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ORCIDBibTeX records: Marco Punta
@article{DBLP:journals/ploscb/RussoBBCPL22,
author = {Elena Tea Russo and
Federico Barone and
Alex Bateman and
Stefano Cozzini and
Marco Punta and
Alessandro Laio},
title = {DPCfam: Unsupervised protein family classification by Density Peak
Clustering of large sequence datasets},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {10},
pages = {1010610},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1010610},
doi = {10.1371/JOURNAL.PCBI.1010610},
timestamp = {Wed, 17 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RussoBBCPL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RussoLP21,
author = {Elena Tea Russo and
Alessandro Laio and
Marco Punta},
title = {Density Peak clustering of protein sequences associated to a Pfam
clan reveals clear similarities and interesting differences with respect
to manual family annotation},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {121},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04013-x},
doi = {10.1186/S12859-021-04013-X},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/RussoLP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnCEEMMPPQSST16,
author = {Robert D. Finn and
Penelope Coggill and
Ruth Y. Eberhardt and
Sean R. Eddy and
Jaina Mistry and
Alex L. Mitchell and
Simon C. Potter and
Marco Punta and
Matloob Qureshi and
Amaia Sangrador{-}Vegas and
Gustavo A. Salazar and
John G. Tate and
Alex Bateman},
title = {The Pfam protein families database: towards a more sustainable future},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {279--285},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1344},
doi = {10.1093/NAR/GKV1344},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnCEEMMPPQSST16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ChiangVPCMFS15,
author = {Zachary Chiang and
{\AA}ke V{\"{a}}stermark and
Marco Punta and
Penelope Coggill and
Jaina Mistry and
Robert D. Finn and
Milton H. Saier Jr.},
title = {The complexity, challenges and benefits of comparing two transporter
classification systems in {TCDB} and Pfam},
journal = {Briefings Bioinform.},
volume = {16},
number = {5},
pages = {865--872},
year = {2015},
url = {https://doi.org/10.1093/bib/bbu053},
doi = {10.1093/BIB/BBU053},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ChiangVPCMFS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/NatarajanPKYGA15,
author = {Padmaja Natarajan and
Marco Punta and
Abhinav Kumar and
Andrew P. Yeh and
Adam Godzik and
L. Aravind},
title = {Structure and sequence analyses of Bacteroides proteins BVU{\_}4064
and {BF1687} reveal presence of two novel predominantly-beta domains,
predicted to be involved in lipid and cell surface interactions},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {7:1--7:9},
year = {2015},
url = {https://doi.org/10.1186/s12859-014-0434-7},
doi = {10.1186/S12859-014-0434-7},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/NatarajanPKYGA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MitchellCDFHLMMNPSSRYBPASRRXKGBLGOHHNWOSMTF15,
author = {Alex L. Mitchell and
Hsin{-}Yu Chang and
Louise C. Daugherty and
Matthew Fraser and
Sarah Hunter and
Rodrigo Lopez and
Craig McAnulla and
Conor McMenamin and
Gift Nuka and
Sebastien Pesseat and
Amaia Sangrador{-}Vegas and
Maxim Scheremetjew and
Claudia Rato and
Siew{-}Yit Yong and
Alex Bateman and
Marco Punta and
Teresa K. Attwood and
Christian J. A. Sigrist and
Nicole Redaschi and
Catherine Rivoire and
Ioannis Xenarios and
Daniel Kahn and
Dominique Guyot and
Peer Bork and
Ivica Letunic and
Julian Gough and
Matt E. Oates and
Daniel H. Haft and
Hongzhan Huang and
Darren A. Natale and
Cathy H. Wu and
Christine A. Orengo and
Ian Sillitoe and
Huaiyu Mi and
Paul D. Thomas and
Robert D. Finn},
title = {The InterPro protein families database: the classification resource
after 15 years},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {213--221},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1243},
doi = {10.1093/NAR/GKU1243},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MitchellCDFHLMMNPSSRYBPASRRXKGBLGOHHNWOSMTF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LewisSABBCCDFGJKKMMMOOPRSSVO15,
author = {Tony E. Lewis and
Ian Sillitoe and
Antonina Andreeva and
Tom L. Blundell and
Daniel W. A. Buchan and
Cyrus Chothia and
Domenico Cozzetto and
Jose M. Dana and
Ioannis Filippis and
Julian Gough and
David T. Jones and
Lawrence A. Kelley and
Gerard J. Kleywegt and
Federico Minneci and
Jaina Mistry and
Alexey G. Murzin and
Bernardo Ochoa{-}Monta{\~{n}}o and
Matt E. Oates and
Marco Punta and
Owen J. L. Rackham and
Jonathan Stahlhacke and
Michael J. E. Sternberg and
Sameer Velankar and
Christine A. Orengo},
title = {Genome3D: exploiting structure to help users understand their sequences},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {382--386},
year = {2015},
url = {https://doi.org/10.1093/nar/gku973},
doi = {10.1093/NAR/GKU973},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LewisSABBCCDFGJKKMMMOOPRSSVO15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TrameCAECPR14,
author = {Christine B. Trame and
Yuanyuan Chang and
Herbert L. Axelrod and
Ruth Y. Eberhardt and
Penelope Coggill and
Marco Punta and
