Preprints

  1. Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D (2019) ‘Open Community Challenge Reveals Molecular Network Modules with Key Roles in Diseases.’ bioRxiv, https://doi.org/10.1101/265553.
  2. Iqbal S, Jespersen JB, Perez-Palma E, May P, Hoksza D, Heyne HO, Ahmed SS, Rifat ZT, Rahman MS, Lage K, Palotie A, Cottrell JR, Wagner FF, Daly MJ, Campbell AJ, Lal D (2019) ‘Insights into protein structural, physicochemical, and functional consequences of missense variants in 1,330 disease-associated human genes.’ bioRxiv, https://doi.org/10.1101/693259.
  3. Tanigawa Y, Li J, Justesen JM, Horn H, Aguirre M, DeBoever C, Chang C, Narasimhan B, Lage K, Hastie T, Park CY, Bejerano G, Ingelsson E, Rivas MA (2019) ‘Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight novel adipocyte biology.’ bioRxiv, https://doi.org/10.1101/442715.
  4. Nguyen, HT, Dobbyn A, Charney AW, Bryois J, Kim A, Mcfadden W, Skene NG, Huckins LM, Wang W, Ruderfer DM, Xu X, Fromer M, Purcell SM, Lage K, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Pinto D, He X, Sullivan PF, Stahl EA (2018) ‘Integrative analysis of rare variants and pathway information shows convergent results between immune pathways, drug targets and epilepsy genes.’ bioRxiv, https://doi.org/10.1101/410100.
  5. Kim A, Malolepsza E, Lim J, Lage K. (2017) ‘Genoppi: a web application for interactive integration of experimental proteomics results with genetic datasets.’ bioRxiv, https://doi.org/10.1101/115576.
  6. Gupta A, Horn H, Razaz P, Kim A, Lawrence M, Getz G, Lage K (2017) ‘Detecting cancer vulnerabilities through gene networks under purifying selection in 4,700 cancer genomes.’ bioRxiv, https://doi.org/10.1101/222687.
  7. Publications

  8. Fernández-Tajes J, Gaulton KJ, van de Bunt M, Torres J, Thurner M, Mahajan A, Gloyn AL, Lage K, McCarthy MI (2019) ‘Developing a network view of type 2 diabetes risk pathways through integration of genetic, genomic and functional data.’ Genome Med, 11 (1): 19. PMID: 30914061 
  9. Viswanathan SR, Nogueira MF, Buss CG, Krill-Burger JM, Wawer MJ, Malolepsza E, Berger AC, Choi PS, Shih J, Taylor AM, Tanenbaum B, Pedamallu CS, Cherniack AD, Tamayo P, Strathdee CA, Lage K, Carr SA, Schenone M, Bhatia SN, Vazquez F, Tsherniak A, Hahn WC, Meyerson M (2018) ‘Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.’ Nat Genet, 50 (7): 937-943. PMID: 29955178 
  10. Li T, Kim A, Rosenbluh J, Horn H, Greenfeld L, An D, Zimmer A, Liberzon A, Bistline J, Natoli T, Li Y, Tsherniak A, Narayan R, Subramanian A, Liefeld T, Wong B, Thompson D, Calvo S, Carr S, Boehm J, Jaffe J, Mesirov J, Hacohen N, Regev A, Lage K (2018) ‘GeNets: a unified web platform for network-based genomic analyses.’ Nat Methods, 15 (7): 543-546. PMID:29915188 
  11. Nguyen HT, Bryois J, Kim A, Dobbyn A, Huckins LM, Munoz-Manchado AB, Ruderfer DM, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Hultman C, Sklar P, Purcell SM, Lage K, He X, Sullivan PF, Stahl EA (2017) ‘Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders.’ Genome Med, 9 (1): 114. PMID: 29262854 
  12. Benajiba L, Fenouille N, Malolepsza E, Ellegast JM, Alexe G, Pikman Y, Luciano F, Galinsky I, DeAngelo DJ, Stone RM, Auberger P, Guirouilh-Barbat J, Lopez B, Khaled M, Lage K, Hermine O, Hemann M, Puissant A, Stegmaier K (2017) ‘Vcp-Regulated Homologous Recombination Represents a New Druggable Vulnerability in Acute Myeloid Leukemia.’ Blood, 130 (Suppl 1): 880.
