{"id":"https://openalex.org/W2615784817","doi":"https://doi.org/10.32657/10356/70489","title":"Machine learning methods for predicting cancer drug effects from signaling and cell fate data","display_name":"Machine learning methods for predicting cancer drug effects from signaling and cell fate data","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2615784817","doi":"https://doi.org/10.32657/10356/70489","mag":"2615784817"},"language":"en","primary_location":{"id":"doi:10.32657/10356/70489","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/70489","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/70489/1/Mishra_Shital_Kumar_Thesis.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},"type":"dissertation","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dr.ntu.edu.sg/bitstream/10356/70489/1/Mishra_Shital_Kumar_Thesis.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Mishra Shital Kumar","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Mishra Shital Kumar","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9980999827384949,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9940000176429749,"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/cancer-drugs","display_name":"Cancer drugs","score":0.562513530254364},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4642506241798401},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3958282172679901},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39028701186180115},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.36773180961608887},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3408118486404419},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32183748483657837},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.2687048614025116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2533153295516968}],"concepts":[{"id":"https://openalex.org/C3020340455","wikidata":"https://www.wikidata.org/wiki/Q974135","display_name":"Cancer drugs","level":3,"score":0.562513530254364},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4642506241798401},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3958282172679901},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39028701186180115},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36773180961608887},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3408118486404419},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32183748483657837},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.2687048614025116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2533153295516968}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.32657/10356/70489","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/70489","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/70489/1/Mishra_Shital_Kumar_Thesis.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/70489","is_oa":false,"landing_page_url":"http://hdl.handle.net/10356/70489","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"}],"best_oa_location":{"id":"doi:10.32657/10356/70489","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/70489","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/70489/1/Mishra_Shital_Kumar_Thesis.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},"sustainable_development_goals":[{"score":0.6600000262260437,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2615784817.pdf","grobid_xml":"https://content.openalex.org/works/W2615784817.grobid-xml"},"referenced_works_count":140,"referenced_works":["https://openalex.org/W35601271","https://openalex.org/W131856359","https://openalex.org/W572230707","https://openalex.org/W1490846006","https://openalex.org/W1502186090","https://openalex.org/W1502677146","https://openalex.org/W1547259510","https://openalex.org/W1556927008","https://openalex.org/W1563577784","https://openalex.org/W1575978816","https://openalex.org/W1591153142","https://openalex.org/W1749623888","https://openalex.org/W1751719206","https://openalex.org/W1940319397","https://openalex.org/W1967142704","https://openalex.org/W1977470105","https://openalex.org/W1984869292","https://openalex.org/W1987388371","https://openalex.org/W1989466762","https://openalex.org/W1990239056","https://openalex.org/W1992844265","https://openalex.org/W1992999500","https://openalex.org/W1993209630","https://openalex.org/W1994239968","https://openalex.org/W1994930469","https://openalex.org/W1999151221","https://openalex.org/W1999677324","https://openalex.org/W2008033461","https://openalex.org/W2008258707","https://openalex.org/W2008610647","https://openalex.org/W2008757142","https://openalex.org/W2010391389","https://openalex.org/W2010478401","https://openalex.org/W2011912935","https://openalex.org/W2015401980","https://openalex.org/W2018252885","https://openalex.org/W2018823286","https://openalex.org/W2020684750","https://openalex.org/W2023098599","https://openalex.org/W2023165046","https://openalex.org/W2023168478","https://openalex.org/W2029069882","https://openalex.org/W2032351190","https://openalex.org/W2035762060","https://openalex.org/W2038264484","https://openalex.org/W2040625744","https://openalex.org/W2041289840","https://openalex.org/W2042409437","https://openalex.org/W2043398720","https://openalex.org/W2045953361","https://openalex.org/W2047094503","https://openalex.org/W2049980433","https://openalex.org/W2050375893","https://openalex.org/W2050902903","https://openalex.org/W2056827131","https://openalex.org/W2057619131","https://openalex.org/W2059721161","https://openalex.org/W2061019845","https://openalex.org/W2062183865","https://openalex.org/W2071274102","https://openalex.org/W2071890257","https://openalex.org/W2076829732","https://openalex.org/W2077206871","https://openalex.org/W2083394284","https://openalex.org/W2083906562","https://openalex.org/W2089442061","https://openalex.org/W2091921805","https://openalex.org/W2095433609","https://openalex.org/W2096561439","https://openalex.org/W2101168190","https://openalex.org/W2103017472","https://openalex.org/W2107208539","https://openalex.org/W2110256992","https://openalex.org/W2111063183","https://openalex.org/W2111871531","https://openalex.org/W2113685289","https://openalex.org/W2116882627","https://openalex.org/W2117692326","https://openalex.org/W2118151336","https://openalex.org/W2118258530","https://openalex.org/W2123183032","https://openalex.org/W2123691571","https://openalex.org/W2129079547","https://openalex.org/W2130240391","https://openalex.org/W2131532199","https://openalex.org/W2134850272","https://openalex.org/W2136701323","https://openalex.org/W2136853888","https://openalex.org/W2139812092","https://openalex.org/W2140484696","https://openalex.org/W2141998683","https://openalex.org/W2142739240","https://openalex.org/W2143721634","https://openalex.org/W2143880249","https://openalex.org/W2146540050","https://openalex.org/W2150749732","https://openalex.org/W2150821867","https://openalex.org/W2152061559","https://openalex.org/W2153893966","https://openalex.org/W2157350782","https://openalex.org/W2158485828","https://openalex.org/W2161636210","https://openalex.org/W2164298117","https://openalex.org/W2167031279","https://openalex.org/W2170158870","https://openalex.org/W2170272380","https://openalex.org/W2224030228","https://openalex.org/W2279299471","https://openalex.org/W2326648943","https://openalex.org/W2335057960","https://openalex.org/W2562878668","https://openalex.org/W2605543710","https://openalex.org/W2622371525","https://openalex.org/W2739999456","https://openalex.org/W3022584652","https://openalex.org/W4210764451","https://openalex.org/W4237335579","https://openalex.org/W4285225950","https://openalex.org/W6608459909","https://openalex.org/W6629898053","https://openalex.org/W6632666831","https://openalex.org/W6633752671","https://openalex.org/W6635261947","https://openalex.org/W6642149768","https://openalex.org/W6652333458","https://openalex.org/W6652400600","https://openalex.org/W6660529481","https://openalex.org/W6662091134","https://openalex.org/W6663014871","https://openalex.org/W6665783544","https://openalex.org/W6675471023","https://openalex.org/W6680241514","https://openalex.org/W6680672010","https://openalex.org/W6683611753","https://openalex.org/W6701569262","https://openalex.org/W6731298883","https://openalex.org/W6776702130","https://openalex.org/W6819133582","https://openalex.org/W7075687836","https://openalex.org/W7075695058"],"related_works":["https://openalex.org/W4206379684","https://openalex.org/W2366105490","https://openalex.org/W2580680567","https://openalex.org/W2961085424","https://openalex.org/W4285170202","https://openalex.org/W114270996","https://openalex.org/W4249200654","https://openalex.org/W2396656278","https://openalex.org/W3011011760","https://openalex.org/W3205561628"],"abstract_inverted_index":{"An":[0],"important":[1,119],"area":[2],"of":[3,8,18,20,47,53,61,67,78,104,110,143,157,164,183,189,201,211,220,238,273,281,335,338,380,387,400,413,438,475,495,511,527,534,552,555,590,600,623],"research":[4,151],"within":[5],"the":[6,9,16,24,74,79,95,108,155,162,209,262,271,279,325,333,353,368,374,398,418,424,444,496,505,512,522,525,588,605,621,630],"discipline":[7],"Computational":[10],"Systems":[11],"Biology":[12],"is":[13,44,57,152,222,479,545,612],"to":[14,137,153,181,260,320,350,481,486,547,580,614],"investigate":[15,154,423],"mechanisms":[17,412],"determination":[19],"cell":[21,29,49,62,76,92,111,174,184,275,384,415,431,464,498,519,592],"fate.":[22,63,385],"As":[23],"cellular":[25],"development":[26,66],"progresses,":[27],"a":[28,45,54,58,251,292,305,435,472,531,559,597],"goes":[30],"through":[31],"several":[32,549],"phenotypes":[33],"(e.g.":[34,453],"Apoptosis,":[35,42],"Proliferation,":[36],"G1,":[37],"S,":[38],"G2":[39],"and":[40,113,141,191,207,213,284,316,367,371,383,402,448,469,567,584,619],"M).":[41],"which":[43,500],"process":[46],"programmed":[48,274],"death":[50,77],"in":[51,69,94,122,125,131,149,169,245,270,287,324,341,484,541,558,572],"case":[52,60],"healthy":[55],"cell,":[56],"special":[59],"For