{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T22:29:46Z","timestamp":1772836186539,"version":"3.50.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,5,13]],"date-time":"2020-05-13T00:00:00Z","timestamp":1589328000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Italian Ministry of Education and University","award":["2010P3S8BR_002"],"award-info":[{"award-number":["2010P3S8BR_002"]}]},{"DOI":"10.13039\/100008968","name":"National Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008968","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the \u2018interactome sequencing\u2019 approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains (\u2018domainome\u2019) or epitopes (\u2018epitome\u2019) from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome\/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural\/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https:\/\/InteractomeSeq.ba.itb.cnr.it\/<\/jats:p>","DOI":"10.1093\/nar\/gkaa363","type":"journal-article","created":{"date-parts":[[2020,5,5]],"date-time":"2020-05-05T19:12:36Z","timestamp":1588705956000},"page":"W200-W207","source":"Crossref","is-referenced-by-count":6,"title":["InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data"],"prefix":"10.1093","volume":"48","author":[{"given":"Simone","family":"Puccio","sequence":"first","affiliation":[{"name":"Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giorgio","family":"Grillo","sequence":"first","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Bari\u00a070100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arianna","family":"Consiglio","sequence":"first","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Bari\u00a070100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria Felicia","family":"Soluri","sequence":"first","affiliation":[{"name":"Department of Health Sciences\u00a0& Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Universit\u00e0 del Piemonte Orientale, Novara\u00a028100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Sblattero","sequence":"first","affiliation":[{"name":"Department of Life Sciences, University of Trieste, Trieste\u00a034100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2714-4744","authenticated-orcid":false,"given":"Diego","family":"Cotella","sequence":"first","affiliation":[{"name":"Department of Health Sciences\u00a0& Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Universit\u00e0 del Piemonte Orientale, Novara\u00a028100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudio","family":"Santoro","sequence":"first","affiliation":[{"name":"Department of Health Sciences\u00a0& Center for TranslationalResearch on Autoimmune and Allergic Disease (CAAD), Universit\u00e0 del Piemonte Orientale, Novara\u00a028100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabino","family":"Liuni","sequence":"first","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Bari\u00a070100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gianluca De","family":"Bellis","sequence":"first","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Segrate (Milan)\u00a020090, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Enrico","family":"Lugli","sequence":"first","affiliation":[{"name":"Laboratory of Translational Immunology, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan), 20089, Italy"},{"name":"Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, IRCCS, Rozzano (Milan)\u00a020089, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clelia","family":"Peano","sequence":"first","affiliation":[{"name":"Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, Rozzano (Milan)\u00a020089, Italy"},{"name":"Genomic Unit, Humanitas Clinical and Research Center, IRCCS,Rozzano (Milan)\u00a020089, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1861-8947","authenticated-orcid":false,"given":"Flavio","family":"Licciulli","sequence":"first","affiliation":[{"name":"Institute for Biomedical Technologies, National Research Council, Bari\u00a070100, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,5,13]]},"reference":[{"key":"2020062614035830300_B1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1128\/IAI.05472-11","article-title":"The intact dupA cluster is a more reliable Helicobacter pylori virulence marker than dupA alone","volume":"80","author":"Jung","year":"2012","journal-title":"Infect. Immun."},{"key":"2020062614035830300_B2","doi-asserted-by":"crossref","first-page":"11221","DOI":"10.3748\/wjg.v21.i40.11221","article-title":"Diagnosis of helicobacter pylori infection: current options and developments","volume":"21","author":"Wang","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"2020062614035830300_B3","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1111\/j.1432-1033.1994.tb20025.x","article-title":"Display of expression products of cDNA libraries on phage surfaces: a versatile screening system for selective isolation of genes by specific gene-product\/ligand interaction","volume":"226","author":"Crameri","year":"1994","journal-title":"Eur. J. Biochem."