Publications
Primary tabs
The Multiple Roles of Waters in Protein Solvation,
, The Journal of Physical Chemistry B, 01/2017, Issue Klaus Schulten Memorial Issue, (2017)
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update,
, Nucleic Acids Research, 04/2017, Volume 45, Issue W1, p.W222-W228, (2017)
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.,
, Nucleic Acids Res, 2016 Jan 4, Volume 44, Issue D1, p.D272-8, (2016)
A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis.,
, Rheumatology (Oxford), 2016 Jun, Volume 55, p.1106-11, (2016)
Genome-Wide Pathway Analysis Identifies Genetic Pathways Associated with Psoriasis.,
, J Invest Dermatol, 2016 Mar, Volume 136, Issue 3, p.593-602, (2016)
Long-timescale dynamics of the Drew-Dickerson dodecamer.,
, Nucleic Acids Res, 2016 May 19, Volume 44, p.4052-66, (2016)
Mutations in JMJD1C are involved in Rett syndrome and intellectual disability.,
, Genet Med, 2016 Apr, Volume 18, Issue 4, p.378-85, (2016)
Parmbsc1: a refined force field for DNA simulations.,
, Nat Methods, 2016 Jan, Volume 13, p.55-8, (2016)
A deletion at ADAMTS9-MAGI1 locus is associated with psoriatic arthritis risk.,
, Ann Rheum Dis, 2015 Oct, Volume 74, p.1875-81, (2015)
Identification of risk loci for Crohn’s disease phenotypes using a genome-wide association study,
, Gastroenterology, 2015 Apr, Volume 148, p.794-805, (2015)
Inntags: small self-structured epitopes for innocuous protein tagging.,
, Nat Methods, 2015 Oct, Volume 12, p.955-8, (2015)
Molecular dynamics simulations: advances and applications.,
, Adv Appl Bioinform Chem, 2015, Volume 8, p.37-47, (2015)
Non-coding recurrent mutations in chronic lymphocytic leukaemia.,
, Nature, 2015 Oct 22, Volume 526, p.519-24, (2015)
PACSAB: Coarse-Grained Force Field for the Study of Protein-Protein Interactions and Conformational Sampling in Multiprotein Systems.,
, J Chem Theory Comput, 2015 Dec 8, Volume 11, p.5929-38, (2015)
BioSWR–semantic web services registry for bioinformatics.,
, PLoS One, 2014, Volume 9, p.e107889, (2014)
Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.,
, Nat Biotechnol, 2014 Nov, Volume 32, p.1106-12, (2014)
A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.,
, Hum Mol Genet, 2014 Dec 20, Volume 23, p.6927-34, (2014)
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations,
, Journal of Chemical Theory and Computation, Volume 9, p.1222-1229, (2013)
Exploring early stages of the chemical unfolding of proteins at the proteome scale.,
, PLoS Computational Biology, 2013/00/01, Volume 9, p.e1003393, (2013)
A genome-wide association study on a southern European population identifies a new Crohn’s disease susceptibility locus at RBX1-EP300.,
, Gut, 2013 Oct, Volume 62, p.1440-5, (2013)
High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure,
, Wiley Interdisciplinary Reviews: Computational Molecular Science, Volume 3, p.364–377, (2013)
NAFlex: a web server for the study of nucleic acid flexibility.,
, Nucleic Acids Res, 2013 Jul, Volume 41, p.W47-55, (2013)
Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Nov, Volume 44, p.1236-42, (2012)
Evidence for transcript networks composed of chimeric RNAs in human cells.,
, PLoS One, 2012, Volume 7, p.e28213, (2012)
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.,
, Nat Genet, 2012 Jan, Volume 44, p.47-52, (2012)
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations,
, Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012)
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.,
, Bioinformatics, 2012 May 1, Volume 28, p.1278-9, (2012)
Risk variants for psoriasis vulgaris in a large case-control collection and association with clinical subphenotypes.,
, Hum Mol Genet, 2012 Oct 15, Volume 21, p.4549-57, (2012)
Unveiling case-control relationships in designing a simple and powerful method for detecting gene-gene interactions.,
, Genet Epidemiol, 2012 Nov, Volume 36, p.710-6, (2012)
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.,
, Nature, 2011 Jul 7, Volume 475, p.101-5, (2011)
Enabling HMMER for the Grid with COMP Superscalar,
, Procedia Computer Science, Volume 1, p.2629–2638, (2010)
MoDEL (Molecular Dynamics Extended Library): a database of atomistic molecular dynamics trajectories.,
, Structure, 2010 Nov 10, Volume 18, p.1399-409, (2010)
FlexServ: an integrated tool for the analysis of protein flexibility.,
, Bioinformatics, 2009 Jul 1, Volume 25, p.1709-10, (2009)
Role of Pre-A motif in nitric oxide scavenging by truncated hemoglobin, HbN, of Mycobacterium tuberculosis.,
, J Biol Chem, 2009 May 22, Volume 284, p.14457-68, (2009)
Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors.,
, ChemMedChem, 2009 May, Volume 4, p.866-76, (2009)
Thienylhalomethylketones: Irreversible glycogen synthase kinase 3 inhibitors as useful pharmacological tools.,
, Bioorg Med Chem, 2009 Oct 1, Volume 17, p.6914-25, (2009)
Interoperability with Moby 1.0–it’s better than sharing your toothbrush!,
, Brief Bioinform, 2008 May, Volume 9, p.220-31, (2008)
A consensus view of protein dynamics.,
, Proc Natl Acad Sci U S A, 2007 Jan 16, Volume 104, p.796-801, (2007)
Dissection of the recognition properties of p38 MAP kinase. Determination of the binding mode of a new pyridinyl-heterocycle inhibitor family.,
, J Med Chem, 2007 Jan 25, Volume 50, p.283-93, (2007)
Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters.,
, J Biol Chem, 2007 May 4, Volume 282, p.13270-81, (2007)
A fast method for the determination of fractional contributions to solvation in proteins.,
, Protein Sci, 2006 Nov, Volume 15, p.2525-33, (2006)
Partition of protein solvation into group contributions from molecular dynamics simulations.,
, Proteins, 2005 Jan 1, Volume 58, p.101-9, (2005)
PMUT: a web-based tool for the annotation of pathological mutations on proteins.,
, Bioinformatics, 2005 Jul 15, Volume 21, p.3176-8, (2005)
SAR and 3D-QSAR studies on thiadiazolidinone derivatives: exploration of structural requirements for glycogen synthase kinase 3 inhibitors.,
, J Med Chem, 2005 Nov 17, Volume 48, p.7103-12, (2005)
Theoretical study of the truncated hemoglobin HbN: exploring the molecular basis of the NO detoxification mechanism.,
, J Am Chem Soc, 2005 Mar 30, Volume 127, p.4433-44, (2005)
Cystinuria-specific rBAT(R365W) mutation reveals two translocation pathways in the amino acid transporter rBAT-b0,+AT.,
, Biochem J, 2004 Feb 1, Volume 377, p.665-74, (2004)
Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?,
, Proteins, 2004 Nov 15, Volume 57, p.458-67, (2004)
Unconventional interactions between water and heterocyclic nitrogens in protein structures.,
, Proteins, 2004 Oct 1, Volume 57, p.1-8, (2004)
Continuum and discrete calculation of fractional contributions to solvation free energy.,
, J Comput Chem, 2003 Oct, Volume 24, p.1610-23, (2003)
Four-stranded DNA structure stabilized by a novel G:C:A:T tetrad.,
, J Am Chem Soc, 2003 May 14, Volume 125, p.5654-62, (2003)