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Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation

BMC Bioinformatics
2021 | Journal article
EID:

2-s2.0-85102388810

Part of ISSN: 14712105
Contributors: Russo, E.T.; Laio, A.; Punta, M.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Author Correction: Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer (Nature Communications, (2020), 11, 1, (139), 10.1038/s41467-019-13915-7)

Nature Communications
2020 | Journal article
EID:

2-s2.0-85078659690

Part of ISSN: 20411723
Contributors: von Loga, K.; Woolston, A.; Punta, M.; Barber, L.J.; Griffiths, B.; Semiannikova, M.; Spain, G.; Challoner, B.; Fenwick, K.; Simon, R. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Clinical brca1/2 reversion analysis identifies hotspot mutations and predicted neoantigens associated with therapy resistance

Cancer Discovery
2020 | Journal article
EID:

2-s2.0-85089866251

Part of ISSN: 21598290 21598274
Contributors: Pettitt, S.J.; Frankum, J.R.; Punta, M.; Lise, S.; Alexander, J.; Chen, Y.; Yap, T.A.; Haider, S.; Tutt, A.N.J.; Lord, C.J.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer

Nature Communications
2020 | Journal article
EID:

2-s2.0-85077941654

Part of ISSN: 20411723
Contributors: von Loga, K.; Woolston, A.; Punta, M.; Barber, L.J.; Griffiths, B.; Semiannikova, M.; Spain, G.; Challoner, B.; Fenwick, K.; Simon, R. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The Immunogenic Potential of Recurrent Cancer Drug Resistance Mutations: An In Silico Study

Frontiers in Immunology
2020 | Journal article
EID:

2-s2.0-85093928432

Part of ISSN: 16643224
Contributors: Punta, M.; Jennings, V.A.; Melcher, A.A.; Lise, S.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer

Cancer Cell
2019 | Journal article
EID:

2-s2.0-85066851075

Part of ISSN: 18783686 15356108
Contributors: Woolston, A.; Khan, K.; Spain, G.; Barber, L.J.; Griffiths, B.; Gonzalez-Exposito, R.; Hornsteiner, L.; Punta, M.; Patil, Y.; Newey, A. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

BMC Medical Genomics
2019 | Journal article
EID:

2-s2.0-85070189815

Part of ISSN: 17558794
Contributors: Kleftogiannis, D.; Punta, M.; Jayaram, A.; Sandhu, S.; Wong, S.Q.; Gasi Tandefelt, D.; Conteduca, V.; Wetterskog, D.; Attard, G.; Lise, S.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity

Nature Communications
2018 | Journal article
EID:

2-s2.0-85053817687

Part of ISSN: 20411723
Contributors: Heindl, A.; Khan, A.M.; Rodrigues, D.N.; Eason, K.; Sadanandam, A.; Orbegoso, C.; Punta, M.; Sottoriva, A.; Lise, S.; Banerjee, S. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Structure-based analysis of CysZ-mediated cellular uptake of sulfate

eLife
2018 | Journal article
EID:

2-s2.0-85051946054

Part of ISSN: 2050084X
Contributors: Sanghai, Z.A.; Liu, Q.; Clarke, O.B.; Belcher-Dufrisne, M.; Wiriyasermkul, P.; Giese, M.H.; Leal-Pinto, E.; Kloss, B.; Tabuso, S.; Love, J. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Carbon dating cancer: Defining the chronology of metastatic progression in colorectal cancer

Annals of Oncology
2017 | Journal article
EID:

2-s2.0-85021125332

Part of ISSN: 15698041 09237534
Contributors: Lote, H.; Spiteri, I.; Ermini, L.; Vatsiou, A.; Roy, A.; McDonald, A.; Maka, N.; Balsitis, M.; Bose, N.; Simbolo, M. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Homology-based annotation of large protein datasets

Methods in Molecular Biology
2016 | Book chapter
EID:

2-s2.0-84985024335

Part of ISSN: 10643745
Contributors: Punta, M.; Mistry, J.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The Pfam protein families database: Towards a more sustainable future

Nucleic Acids Research
2016 | Journal article
EID:

2-s2.0-84976865403

Part of ISSN: 13624962 03051048
Contributors: Finn, R.D.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Mistry, J.; Mitchell, A.L.; Potter, S.C.; Punta, M.; Qureshi, M.; Sangrador-Vegas, A. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Genome3D: Exploiting structure to help users understand their sequences

