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Center director:
Prof. Niels Tommerup
tommerup@imbg.ku.dk







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Mads Bak

Mads Bak

Post.doc / Post.doc

Homeobox and microRNA gene expression in the mammalian central nervous system. High throughput (Illumina Genome Analyzer) sequencing

Emailmadsba@sund.ku.dk
Office24.4.32
Phone27827

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Publications related to WJC

31.   Hansen L, Tawamie H, Murakami Y, Mang Y, ur Rehman S, Buchert R, Schaffer S, Muhammad S, Bak M, Nöthen MM, Bennett E, Maeda Y, Aigner M, Reis A, Kinoshita T, Kinoshita T, Tommerup N, Baig SM, Jamra RA. Hypomorphic Mutations in PGAP2, Encoding a GPI-Anchor-Remodeling Protein, Cause Autosomal-Recessive Intellectual Disability. Am J Hum Genet. 2013;92(4):575-83.
 
30.   Rieneck K, Bak M, Jønson L, Clausen FB, Krog GR, Tommerup N, Nielsen LK, Hedegaard M, Dziegiel MH. Next-generation sequencing: proof of concept for antenatal prediction of the fetal Kell blood group phenotype from cell-free fetal DNA in maternal plasma. Transfusion. 2013 Apr 3. doi: 10.1111/trf.12172. [Epub ahead of print].
 
29.   Mogensen MS, Scheibye-Alsing K, Karlskov-Mortensen P, Proschowsky HF, Jensen VF, Bak M, Tommerup N, Kadarmideen HN, Fredholm M. Validation of genome-wide intervertebral disk calcification associations in dachshund and further investigation of the chromosome 12 susceptibility locus. Front Genet. 2012;3:225. doi: 10.3389/fgene.2012.00225. Epub 2012 Nov 1.
 
28.   Podolska A, Anthon C, Bak M, Tommerup N, Skovgaard K, Heegaard PM, Gorodkin J, Cirera S, Fredholm M. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics. 2012;13:459.
 
27.   Halgren C, Kjaergaard S, Bak M, Hansen C, El-Schich Z, Anderson CM, Henriksen KF, Hjalgrim H, Kirchhoff M, Bijlsma EK, Nielsen M, den Hollander NS, Ruivenkamp CA, Isidor B, Le Caignec C, Zannolli R, Mucciolo M, Renieri A, Mari F, Anderlid BM, Andrieux J, Dieux A, Tommerup N, Bache I. Corpus Callosum Abnormalities, Mental Retardation, Speech Impairment, and Autism in Patients with Haploinsufficiency of ARID1B. Clin Genet. 2012 Sep;82(3):248-55.
 
26.   Jakobsen LP, Pfeiffer P, Andersen M, Eiberg H, Hansen L, Mang Y, Bak M, Møller RS, Klitten LL, Tommerup N. Genetic studies in congenital anterior midline cervical cleft. Am J Med Genet A. 2012;158A:2021-6.
 
25.   Halgren C, Bache I, Bak M, Myatt MW, Anderson CM, Brøndum-Nielsen K, Tommerup N. Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity. Eur J Hum Genet. 2012 May 23. doi: 10.1038/ejhg.2012.92. [Epub ahead of print].
 
24.   Minocherhomji S, Seeman S, Mang Y, El-schich Z, Bak M, Hansen C, Papadopolous N, Nielsen H, Josefsen K, Gorodkin J, Tommerup N, Silahtaroglu A. Sequence and expression analysis of gaps in human chromosome 20. Nucleic Acids Res. 2012 Apr 17. [Epub ahead of print].
 
23.   Mercader JM, González JR, Lozano JJ, Bak M, Kauppinen S, Sumoy L, Dierssen M, Fernández-Aranda F, Visa J, Gratacòs M, Estivill X. Aberrant brain microRNA target and miRISC gene expression in the anx/anx anorexia mouse model. Gene. 2012;497:181-90.
 
22.   Brøchner CB, Johansen JS, Larsen LA, Bak M, Mikkelsen HB, Byskov AG, Andersen CY, Møllgård K. Ykl-40 is Differentially Expressed in Human Embryonic Stem Cells and in Cell Progeny of the Three Germ Layers. J Histochem Cytochem. 2012;60:188-204.
 
21.   Dietrich N, Lerdrup M, Landt E, Agrawal-Singh S, Bak M, Tommerup N, Rappsilber J, Södersten E, Hansen K. REST-Mediated Recruitment of Polycomb Repressor Complexes in Mammalian Cells. PLoS Genet. 2012;8:e1002494.
 
