Author details

Full Name

Marco Punta

Affiliation

ORCID

Career Start Year

2002

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37350667	Preexisting Immunity Drives the Response to Neoadjuvant Chemotherapy in Esophageal Adenocarcinoma.		2023
37539479	Phase II trial of hypomethylating agent combined with nivolumab for acute myeloid leukaemia relapse after allogeneic haematopoietic cell transplantation-Immune signature correlates with response.		2023
34968022	Solution Structure of the BPSL1445 Protein of <i>Burkholderia pseudomallei</i> Reveals the SYLF Domain Three-Dimensional Fold.	ACS Chem Biol	2022
36260616	DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets.	PLoS Comput Biol	2022
33711918	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
33133066	The Immunogenic Potential of Recurrent Cancer Drug Resistance Mutations: An <i>In Silico</i> Study.	Front Immunol	2020
31949146	Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer.	Nat Commun	2020
31996672	Author Correction: Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer.	Nat Commun	2020
32699032	Clinical <i>BRCA1/2</i> Reversion Analysis Identifies Hotspot Mutations and Predicted Neoantigens Associated with Therapy Resistance.	Cancer Discov	2020
31375105	Identification of single nucleotide variants using position-specific error estimation in deep sequencing data.	BMC Med Genomics	2019
31287991	Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer.	Cancer Cell	2019
29792261	Structure-based analysis of CysZ-mediated cellular uptake of sulfate.	Elife	2018
30254278	Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity.	Nat Commun	2018
28327965	Carbon dating cancer: defining the chronology of metastatic progression in colorectal cancer.	Ann Oncol	2017
26673716	The Pfam protein families database: towards a more sustainable future.	Nucleic Acids Res	2016
27115632	Homology-Based Annotation of Large Protein Datasets.	Methods in Molecular Biology	2016
25348407	Genome3D: exploiting structure to help users understand their sequences.	Nucleic Acids Res	2015
25592227	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
25502193	Prediction and analysis of intrinsically disordered proteins.	Methods in Molecular Biology	2015
25614388	The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.	Brief Bioinform	2015
25428371	The InterPro protein families database: the classification resource after 15 years.	Nucleic Acids Res	2015
25044324	Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.	Protein Sci	2014
24383880	New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.	BMC Bioinformatics	2014
24288371	Pfam: the protein families database.	Nucleic Acids Res	2014
24799431	PredictProtein--an open resource for online prediction of protein structural and functional features.	Nucleic Acids Res	2014
23451277	The SHOCT domain: a widespread domain under-represented in model organisms.	PLoS One	2013
24189229	An estimated 5% of new protein structures solved today represent a new Pfam family.	Acta Crystallogr D Biol Crystallogr	2013
24274019	LUD, a new protein domain associated with lactate utilization.	BMC Bioinformatics	2013
23603847	The challenge of increasing Pfam coverage of the human proteome.	Database (Oxford)	2013
23598997	Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.	Nucleic Acids Res	2013
23376229	Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.	J Proteomics	2013
22096229	InterPro in 2011: new developments in the family and domain prediction database.	Nucleic Acids Res	2012
22434837	AntiFam: a tool to help identify spurious ORFs in protein annotation.	Database (Oxford)	2012
22693626	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
22622032	Structural genomics plucks high-hanging membrane proteins.	Curr Opin Struct Biol	2012
22127870	The Pfam protein families database.	Nucleic Acids Res	2012
21514145	Protein disorder--a breakthrough invention of evolution?	Curr Opin Struct Biol	2011
21482623	Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy.	Genome Res	2011
21471968	Crystal structure of a phosphorylation-coupled saccharide transporter.	Nature	2011
21317882	Crystal structure of a potassium ion transporter, TrkH.	Nature	2011
19927321	Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.	Proteins	2010
20690043	The New York Consortium on Membrane Protein Structure (NYCOMPS): a high-throughput platform for structural genomics of integral membrane proteins.	J Struct Funct Genomics	2010
20981093	Homologue structure of the SLAC1 anion channel for closing stomata in leaves.	Nature	2010
19859826	Structural genomics target selection for the New York consortium on membrane protein structure.	J Struct Funct Genomics	2009
19209228	Improved disorder prediction by combination of orthogonal approaches.	PLoS One	2009
19067583	Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome.	J Proteome Res	2009
19191354	Structural genomics reveals EVE as a new ASCH/PUA-related domain.	Proteins	2009
18635571	MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.	Bioinformatics	2008
19065812	Neural networks predict protein structure and function.	Methods Mol Biol	2008
19015738	Erratum.	PLoS Computational Biology	2008