Pages tagged "Article"
2019
Federated discovery and sharing of genomic data using Beacons
Miroslav Cupak , Stephen Keenan , Jordi Rambla , Sabela de la Torre , Stephanie Dyke , Anthony Brookes , Knox Carey , David Lloyd , Peter Goodhand , Maximilian Haeussler , Michael Baudis , Heinz Stockinger , Lena Dolman , Ilkka Lappalainen , Juha Törnroos , Mikael Linden , John Spalding , Saif Ur-Rehman , Angela Page , Paul Flicek , Susheel Varma , Gary Saunders , Serena Scollen , Stephen Sherry , David Haussler , Beacon Project Team
Nat Biotechnol (2019), accepted 2019-01-23
DNA copy number imbalances in primary cutaneous lymphomas (PCL)
Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2019)
JEADV, 2019-01-19. https://doi.org/10.1111/jdv.15442
Enabling population assignment from cancer genomes with SNP2pop.
Huang Q and Baudis M. (2019)
bioRxiv, 2019-01-14. https://doi.org/10.1101/368647 (first version 2018-07-14)
2018
DNA copy number imbalances in primary cutaneous lymphomas (PCL)
Gug G, Huang Q, Chiticariu E, Solovan C and Baudis M (2018)
bioRxiv, 2018-09-14. doi:10.1101/417766
Registered access: authorizing data access
Dyke SOM, Linden M, Lappalainen I, De Argila JR, Carey K, Lloyd D, Spalding JD, Cabili MN, Kerry G, Foreman J, Cutts T, Shabani M, Rodriguez LL, Haeussler M, Walsh B, Jiang X, Wang S, Perrett D, Boughtwood T, Matern A, Brookes AJ, Cupak M, Fiume M, Pandya R, Tulchinsky I, Scollen S, Törnroos J, Das S, Evans AC, Malin BA, Beck S, Brenner SE, Nyrönen T, Blomberg N, Firth HV, Hurles M, Philippakis AA, Rätsch G, Brudno M, Boycott KM, Rehm HL, Baudis M, Sherry ST, Kato K, Knoppers BM, Baker D, and Flicek P
European Journal of Human Genetics (2018)
Mountains and Chasms - Surveying the Oncogenomic Publication Landscape
Carrio Cordo P and Baudis M. (2018)
Preprints 2018, 2018070618 (doi: 10.20944/preprints201807.0618.v1).
Oncology (2018; online Oct 26)
Population assignment from cancer genome profiling data.
Huang Q and Baudis M. (2018)
bioRxiv, 2018-07-14. doi:10.1101/368647
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu Pons J, Duren R, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Sezerman OU, Warner J, Rieke DT, Aittokallio T, Cerami E, Ritter D, Schriml LM, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus SM, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, and Margolin A
bioRxiv. doi:10.1101/366856
Krüppel-Like Factor 10 participates in cervical cancer immunoediting through transcriptional regulation of Pregnancy-Specific Beta-1 Glycoproteins.
Marrero-Rodríguez D, Taniguchi-Ponciano K, Subramaniam M, Hawse JR, Pitel KS, Arreola-De la Cruz H, Huerta-Padilla V, Ponce-Navarrete G, Figueroa-Corona MDP, Gomez-Virgilio L, Martinez-Cuevas TI, Mendoza-Rodriguez M, Rodriguez-Esquivel M, Romero-Morelos P, Ramirez-Salcedo J, Baudis M, Meraz-Rios M, Jimenez-Vega F, Salcedo M.
Gao B, Huang Q and Baudis M
2017
Mackay A, Burford A, Carvalho D, Izquierdo E, Fazal-Salom J, Taylor KR, Bjerke L, Clarke M, Vinci M, Nandhabalan M, Temelso S, Popov S, Molinari V, Raman P, Waanders AJ, Han HJ, Gupta S, Marshall L, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Ng HK, Li X, Mu K, Trabelsi S, Brahim DH, Kisljakov AN, Konovalov DM, Moore AS, Carcaboso AM, Sunol M, de Torres C, Cruz O, Mora J, Shats LI, Stavale JN, Bidinotto LT, Reis RM, Entz-Werle N, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Monje M, Debily MA, Castel D, Grill J, Hawkins C, Nikbakht H, Jabado N, Baker SJ, Pfister SM, Jones DTW, Fouladi M, von Bueren AO, Baudis M, Resnick A, Jones C.