20.   Schmitz SU, Albert M, Malatesta M, Morey L, Johansen JV, Bak M, Tommerup N, Abarrategui I, Helin K. Jarid1b targets genes regulating development and is involved in neural differentiation. EMBO J. 2011;30:4586-600.
 
19.   Skovgaard O, Bak M, Løbner-Olesen A, Tommerup N. Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing. Genome Res. 2011;21:1388-93.
 
18.   Eskildsen T, Taipaleenmäki H, Stenvang J, Abdallah BM, Ditzel N, Nossent AY, Bak M, Kauppinen S, Kassem M. MicroRNA-138 regulates osteogenic differentiation of human stromal (mesenchymal) stem cells in vivo. PNAS 2011;108:6139-44.
 
17.   Gilling M, Lind-Thomsen A, Mang Y, Bak M, Møller M, Ullmann R, Kristoffersson U, Kalscheuer VM, Henriksen KF, Bugge M, Tümer Z, Tommerup N. Biparental inheritance of chromosomal abnormalities in male twins with non-syndromic mental retardation. Eur J Med Genet. 2011;54:e383-8.
 
16.   Wesolowska A, Dalgaard MD, Borst L, Gautier L, Bak M, Weinhold N, Nielsen BF, Helt LR, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R. Cost-effective multiplexing before capture allows screening of 25 000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia. 2011;25:1001-6.
 
15.   Boyd M, Hansen M, Jensen TG, Perearnau A, Olsen AK, Bram LL, Bak M, Tommerup N, Olsen J, Troelsen JT. Genome-wide analysis of CDX2 binding in intestinal epithelial cells (Caco-2). J Biol Chem. 2010;285:25115-25.
 
14.   Kleine-Kohlbrecher D, Christensen J, Vandamme J, Abarrategui I, Bak M, Tommerup N, Shi X, Gozani O, Rappsilber J, Salcini AE, Helin K. A Functional Link between the Histone Demethylase PHF8 and the Transcription Factor ZNF711 in X-Linked Mental Retardation. Mol Cell 2010;38:165-78.
 
13.   Pasini D, Cloos PAC, Walfridsson J, Olsson L, Bukowski J-P, Johansen JV, Bak M, Tommerup N, Rappsilber J, Helin K. JARID2 regulates binding of the Polycomb repressive complex 2 to target genes in ES cells. Nature. 2010;464:306-10.
 
12.   Liu X, Sempere LF, Ouyang H, Memoli VA, Andrew AS, Luo Y, Demidenko E, Korc M, Shi W, Preis M, Dragnev KH, Li H, Direnzo J, Bak M, Freemantle SJ, Kauppinen S, Dmitrovsky E. MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest. 2010;120:1298-1309.
 
11.   Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos P, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li X, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre T, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham T, Ramsey CB, Hansen TvO, Nielsen FC, Crawford M, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010;463:757-62.
 
10.   Liu X, Sempere LF, Galimberti F, Freemantle SJ, Black C, Dragnev KH, Ma Y, Fiering S, Memoli V, Li H, Direnzo J, Korc M, Cole CN, Bak M, Kauppinen S, Dmitrovsky E. Uncovering Growth-Suppressive MicroRNAs in Lung Cancer. Clin Cancer Res. 2009;15:1177-83.
 
9.   Vestergaard J, Lind-Thomsen A, Pedersen MW, Ostergaard Jarmer H, Bak M, Hasholt L, Tommerup N, Tümer Z, Larsen LA. GLI1 Is Involved in Cell Cycle Regulation and Proliferation of NT2 Embryonal Carcinoma Stem Cells. DNA Cell Biol. 2008;27:251-6.
 
8.   Elmén J, Lindow M, Silahtaroglu A, Bak M, Christensen M, Lind-Thomsen A, Hedtjärn M, Hansen JB, Hansen HF, Straarup EM, McCullagh K, Kearney P, Kauppinen S. Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res. 2008;36:1153-62.
 
7.   Bak M, Silahtaroglu A, Møller M, Christensen M, Rath MF, Skryabin B, Tommerup N, Kauppinen S. MicroRNA expression in the adult mouse central nervous system. RNA. 2008;14:432-44.
 
6.   Sempere LF, Christensen M, Silahtaroglu A, Bak M, Heath CV, Schwartz G, Wells W, Kauppinen S, Cole CN. Altered MicroRNA expression confined to specific epithelial cell subpopulations in breast cancer. Cancer Res. 2007;67:11612-20.
 
5.   Bugge M, Collins A, Hertz JM, Eiberg H, Lundsteen C, Brandt CA, Bak M, Hansen C, Delozier CD, Lespinasse J, Tranebjaerg L, Hahnemann JM, Rasmussen K, Bruun-Petersen G, Duprez L, Tommerup N, Petersen MB. Non-disjunction of chromosome 13. Hum Mol Genet. 2007;16:2004-10.
 