Nucleic Acids Research
2015 | Journal article
EID:

2-s2.0-84941051798

Part of ISSN: 13624962 03051048
Contributors: Lewis, T.E.; Sillitoe, I.; Andreeva, A.; Blundell, T.L.; Buchan, D.W.A.; Chothia, C.; Cozzetto, D.; Dana, J.M.; Filippis, I.; Gough, J. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

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

BMC Bioinformatics
2015 | Journal article
EID:

2-s2.0-84926289314

Part of ISSN: 14712105
Contributors: Natarajan, P.; Punta, M.; Kumar, A.; Yeh, A.P.; Godzik, A.; Aravind, L.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The InterPro protein families database: The classification resource after 15 years

Nucleic Acids Research
2015 | Journal article
EID:

2-s2.0-84946074739

Part of ISSN: 13624962 03051048
Contributors: Mitchell, A.; Chang, H.-Y.; Daugherty, L.; Fraser, M.; Hunter, S.; Lopez, R.; McAnulla, C.; McMenamin, C.; Nuka, G.; Pesseat, S. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake

Protein Science
2014 | Journal article
EID:

2-s2.0-84928969903

Part of ISSN: 1469896X 09618368
Contributors: Kumar, A.; Punta, M.; Axelrod, H.L.; Das, D.; Farr, C.L.; Grant, J.C.; Chiu, H.-J.; Miller, M.D.; Coggill, P.C.; Klock, H.E. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

BMC Bioinformatics
2014 | Journal article
EID:

2-s2.0-84891933049

Part of ISSN: 14712105
Contributors: Trame, C.B.; Chang, Y.; Axelrod, H.L.; Eberhardt, R.Y.; Coggill, P.; Punta, M.; Rawlings, N.D.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Pfam: The protein families database

Nucleic Acids Research
2014 | Journal article
EID:

2-s2.0-84891782659

Part of ISSN: 03051048 13624962
Contributors: Finn, R.D.; Bateman, A.; Clements, J.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Heger, A.; Hetherington, K.; Holm, L.; Mistry, J. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Prediction and analysis of intrinsically disordered proteins

Structural Proteomics: High-Throughput Methods: Second Edition
2014 | Book chapter
EID:

2-s2.0-84954616522

Contributors: Punta, M.; Simon, I.; Dosztányi, Z.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

PredictProtein - An open resource for online prediction of protein structural and functional features

Nucleic Acids Research
2014 | Journal article
EID:

2-s2.0-84904418029

Part of ISSN: 13624962 03051048
Contributors: Yachdav, G.; Kloppmann, E.; Kajan, L.; Hecht, M.; Goldberg, T.; Hamp, T.; Hönigschmid, P.; Schafferhans, A.; Roos, M.; Bernhofer, M. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam

Briefings in Bioinformatics
2014 | Journal article
EID:

2-s2.0-84941790190

Part of ISSN: 14774054 14675463
Contributors: Chiang, Z.; Vastermark, A.; Punta, M.; Coggill, P.C.; Mistry, J.; Finn, R.D.; Saier, M.H.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

An estimated 5% of new protein structures solved today represent a new Pfam family

Acta Crystallographica Section D: Biological Crystallography
2013 | Journal article
EID:

2-s2.0-84887378313

Part of ISSN: 09074449 13990047
Contributors: Mistry, J.; Kloppmann, E.; Rost, B.; Punta, M.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

Nucleic Acids Research
2013 | Journal article
EID:

2-s2.0-84880213068

Part of ISSN: 03051048 13624962
Contributors: Mistry, J.; Finn, R.D.; Eddy, S.R.; Bateman, A.; Punta, M.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report

Journal of Proteomics
2013 | Journal article
EID:

2-s2.0-84879501266

Part of ISSN: 18743919 18767737
Contributors: Perez-Riverol, Y.; Hermjakob, H.; Kohlbacher, O.; Martens, L.; Creasy, D.; Cox, J.; Leprevost, F.; Shan, B.P.; Pérez-Nueno, V.I.; Blazejczyk, M. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

LUD, a new protein domain associated with lactate utilization

BMC Bioinformatics
2013 | Journal article
EID:

2-s2.0-84888191271

Part of ISSN: 14712105
Contributors: Hwang, W.C.; Bakolitsa, C.; Punta, M.; Coggill, P.C.; Bateman, A.; Axelrod, H.L.; Rawlings, N.D.; Sedova, M.; Peterson, S.N.; Eberhardt, R.Y. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The challenge of increasing Pfam coverage of the human proteome