2016
CNARA: reliability assessment for genomic copy number profiles.
Ai N, Cai H, Solovan C, Baudis M.
Andersson A, Bluwstein A, Kumar N, Teloni F, Traenkle J, Baudis M, Altmeyer M, Hottiger MO.
2015
A Biobank Supporting Rare Disease Research In Dermatopathology. Our Experience In Establishing A Biobank.
Beleut M, Seclaman E, Baudis M, Nicula A, and Solovan C
RoJCED 2, 202-206 (2015)
arrayMap 2014: an updated cancer genome resource.
Cai H, Gupta S, Rath P, Ai N, Baudis M.
Muff R, Rath P, Ram Kumar RM, Husmann K, Born W, Baudis M, Fuchs B.
2014
Progenetix: 12 years of oncogenomic data curation.
Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M.
Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens.
Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M.
Biopsying parapsoriasis: quo vadis? Are morphological stains enough or are ancillary tests needed?
Baderca F, Chiticariu E, Baudis M, Solovan C.
2013
SIL1 mutations and clinical spectrum in patients with Marinesco-Sjogren syndrome.
Krieger M, Roos A, Stendel C, Claeys KG, Sonmez FM, Baudis M, Bauer P, Bornemann A, de Goede C, Dufke A, Finkel RS, Goebel HH, Häussler M, Kingston H, Kirschner J, Medne L, Muschke P, Rivier F, Rudnik-Schöneborn S, Spengler S, Inzana F, Stanzial F, Benedicenti F, Synofzik M, Lia Taratuto A, Pirra L, Tay SK, Topaloglu H, Uyanik G, Wand D, Williams D, Zerres K, Weis J, Senderek J.
Recurrent loss of heterozygosity in 1p36 associated with TNFRSF14 mutations in IRF4 translocation negative pediatric follicular lymphomas.
Martin-Guerrero I, Salaverria I, Burkhardt B, Szczepanowski M, Baudis M, Bens S, de Leval L, Garcia-Orad A, Horn H, Lisfeld J, Pellissery S, Klapper W, Oschlies I, Siebert R.
High resolution copy number analysis of IRF4 translocation-positive diffuse large B-cell and follicular lymphomas.
Salaverria I, Martin-Guerrero I, Burkhardt B, Kreuz M, Zenz T, Oschlies I, Arnold N, Baudis M, Bens S, García-Orad A, Lisfeld J, Schwaenen C, Szczepanowski M, Wessendorf S, Pfreundschuh M, Trümper L, Klapper W, Siebert R.
PKC signaling prevents irradiation-induced apoptosis of primary human fibroblasts.
Bluwstein A, Kumar N, Léger K, Traenkle J, Oostrum Jv, Rehrauer H, Baudis M, Hottiger MO.
2012
Spengler S, Begemann M, Ortiz Brüchle N, Baudis M, Denecke B, Kroisel PM, Oehl-Jaschkowitz B, Schulze B, Raabe-Meyer G, Spaich C, Blümel P, Jauch A, Moog U, Zerres K, Eggermann T.
2p21 Deletions in hypotonia-cystinuria syndrome.
Eggermann T, Spengler S, Venghaus A, Denecke B, Zerres K, Baudis M, Ensenauer R.
Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL.
Wernstedt A, Valtorta E, Armelao F, Togni R, Girlando S, Baudis M, Heinimann K, Messiaen L, Staehli N, Zschocke J, Marra G, Wimmer K.
arrayMap: a reference resource for genomic copy number imbalances in human malignancies.
Cai H, Kumar N, Baudis M.
Specific genomic regions are differentially affected by copy number alterations across distinct cancer types, in aggregated cytogenetic data.
Kumar N, Cai H, von Mering C, Baudis M.
Losses at chromosome 4q are associated with poor survival in operable ductal pancreatic adenocarcinoma.
Luebke AM, Baudis M, Matthaei H, Vashist YK, Verde PE, Hosch SB, Erbersdobler A, Klein CA, Izbicki JR, Knoefel WT, Stoecklein NH.
Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome.
Beleut M, Zimmermann P, Baudis M, Bruni N, Bühlmann P, Laule O, Luu VD, Gruissem W, Schraml P, Moch H.
2011
Silver-Russell patients showing a broad range of ICR1 and ICR2 hypomethylation in different tissues.
Begemann M, Spengler S, Kanber D, Haake A, Baudis M, Leisten I, Binder G, Markus S, Rupprecht T, Segerer H, Fricke-Otto S, Mühlenberg R, Siebert R, Buiting K, Eggermann T.
CDCOCA: a statistical method to define complexity dependence of co-occuring chromosomal aberrations.
Kumar N, Rehrauer H, Cai H, Baudis M.
2010
MUC1 oncogene amplification correlates with protein overexpression in invasive breast carcinoma cells.
Lacunza E, Baudis M, Colussi AG, Segal-Eiras A, Croce MV, Abba MC.
Chromosome 11p15 duplication in Silver-Russell syndrome due to a maternally inherited translocation t(11;15).
Eggermann T, Spengler S, Bachmann N, Baudis M, Mau-Holzmann UA, Singer S, Rossier E.
Increased expression of cellular retinol-binding protein 1 in laryngeal squamous cell carcinoma.
Peralta R, Baudis M, Vazquez G, Juárez S, Ortiz R, Decanini H, Hernandez D, Gallegos F, Valdivia A, Piña P, Salcedo M.
Submicroscopic chromosomal imbalances in idiopathic Silver-Russell syndrome (SRS): the SRS phenotype overlaps with the 12q14 microdeletion syndrome.
Spengler S, Schönherr N, Binder G, Wollmann HA, Fricke-Otto S, Mühlenberg R, Denecke B, Baudis M, Eggermann T.
Identification of a 21q22 duplication in a Silver-Russell syndrome patient further narrows down the Down syndrome critical region.
Eggermann T, Schönherr N, Spengler S, Jäger S, Denecke B, Binder G, Baudis M.
2009
Quantifying cancer progression with conjunctive Bayesian networks.
Gerstung M, Baudis M, Moch H, Beerenwinkel N.
Inferring progression models for CGH data.
Liu J, Bandyopadhyay N, Ranka S, Baudis M, Kahveci T.
Recurrent loss, but lack of mutations, of the SMARCB1 tumor suppressor gene in T-cell prolymphocytic leukemia with TCL1A-TCRAD juxtaposition.
Bug S, Dürig J, Oyen F, Klein-Hitpass L, Martin-Subero JI, Harder L, Baudis M, Arnold N, Kordes U, Dührsen U, Schneppenheim R, Siebert R.
Translocations involving 8q24 in Burkitt lymphoma and other malignant lymphomas: a historical review of cytogenetics in the light of todays knowledge.
Boerma EG, Siebert R, Kluin PM, Baudis M.
2008
Chromosomal changes characterize head and neck cancer with poor prognosis.
Bauer VL, Braselmann H, Henke M, Mattern D, Walch A, Unger K, Baudis M, Lassmann S, Huber R, Wienberg J, Werner M, Zitzelsberger HF.
Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH.
Hoischen A, Ehrler M, Fassunke J, Simon M, Baudis M, Landwehr C, Radlwimmer B, Lichter P, Schramm J, Becker AJ, Weber RG.
Recurrent loss of the Y chromosome and homozygous deletions within the pseudoautosomal region 1: association with male predominance in mantle cell lymphoma.
Nieländer I, Martín-Subero JI, Wagner F, Baudis M, Gesk S, Harder L, Hasenclever D, Klapper W, Kreuz M, Pott C, Martinez-Climent JA, Dreyling M, Arnold N, Siebert R.
2007
Combined single nucleotide polymorphism-based genomic mapping and global gene expression profiling identifies novel chromosomal imbalances, mechanisms and candidate genes important in the pathogenesis of T-cell prolymphocytic leukemia with inv(14)(q11q32).
Dürig J, Bug S, Klein-Hitpass L, Boes T, Jöns T, Martin-Subero JI, Harder L, Baudis M, Dührsen U, Siebert R.
Baudis M.
2006
ABCB1 over-expression and drug-efflux in acute lymphoblastic leukemia cell lines with t(17;19) and E2A-HLF expression.