4.   Bak M, Conley L, Hedegaard J, Larsen LA, Sørensen P, Bendixen C, Tommerup N. Evaluation of two methods for generating cRNA for microarray experiments from nanogram amounts of total RNA. Anal Biochem. 2006;358:111-9.
 
3.   Bugge M, Delozier-Blanchet C, Bak M, Brandt CA, Hertz JM, Nielsen JB, Duprez L, Petersen MB. Trisomy 13 due to rea(13q;13q) is caused by i(13) and not rob(13;13)(q10;q10) in the majority of cases. Am J Med Genet A. 2005;132A:310-3.
 
2.   Bak M, Hansen C, Henriksen KF, Hansen L, Pakkenberg H, Eiberg H, Tommerup N. Mutation analysis of the Sonic hedgehog promoter and putative enhancer elements in Parkinsons disease patients. Brain Res Mol Brain Res. 2004;126:207-11.
 
1.   Bak M, Hansen C, Tommerup N, Larsen LA. The Hedgehog signaling pathway-implications for drug targets in cancer and neurodegenerative disorders. Pharmacogenomics. 2003;4:411-29 (Review).
 

Book chapters related to WJC

1.   Vestergaard J, Bak M, Larsen LA. The Hedgehog Signaling Pathway in Cancer. In: Macieira-Coelho, Alvaro (eds.). Developmental Biology of Neoplastic Growth, Progress in Molecular and Subcellular Biology, Vol. 40. Heidelberg 2005, Springer.
 

Presentations related to WJC

71st CSHL SYMPOSIUM: Regulatory RNAs
Cold Spring Harbor Laboratory, May 31, 2006
Posters
7.   Bak M, Silahtaroglu AN, Christensen M, Møller M, Skryabin B, Kloosterman W, Nolting D, Rath MF, Brosius J, Plasterk R, Tommerup N, Kauppinen S. microRNAs in the mammalian brain.
 
Keystone Symposia: RNAi and Related Pathways
Vancouver, British Columbia, Canada, January 26, 2006
Posters
6.   Christensen M, Bak M, Silahatroglu A, Kloostermann W, Skryapin B, Nolting D, Nørremølle A, Lassen A-C, Hasholt L, Brosius J, Tommerup N, Plasterk R, Kauppinen S. miRNAs in mammalian brain.
 
54th Meeting of the American Society of Human Genetics
Toronto, Canada, October 25, 2004
Posters
5.PDF  Bugge M, deLozier-Blanchet C, Bak M, Brandt CA, Hertz JM, Nielsen JB, Duprez L, Petersen MB. Trisomy 13 due to rea(13;13) de novo is caused by i(13;13) and not t(13;13) in the majority of cases.
 
XVIIième Colloque de L'Association des Cytogénéticiens de Langue Francaise
Université de Versailles Saint Quentin en Yvelines, September 19, 2004
Posters
4.PDF  Bugge M, deLozier-Blanchet C, Bak M, Brandt CA, Hertz JM, Nielsen JB, Duprez L, Petersen MB. La trisomie 13 due à rea(13;13) de novo est causée par un isochromosome (13;13) et non pas par translocation (13;13) dans la majorité des cas.
 
European Human Genetics Conference 2003
Birmingham, England, May 02, 2003
Posters
3.PDF  Gilling M, Tumer Z, Bache I, Bak M, Niebuhr E, Bugge M, Cotterill R M J K. Brøndum-Nielsen3, U. Kristoffersson4, H-H. Ropers 5, N. Tommerup1. FISH-mapping of translocation breakpoints associated with autism.
 
52nd Annual Meeting of The American Society of Human Genetics
Baltimore, Maryland, USA, October 14, 2002
Posters
2.   Bugge M, Petersen MB, Bak M, Brandt CA, Hertz JM, Tranebjaerg L, Delozier-Blanchet CD, Petersen GB, Lundsteen C, Lespinasse J, Rasmussen K, Mikkelsen M. Nondisjunction studies in trisomy 13. Am J Human Genet 2002;71 (supp): 292 (Poster 704).
 
Association des Cytogénéticiens de Langue Francaise
Toulouse, France, September 15, 2002
Posters
1.   Bugge M, Petersen MB, Bak M, Brandt CA, Hertz JM, Tranebjaerg L, Delozier-Blanchet CD, Petersen GB, Lundsteen C, Lespinasse J, Rasmussen K, Mikkelsen M. Non-disjonction de trisomie 13.
 

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