ProfessorBorisLenhard

Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DAet al., 2007, Mammalian RNA polymerase II core promoters: insights from genome-wide studies, NATURE REVIEWS GENETICS, Vol: 8, Pages: 424-436, ISSN: 1471-0056

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• Citations: 386

Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engstrom PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TSet al., 2007, Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates, GENOME RESEARCH, Vol: 17, Pages: 545-555, ISSN: 1088-9051

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• Citations: 254

Vidal OM, Merino R, Rico-Bautista E, Fernandez-Perez L, Chia DJ, Woelfle J, Ono M, Lenhard B, Norstedt G, Rotwein P, Flores-Morales Aet al., 2007, <i>In</i> <i>vivo</i> transcript profiling and phylogenetic analysis identifies suppressor of cytokine signaling 2 as a direct signal transducer and activator of transcription 5b target in liver, MOLECULAR ENDOCRINOLOGY, Vol: 21, Pages: 293-311, ISSN: 0888-8809

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• Citations: 59

Pang KC, Stephen S, Dinger ME, Engstrom PG, Lenhard B, Mattick JSet al., 2007, RNAdb 2.0-an expanded database of mammalian non-coding RNAs, NUCLEIC ACIDS RESEARCH, Vol: 35, Pages: D178-D182, ISSN: 0305-1048

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• Citations: 127

Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TSet al., 2007, Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes, GENOME BIOLOGY, Vol: 8, ISSN: 1474-760X

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• Citations: 37

Bailey PJ, Klos JM, Andersson E, Karlen M, Kallstrom M, Ponjavic J, Muhr J, Lenhard B, Sandelin A, Ericson Jet al., 2006, A global genomic transcriptional code associated with CNS-expressed genes, EXPERIMENTAL CELL RESEARCH, Vol: 312, Pages: 3108-3119, ISSN: 0014-4827

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• Citations: 40

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CAM, Taylor MS, