Jussi Taipale

About me
Publications
Public outreach and news

About me

Professor of Medical System Biology

Articles

Article: NATURE BIOTECHNOLOGY. 2023;41(2):197-203
A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites
Pihlajamaa P; Kauko O; Sahu B; Kivioja T; Taipale J
Article: CELL GENOMICS. 2022;2(12):100214
Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
Benaglio P; Zhu H; Okino M-L; Yan J; Elgamal R; Nariai N; Beebe E; Korgaonkar K; Qiu Y; Donovan MKR; Chiou J; Wang G; Newsome J; Kaur J; Miller M; Preissl S; Corban S; Aylward A; Taipale J; Ren B; Frazer KA; Sander M; Gaulton KJ
Article: DEVELOPMENTAL CELL. 2022;57(8):1024-1036.e5
Upregulation of ribosome biogenesis via canonical E-boxes is required for Myc-driven proliferation
Zielke N; Vaharautio A; Liu J; Kivioja T; Taipale J
Article: NATURE GENETICS. 2022;54(3):283-294
Sequence determinants of human gene regulatory elements
Sahu B; Hartonen T; Pihlajamaa P; Wei B; Dave K; Zhu F; Kaasinen E; Lidschreiber K; Lidschreiber M; Daub CO; Cramer P; Kivioja T; Taipale J
Article: ELIFE. 2021;10:e75415
Rapid genome editing by CRISPR-Cas9-POLD3 fusion
Reint G; Li Z; Labun K; Keskitalo S; Soppa I; Mamia K; Tolo E; Szymanska M; Meza-Zepeda LA; Lorenz S; Cieslar-Pobuda A; Hu X; Bordin DL; Staerk J; Valen E; Schmierer B; Varjosalo M; Taipale J; Haapaniemi E
Article: CURRENT OPINION IN STRUCTURAL BIOLOGY. 2021;71:171-179
Structural insights into the interaction between transcription factors and the nucleosome
Morgunova E; Taipale J
Article: HUMAN MOLECULAR GENETICS. 2021;30(24):2429-2440
WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas
Aavikko M; Kaasinen E; Andersson N; Pentinmikko N; Sulo P; Donner I; Pihlajamaa P; Kuosmanen A; Bramante S; Katainen R; Sipila LJ; Martin S; Arola J; Carpen O; Heiskanen I; Mecklin J-P; Taipale J; Ristimaki A; Lehti K; Gucciardo E; Katajisto P; Schalin-Jantti C; Vahteristo P; Aaltonen LA
Article: NATURE COMMUNICATIONS. 2021;12(1):5448
Parity associates with chromosomal damage in uterine leiomyomas
Kuisma H; Bramante S; Rajamaki K; Sipila LJ; Kaasinen E; Kaukomaa J; Palin K; Makinen N; Sjoberg J; Sarvilinna N; Taipale J; Kauppi L; Tumiati M; Hassinen A; Pitkaniemi J; Jalkanen J; Heikkinen S; Pasanen A; Heikinheimo O; Butzow R; Valimaki N; Aaltonen LA
Article: CANCERS. 2021;13(18):4569
Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer
Wu Y; Kroller L; Miao B; Boekhoff H; Bauer AS; Buechler MW; Hackert T; Giese NA; Taipale J; Hoheisel JD
Article: ONCOGENE. 2021;40(36):5533-5547
Human cell transformation by combined lineage conversion and oncogene expression
Sahu B; Pihlajamaa P; Zhang K; Palin K; Ahonen S; Cervera A; Ristimaki A; Aaltonen LA; Hautaniemi S; Taipale J
Article: NATURE. 2021;596(7872):398-403
Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma
Berta DG; Kuisma H; Valimaki N; Raisanen M; Jantti M; Pasanen A; Karhu A; Kaukomaa J; Taira A; Cajuso T; Nieminen S; Penttinen R-M; Ahonen S; Lehtonen R; Mehine M; Vahteristo P; Jalkanen J; Sahu B; Ravantti J; Makinen N; Rajamaki K; Palin K; Taipale J; Heikinheimo O; Butzow R; Kaasinen E; Aaltonen LA
Article: GASTROENTEROLOGY. 2021;161(2):592-607
Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer
Rajamaki K; Taira A; Katainen R; Valimaki N; Kuosmanen A; Plaketti R-M; Seppala TT; Ahtiainen M; Wirta E-V; Vartiainen E; Sulo P; Ravantti J; Lehtipuro S; Granberg KJ; Nykter M; Tanskanen T; Ristimaki A; Koskensalo S; Renkonen-Sinisalo L; Lepisto A; Bohm J; Taipale J; Mecklin J-P; Aavikko M; Palin K; Aaltonen LA
Article: NATURE BIOTECHNOLOGY. 2021;39(4):510-519
A comprehensive library of human transcription factors for cell fate engineering
Ng AHM; Khoshakhlagh P; Arias JER; Pasquini G; Wang K; Swiersy A; Shipman SL; Appleton E; Kiaee K; Kohman RE; Vernet A; Dysart M; Leeper K; Saylor W; Huang JY; Graveline A; Taipale J; Hill DE; Vidal M; Melero-Martin JM; Busskamp V; Church GM
Article: NATURE. 2021;591(7848):147-151
Systematic analysis of binding of transcription factors to noncoding variants
Yan J; Qiu Y; Ribeiro dos Santos AM; Yin Y; Li YE; Vinckier N; Nariai N; Benaglio P; Raman A; Li X; Fan S; Chiou J; Chen F; Frazer KA; Gaulton KJ; Sander M; Taipale J; Ren B