  13. Horn H, Lawrence MS, Chouinard CR, Shrestha Y, Hu JX, Worstell E, Shea E, Ilic N, Kim E, Kamburov A, Kashani A, Hahn WC, Campbell JD, Boehm JS, Getz G, Lage K (2018) ‘NetSig: network-based discovery from cancer genomes.’ Nat Methods, 15 (1): 61-66. PMID: 29200198 
  14. Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K (2017) ‘A scored human protein-protein interaction network to catalyze genomic interpretation.’ Nat Methods, 14 (1): 61-64. PMID: 27892958 
  15. Rosenbluh J, Mercer J, Shrestha Y, Oliver R, Tamayo P, Doench JG, Tirosh I, Piccioni F, Hartenian E, Horn H, Fagbami L, Root DE, Jaffe J, Lage K, Boehm JS, Hahn WC (2016) ‘Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers.’ Cell Syst, 3 (3): 302-316.e4. PMID: 27684187 
  16. van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio LA, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW (2016) ’52 Genetic Loci Influencing Myocardial Mass.’ J Am Coll Cardiol, 68 (13): 1435-1448. PMID: 27659466 
  17. Sosulski A, Horn H, Zhang L, Coletti C, Vathipadiekal V, Castro CM, Birrer MJ, Nagano O, Saya H, Lage K, Donahoe PK, Pépin D (2016) ‘CD44 Splice Variant v8-10 as a Marker of Serous Ovarian Cancer Prognosis.’ PLoS One, 11 (6): e0156595. PMID: 27253518 
  18. Kim E, Ilic N, Shrestha Y, Zou L, Kamburov A, Zhu C, Yang X, Lubonja R, Tran N, Nguyen C, Lawrence MS, Piccioni F, Bagul M, Doench JG, Chouinard CR, Wu X, Hogstrom L, Natoli T, Tamayo P, Horn H, Corsello SM, Lage K, Root DE, Subramanian A, Golub TR, Getz G, Boehm JS, Hahn WC (2016) ‘Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.’ Cancer Discov, 6 (7): 714-26. PMID: 27147599 
  19. Won HH, Natarajan P, Dobbyn A, Jordan DM, Roussos P, Lage K, Raychaudhuri S, Stahl E, Do R (2015) ‘Disproportionate Contributions of Select Genomic Compartments and Cell Types to Genetic Risk for Coronary Artery Disease.’ PLoS Genet, 11 (10): e1005622. PMID: 26509271 
  20. 1000 Genomes Project Consortium., Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) ‘A global reference for human genetic variation.’ Nature, 526 (7571): 68-74. PMID: 26432245 
  21. Kamburov A, Lawrence MS, Polak P, Leshchiner I, Lage K, Golub TR, Lander ES, Getz G (2015) ‘Comprehensive assessment of cancer missense mutation clustering in protein structures.’ Proc Natl Acad Sci U S A, 112 (40): E5486-95. PMID: 26392535 
  22. Quintero-Rivera F, Xi QJ, Keppler-Noreuil KM, Lee JH, Higgins AW, Anchan RM, Roberts AE, Seong IS, Fan X, Lage K, Lu LY, Tao J, Hu X, Berezney R, Gelb BD, Kamp A, Moskowitz IP, Lacro RV, Lu W, Morton CC, Gusella JF, Maas RL (2015) ‘MATR3 disruption in human and mouse associated with bicuspid aortic valve, aortic coarctation and patent ductus arteriosus.’ Hum Mol Genet, 24 (8): 2375-89. PMID: 25574029 
  23. Longoni M, High FA, Russell MK, Kashani A, Tracy AA, Coletti CM, Hila R, Shamia A, Wells J, Ackerman KG, Wilson JM, Bult CJ, Lee C, Lage K, Pober BR, Donahoe PK (2014) ‘Molecular pathogenesis of congenital diaphragmatic hernia revealed by exome sequencing, developmental data, and bioinformatics.’ Proc Natl Acad Sci U S A, 111 (34): 12450-5. PMID:25107291 
  24. Lundby A, Rossin EJ, Steffensen AB, Acha MR, Newton-Cheh C, Pfeufer A, Lynch SN, QT Interval International GWAS Consortium (QT-IGC)., Olesen SP, Brunak S, Ellinor PT, Jukema JW, Trompet S, Ford I, Macfarlane PW, Krijthe BP, Hofman A, Uitterlinden AG, Stricker BH, Nathoe HM, Spiering W, Daly MJ, Asselbergs FW, van der Harst P, Milan DJ, de Bakker PI, Lage K, Olsen JV (2014) ‘Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics.’ Nat Methods, 11 (8): 868-74. PMID: 24952909 