Baudis M, Prima V, Tung YH, Hunger SP.
Distance-based clustering of CGH data.
Liu J, Mohammed J, Carter J, Ranka S, Kahveci T, Baudis M.
Allele-specific loss of heterozygosity in multiple colorectal adenomas: toward an integrated molecular cytogenetic map II.
Mao X, Hamoudi RA, Talbot IC, Baudis M.
Baudis M.
2005
Genetic losses in breast cancer: toward an integrated molecular cytogenetic map.
Mao X, Hamoudi RA, Zhao P, Baudis M.
Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma.
Vandesompele J, Baudis M, De Preter K, Van Roy N, Ambros P, Bown N, Brinkschmidt C, Christiansen H, Combaret V, Lastowska M, Nicholson J, O’Meara A, Plantaz D, Stallings R, Brichard B, Van den Broecke C, De Bie S, De Paepe A, Laureys G, Speleman F.
Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma.
Hidalgo A, Baudis M, Petersen I, Arreola H, Piña P, Vázquez-Ortiz G, Hernández D, González J, Lazos M, López R, Pérez C, García J, Vázquez K, Alatorre B, Salcedo M.
2002
Randomized study to evaluate the use of high-dose therapy as part of primary treatment for “aggressive” lymphoma.
Kaiser U, Uebelacker I, Abel U, Birkmann J, Trümper L, Schmalenberg H, Karakas T, Metzner B, Hossfeld DK, Bischoff HG, Franke A, Reiser M, Müller P, Mantovani L, Grundeis M, Rothmann F, von Seydewitz CU, Mesters RM, Steinhauer EU, Krahl D, Schumacher K, Kneba M, Baudis M, Schmitz N, Pfab R, Köppler H, Parwaresch R, Pfreundschuh M, Havemann K.
2001
Progenetix.net: an online repository for molecular cytogenetic aberration data.
Baudis M, Cleary ML.
Bentz M, Barth TF, Brüderlein S, Bock D, Schwerer MJ, Baudis M, Joos S, Viardot A, Feller AC, Müller-Hermelink HK, Lichter P, Döhner H, Möller P.
Comparative genomic hybridization for the analysis of leukemias and lymphomas.
Baudis M, Bentz M.
Potential of chromosomal and matrix-based comparative genomic hybridization for molecular diagnostics in lymphomas.
Wessendorf S, Lichter P, Schwänen C, Fritz B, Baudis M, Walenta K, Kloess M, Döhner H, Bentz M.
2000
t(11;14)-positive mantle cell lymphomas exhibit complex karyotypes and share similarities with B-cell chronic lymphocytic leukemia.
Bentz M, Plesch A, Bullinger L, Stilgenbauer S, Ott G, Müller-Hermelink HK, Baudis M, Barth TF, Möller P, Lichter P, Döhner H.
1997
Analysis of genomic alterations in benign, atypical, and anaplastic meningiomas: toward a genetic model of meningioma progression.
Weber RG, Boström J, Wolter M, Baudis M, Collins VP, Reifenberger G, Lichter P.
High-level DNA amplifications are common genetic aberrations in B-cell neoplasms.
Werner CA, Döhner H, Joos S, Trümper LH, Baudis M, Barth TF, Ott G, Möller P, Lichter P, Bentz M.
1996
Efficacy of current molecular cytogenetic protocols for the diagnosis of chromosome aberrations in tumor specimens.
Lichter P, Fischer K, Joos S, Fink T, Baudis M, Potkul RK, Ohl S, Solinas-Toldo S, Weber R, Stilgenbauer S, Bentz M, Döhner H.
Chromosome imbalances in papillary renal cell carcinoma and first cytogenetic data of familial cases analyzed by comparative genomic hybridization.
Bentz M, Bergerheim US, Li C, Joos S, Werner CA, Baudis M, Gnarra J, Merino MJ, Zbar B, Linehan WM, Lichter P.
1995
Identification of genetic imbalances in malignant lymphoma using comparative genomic hybridization.
Bentz M, Döhner H, Werner CA, Huck K, Baudis M, Joos S, Schlegelberger B, Trümper LH, Feller AC, Pfreundschuh M.