":[64],"example,":[65],"fingers":[68],"human":[70],"embryo":[71],"occurs":[72],"due":[73],"apoptotic":[75,247,326,445],"cells":[80,127,340,557,628],"between":[81],"digits.":[82],"Regulatory":[83],"networks":[84,99],"such":[85,489],"as":[86,177,490,565],"transcriptional":[87],"regulatory":[88,120,268],"network":[89,322,356,370,447],"for":[90,100,224,332,352,443,460,493,603,617],"regulating":[91,101],"differentiation":[93],"embryonic":[96],"development,":[97],"signaling":[98,128,158,170,205,239,243,382,446],"activity":[102],"level":[103],"proteins,":[105],"etc.,":[106],"determine":[107],"course":[109],"fate":[112,416],"lineage":[114],"commitment.":[115],"Signaling":[116],"pathways":[117,129,159,171,195,240,327],"play":[118],"roles":[121,263],"apoptosis.":[123],"However,":[124],"cancer":[126,150,202,288,381,414,430,591,627],"are":[130,390],"an":[132,246],"atypical":[133],"forms":[134],"that":[135,160,328,539,564],"lead":[136,180],"continuous":[138],"survival,":[139],"growth":[140],"proliferation":[142],"tumor":[144,165,463,556],"cells.":[145,166],"A":[146,217],"major":[147],"objective":[148],"dynamics":[156,200],"influence":[161],"apoptosis":[163,483,543],"The":[167,477,508],"changes":[168,206,510],"supporting":[172],"uncontrolled":[173],"growth,":[175],"termed":[176],"rewiring,":[178],"can":[179,408,501,577],"dysregulation":[182],"fates.":[185],"Hence":[186],"comparative":[187],"analysis":[188,286],"normal":[190],"oncogenic":[192],"signal":[193],"transduction":[194],"may":[196,329],"provide":[197],"insights":[198],"into":[199],"drug":[203,336,426,515,526,553],"induced":[204],"enable":[208],"discovery":[210],"novel":[212,598],"effective":[214,226],"anti-cancer":[215,227,624],"therapies.":[216],"better":[218],"understanding":[219,586],"rewiring":[221,237,323],"essential":[223,267],"developing":[225],"therapeutic":[228],"strategies.":[229],"In":[230],"this":[231],"thesis,":[232],"we":[233,290,422,537],"first":[234],"demonstrate":[235],"how":[236],"regulate":[241],"diverse":[242,429,518],"molecules":[244],"network.":[248],"We":[249,303,433,562],"use":[250,304],"simple":[252],"yet":[253],"intuitive":[254],"differential":[255,312,440],"equation":[256,313],"based":[257,309],"computational":[258,297,606],"model":[259,407,437,451,478,544,576,607],"understand":[261],"played":[264],"by":[265,278,358],"certain":[266],"proteins":[269],"regulation":[272,589],"death.":[276,593],"Inspired":[277],"success":[280],"dynamical":[282],"modeling":[283,294,307,602],"data":[285,364,376,379,459],"biology,":[289],"propose":[291],"hybrid":[293,306,406,601],"approach":[295,308],"combining":[296],"models":[298,315],"with":[299,377,392,524,608],"experimental":[300,393,506],"phosphoproteomics":[301,458],"data.":[302,610],"on":[310,428,517,626],"ordinary":[311,439],"(ODE)":[314],"machine":[317],"learning":[318],"techniques":[319],"map":[321],"be":[330,502,578,615],"responsible":[331],"increase":[334],"sensitivity":[337,554],"tumour":[339],"triple-negative":[342],"breast":[343,462],"cancer.":[344],"Our":[345,594],"method":[346,599],"employs":[347],"Genetic":[348],"Algorithm":[349],"search":[351],"most":[354],"likely":[355],"topologies":[357],"iteratively":[359],"generating":[360],"simulated":[361,375],"protein":[362],"phosphorylation":[363],"using":[365,471,504],"ODEs":[366],"rewired":[369],"then":[372],"fitting":[373],"real":[378,457,535],"Most":[386],"our":[388,405,540,574],"predictions":[389],"consistent":[391],"evidence":[394],"from":[395,456],"literature.":[396,507],"Combining":[397],"strengths":[399],"knowledge-driven":[401],"data-driven":[403],"approaches,":[404],"help":[409],"uncover":[410],"molecular":[411],"at":[417,629],"systems":[419,631],"level.":[420,632],"Secondly,":[421],"context-specific":[425],"effects":[427,516],"lines.":[432],"construct":[434],"knowledge-based":[436],"equations":[441],"(ODEs)":[442],"subsequently":[449],"infer":[450],"parameters":[452,513],"reaction":[454],"rates)":[455],"three":[461,497],"lines,":[465],"i.e.":[466],"BT-20,":[467],"MCF7":[468],"MDA-MB-453":[470],"Bayesian":[473],"framework":[474],"inference.":[476],"used":[480,579],"predict":[482],"response":[485],"various":[487],"perturbations":[488],"caspase":[491],"knockdown":[492],"each":[494],"lines":[499,520],"validated":[503],"inferred":[509],"reveal":[514],"under":[521],"treatment":[523],"Erlotinib.":[528],"Despite":[529],"having":[530],"limited":[532],"amount":[533],"data,":[536],"believe":[538],"silico":[542],"able":[546],"capture":[548],"dynamic":[550],"characteristics":[551],"coherent":[560],"way.":[561],"hope":[563],"new":[566],"larger":[568],"datasets":[569],"become":[570],"available":[571],"future,":[573],"proposed":[575],"gain":[581],"more":[582],"in-depth":[583],"quantitative":[585],"about":[587],"studies":[595],"offer":[596],"linking":[604],"biological":[609],"It":[611],"demonstrated":[613],"promising":[616],"explaining":[618],"predicting":[620],"impact":[622],"therapies":[625]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2017-05-26T00:00:00"}