  25. Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, Sotoodehnia N, Rossin EJ, Morley M, Wang X, Johnson AD, Lundby A, Gudbjartsson DF, Noseworthy PA, Eijgelsheim M, Bradford Y, Tarasov KV, Dörr M, Müller-Nurasyid M, Lahtinen AM, Nolte IM, Smith AV, Bis JC, Isaacs A, Newhouse SJ, Evans DS, Post WS, Waggott D, Lyytikäinen LP, Hicks AA, Eisele L, Ellinghaus D, Hayward C, Navarro P, Ulivi S, Tanaka T, Tester DJ, Chatel S, Gustafsson S, Kumari M, Morris RW, Naluai ÅT, Padmanabhan S, Kluttig A, Strohmer B, Panayiotou AG, Torres M, Knoflach M, Hubacek JA, Slowikowski K, Raychaudhuri S, Kumar RD, Harris TB, Launer LJ, Shuldiner AR, Alonso A, Bader JS, Ehret G, Huang H, Kao WH, Strait JB, Macfarlane PW, Brown M, Caulfield MJ, Samani NJ, Kronenberg F, Willeit J, CARe Consortium., COGENT Consortium., Smith JG, Greiser KH, Meyer Zu Schwabedissen H, Werdan K, Carella M, Zelante L, Heckbert SR, Psaty BM, Rotter JI, Kolcic I, Polašek O, Wright AF, Griffin M, Daly MJ, DCCT/EDIC., Arnar DO, Hólm H, Thorsteinsdottir U, eMERGE Consortium., Denny JC, Roden DM, Zuvich RL, Emilsson V, Plump AS, Larson MG, O’Donnell CJ, Yin X, Bobbo M, D’Adamo AP, Iorio A, Sinagra G, Carracedo A, Cummings SR, Nalls MA, Jula A, Kontula KK, Marjamaa A, Oikarinen L, Perola M, Porthan K, Erbel R, Hoffmann P, Jöckel KH, Kälsch H, Nöthen MM, HRGEN Consortium., den Hoed M, Loos RJ, Thelle DS, Gieger C, Meitinger T, Perz S, Peters A, Prucha H, Sinner MF, Waldenberger M, de Boer RA, Franke L, van der Vleuten PA, Beckmann BM, Martens E, Bardai A, Hofman N, Wilde AA, Behr ER, Dalageorgou C, Giudicessi JR, Medeiros-Domingo A, Barc J, Kyndt F, Probst V, Ghidoni A, Insolia R, Hamilton RM, Scherer SW, Brandimarto J, Margulies K, Moravec CE, del Greco M F, Fuchsberger C, O’Connell JR, Lee WK, Watt GC, Campbell H, Wild SH, El Mokhtari NE, Frey N, Asselbergs FW, Mateo Leach I, Navis G, van den Berg MP, van Veldhuisen DJ, Kellis M, Krijthe BP, Franco OH, Hofman A, Kors JA, Uitterlinden AG, Witteman JC, Kedenko L, Lamina C, Oostra BA, Abecasis GR, Lakatta EG, Mulas A, Orrú M, Schlessinger D, Uda M, Markus MR, Völker U, Snieder H, Spector TD, Ärnlöv J, Lind L, Sundström J, Syvänen AC, Kivimaki M, Kähönen M, Mononen N, Raitakari OT, Viikari JS, Adamkova V, Kiechl S, Brion M, Nicolaides AN, Paulweber B, Haerting J, Dominiczak AF, Nyberg F, Whincup PH, Hingorani AD, Schott JJ, Bezzina CR, Ingelsson E, Ferrucci L, Gasparini P, Wilson JF, Rudan I, Franke A, Mühleisen TW, Pramstaller PP, Lehtimäki TJ, Paterson AD, Parsa A, Liu Y, van Duijn CM, Siscovick DS, Gudnason V, Jamshidi Y, Salomaa V, Felix SB, Sanna S, Ritchie MD, Stricker BH, Stefansson K, Boyer LA, Cappola TP, Olsen JV, Lage K, Schwartz PJ, Kääb S, Chakravarti A, Ackerman MJ, Pfeufer A, de Bakker PI, Newton-Cheh C (2014) ‘Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.’ Nat Genet, 46 (8): 826-36. PMID: 24952745 
  26. Lage K (2014) ‘Protein-protein interactions and genetic diseases: The interactome.’ Biochim Biophys Acta, 1842 (10): 1971-1980. PMID: 24892209 
  27. Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM (2014) ‘An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.’ Genome Biol, 15 (3): R53. PMID: 24667040 