Article: MOLECULAR SYSTEMS BIOLOGY. 2021;17(1):e9873
Transcriptionally active enhancers in human cancer cells
Lidschreiber K; Jung LA; von der Emde H; Dave K; Taipale J; Cramer P; Lidschreiber M
Article: NATURE. 2020;587(7833):240-245
A comparative genomics multitool for scientific discovery and conservation
Genereux DP; Serres A; Armstrong J; Johnson J; Marinescu VD; Muren E; Juan D; Bejerano G; Casewell NR; Chemnick LG; Damas J; Di Palma F; Diekhans M; Fiddes IT; Garber M; Gladyshev VN; Goodman L; Haerty W; Houck ML; Hubley R; Kivioja T; Koepfli K-P; Kuderna LFK; Lander ES; Meadows JRS; Murphy WJ; Nash W; Noh HJ; Nweeia M; Pfenning AR; Pollard KS; Ray DA; Shapiro B; Smit AFA; Springer MS; Steiner CC; Swofford R; Taipale J; Teeling EC; Turner-Maier J; Alfoldi J; Birren B; Ryder OA; Lewin HA; Paten B; Marques-Bonet T; Lindblad-Toh K; Karlsson EK
Article: GENOME RESEARCH. 2020;30(7):962-973
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences
Jolma A; Zhang J; Mondragon E; Morgunova E; Kivioja T; Laverty KU; Yin Y; Zhu F; Bourenkov G; Morris Q; Hughes TR; Maher III LJ; Taipale J
Article: NATURE METHODS. 2020;17(7):685-688
CRISPR-assisted detection of RNA-protein interactions in living cells
Yi W; Li J; Zhu X; Wang X; Fan L; Sun W; Liao L; Zhang J; Li X; Ye J; Chen F; Taipale J; Chan KM; Zhang L; Yan J
Article: INTERNATIONAL JOURNAL OF CANCER. 2020;147(1):189-201
The transcription factor FLI1 promotes cancer progression by affecting cell cycle regulation
Miao B; Bauer AS; Hufnagel K; Wu Y; Trajkovic-Arsic M; Pirona AC; Giese N; Taipale J; Siveke JT; Hoheisel JD; Lueong S
Article: BIOINFORMATICS. 2020;36(9):2690-2696
MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs
Toivonen J; Das PK; Taipale J; Ukkonen E
Article: NATURE. 2020;580(7805):669-672
Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function.
Dodonova SO; Zhu F; Dienemann C; Taipale J; Cramer P
Article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2019;144(5):1364-1376
Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy
Goos H; Fogarty CL; Sahu B; Plagnol V; Rajamaki K; Nurmi K; Liu X; Einarsdottir E; Jouppila A; Pettersson T; Vihinen H; Krjutskov K; Saavalainen P; Jarvinen A; Muurinen M; Greco D; Scala G; Curtis J; Nordstrom D; Flaumenhaft R; Vaarala O; Kovanen PE; Keskitalo S; Ranki A; Kere J; Lehto M; Notarangelo LD; Nejentsev S; Eklund KK; Varjosalo M; Taipale J; Seppanen MRJ
Article: NATURE COMMUNICATIONS. 2019;10(1):1252
Impact of constitutional TET2 haploinsufficiency on molecular and clinical phenotype in humans
Kaasinen E; Kuismin O; Rajamaki K; Ristolainen H; Aavikko M; Kondelin J; Saarinen S; Berta DG; Katainen R; Hirvonen EAM; Karhu A; Taira A; Tanskanen T; Alkodsi A; Taipale M; Morgunova E; Franssila K; Lehtonen R; Makinen M; Aittomaki K; Palotie A; Kurki MI; Pietilainen O; Hilpert M; Saarentaus E; Niinimaki J; Junttila J; Kaikkonen K; Vahteristo P; Skoda RC; Seppanen MRJ; Eklund KK; Taipale J; Kilpivaara O; Aaltonen LA
Article: NATURE. 2018;562(7725):76-81
The interaction landscape between transcription factors and the nucleosome
Zhu F; Farnung L; Kaasinen E; Sahu B; Yin Y; Wei B; Dodonova SO; Nitta KR; Morgunova E; Taipale M; Cramer P; Taipale J
Article: NATURE GENETICS. 2018;50(10):1375-1380
Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer
Orlando G; Law PJ; Cornish AJ; Dobbins SE; Chubb D; Broderick P; Litchfield K; Hariri F; Pastinen T; Osborne CS; Taipale J; Houlston RS
Article: NATURE COMMUNICATIONS. 2018;9(1):3664
Contribution of allelic imbalance to colorectal cancer
Palin K; Pitkanen E; Turunen M; Sahu B; Pihlajamaa P; Kivioja T; Kaasinen E; Valimaki N; Hanninen UA; Cajuso T; Aavikko M; Tuupanen S; Kilpivaara O; van den Berg L; Kondelin J; Tanskanen T; Katainen R; Grau M; Rauanheimo H; Plaketti R-M; Taira A; Sulo P; Hartonen T; Dave K; Schmierer B; Botla S; Sokolova M; Vaharautio A; Gladysz K; Ongen H; Dermitzakis E; Bramsen JB; Orntoft TF; Andersen CL; Ristimaki A; Lepisto A; Renkonen-Sinisalo L; Mecklin J-P; Taipale J; Aaltonen LA
Article: EMBO MOLECULAR MEDICINE. 2018;10(9):emmm201708552
Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer.