Database
2013 | Journal article
EID:

2-s2.0-84891791773

Part of ISSN: 17580463
Contributors: Mistry, J.; Coggill, P.; Eberhardt, R.Y.; Deiana, A.; Giansanti, A.; Finn, R.D.; Bateman, A.; Punta, M.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The SHOCT Domain: A Widespread Domain Under-Represented in Model Organisms

PLoS ONE
2013 | Journal article
EID:

2-s2.0-84874378790

Part of ISSN: 19326203
Contributors: Eberhardt, R.Y.; Bartholdson, S.J.; Punta, M.; Bateman, A.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

AntiFam: A tool to help identify spurious ORFs in protein annotation

Database
2012 | Journal article
EID:

2-s2.0-84864030677

Part of ISSN: 17580463
Contributors: Eberhardt, R.Y.; Haft, D.H.; Punta, M.; Martin, M.; O'Donovan, C.; Bateman, A.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Erratum: InterPro in 2011: New developments in the family and domain prediction database (Nucleic Acids Research (2011) 40 (D306-D312) DOI: 10.1093/nar/gkr948)

Nucleic Acids Research
2012 | Journal article
EID:

2-s2.0-84861565311

Part of ISSN: 03051048 13624962
Contributors: Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, T.K.; Bateman, A.; Bernard, T.; Binns, D.; Bork, P.; Burge, S. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

InterPro in 2011: New developments in the family and domain prediction database

Nucleic Acids Research
2012 | Journal article
EID:

2-s2.0-84858602406

Part of ISSN: 13624962 03051048
Contributors: Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, T.K.; Bateman, A.; Bernard, T.; Binns, D.; Bork, P.; Burge, S. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Metal binding in proteins: Machine learning complements X-ray absorption spectroscopy

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2012 | Book
EID:

2-s2.0-84866850791

Part of ISSN: 03029743 16113349
Contributors: Lippi, M.; Passerini, A.; Punta, M.; Frasconi, P.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Nmr structure of lipoprotein YxeF from bacillus subtilis reveals a calycin fold and distant homology with the lipocalin blc from escherichia coli

PLoS ONE
2012 | Journal article
EID:

2-s2.0-84861917479

Part of ISSN: 19326203
Contributors: Wu, Y.; Punta, M.; Xiao, R.; Acton, T.B.; Sathyamoorthy, B.; Dey, F.; Fischer, M.; Skerra, A.; Rost, B.; Montelione, G.T. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Structural genomics plucks high-hanging membrane proteins

Current Opinion in Structural Biology
2012 | Journal article
EID:

2-s2.0-84862601592

Part of ISSN: 0959440X 1879033X
Contributors: Kloppmann, E.; Punta, M.; Rost, B.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The Pfam protein families database

Nucleic Acids Research
2012 | Journal article
EID:

2-s2.0-84858077472

Part of ISSN: 03051048 13624962
Contributors: Punta, M.; Coggill, P.C.; Eberhardt, R.Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G.; Clements, J. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Toward community standards in the quest for orthologs

Bioinformatics
2012 | Journal article
EID:

2-s2.0-84859038699

Part of ISSN: 13674803 14602059
Contributors: Dessimoz, C.; Gabaldón, T.; Roos, D.S.; Sonnhammer, E.L.L.; Herrero, J.; Altenhoff, A.; Apweiler, R.; Ashburner, M.; Blake, J.; Boeckmann, B. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy

Genome Research
2011 | Journal article
EID:

2-s2.0-79957939897

Part of ISSN: 10889051 15495469
Contributors: Shi, W.; Punta, M.; Bohon, J.; Sauder, J.M.; D'Mello, R.; Sullivan, M.; Toomey, J.; Abel, D.; Lippi, M.; Passerini, A. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Crystal structure of a phosphorylation-coupled saccharide transporter

Nature
2011 | Journal article
EID:

2-s2.0-79955593495

Part of ISSN: 00280836 14764687
Contributors: Cao, Y.; Jin, X.; Levin, E.J.; Huang, H.; Zong, Y.; Quick, M.; Weng, J.; Pan, Y.; Love, J.; Punta, M. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Crystal structure of a potassium ion transporter, TrkH

Nature
2011 | Journal article
EID:

2-s2.0-79952818073

Part of ISSN: 00280836 14764687
Contributors: Cao, Y.; Jin, X.; Huang, H.; Derebe, M.G.; Levin, E.J.; Kabaleeswaran, V.; Pan, Y.; Punta, M.; Love, J.; Weng, J. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Protein disorder-a breakthrough invention of evolution?