},{"key":"2020062614035830300_B4","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0022-1759(99)00139-8","article-title":"Phage display of cDNA repertoires: The pVI display system and its applications for the selection of immunogenic ligands","volume":"231","author":"Hufton","year":"1999","journal-title":"J. Immunol. Methods"},{"key":"2020062614035830300_B5","first-page":"378","article-title":"Surface expression and ligand-based selection of cDNAs fused to filamentous phage gene VI","volume":"13","author":"Jespers","year":"1995","journal-title":"Bio\/Technology"},{"key":"2020062614035830300_B6","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1016\/S0022-2836(02)00851-3","article-title":"Searching for DNA-protein interactions by lambda phage display","volume":"322","author":"Cicchini","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2020062614035830300_B7","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1007\/s00253-009-2277-0","article-title":"New perspective for phage display as an efficient and versatile technology of functional proteomics","volume":"85","author":"Li","year":"2010","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"2020062614035830300_B8","doi-asserted-by":"crossref","first-page":"e110","DOI":"10.1093\/nar\/gkq052","article-title":"Rapid interactome profiling by massive sequencing","volume":"38","author":"Di\u00a0Niro","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020062614035830300_B9","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.2144\/04366RR03","article-title":"Phage display of cDNA libraries: enrichment of cDNA expression using open reading frame selection","volume":"36","author":"Faix","year":"2004","journal-title":"BioTechniques"},{"key":"2020062614035830300_B10","doi-asserted-by":"crossref","first-page":"335","DOI":"10.2144\/000112225","article-title":"Enrichment of open reading frames presented on bacteriophage M13 using Hyperphage","volume":"41","author":"Hust","year":"2006","journal-title":"BioTechniques"},{"key":"2020062614035830300_B11","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1007\/978-1-4939-7447-4_27","article-title":"ORFeome phage display","volume":"1701","author":"Zantow","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"2020062614035830300_B12","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.clim.2013.04.009","article-title":"Profiling celiac disease antibody repertoire","volume":"148","author":"D\u2019Angelo","year":"2013","journal-title":"Clin. Immunol."},{"key":"2020062614035830300_B13","doi-asserted-by":"crossref","first-page":"e1614856","DOI":"10.1080\/2162402X.2019.1614856","article-title":"High-throughput assessment of the antibody profile in ovarian cancer ascitic fluids","volume":"8","author":"Antony","year":"2019","journal-title":"Oncoimmunology"},{"key":"2020062614035830300_B14","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1080\/15476286.2015.1107702","article-title":"Identification of novel proteins binding the AU-rich element of \u03b1-prothymosin mRNA through the selection of open reading frames (RIDome)","volume":"12","author":"Patrucco","year":"2015","journal-title":"RNA Biol."},{"key":"2020062614035830300_B15","doi-asserted-by":"crossref","first-page":"13572","DOI":"10.1096\/fj.201901618RR","article-title":"The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs","volume":"33","author":"Fasolo","year":"2019","journal-title":"FASEB J."},{"key":"2020062614035830300_B16","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/msb4100134","article-title":"Large-scale mapping of human protein-protein interactions by mass spectrometry","volume":"3","author":"Ewing","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2020062614035830300_B17","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1107\/S1399004715015680","article-title":"Selecting soluble\/foldable protein domains through single-gene or genomic ORF filtering: Structure of the head domain of Burkholderia pseudomallei antigen BPSL2063","volume":"71","author":"Gourlay","year":"2015","journal-title":"Acta Crystallogr. Sect. D Biol. Crystallogr."},{"key":"2020062614035830300_B18","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2164-12-S1-S5","article-title":"Filtering \u2018genic\u2019 open reading frames from genomic DNA samples for advanced annotation","volume":"15","author":"D\u2019Angelo","year":"2011","journal-title":"BMC Genomics"},{"key":"2020062614035830300_B19","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2105-14-S7-S10","article-title":"NGS-Trex: Next generation sequencing transcriptome profile explorer","volume":"14","author":"Boria","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2020062614035830300_B20","doi-asserted-by":"crossref","first-page":"e308","DOI":"10.1038\/emm.2017.22","article-title":"Next-generation sequencing enables the discovery of more diverse positive clones from a phage-displayed antibody library","volume":"49","author":"Yang","year":"2017","journal-title":"Exp. Mol. Med."},{"key":"2020062614035830300_B21","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"2020062614035830300_B22","first-page":"56981","article-title":"Interactome-Seq: A protocol for domainome library construction, validation and selection by phage display and next generation sequencing","volume":"3","author":"Soluri","year":"2018","journal-title":"J. Vis. Exp."