Kondelin J; Salokas K; Saarinen L; Ovaska K; Rauanheimo H; Plaketti R-M; Hamberg J; Liu X; Yadav L; Gylfe AE; Cajuso T; Hänninen UA; Palin K; Ristolainen H; Katainen R; Kaasinen E; Tanskanen T; Aavikko M; Taipale M; Taipale J; Renkonen-Sinisalo L; Lepistö A; Koskensalo S; Böhm J; Mecklin J-P; Ongen H; Dermitzakis ET; Kilpivaara O; Vahteristo P; Turunen M; Hautaniemi S; Tuupanen S; Karhu A; Välimäki N; Varjosalo M; Pitkänen E; Aaltonen LA
Article: NATURE BIOTECHNOLOGY. 2018;36(6):521-529
A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility
Wei B; Jolma A; Sahu B; Orre LM; Zhong F; Zhu F; Kivioja T; Sur I; Lehtio J; Taipale M; Taipale J
Article: NATURE MEDICINE. 2018;24(7):927-930
CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response
Haapaniemi E; Botla S; Persson J; Schmierer B; Taipale J
Article: EMBO JOURNAL. 2018;37(10):e96114
Informational limits of biological organisms
Taipale J
Article: NUCLEIC ACIDS RESEARCH (NAR). 2018;46(8):e44
Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets
Toivonen J; Kivioja T; Jolma A; Yin Y; Taipale J; Ukkonen E
Article: ELIFE. 2018;7:e32963
Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima
Morgunova E; Yin Y; Das PK; Jolma A; Zhu F; Popov A; Xu Y; Nilsson L; Taipale J
Article: CURRENT OPINION IN STRUCTURAL BIOLOGY. 2017;47:1-8
Structural perspective of cooperative transcription factor binding
Morgunova E; Taipale J
Article: MOLECULAR SYSTEMS BIOLOGY. 2017;13(10):945
CRISPR/Cas9 screening using unique molecular identifiers
Schmierer B; Botla SK; Zhang J; Turunen M; Kivioja T; Taipale J
Article: JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2017;140(3):782-796
Damaging heterozygous mutations in NFKB1 lead to diverse immunologic phenotypes
Kaustio M; Haapaniemi E; Goos H; Hautala T; Park G; Syrjanen J; Einarsdottir E; Sahu B; Kilpinen S; Rounioja S; Fogarty CL; Glumoff V; Kulmala P; Katayama S; Tamene F; Trotta L; Morgunova E; Krjutskov K; Nurmi K; Eklund K; Lagerstedt A; Helminen M; Martelius T; Mustjoki S; Taipale J; Saarela J; Kere J; Varjosalo M; Seppanen M
Article: CANCER RESEARCH. 2017;77(15):4078-4088
Comprehensive Evaluation of Protein Coding Mononucleotide Microsatellites in Microsatellite-Unstable Colorectal Cancer
Kondelin J; Gylfe AE; Lundgren S; Tanskanen T; Hamberg J; Aavikko M; Palin K; Ristolainen H; Katainen R; Kaasinen E; Taipale M; Taipale J; Renkonen-Sinisalo L; Jarvinen H; Bohm J; Mecklin J-P; Vahteristo P; Tuupanen S; Aaltonen LA; Pitkanen E
Article: ELIFE. 2017;6:e23382
Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth
Dave K; Sur I; Yan J; Zhang J; Kaasinen E; Zhong F; Blaas L; Li X; Kharazi S; Gustafsson C; De Paep A; Mansson R; Taipale J
Article: SCIENCE. 2017;356(6337):eaaj2239
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Yin Y; Morgunova E; Jolma A; Kaasinen E; Sahu B; Khund-Sayeed S; Das PK; Kivioja T; Dave K; Zhong F; Nitta KR; Taipale M; Popov A; Ginno PA; Domcke S; Yan J; Schubeler D; Vinson C; Taipale J
Article: NATURE. 2017;544(7649):245-249
Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates
Mall M; Kareta MS; Chanda S; Ahlenius H; Perotti N; Zhou B; Grieder SD; Ge X; Drake S; Ang CE; Walker BM; Vierbuchen T; Fuentes DR; Brennecke P; Nitta KR; Jolma A; Steinmetz LM; Taipale J; Sudhof TC; Wernig M
Article: HUMAN MUTATION. 2017;38(3):269-274
Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry
Heikkinen T; Kaempjaervi K; Keskitalo S; von Nandelstadh P; Liu X; Rantanen V; Pitkaenen E; Kinnunen M; Kuusanmaeki H; Kontro M; Turunen M; Maekinen N; Taipale J; Heckman C; Lehti K; Mustjoki S; Varjosalo M; Vahteristo P
Article: BIOINFORMATICS. 2017;33(4):514-521
Fast motif matching revisited: high-order PWMs, SNPs and indels
Korhonen JH; Palin K; Taipale J; Ukkonen E
Article: NATURE COMMUNICATIONS. 2017;8:14418
The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression
Liu NQ; ter Huurne M; Nguyen LN; Peng T; Wang S-Y; Studd JB; Joshi O; Ongen H; Bramsen JB; Yan J; Andersen CL; Taipale J; Dermitzakis ET; Houlston RS; Hubner NC; Stunnenberg HG
Article: MOLECULAR SYSTEMS BIOLOGY. 2017;13(2):910
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models
Yang L; Orenstein Y; Jolma A; Yin Y; Taipale J; Shamir R; Rohs R
Article: CELL CYCLE. 2017;16(2):189-199
Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion
Sokolova M; Turunen M; Mortusewicz O; Kivioja T; Herr P; Vaharautio A; Bjorklund M; Taipale M; Helleday T; Taipale J