  28. Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium., Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M (2013) ‘Integrative annotation of variants from 1092 humans: application to cancer genomics.’ Science, 342 (6154): 1235587. PMID: 24092746 
  29. Rondas D, Bugliani M, D’Hertog W, Lage K, Masini M, Waelkens E, Marchetti P, Mathieu C, Overbergh L (2013) ‘Glucagon-like peptide-1 protects human islets against cytokine-mediated β-cell dysfunction and death: a proteomic study of the pathways involved.’ J Proteome Res, 12 (9): 4193-206. PMID: 23937086 
  30. Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G, Medland SE, Todt U, McArdle WL, Quaye L, Koiranen M, Ikram MA, Lehtimäki T, Stam AH, Ligthart L, Wedenoja J, Dunham I, Neale BM, Palta P, Hamalainen E, Schürks M, Rose LM, Buring JE, Ridker PM, Steinberg S, Stefansson H, Jakobsson F, Lawlor DA, Evans DM, Ring SM, Färkkilä M, Artto V, Kaunisto MA, Freilinger T, Schoenen J, Frants RR, Pelzer N, Weller CM, Zielman R, Heath AC, Madden PAF, Montgomery GW, Martin NG, Borck G, Göbel H, Heinze A, Heinze-Kuhn K, Williams FMK, Hartikainen AL, Pouta A, van den Ende J, Uitterlinden AG, Hofman A, Amin N, Hottenga JJ, Vink JM, Heikkilä K, Alexander M, Muller-Myhsok B, Schreiber S, Meitinger T, Wichmann HE, Aromaa A, Eriksson JG, Traynor B, Trabzuni D, North American Brain Expression Consortium., UK Brain Expression Consortium., Rossin E, Lage K, Jacobs SBR, Gibbs JR, Birney E, Kaprio J, Penninx BW, Boomsma DI, van Duijn C, Raitakari O, Jarvelin MR, Zwart JA, Cherkas L, Strachan DP, Kubisch C, Ferrari MD, van den Maagdenberg AMJM, Dichgans M, Wessman M, Smith GD, Stefansson K, Daly MJ, Nyholt DR, Chasman D, Palotie A (2013) ‘Genome-wide meta-analysis identifies new susceptibility loci for migraine.’ Nat Genet, 45 (8): 912-917. PMID: 23793025 
  31. Pers TH, Dworzyński P, Thomas CE, Lage K, Brunak S (2013) ‘MetaRanker 2.0: a web server for prioritization of genetic variation data.’ Nucleic Acids Res, 41 (Web Server issue): W104-8. PMID: 23703204 
  32. Margolin DH, Kousi M, Chan YM, Lim ET, Schmahmann JD, Hadjivassiliou M, Hall JE, Adam I, Dwyer A, Plummer L, Aldrin SV, O’Rourke J, Kirby A, Lage K, Milunsky A, Milunsky JM, Chan J, Hedley-Whyte ET, Daly MJ, Katsanis N, Seminara SB (2013) ‘Ataxia, dementia, and hypogonadotropism caused by disordered ubiquitination.’ N Engl J Med, 368 (21): 1992-2003. PMID: 23656588 
  33. Miraoui H, Dwyer AA, Sykiotis GP, Plummer L, Chung W, Feng B, Beenken A, Clarke J, Pers TH, Dworzynski P, Keefe K, Niedziela M, Raivio T, Crowley WF Jr, Seminara SB, Quinton R, Hughes VA, Kumanov P, Young J, Yialamas MA, Hall JE, Van Vliet G, Chanoine JP, Rubenstein J, Mohammadi M, Tsai PS, Sidis Y, Lage K, Pitteloud N (2013) ‘Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 are identified in individuals with congenital hypogonadotropic hypogonadism.’ Am J Hum Genet, 92 (5): 725-43. PMID: 23643382 
  34. Longoni M, Lage K, Russell MK, Loscertales M, Abdul-Rahman OA, Baynam G, Bleyl SB, Brady PD, Breckpot J, Chen CP, Devriendt K, Gillessen-Kaesbach G, Grix AW, Rope AF, Shimokawa O, Strauss B, Wieczorek D, Zackai EH, Coletti CM, Maalouf FI, Noonan KM, Park JH, Tracy AA, Lee C, Donahoe PK, Pober BR (2012) ‘Congenital diaphragmatic hernia interval on chromosome 8p23.1 characterized by genetics and protein interaction networks.’ Am J Med Genet A, 158A (12): 3148-58. PMID: 23165946 
