{"id":"https://openalex.org/W2936496314","doi":"https://doi.org/10.1142/s0219720019500197","title":"PyPredT6: A python-based prediction tool for identification of Type VI effector proteins","display_name":"PyPredT6: A python-based prediction tool for identification of Type VI effector proteins","publication_year":2019,"publication_date":"2019-04-10","ids":{"openalex":"https://openalex.org/W2936496314","doi":"https://doi.org/10.1142/s0219720019500197","mag":"2936496314","pmid":"https://pubmed.ncbi.nlm.nih.gov/31288641"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019500197","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500197","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080371731","display_name":"Rishika Sen","orcid":"https://orcid.org/0000-0001-6549-015X"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Rishika Sen","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India","institution_ids":["https://openalex.org/I6498739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068311817","display_name":"Losiana Nayak","orcid":"https://orcid.org/0000-0003-1154-2561"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Losiana Nayak","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India","institution_ids":["https://openalex.org/I6498739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000655826","display_name":"Rajat K. De","orcid":"https://orcid.org/0000-0001-6080-1131"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Rajat K. De","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India"],"raw_orcid":"https://orcid.org/0000-0001-6080-1131","affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, 103 B.T. Road, Kolkata-700108, India","institution_ids":["https://openalex.org/I6498739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5080371731"],"corresponding_institution_ids":["https://openalex.org/I6498739"],"apc_list":null,"apc_paid":null,"fwci":1.7235,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.81535831,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"17","issue":"03","first_page":"1950019","last_page":"1950019"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11684","display_name":"Vibrio bacteria research studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11684","display_name":"Vibrio bacteria research studies","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12232","display_name":"Yersinia bacterium, plague, ectoparasites research","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.9602470397949219},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.776790976524353},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.674964427947998},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6095920205116272},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5802786350250244},{"id":"https://openalex.org/keywords/type-three-secretion-system","display_name":"Type three secretion system","score":0.5119534730911255},{"id":"https://openalex.org/keywords/vibrio-cholerae","display_name":"Vibrio cholerae","score":0.5067933201789856},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.487050324678421},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3221074938774109},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23523548245429993},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21958434581756592},{"id":"https://openalex.org/keywords/virulence","display_name":"Virulence","score":0.1697463095188141},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.16354885697364807},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16159743070602417},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.13550147414207458}],"concepts":[{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.9602470397949219},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.776790976524353},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.674964427947998},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6095920205116272},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5802786350250244},{"id":"https://openalex.org/C130211564","wikidata":"https://www.wikidata.org/wiki/Q21199165","display_name":"Type three secretion system","level":4,"score":0.5119534730911255},{"id":"https://openalex.org/C2778643871","wikidata":"https://www.wikidata.org/wiki/Q160821","display_name":"Vibrio cholerae","level":3,"score":0.5067933201789856},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.487050324678421},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3221074938774109},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23523548245429993},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21958434581756592},{"id":"https://openalex.org/C60987743","wikidata":"https://www.wikidata.org/wiki/Q1460232","display_name":"Virulence","level":3,"score":0.1697463095188141},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.16354885697364807},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16159743070602417},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.13550147414207458},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D014734","descriptor_name":"Vibrio cholerae","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D015010","descriptor_name":"Yersinia pestis","qualifier_ui":"Q000472","qualifier_name":"pathogenicity","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058947","descriptor_name":"Bacterial Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058947","descriptor_name":"Bacterial Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058947","descriptor_name":"Bacterial Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720019500197","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019500197","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31288641","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31288641","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320767","display_name":"University Grants Commission","ror":"https://ror.org/04p800546"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1520812622","https://openalex.org/W1530147790","https://openalex.org/W1983690863","https://openalex.org/W1988272131","https://openalex.org/W1996480990","https://openalex.org/W1996609261","https://openalex.org/W1997870466","https://openalex.org/W2008708467","https://openalex.org/W2016645527","https://openalex.org/W2024077215","https://openalex.org/W2025635459","https://openalex.org/W2032522809","https://openalex.org/W2050745211","https://openalex.org/W2055764609","https://openalex.org/W2063274819","https://openalex.org/W2068532894","https://openalex.org/W2081413516","https://openalex.org/W2087075211","https://openalex.org/W2095131353","https://openalex.org/W2102357455","https://openalex.org/W2115434912","https://openalex.org/W2130599662","https://openalex.org/W2132791018","https://openalex.org/W2142120104","https://openalex.org/W2155331065","https://openalex.org/W2156237648","https://openalex.org/W2157825442","https://openalex.org/W2163670463","https://openalex.org/W2170482677","https://openalex.org/W2171526970","https://openalex.org/W2336505047","https://openalex.org/W2532873024","https://openalex.org/W2560746362","https://openalex.org/W2582563843","https://openalex.org/W2588467130","https://openalex.org/W2620636232","https://openalex.org/W2622345236","https://openalex.org/W2756038181","https://openalex.org/W2791378714","https://openalex.org/W2898454434","https://openalex.org/W4246984456","https://openalex.org/W4251184400"],"related_works":["https://openalex.org/W2153919606","https://openalex.org/W2470108822","https://openalex.org/W3216004349","https://openalex.org/W4224305457","https://openalex.org/W2116909324","https://openalex.org/W4244161128","https://openalex.org/W1549873021","https://openalex.org/W2115997854","https://openalex.org/W1577035833","https://openalex.org/W2120190359"],"abstract_inverted_index":{"Prediction":[0,28],"of":[1,5,25,29,40,48,73,86,107,121],"effector":[2,31,69,90,109],"proteins":[3,32,110],"is":[4,33,124],"paramount":[6],"importance":[7],"due":[8],"to":[9,23,66,117],"their":[10],"crucial":[11],"role":[12],"as":[13],"first-line":[14],"invaders":[15],"while":[16],"establishing":[17],"a":[18,34,60],"pathogen-host":[19],"interaction,":[20],"often":[21],"leading":[22],"infection":[24],"the":[26,38,45,49,81,87,119],"host.":[27],"T6":[30,41,68,108],"new":[35],"challenge":[36],"since":[37],"discovery":[39],"Secretion":[42],"System":[43],"and":[44,83,96,114],"unique":[46,75],"nature":[47],"particular":[50],"secretion":[51],"system.":[52],"In":[53],"this":[54],"paper,":[55],"we":[56,101],"have":[57,102],"first":[58],"designed":[59],"Python-based":[61],"standalone":[62],"tool,":[63],"called":[64],"PyPredT6,":[65],"predict":[67],"proteins.":[70,91],"A":[71],"total":[72],"873":[74],"features":[76,95],"has":[77],"been":[78],"extracted":[79],"from":[80],"peptide":[82],"nucleotide":[84],"sequences":[85],"experimentally":[88],"verified":[89],"Based":[92],"on":[93],"these":[94],"using":[97],"machine":[98],"learning":[99],"algorithms,":[100],"performed":[103],"in":[104,111],"silico":[105],"prediction":[106],"Vibrio":[112],"cholerae":[113],"Yersinia":[115],"pestis":[116],"establish":[118],"applicability":[120],"PyPredT6.":[122],"PyPredT6":[123],"available":[125],"at":[126],"http://projectphd.droppages.com/PyPredT6.html":[127],".":[128]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