Article: GENOME RESEARCH. 2016;26(12):1742-1752
Multiparameter functional diversity of human C2H2 zinc finger proteins
Schmitges FW; Radovani E; Najafabadi HS; Barazandeh M; Campitelli LF; Yin Y; Jolma A; Zhong G; Guo H; Kanagalingam T; Dai WF; Taipale J; Emili A; Greenblatt JF; Hughes TR
Article: BRITISH JOURNAL OF CANCER. 2016;115(2):266-272
Mendelian randomisation analysis strongly implicates adiposity with risk of developing colorectal cancer
Jarvis D; Mitchell JS; Law PJ; Palin K; Tuupanen S; Gylfe A; Hanninen UA; Cajuso T; Tanskanen T; Kondelin J; Kaasinen E; Sarin A-P; Kaprio J; Eriksson JG; Rissanen H; Knekt P; Pukkala E; Jousilahti P; Salomaa V; Ripatti S; Palotie A; Jarvinen H; Renkonen-Sinisalo L; Lepisto A; Bohm J; Mecklin J-P; Al-Tassan NA; Palles C; Martin L; Barclay E; Farrington SM; Timofeeva MN; Meyer BF; Wakil SM; Campbell H; Smith CG; Idziaszczyk S; Maughan TS; Kaplan R; Kerr R; Kerr D; Buchanan DD; Win AK; Hopper JL; Jenkins MA; Lindor NM; Newcomb PA; Gallinger S; Conti D; Schumacher F; Casey G; Taipale J; Aaltonen LA; Cheadle JP; Dunlop MG; Tomlinson IP; Houlston RS
Article: HUMAN MOLECULAR GENETICS. 2016;25(11):2349-2359
Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease
Orlando G; Law PJ; Palin K; Tuupanen S; Gylfe A; Hanninen UA; Cajuso T; Tanskanen T; Kondelin J; Kaasinen E; Sarin A-P; Kaprio J; Eriksson JG; Rissanen H; Knekt P; Pukkala E; Jousilahti P; Salomaa V; Ripatti S; Palotie A; Jarvinen H; Renkonen-Sinisalo L; Lepisto A; Bohm J; Mecklin J-P; Al-Tassan NA; Palles C; Martin L; Barclay E; Tenesa A; Farrington S; Timofeeva MN; Meyer BF; Wakil SM; Campbell H; Smith CG; Idziaszczyk S; Maughan TS; Kaplan R; Kerr R; Kerr D; Buchanan DD; Win AK; Hopper J; Jenkins M; Lindor NM; Newcomb PA; Gallinger S; Conti D; Schumacher F; Casey G; Taipale J; Cheadle JP; Dunlop MG; Tomlinson IP; Aaltonen LA; Houlston RS
Article: PLOS PATHOGENS. 2016;12(2):e1005424
Oncogenic Herpesvirus Utilizes Stress-Induced Cell Cycle Checkpoints for Efficient Lytic Replication.
Balistreri G; Viiliäinen J; Turunen M; Diaz R; Lyly L; Pekkonen P; Rantala J; Ojala K; Sarek G; Teesalu M; Denisova O; Peltonen K; Julkunen I; Varjosalo M; Kainov D; Kallioniemi O; Laiho M; Taipale J; Hautaniemi S; Ojala PM
Article: PLOS GENETICS. 2016;12(2):e1005850
Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12
Makinen N; Aavikko M; Heikkinen T; Taipale M; Taipale J; Koivisto-Korander R; Butzow R; Vahteristo P
Article: PROSTATE. 2016;76(1):22-31
Somatic MED12 mutations in prostate cancer and uterine leiomyomas promote tumorigenesis through distinct mechanisms.
Kämpjärvi K; Kim NH; Keskitalo S; Clark AD; von Nandelstadh P; Turunen M; Heikkinen T; Park MJ; Mäkinen N; Kivinummi K; Lintula S; Hotakainen K; Nevanlinna H; Hokland P; Böhling T; Bützow R; Böhm J; Mecklin J-P; Järvinen H; Kontro M; Visakorpi T; Taipale J; Varjosalo M; Boyer TG; Vahteristo P
Article: NATURE COMMUNICATIONS. 2015;6:10050
Structural insights into the DNA-binding specificity of E2F family transcription factors
Morgunova E; Yin Y; Jolma A; Dave K; Schmierer B; Popov A; Eremina N; Nilsson L; Taipale J
Article: NATURE. 2015;527(7578):384-388
DNA-dependent formation of transcription factor pairs alters their binding specificity
Jolma A; Yin Y; Nitta KR; Dave K; Popov A; Taipale M; Enge M; Kivioja T; Morgunova E; Taipale J
Article: NATURE GENETICS. 2015;47(7):818-821
CTCF/cohesin-binding sites are frequently mutated in cancer
Katainen R; Dave K; Pitkanen E; Palin K; Kivioja T; Valimaki N; Gylfe AE; Ristolainen H; Hanninen UA; Cajuso T; Kondelin J; Tanskanen T; Mecklin J-P; Jarvinen H; Renkonen-Sinisalo L; Lepisto A; Kaasinen E; Kilpivaara O; Tuupanen S; Enge M; Taipale J; Aaltonen LA
Article: ELIFE. 2015;4:e04837
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
Nitta KR; Jolma A; Yin Y; Morgunova E; Kivioja T; Akhtar J; Hens K; Toivonen J; Deplancke B; Furlong EEM; Taipale J
Article: NATURE COMMUNICATIONS. 2015;6:6178
Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci
Jaeger R; Migliorini G; Henrion M; Kandaswamy R; Speedy HE; Heindl A; Whiffin N; Carnicer MJ; Broome L; Dryden N; Nagano T; Schoenfelder S; Enge M; Yuan Y; Taipale J; Fraser P; Fletcher O; Houlston RS
Article: BRITISH JOURNAL OF CANCER. 2014;111(8):1657-1662
Identification of 33 candidate oncogenes by screening for base-specific mutations