  35. Lage K, Greenway SC, Rosenfeld JA, Wakimoto H, Gorham JM, Segrè AV, Roberts AE, Smoot LB, Pu WT, Pereira AC, Mesquita SM, Tommerup N, Brunak S, Ballif BC, Shaffer LG, Donahoe PK, Daly MJ, Seidman JG, Seidman CE, Larsen LA (2012) ‘Genetic and environmental risk factors in congenital heart disease functionally converge in protein networks driving heart development.’ Proc Natl Acad Sci U S A, 109 (35): 14035-40. PMID: 22904188 
  36. Lundby A, Lage K, Weinert BT, Bekker-Jensen DB, Secher A, Skovgaard T, Kelstrup CD, Dmytriyev A, Choudhary C, Lundby C, Olsen JV (2012) ‘Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns.’ Cell Rep, 2 (2): 419-31. PMID: 22902405 
  37. Lundby A, Secher A, Lage K, Nordsborg NB, Dmytriyev A, Lundby C, Olsen JV (2012) ‘Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.’ Nat Commun, 3 (): 876. PMID: 22673903 
  38. Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, Heilbut A, Ernst C, Hanscom C, Rossin E, Lindgren AM, Pereira S, Ruderfer D, Kirby A, Ripke S, Harris DJ, Lee JH, Ha K, Kim HG, Solomon BD, Gropman AL, Lucente D, Sims K, Ohsumi TK, Borowsky ML, Loranger S, Quade B, Lage K, Miles J, Wu BL, Shen Y, Neale B, Shaffer LG, Daly MJ, Morton CC, Gusella JF (2012) ‘Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries.’ Cell, 149 (3): 525-37. PMID: 22521361 
  39. Russell MK, Longoni M, Wells J, Maalouf FI, Tracy AA, Loscertales M, Ackerman KG, Pober BR, Lage K, Bult CJ, Donahoe PK (2012) ‘Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes.’ Proc Natl Acad Sci U S A, 109 (8): 2978-83. PMID: 22315423 
  40. Ferreira GB, Kleijwegt FS, Waelkens E, Lage K, Nikolic T, Hansen DA, Workman CT, Roep BO, Overbergh L, Mathieu C (2012) ‘Differential protein pathways in 1,25-dihydroxyvitamin d(3) and dexamethasone modulated tolerogenic human dendritic cells.’ J Proteome Res, 11 (2): 941-71. PMID: 22103328 
  41. Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, Daly MJ, Daly MJ (2011) ‘Pervasive sharing of genetic effects in autoimmune disease.’ PLoS Genet, 7 (8): e1002254. PMID: 21852963 
  42. Berchtold LA, Størling ZM, Ortis F, Lage K, Bang-Berthelsen C, Bergholdt R, Hald J, Brorsson CA, Eizirik DL, Pociot F, Brunak S, Størling J (2011) ‘Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis.’ Proc Natl Acad Sci U S A, 108 (37): E681-8. PMID: 21705657 
  43. Pers TH, Hansen NT, Lage K, Koefoed P, Dworzynski P, Miller ML, Flint TJ, Mellerup E, Dam H, Andreassen OA, Djurovic S, Melle I, Børglum AD, Werge T, Purcell S, Ferreira MA, Kouskoumvekaki I, Workman CT, Hansen T, Mors O, Brunak S (2011) ‘Meta-analysis of heterogeneous data sources for genome-scale identification of risk genes in complex phenotypes.’ Genet Epidemiol, 35 (5): 318-32. PMID: 21484861 
  44. Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, International Inflammatory Bowel Disease Genetics Constortium., Cotsapas C, Daly MJ (2011) ‘Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology.’ PLoS Genet, 7 (1): e1001273. PMID: 21249183 
  45. Ferreira GB, Overbergh L, van Etten E, Lage K, D’Hertog W, Hansen DA, Maris M, Moreau Y, Workman CT, Waelkens E, Mathieu C (2008) ‘Protein-induced changes during the maturation process of human dendritic cells: A 2-D DIGE approach.’ Proteomics Clin Appl, 2 (9): 1349-60. PMID: 21136928 
  46. Riley BE, Kaiser SE, Shaler TA, Ng AC, Hara T, Hipp MS, Lage K, Xavier RJ, Ryu KY, Taguchi K, Yamamoto M, Tanaka K, Mizushima N, Komatsu M, Kopito RR (2010) ‘Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection.’ J Cell Biol, 191(3): 537-52. PMID: 21041446 