Neil D. Rawlings},
title = {New mini- zincin structures provide a minimal scaffold for members
of this metallopeptidase superfamily},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {1},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-1},
doi = {10.1186/1471-2105-15-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TrameCAECPR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FinnBCCEEHHHMSTP14,
author = {Robert D. Finn and
Alex Bateman and
Jody Clements and
Penelope Coggill and
Ruth Y. Eberhardt and
Sean R. Eddy and
Andreas Heger and
Kirstie Hetherington and
Liisa Holm and
Jaina Mistry and
Erik L. L. Sonnhammer and
John G. Tate and
Marco Punta},
title = {Pfam: the protein families database},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {222--230},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1223},
doi = {10.1093/NAR/GKT1223},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FinnBCCEEHHHMSTP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/YachdavKKHGHHSRBRAPSB0VSBR14,
author = {Guy Yachdav and
Edda Kloppmann and
L{\'{a}}szl{\'{o}} Kaj{\'{a}}n and
Maximilian Hecht and
Tatyana Goldberg and
Tobias Hamp and
Peter H{\"{o}}nigschmid and
Andrea Schafferhans and
Manfred Roos and
Michael Bernhofer and
Lothar Richter and
Haim Ashkenazy and
Marco Punta and
Avner Schlessinger and
Yana Bromberg and
Reinhard Schneider and
Gerrit Vriend and
Chris Sander and
Nir Ben{-}Tal and
Burkhard Rost},
title = {PredictProtein - an open resource for online prediction of protein
structural and functional features},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Webserver-Issue},
pages = {337--343},
year = {2014},
url = {https://doi.org/10.1093/nar/gku366},
doi = {10.1093/NAR/GKU366},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/YachdavKKHGHHSRBRAPSB0VSBR14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MistryCEDGFBP13,
author = {Jaina Mistry and
Penny C. Coggill and
Ruth Y. Eberhardt and
Antonio Deiana and
Andrea Giansanti and
Robert D. Finn and
Alex Bateman and
Marco Punta},
title = {The challenge of increasing Pfam coverage of the human proteome},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat023},
doi = {10.1093/DATABASE/BAT023},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MistryCEDGFBP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MistryCEDGFBP13a,
author = {Jaina Mistry and
Penny C. Coggill and
Ruth Y. Eberhardt and
Antonio Deiana and
Andrea Giansanti and
Robert D. Finn and
Alex Bateman and
Marco Punta},
title = {The challenge of increasing Pfam coverage of the human proteome},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat040},
doi = {10.1093/DATABASE/BAT040},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MistryCEDGFBP13a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HwangBPCBARSPEAPG13,
author = {William C. Hwang and
Constantina Bakolitsa and
Marco Punta and
Penelope Coggill and
Alex Bateman and
Herbert L. Axelrod and
Neil D. Rawlings and
Mayya Sedova and
Scott N. Peterson and
Ruth Y. Eberhardt and
L. Aravind and
Jaime Pascual and
Adam Godzik},
title = {LUD, a new protein domain associated with lactate utilization},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {341},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-341},
doi = {10.1186/1471-2105-14-341},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HwangBPCBARSPEAPG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/EberhardtHPMOB12,
author = {Ruth Y. Eberhardt and
Daniel H. Haft and
Marco Punta and
Maria Jesus Martin and
Claire O'Donovan and
Alex Bateman},
title = {AntiFam: a tool to help identify spurious ORFs in protein annotation},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas003},
doi = {10.1093/DATABASE/BAS003},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/EberhardtHPMOB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PuntaCEMTBPFCCHHSEBF12,
author = {Marco Punta and
Penny C. Coggill and
Ruth Y. Eberhardt and
Jaina Mistry and
John G. Tate and
Chris Boursnell and
Ningze Pang and
Kristoffer Forslund and
Goran Ceric and
Jody Clements and
Andreas Heger and
Liisa Holm and
Erik L. L. Sonnhammer and
Sean R. Eddy and
Alex Bateman and
Robert D. Finn},
title = {The Pfam protein families database},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {290--301},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1065},
doi = {10.1093/NAR/GKR1065},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/PuntaCEMTBPFCCHHSEBF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HunterJM12,
author = {Sarah Hunter and
Philip Jones and
Alex L. Mitchell and
Rolf Apweiler and
Teresa K. Attwood and
Alex Bateman and
Thomas Bernard and
David Binns and
Peer Bork and
Sarah W. Burge and
Edouard De Castro and
Penny C. Coggill and
Matthew Corbett and
Ujjwal Das and
Louise C. Daugherty and
Lauranne Duquenne and
Robert D. Finn and
Matthew Fraser and
Julian Gough and
Daniel H. Haft and
Nicolas Hulo and
Daniel Kahn and
Elizabeth Kelly and
Ivica Letunic and
David Lonsdale and
Rodrigo Lopez and
Martin Madera and
John Maslen and
Craig McAnulla and
Jennifer McDowall and
Conor McMenamin and
Huaiyu Mi and
Prudence Mutowo{-}Meullenet and
Nicola J. Mulder and
Darren A. Natale and
Christine A. Orengo and
Sebastien Pesseat and
Marco Punta and