Tuupanen S; Hanninen UA; Kondelin J; von Nandelstadh P; Cajuso T; Gylfe AE; Katainen R; Tanskanen T; Ristolainen H; Bohm J; Mecklin J-P; Jarvinen H; Renkonen-Sinisalo L; Andersen CL; Taipale M; Taipale J; Vahteristo P; Lehti K; Pitkanen E; Aaltonen LA
Article: INTERNATIONAL JOURNAL OF CANCER. 2014;135(3):611-623
Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer
Cajuso T; Hanninen UA; Kondelin J; Gylfe AE; Tanskanen T; Katainen R; Pitkanen E; Ristolainen H; Kaasinen E; Taipale M; Taipale J; Bohm J; Renkonen-Sinisalo L; Mecklin J-P; Jarvinen H; Tuupanen S; Kilpivaara O; Vahteristo P
Article: CELL REPORTS. 2014;7(3):654-660
Uterine Leiomyoma-Linked MED12 Mutations Disrupt Mediator-Associated CDK Activity
Turunen M; Spaeth JM; Keskitalo S; Park MJ; Kivioja T; Clark AD; Makinen N; Gao F; Palin K; Nurkkala H; Vaharautio A; Aavikko M; Kampjarvi K; Vahteristo P; Kim CA; Aaltonen LA; Varjosalo M; Taipale J; Boyer TG
Article: BRITISH JOURNAL OF CANCER. 2014;110(9):2246-2249
Mutation analysis of components of the Mediator kinase module in MED12 mutation-negative uterine leiomyomas
Makinen N; Heinonen H-R; Sjoberg J; Taipale J; Vahteristo P; Aaltonen LA
Article: ONCOTARGET. 2014;5(3):853-859
Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer
Pitkanen E; Cajuso T; Katainen R; Kaasinen E; Valimaki N; Palin K; Taipale J; Aaltonen LA; Kilpivaara O
Article: NATURE GENETICS. 2014;46(2):126-135
A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding
Huang Q; Whitington T; Gao P; Lindberg JF; Yang Y; Sun J; Vaisanen M-R; Szulkin R; Annala M; Yan J; Egevad LA; Zhang K; Lin R; Jolma A; Nykter M; Manninen A; Wiklund F; Vaarala MH; Visakorpi T; Xu J; Taipale J; Wei G-H
Article: INNATE IMMUNITY. 2013;19(5):516-530
Human kinome analysis reveals novel kinases contributing to virus infection and retinoic-acid inducible gene I-induced type I and type III IFN gene expression
Nousiainen L; Sillanpaeae M; Jiang M; Thompson J; Taipale J; Julkunen I
Article: GASTROENTEROLOGY. 2013;145(3):540-3.e22
Identification of Candidate Oncogenes in Human Colorectal Cancers With Microsatellite Instability
Gylfe AE; Kondelin J; Turunen M; Ristolainen H; Katainen R; Pitkanen E; Kaasinen E; Rantanen V; Tanskanen T; Varjosalo M; Lehtonen H; Palin K; Taipale M; Taipale J; Renkonen-Sinisalo L; Jarvinen H; Bohm J; Mecklin J-P; Ristimaki A; Kilpivaara O; Tuupanen S; Karhu A; Vahteristo P; Aaltonen LA
Article: CELL. 2013;154(4):801-813
Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites
Yan J; Enge M; Whitington T; Dave K; Liu J; Sur I; Schmierer B; Jolma A; Kivioja T; Taipale M; Taipale J
Article: DEVELOPMENT. 2013;140(11):2434-2442
A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila
Bischof J; Bjorklund M; Furger E; Schertel C; Taipale J; Basler K
Article: DEVELOPMENTAL CELL. 2013;25(2):207-219
Systematic Screening of a Drosophila ORF Library In Vivo Uncovers Wnt/Wg Pathway Components
Schertel C; Huang D; Bjorklund M; Bischof J; Yin D; Li R; Wu Y; Zeng R; Wu J; Taipale J; Song H; Basler K
Article: CELL. 2013;152(1-2):327-339
DNA-Binding Specificities of Human Transcription Factors
Jolma A; Yan J; Whitington T; Toivonen J; Nitta KR; Rastas P; Morgunova E; Enge M; Taipale M; Wei G; Palin K; Vaquerizas JM; Vincentelli R; Luscombe NM; Hughes TR; Lemaire P; Ukkonen E; Kivioja T; Taipale J
Article: PLOS GENETICS. 2013;9(10):e1003876
Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer
Gylfe AE; Katainen R; Kondelin J; Tanskanen T; Cajuso T; Hanninen U; Taipale J; Taipale M; Renkonen-Sinisalo L; Jarvinen H; Mecklin J-P; Kilpivaara O; Pitkanen E; Vahteristo P; Tuupanen S; Karhu A; Aaltonen LA
Article: G3: GENES, GENOMES, GENETICS. 2013;3(1):75-90
Transcriptional Networks Controlling the Cell Cycle
Bonke M; Turunen M; Sokolova M; Vaharautio A; Kivioja T; Taipale M; Bjorklund M; Taipale J
Article: SCIENCE. 2012;338(6112):1360-1363
Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors
Sur IK; Hallikas O; Vaharautio A; Yan J; Turunen M; Enge M; Taipale M; Karhu A; Aaltonen LA; Taipale J
Article: CELL DEATH AND DIFFERENTIATION. 2012;19(12):1992-2002
Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis
Nikulenkov F; Spinnler C; Li H; Tonelli C; Shi Y; Turunen M; Kivioja T; Ignatiev I; Kel A; Taipale J; Selivanova G
Article: AMERICAN JOURNAL OF HUMAN GENETICS. 2012;91(3):520-526
Loss of SUFU Function in Familial Multiple Meningioma