  47. D’Hertog W, Maris M, Ferreira GB, Verdrengh E, Lage K, Hansen DA, Cardozo AK, Workman CT, Moreau Y, Eizirik DL, Waelkens E, Overbergh L, Mathieu C (2010) ‘Novel insights into the global proteome responses of insulin-producing INS-1E cells to different degrees of endoplasmic reticulum stress.’ J Proteome Res, 9 (10): 5142-52. PMID: 20839851 
  48. Lage K, Møllgård K, Greenway S, Wakimoto H, Gorham JM, Workman CT, Bendsen E, Hansen NT, Rigina O, Roque FS, Wiese C, Christoffels VM, Roberts AE, Smoot LB, Pu WT, Donahoe PK, Tommerup N, Brunak S, Seidman CE, Seidman JG, Larsen LA (2010) ‘Dissecting spatio-temporal protein networks driving human heart development and related disorders.’ Mol Syst Biol,6 (): 381. PMID: 20571530 
  49. Ferreira GB, van Etten E, Lage K, Hansen DA, Moreau Y, Workman CT, Waer M, Verstuyf A, Waelkens E, Overbergh L, Mathieu C (2009) ‘Proteome analysis demonstrates profound alterations in human dendritic cell nature by TX527, an analogue of vitamin D.’ Proteomics, 9 (14): 3752-64. PMID: 19639594 
  50. Bergholdt R, Brorsson C, Lage K, Nielsen JH, Brunak S, Pociot F (2009) ‘Expression profiling of human genetic and protein interaction networks in type 1 diabetes.’ PLoS One, 4 (7): e6250. PMID: 19609442 
  51. Jakobsen LP, Borup R, Vestergaard J, Larsen LA, Lage K, Maroun LL, Kjaer I, Niemann CU, Andersen M, Knudsen MA, Møllgård K, Tommerup N (2009) ‘Expression analyses of human cleft palate tissue suggest a role for osteopontin and immune related factors in palatal development.’ Exp Mol Med, 41 (2): 77-85. PMID: 19287188 
  52. Donahoe PK, Noonan KM, Lage K (2009) ‘Genetic tools and algorithms for gene discovery in major congenital anomalies.’ Birth Defects Res A Clin Mol Teratol, 85 (1): 6-12. PMID: 19107955 
  53. Lage K, Hansen NT, Karlberg EO, Eklund AC, Roque FS, Donahoe PK, Szallasi Z, Jensen TS, Brunak S (2008) ‘A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes.’ Proc Natl Acad Sci U S A, 105 (52): 20870-5. PMID: 19104045 
  54. Bergholdt R, Størling ZM, Lage K, Karlberg EO, Olason PI, Aalund M, Nerup J, Brunak S, Workman CT, Pociot F (2007) ‘Integrative analysis for finding genes and networks involved in diabetes and other complex diseases.’ Genome Biol, 8 (11): R253. PMID: 18045462 
  55. D’Hertog W, Overbergh L, Lage K, Ferreira GB, Maris M, Gysemans C, Flamez D, Cardozo AK, Van den Bergh G, Schoofs L, Arckens L, Moreau Y, Hansen DA, Eizirik DL, Waelkens E, Mathieu C (2007) ‘Proteomics analysis of cytokine-induced dysfunction and death in insulin-producing INS-1E cells: new insights into the pathways involved.’ Mol Cell Proteomics, 6 (12): 2180-99. PMID: 17921177 
  56. Sanggaard KM, Rendtorff ND, Kjaer KW, Eiberg H, Johnsen T, Gimsing S, Dyrmose J, Nielsen KO, Lage K, Tranebjaerg L (2007) ‘Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses.’ Eur J Hum Genet, 15 (11): 1121-31. PMID: 17637804 
  57. Lage K, Karlberg EO, Størling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tümer Z, Pociot F, Tommerup N, Moreau Y, Brunak S (2007) ‘A human phenome-interactome network of protein complexes implicated in genetic disorders.’ Nat Biotechnol, 25 (3): 309-16. PMID: 17344885 
  58. Hinsby AM, Kiemer L, Karlberg EO, Lage K, Fausbøll A, Juncker AS, Andersen JS, Mann M, Brunak S (2006) ‘A wiring of the human nucleolus.’ Mol Cell, 22 (2): 285-95. PMID: 16630896