Antony F. Quinn and
Catherine Rivoire and
Amaia Sangrador{-}Vegas and
Jeremy D. Selengut and
Christian J. A. Sigrist and
Maxim Scheremetjew and
John G. Tate and
Manjulapramila Thimmajanarthanan and
Paul D. Thomas and
Cathy H. Wu and
Corin Yeats and
Siew{-}Yit Yong},
title = {InterPro in 2011: new developments in the family and domain prediction
database},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {306--312},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr948},
doi = {10.1093/NAR/GKR948},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HunterJM12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pkdd/LippiPPF12,
author = {Marco Lippi and
Andrea Passerini and
Marco Punta and
Paolo Frasconi},
editor = {Peter A. Flach and
Tijl De Bie and
Nello Cristianini},
title = {Metal Binding in Proteins: Machine Learning Complements X-Ray Absorption
Spectroscopy},
booktitle = {Machine Learning and Knowledge Discovery in Databases - European Conference,
{ECML} {PKDD} 2012, Bristol, UK, September 24-28, 2012. Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {7524},
pages = {854--857},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33486-3\_63},
doi = {10.1007/978-3-642-33486-3\_63},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/pkdd/LippiPPF12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/09/PuntaR09,
author = {Marco Punta and
Burkhard Rost},
editor = {David J. Livingstone},
title = {Neural Networks Predict Protein Structure and Function},
booktitle = {Artificial Neural Networks},
series = {Methods in Molecular Biology},
volume = {458},
pages = {198--225},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-1-60327-101-1\_11},
doi = {10.1007/978-1-60327-101-1\_11},
timestamp = {Wed, 16 Dec 2020 16:45:37 +0100},
biburl = {https://dblp.org/rec/books/sp/09/PuntaR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LippiPPRF08,
author = {Marco Lippi and
Andrea Passerini and
Marco Punta and
Burkhard Rost and
Paolo Frasconi},
title = {MetalDetector: a web server for predicting metal-binding sites and
disulfide bridges in proteins from sequence},
journal = {Bioinform.},
volume = {24},
number = {18},
pages = {2094--2095},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn371},
doi = {10.1093/BIOINFORMATICS/BTN371},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LippiPPRF08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PuntaO08,
author = {Marco Punta and
Yanay Ofran},
title = {The Rough Guide to In Silico Function Prediction, or How To Use Sequence
and Structure Information To Predict Protein Function},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {10},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000160},
doi = {10.1371/JOURNAL.PCBI.1000160},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/PuntaO08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LussierLROPBK08,
author = {Yves A. Lussier and
Younghee Lee and
Predrag Radivojac and
Yanay Ofran and
Marco Punta and
Atul J. Butte and
Maricel G. Kann},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2008, Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, 4-8 January 2008},
pages = {228--230},
publisher = {World Scientific},
year = {2008},
url = {http://psb.stanford.edu/psb-online/proceedings/psb08/bioinfo.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LussierLROPBK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SchlessingerPR07,
author = {Avner Schlessinger and
Marco Punta and
Burkhard Rost},
title = {Natively unstructured regions in proteins identified from contact
predictions},
journal = {Bioinform.},
volume = {23},
number = {18},
pages = {2376--2384},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm349},
doi = {10.1093/BIOINFORMATICS/BTM349},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SchlessingerPR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KannOPR07,
author = {Maricel G. Kann and
Yanay Ofran and
Marco Punta and
Predrag Radivojac},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2007},
pages = {1--3},
publisher = {World Scientific},
year = {2007},
url = {http://psb.stanford.edu/psb-online/proceedings/psb07/intro-protein.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KannOPR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/KannOPR06,
author = {Maricel G. Kann and
Yanay Ofran and
Marco Punta and
Predrag Radivojac},
editor = {Russ B. Altman and
Tiffany Murray and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {Session Introduction},
booktitle = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2006},
pages = {351--353},
publisher = {World Scientific},
year = {2006},
url = {http://psb.stanford.edu/psb-online/proceedings/psb06/intro-protein.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/KannOPR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PuntaR05,
author = {Marco Punta and
Burkhard Rost},
title = {PROFcon: novel prediction of long-range contacts},
journal = {Bioinform.},
volume = {21},
number = {13},
pages = {2960--2968},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti454},
doi = {10.1093/BIOINFORMATICS/BTI454},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PuntaR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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