Marco Punta

Fellowship
Carl von Linde Junior Fellow

Appointment
2009

Institution
IRCCS Ospedale San Raffaele

Department
Immunogenetics Lab

Host
Burkhard Rost

Focus Group
Computational Biology

Short CV

Marco Punta received his Bachelor of Science and his Master of Science in physics (of biosystems) in1998 from the University of Rome “La Sapienza”. In 2002 he was awarded his Ph.D. degree in biophysics at the International School for Advanced Studies, Trieste, Italy (dissertation: “Structure and function of cyclic nucleotide gated channels: insights from molecular modeling”. Thesis Advisors: Prof. Paolo Carloni, Prof. Vincent Torre). Punta joined the group of Prof. Burkhard Rost at the Department of Biochemistry and Molecular Biophysics at Columbia University, New York, USA, as Postdoctoral Researcher in that same year. He was an Associate Research Scientist at the Herbert Irving Cancer Center of Columbia University. From 2009 to 2011 he was a Carl von Linde Junior Fellow at the Bioinformatic and Computational Biology Department at TUM. After having worked at the Wellcome Trust Sanger Institute, Cambridge, UK, he is now a research scientist at Université Pierre et Marie Curie in Paris, France.


Research Interests

At TUM-IAS Punta will study how protein sequence is modified by evolutionary processes under structural and functional constraints. On the one hand, he will try to detect evolutionary signals in sequences and structures that may help to better characterize individual protein families. On the other, he intends to develop new methods and strategies to study remote relationships between families, using structural information as a key. Applications include proteins function annotation and protein design.


Selected Publications

  • Punta, Marco; Ofran, Yanay: The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function. PLoS Comput Biol 4 (10), 2008, e1000160.
  • Punta, Marco; Forrest, Lucy R.; Bigelow, Henry; Kernytsky, Andrew; Liu, Jinfeng; Rost, Burkhard: Membrane protein prediction methods. Methods 41 (4), 2007, 460-474.
  • Passerini, Andrea; Punta, Marco; Ceroni, Alessio; Rost, Burkhard; Frasconi, Paolo: Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks. Proteins 65 (2), 2006, 305-316.
  • Punta, M.; Rost, B.: PROFcon: novel prediction of long-range contacts. Bioinformatics 21 (13), 2005, 2960-2968.
  • Punta, Marco; Rost, Burkhard: Protein Folding Rates Estimated from Contact Predictions. Journal of Molecular Biology 348 (3), 2005, 507-512.
  • Punta, Marco; Maritan, Amos: A knowledge-based scale for amino acid membrane propensity. Proteins 50 (1), 2002, 114-121.

Publications as TUM-IAS-Fellow

2009

  • Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard: Structural genomics reveals EVE as a new ASCH/PUA-related domain. Proteins 75 (3), 2009, 760-773 mehr… BibTeX Volltext ( DOI )
  • Galea, Charles A.; High, Anthony A.; Obenauer, John C.; Mishra, Ashutosh; Park, Cheon-Gil; Punta, Marco; Schlessinger, Avner; Ma, Jing; Rost, Burkhard; Slaughter, Clive A.; Kriwacki, Richard W.: Large-Scale Analysis of Thermostable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome. J. Proteome Res. 8 (1), 2009, 211-226 mehr… BibTeX Volltext ( DOI )
  • Schlessinger, Avner; Punta, Marco; Yachdav, Guy; Kajan, Laszlo; Rost, Burkhard: Improved Disorder Prediction by Combination of Orthogonal Approaches. PLoS ONE 4 (2), 2009, e4433 mehr… BibTeX Volltext ( DOI )