Aavikko M; Li S-P; Saarinen S; Alhopuro P; Kaasinen E; Morgunova E; Li Y; Vesanen K; Smith MJ; Evans DGR; Poyhonen M; Kiuru A; Auvinen A; Aaltonen LA; Taipale J; Vahteristo P
Article: CANCER GENETICS. 2012;205(1-2):25-33
Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583
Tuupanen S; Yan J; Turunen M; Gylfe AE; Kaasinen E; Li L; Eng C; Culver DA; Kalady MF; Pennison MJ; Pasche B; Manne U; de la Chapelle A; Hampel H; Henderson BE; Le Marchand L; Hautaniemi S; Askhtorab H; Smoot D; Sandler RS; Keku T; Kupfer SS; Ellis NA; Haiman CA; Taipale J; Aaltonen LA
Article: NATURE METHODS. 2011;9(1):72-74
Counting absolute numbers of molecules using unique molecular identifiers
Kivioja T; Vaharautio A; Karlsson K; Bonke M; Enge M; Linnarsson S; Taipale J
Article: SCIENCE. 2011;334(6053):252-255
MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas
Makinen N; Mehine M; Tolvanen J; Kaasinen E; Li Y; Lehtonen HJ; Gentile M; Yan J; Enge M; Taipale M; Aavikko M; Katainen R; Virolainen E; Bohling T; Koski TA; Launonen V; Sjoberg J; Taipale J; Vahteristo P; Aaltonen LA
Article: SCIENCE SIGNALING. 2011;4(176):pe29
Beyond the Balance of Activator and Repressor
Whitington T; Jolma A; Taipale J
Article: JOURNAL OF CELL SCIENCE. 2011;124(Pt 8):1245-1255
Missing-in-metastasis MIM/MTSS1 promotes actin assembly at intercellular junctions and is required for integrity of kidney epithelia.
Saarikangas J; Mattila PK; Varjosalo M; Bovellan M; Hakanen J; Calzada-Wack J; Tost M; Jennen L; Rathkolb B; Hans W; Horsch M; Hyvönen ME; Perälä N; Fuchs H; Gailus-Durner V; Esposito I; Wolf E; de Angelis MH; Frilander MJ; Savilahti H; Sariola H; Sainio K; Lehtonen S; Taipale J; Salminen M; Lappalainen P
Article: CANCER RESEARCH. 2010;70(20):7851-7861
Fibroblast Growth Factor Receptor 4 Regulates Tumor Invasion by Coupling Fibroblast Growth Factor Signaling to Extracellular Matrix Degradation
Sugiyama N; Varjosalo M; Meller P; Lohi J; Hyytiainen M; Kilpinen S; Kallioniemi O; Ingvarsen S; Engelholm LH; Taipale J; Alitalo K; Keski-Oja J; Lehti K
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2010;107(36):15786-15791
FGF receptor-4 (FGFR4) polymorphism acts as an activity switch of a membrane type 1 matrix metalloproteinase-FGFR4 complex
Sugiyama N; Varjosalo M; Meller P; Lohi J; Chan KM; Zhou Z; Alitalo K; Taipale J; Keski-Oja J; Lehti K
Article: EMBO JOURNAL. 2010;29(13):2147-2160
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Wei G-H; Badis G; Berger MF; Kivioja T; Palin K; Enge M; Bonke M; Jolma A; Varjosalo M; Gehrke AR; Yan J; Talukder S; Turunen M; Taipale M; Stunnenberg HG; Ukkonen E; Hughes TR; Bulyk ML; Taipale J
Article: MOLECULAR CANCER RESEARCH. 2010;8(7):952-960
Mutations in the Circadian Gene CLOCK in Colorectal Cancer
Alhopuro P; Bjorklund M; Sammalkorpi H; Turunen M; Tuupanen S; Bistrom M; Niittymaki I; Lehtonen HJ; Kivioja T; Launonen V; Saharinen J; Nousiainen K; Hautaniemi S; Nuorva K; Mecklin J-P; Jarvinen H; Orntoft T; Arango D; Lehtonen R; Karhu A; Taipale J; Aaltonen LA
Article: GENOME RESEARCH. 2010;20(6):861-873
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Jolma A; Kivioja T; Toivonen J; Cheng L; Wei G; Enge M; Taipale M; Vaquerizas JM; Yan J; Sillanpaa MJ; Bonke M; Palin K; Talukder S; Hughes TR; Luscombe NM; Ukkonen E; Taipale J
Article: NATURE GENETICS. 2009;41(8):885-890
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling
Tuupanen S; Turunen M; Lehtonen R; Hallikas O; Vanharanta S; Kivioja T; Bjorklund M; Wei G; Yan J; Niittymaki I; Mecklin J-P; Jarvinen H; Ristimaki A; Di-Bernardo M; East P; Carvajal-Carmona L; Houlston RS; Tomlinson I; Palin K; Ukkonen E; Karhu A; Taipale J; Aaltonen LA
Article: PLOS PATHOGENS. 2009;5(3):e1000324
KSHV reactivation from latency requires Pim-1 and Pim-3 kinases to inactivate the latency-associated nuclear antigen LANA.
Cheng F; Weidner-Glunde M; Varjosalo M; Rainio E-M; Lehtonen A; Schulz TF; Koskinen PJ; Taipale J; Ojala PM
Article: MOLECULAR AND CELLULAR BIOLOGY. 2008;28(15):4843-4850
Deletion of vascular endothelial growth factor C (VEGF-C) and VEGF-D is not equivalent to VEGF receptor 3 deletion in mouse embryos.
Haiko P; Makinen T; Keskitalo S; Taipale J; Karkkainen MJ; Baldwin ME; Stacker SA; Achen MG; Alitalo K
Article: CELL. 2008;133(3):537-548
Application of active and kinase-deficient kinome collection for identification of kinases regulating hedgehog signaling.
