoire de structures d'ARN".

Feb 9, 2007: Talk of W.A. Lorenz and Y. Ponty in Mathematics Department of Boston College. Talk entitled "Asymptotics of RNA shapes".

Nov 13, 2006: After more than 3 years as a co-worker in the Structural Bioinformatics Lab, Dr. Fabrizio Ferre begins new bioinformatics position at Harvard University/Children's Hospital in Boston.

Nov 7, 2006: Colloqium talk of Prof. Ken Dill, invited speaker in Biology Department colloquium.

Oct 20, 2006: Talk of P. Clote entitled "Some new aspects of protein and RNA structure", at Brenner Lab, Biology Department, University of California at Berkeley, P. Clote.

Nov 2, 2006: Talk of P. Clote entitled "Some new aspects of protein and RNA structure", at Bioinformatics Institute of Iowa State University, Ames IA.

Oct 30, 2006: Talk of William A. Lorenz entitled "A Self-adaptive Random Walk Algorithm to Identify Genetic Epistatic Effects" at the MIT Bioinformatics Seminar.

Oct 1, 2006: Yann Ponty joins our Structural Bioinformatics Lab. Doctoral dissertation (submitted) in Computer Science from University of Paris-Sud (Orsay) concerns combinatorial asysmptotics for RNA structures and novel algorithms to sample RNA secondary structures.

Sep 1, 2006: William A. Lorenz PhD. joins our Structural Bioinformatics Lab. Doctoral dissertation in Mathematics from University of Michigan at Ann Arbor concerns computational methods to determine epistasis, a topic in computational genomics.

Sep 1, 2006: Jerome Waldispühl takes position as Lecturer in the Department of Mathematics at the Massachusetts Institute of Technology, with positions at MIT's Computational and Systems Biology (CSBI) and Computer Science and Artificial Intelligence Laboratory (CSAIL). Jerome remains affiliated with our Structural Bioinformatics Lab as a Visiting Scientist.

June 2, 2006: Talk entitled "Some new aspects of RNA structure and gene finders", P. Clote, in Department of Biology, Ecole Normale Superieure, Paris.

May 18, 2006: Talk entitled "Some new aspects of protein and RNA structure", P. Clote, at the Genome Center, University of California at Davis.

April 28, 2006: Friday from 1:15 - 1:45 in O'Neill Plaza at Boston College, Sharp Eleventh plays jazz. Ned Rosen (piano), Peter Clote (sax - alto and soprano).

April 13, 2006: Talk of P. Clote at Carleton University, Ottawa, entitled "RNA: k-locally optimal structures and k-point mutants".

March 14 2006: Sharp Eleventh played for banquet of Boston College Biology Landmark Seminar. Inaugural seminar given by Susan Lindquist, Ph.D., Professor of Biology at MIT.

February 13, 2006: Invited talk of P. Clote at conference BIFI 2006 in Zaragoza (Spain). Conference title: "From Physics to Biology: the interface between experiment and computation". Title of talk: "RNA secondary structure: energetic study of kinetic traps and k-point mutants".

January 16, 2006: The new website is online.

January 13, 2006: Renovation and extension of the Structural Bioinformatics Lab space in Higgins 581.

December 14, 2005: Invited talk of P. Clote at the 2005 LIX Worshop. Conference title: "Bioinformatics: algorithms, structures and statistics". Title of talk: "Aspects of the energy landscape for RNA secondary structures".

December 14, 2005: Invited talk of J. Waldispühl at the 2005 LIX Worshop. Conference title: "Bioinformatics: algorithms, structures and statistics". Title of talk: "Fast In-Silico Folding of Transmembrane beta-barrel Proteins"

December 9, 2005: Talk of J. Waldispühl at the Boston College Biology department Data Club.

October 31, 2005: Talk of P. Clote and J. Waldispühl at the M.I.T. Bioinformatics Seminar.