Current Opinion in Structural Biology
2011 | Journal article
EID:

2-s2.0-79958059909

Part of ISSN: 0959440X 1879033X
Contributors: Schlessinger, A.; Schaefer, C.; Vicedo, E.; Schmidberger, M.; Punta, M.; Rost, B.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Homologue structure of the SLAC1 anion channel for closing stomata in leaves

Nature
2010 | Journal article
EID:

2-s2.0-78049413361

Part of ISSN: 00280836 14764687
Contributors: Chen, Y.-H.; Hu, L.; Punta, M.; Bruni, R.; Hillerich, B.; Kloss, B.; Rost, B.; Love, J.; Siegelbaum, S.A.; Hendrickson, W.A.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175

Proteins: Structure, Function and Bioinformatics
2010 | Journal article
EID:

2-s2.0-77949900189

Part of ISSN: 08873585 10970134
Contributors: Singarapu, K.K.; Mills, J.L.; Xiao, R.; Acton, T.; Punta, M.; Fischer, M.; Honig, B.; Rost, B.; Montelione, G.T.; Szyperski, T.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The New York Consortium on Membrane Protein Structure (NYCOMPS): A high-throughput platform for structural genomics of integral membrane proteins

Journal of Structural and Functional Genomics
2010 | Journal article
EID:

2-s2.0-77956613642

Part of ISSN: 1345711X
Contributors: Love, J.; Mancia, F.; Shapiro, L.; Punta, M.; Rost, B.; Girvin, M.; Wang, D.-N.; Zhou, M.; Hunt, J.F.; Szyperski, T. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Improved disorder prediction by combination of orthogonal approaches

PLoS ONE
2009 | Journal article
EID:

2-s2.0-84885949386

Part of ISSN: 19326203
Contributors: Schlessinger, A.; Punta, M.; Yachdav, G.; Kajan, L.; Rost, B.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome

Journal of Proteome Research
2009 | Journal article
EID:

2-s2.0-60849128834

Part of ISSN: 15353893
Contributors: Galea, C.A.; High, A.A.; Obenauer, J.C.; Mlshra, A.; Park, C.-G.; Punta, M.; Schlesslnger, A.; Jing, M.; Rost, B.; Slaughter, C.A. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Structural genomics reveals EVE as a new ASCH/PUA-related domain

Proteins: Structure, Function and Bioinformatics
2009 | Journal article
EID:

2-s2.0-66149121080

Part of ISSN: 08873585 10970134
Contributors: Bertonati, C.; Punta, M.; Fischer, M.; Yachdav, G.; Forouhar, F.; Zhou, W.; Kuzin, A.P.; Seetharaman, J.; Abashidze, M.; Ramelot, T.A. et al.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Structural genomics target selection for the New York consortium on membrane protein structure

Journal of Structural and Functional Genomics
2009 | Journal article
EID:

2-s2.0-71049118492

Part of ISSN: 1345711X
Contributors: Punta, M.; Love, J.; Handelman, S.; Hunt, J.F.; Shapiro, L.; Hendrickson, W.A.; Rost, B.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

MetalDetector: A web server for predicting metal-binding sites and disulfide bridges in proteins from sequence

Bioinformatics
2008 | Journal article
EID:

2-s2.0-51749116964

Part of ISSN: 13674803 14602059
Contributors: Lippi, M.; Passerini, A.; Punta, M.; Rost, B.; Frasconi, P.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Molecular bioinformatics for disease: Protein interactions and phenomics

Pacific Symposium on Biocomputing 2008, PSB 2008
2008 | Conference paper
EID:

2-s2.0-84873050670

Contributors: Lussier, Y.A.; Lee, Y.; Radivojac, P.; Ofran, Y.; Punta, M.; Butte, A.; Kann, M.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

Neural networks predict protein structure and function

Methods in Molecular Biology
2008 | Book
EID:

2-s2.0-84934439235

Part of ISSN: 10643745
Contributors: Punta, M.; Rost, B.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier

The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function

PLoS Computational Biology
2008 | Journal article
EID:

2-s2.0-55449125498

Part of ISSN: 1553734X 15537358
Contributors: Punta, M.; Ofran, Y.
Source: Self-asserted source
Marco Punta via Scopus - Elsevier
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