Varjosalo M; Björklund M; Cheng F; Syvänen H; Kivioja T; Kilpinen S; Sun Z; Kallioniemi O; Stunnenberg HG; He W-W; Ojala P; Taipale J
Article: CANCER CELL. 2008;13(5):407-419
Transcription factor PROM induces colon cancer progression by promoting the transition from benign to highly dysplastic phenotype
Petrova TV; Nykanen A; Norrmen C; Ivanov KI; Andersson LC; Haglund C; Puolakkainen P; Wempe F; von Melchner H; Gradwohl G; Vanharanta S; Aaltonen LA; Saharinen J; Gentile M; Clarke A; Taipale J; Oliver G; Alitalo K
Article: NATURE METHODS. 2006;3(10):777-779
Minimizing the risk of reporting false positives in large-scale RNAi screens.
Echeverri CJ; Beachy PA; Baum B; Boutros M; Buchholz F; Chanda SK; Downward J; Ellenberg J; Fraser AG; Hacohen N; Hahn WC; Jackson AL; Kiger A; Linsley PS; Lum L; Ma Y; Mathey-Prévôt B; Root DE; Sabatini DM; Taipale J; Perrimon N; Bernards R
Article: NATURE. 2006;439(7079):1009-1013
Identification of pathways regulating cell size and cell-cycle progression by RNAi
Björklund M; Taipale M; Varjosalo M; Saharinen J; Lahdenperä J; Taipale J
Article: DEVELOPMENTAL CELL. 2006;10(2):177-186
Divergence of hedgehog signal transduction mechanism between Drosophila and mammals.
Varjosalo M; Li S-P; Taipale J
Article: CELL. 2006;124(1):47-59
Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity.
Hallikas O; Palin K; Sinjushina N; Rautiainen R; Partanen J; Ukkonen E; Taipale J
Article: NATURE PROTOCOLS. 2006;1(1):368-374
Locating potential enhancer elements by comparative genomics using the EEL software.
Palin K; Taipale J; Ukkonen E
Article: NATURE PROTOCOLS. 2006;1(1):215-222
High-throughput assay for determining specificity and affinity of protein-DNA binding interactions.
Hallikas O; Taipale J
Article: NATURE IMMUNOLOGY. 2004;5(1):74-80
Vascular endothelial growth factor C is required for sprouting of the first lymphatic vessels from embryonic veins.
Karkkainen MJ; Haiko P; Sainio K; Partanen J; Taipale J; Petrova TV; Jeltsch M; Jackson DG; Talikka M; Rauvala H; Betsholtz C; Alitalo K
Article: MOLECULAR CELL. 2003;12(5):1261-1274
Hedgehog signal transduction via Smoothened association with a cytoplasmic complex scaffolded by the atypical kinesin, Costal-2.
Lum L; Zhang C; Oh S; Mann RK; von Kessler DP; Taipale J; Weis-Garcia F; Gong R; Wang B; Beachy PA
Article: NATURE GENETICS. 2003;33(4):508-513
A defective response to Hedgehog signaling in disorders of cholesterol biosynthesis.
Cooper MK; Wassif CA; Krakowiak PA; Taipale J; Gong R; Kelley RI; Porter FD; Beachy PA
Article: GENES & DEVELOPMENT. 2002;16(21):2743-2748
Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened.
Chen JK; Taipale J; Cooper MK; Beachy PA
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2002;99(22):14071-14076
Small molecule modulation of Smoothened activity.
Chen JK; Taipale J; Young KE; Maiti T; Beachy PA
Article: CELL. 2002;111(1):63-75
Hedgehog-mediated patterning of the mammalian embryo requires transporter-like function of dispatched.
Ma Y; Erkner A; Gong R; Yao S; Taipale J; Basler K; Beachy PA
Article: SCIENCE. 2002;297(5586):1559-1561
Medulloblastoma growth inhibition by hedgehog pathway blockade.
Berman DM; Karhadkar SS; Hallahan AR; Pritchard JI; Eberhart CG; Watkins DN; Chen JK; Cooper MK; Taipale J; Olson JM; Beachy PA
Article: NATURE. 2002;418(6900):892-897
Patched acts catalytically to suppress the activity of Smoothened.
Taipale J; Cooper MK; Maiti T; Beachy PA
Article: NATURE. 2001;411(6835):349-354
The Hedgehog and Wnt signalling pathways in cancer.
Taipale J; Beachy PA
Article: THE FASEB JOURNAL. 2001;15(6):1028-1036
VEGFR3 gene structure, regulatory region, and sequence polymorphisms.
Iljin K; Karkkainen MJ; Lawrence EC; Kimak MA; Uutela M; Taipale J; Pajusola K; Alhonen L; Halmekytö M; Finegold DN; Ferrell RE; Alitalo K
Article: NATURE. 2000;406(6799):1005-1009
Effects of oncogenic mutations in Smoothened and Patched can be reversed by cyclopamine.
Taipale J; Chen JK; Cooper MK; Wang B; Mann RK; Milenkovic L; Scott MP; Beachy PA
Article: AMERICAN JOURNAL OF PATHOLOGY. 1999;154(5):1381-1390
VEGFR-3 and its ligand VEGF-C are associated with angiogenesis in breast cancer.
Valtola R; Salven P; Heikkilä P; Taipale J; Joensuu H; Rehn M; Pihlajaniemi T; Weich H; deWaal R; Alitalo K
Article: MOLECULAR AND CELLULAR BIOLOGY. 1999;19(5):3654-3663
Hepatocyte growth factor releases mink epithelial cells from transforming growth factor β1-induced growth arrest by restoring Cdk6 expression and cyclin E-associated Cdk2 activity
Tsubari M; Taipale J; Tiihonen E; Keski-Oja J; Laiho M
Article: SCIENCE. 1998;282(5390):946-949
Cardiovascular failure in mouse embryos deficient in VEGF receptor-3.