},{"key":"2020062614035830300_B23","doi-asserted-by":"crossref","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"2020062614035830300_B24","doi-asserted-by":"crossref","first-page":"7762","DOI":"10.1093\/nar\/gkv784","article-title":"High speed BLASTN: An accelerated MegaBLAST search tool","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020062614035830300_B25","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1038\/nbt.3519","article-title":"Near-optimal probabilistic RNA-seq quantification","volume":"34","author":"Bray","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2020062614035830300_B26","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1186\/s12864-018-4869-5","article-title":"Limitations of alignment-free tools in total RNA-seq quantification","volume":"19","author":"Wu","year":"2018","journal-title":"BMC Genomics."},{"key":"2020062614035830300_B27","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: A flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2020062614035830300_B28","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2009","journal-title":"Bioinformatics"},{"key":"2020062614035830300_B29","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/s13059-016-0924-1","article-title":"JBrowse: a dynamic web platform for genome visualization and analysis","volume":"17","author":"Buels","year":"2016","journal-title":"Genome Biol."},{"key":"2020062614035830300_B30","doi-asserted-by":"crossref","first-page":"e94","DOI":"10.1038\/oncsis.2014.6","article-title":"Lamin B2 prevents chromosome instability by ensuring proper mitotic chromosome segregation","volume":"3","author":"Kuga","year":"2014","journal-title":"Oncogenesis"},{"key":"2020062614035830300_B31","doi-asserted-by":"crossref","first-page":"e11","DOI":"10.1016\/j.devcel.2020.01.030","article-title":"Lamin B2 levels regulate polyploidization of cardiomyocyte nuclei and myocardial regeneration","volume":"53","author":"Han","year":"2020","journal-title":"Dev Cell."},{"key":"2020062614035830300_B32","doi-asserted-by":"crossref","first-page":"7672","DOI":"10.2174\/0929867325666180629123117","article-title":"Development and application of computational methods in phage display technology","volume":"26","author":"He","year":"2018","journal-title":"Curr. Med. Chem."},{"key":"2020062614035830300_B33","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1002\/pmic.200300680","article-title":"RELIC - a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites","volume":"4","author":"Mandava","year":"2004","journal-title":"Proteomics"},{"key":"2020062614035830300_B34","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1002\/bip.360360513","article-title":"Mapping epitopes on protein surfaces","volume":"36","author":"Pizzi","year":"1995","journal-title":"Biopolymers"},{"key":"2020062614035830300_B35","first-page":"71","article-title":"DNASTAR\u2019s Lasergene sequence analysis software","volume":"132","author":"Burland","year":"2000","journal-title":"Methods Mol. Biol."},{"key":"2020062614035830300_B36","doi-asserted-by":"crossref","first-page":"1344","DOI":"10.1110\/ps.0237103","article-title":"SiteLight: binding-site prediction using phage display libraries","volume":"12","author":"Halperin","year":"2003","journal-title":"Protein Sci."},{"key":"2020062614035830300_B37","doi-asserted-by":"crossref","first-page":"e967","DOI":"10.1371\/journal.pone.0000967","article-title":"SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins","volume":"2","author":"Edwards","year":"2007","journal-title":"PLoS One"},{"key":"2020062614035830300_B38","doi-asserted-by":"crossref","first-page":"e0155244","DOI":"10.1371\/journal.pone.0155244","article-title":"PHASTpep: analysis software for discovery of cell-selective peptides via phage display and next-generation sequencing","volume":"11","author":"Brinton","year":"2016","journal-title":"PLoS One"},{"key":"2020062614035830300_B39","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.3389\/fphys.2019.01160","article-title":"A computational pipeline for the extraction of actionable biological information from NGS-phage display experiments","volume":"10","author":"Vekris","year":"2019","journal-title":"Front. Physiol."},{"key":"2020062614035830300_B40","doi-asserted-by":"crossref","first-page":"e0193332","DOI":"10.1371\/journal.pone.0193332","article-title":"PuLSE: quality control and quantification of peptide sequences explored by phage display libraries","volume":"13","author":"Shave","year":"2018","journal-title":"PLoS One"},{"key":"2020062614035830300_B41","doi-asserted-by":"crossref","first-page":"1214","DOI":"10.1038\/s41598-018-19439-2","article-title":"Compositional bias in na\u00efve and chemically-modified phage-displayed libraries uncovered by paired-end deep sequencing","volume":"8","author":"He","year":"2018","journal-title":"Sci. Rep."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W200\/33432924\/gkaa363.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/W1\/W200\/33432924\/gkaa363.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,6,27]],"date-time":"2020-06-27T06:19:52Z","timestamp":1593238792000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/W1\/W200\/5836767"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,5,13]]},"references-count":41,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2020,5,13]]},"published-print":{"date-parts":[[2020,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa363","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,2]]},"published":{"date-parts":[[2020,5,13]]}}}