Dumont DJ; Jussila L; Taipale J; Lymboussaki A; Mustonen T; Pajusola K; Breitman M; Alitalo K
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 1998;273(32):20669-20676
Recombinant latent transforming growth factor beta-binding protein 2 assembles to fibroblast extracellular matrix and is susceptible to proteolytic processing and release.
Hyytiäinen M; Taipale J; Heldin CH; Keski-Oja J
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 1998;273(29):18459-18469
Identification and characterization of a new latent transforming growth factor-beta-binding protein, LTBP-4.
Saharinen J; Taipale J; Monni O; Keski-Oja J
Article: JOURNAL OF HISTOCHEMISTRY AND CYTOCHEMISTRY. 1996;44(8):875-889
Latent transforming growth factor-beta 1 and its binding protein are components of extracellular matrix microfibrils.
Taipale J; Saharinen J; Hedman K; Keski-Oja J
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 1996;271(8):4342-4348
Hepatocyte growth factor releases epithelial and endothelial cells from growth arrest induced by transforming growth factor-beta1.
Taipale J; Keski-Oja J
Article: EMBO JOURNAL. 1996;15(2):245-253
Association of the small latent transforming growth factor-beta with an eight cysteine repeat of its binding protein LTBP-1.
Saharinen J; Taipale J; Keski-Oja J
Article: JOURNAL OF BIOLOGICAL CHEMISTRY. 1995;270(9):4689-4696
Human mast cell chymase and leukocyte elastase release latent transforming growth factor-beta 1 from the extracellular matrix of cultured human epithelial and endothelial cells.
Taipale J; Lohi J; Saarinen J; Kovanen PT; Keski-Oja J
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Corrigendum: NATURE METHODS. 2021;18(2):219
CRISPR-assisted detection of RNA-protein interactions in living cells (vol 17, pg 685, 2020)
Yi W; Li J; Zhu X; Wang X; Fan L; Sun W; Liao L; Zhang J; Li X; Ye J; Chen F; Taipale J; Chan KM; Zhang L; Yan J
Letter: MOLECULAR SYSTEMS BIOLOGY. 2019;15(8):e9059
Reply to "CRISPR screens are feasible in TP53 wild-type cells"
Haapaniemi E; Botla S; Persson J; Schmierer B; Taipale J
Editorial comment: SCIENCE. 2018;362(6413):401-402
The chromatin of cancer
Taipale J
Corrigendum: CELL. 2018;175(2):598-599
The Human Transcription Factors (vol 172, pg 650, 2018)
Lambert SA; Jolma A; Campitelli LF; Das PK; Yin Y; Albu M; Chen X; Taipale J; Hughes TR; Weirauch MT
Review: CELL. 2018;172(4):650-665
The Human Transcription Factors
Lambert SA; Jolma A; Campitelli LF; Das PK; Yin Y; Albu M; Chen X; Taipale J; Hughes TR; Weirauch MT
Published conference paper: BIOINFORMATICS. 2016;32(17):i629-i638
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments
Hartonen T; Sahu B; Dave K; Kivioja T; Taipale J
Review: NATURE REVIEWS CANCER. 2016;16(8):483-493
The role of enhancers in cancer
Sur I; Taipale J
Editorial comment: SCIENCE. 2014;346(6215):1291-1292
Cancer by super-enhancer
Vaehaerautio A; Taipale J
Review: CANCER RESEARCH. 2013;73(14):4180-4184
Lessons from Functional Analysis of Genome-Wide Association Studies
Sur I; Tuupanen S; Whitington T; Aaltonen LA; Taipale J
Review: SUB-CELLULAR BIOCHEMISTRY. 2011;52:155-173
Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.
Jolma A; Taipale J
Review: GENES & DEVELOPMENT. 2008;22(18):2454-2472
Hedgehog: functions and mechanisms.
Varjosalo M; Taipale J
Editorial comment: JOURNAL OF CELL SCIENCE. 2007;120(Pt 1):3-6
Hedgehog signaling.
Varjosalo M; Taipale J
Editorial comment: DUODECIM; LAAKETIETEELLINEN AIKAKAUSKIRJA. 2004;120(4):373-375
[Epithelial stem cell and cancer].
Taipale J
Review: CYTOKINE AND GROWTH FACTOR REVIEWS. 1999;10(2):99-117
Latent transforming growth factor-beta binding proteins (LTBPs)--structural extracellular matrix proteins for targeting TGF-beta action.
Saharinen J; Hyytiäinen M; Taipale J; Keski-Oja J
Review: CURRENT TOPICS IN MICROBIOLOGY AND IMMUNOLOGY. 1999;237:85-96
Vascular endothelial growth factor receptor-3.
Taipale J; Makinen T; Arighi E; Kukk E; Karkkainen M; Alitalo K
Review: ADVANCES IN CANCER RESEARCH. 1998;75:87-134
Extracellular matrix-associated transforming growth factor-beta: role in cancer cell growth and invasion.
Taipale J; Saharinen J; Keski-Oja J
Review: THE FASEB JOURNAL. 1997;11(1):51-59
Growth factors in the extracellular matrix.
Taipale J; Keski-Oja J
Review: TRENDS IN GLYCOSCIENCE AND GLYCOTECHNOLOGY. 1995;7(36):277-289
Association of latent transforming growth factor-beta to fibroblast extracellular matrix - An insight to proteolytic activation
KeskiOja J; Koli K; Lohi J; Saharinen J; Taipale J

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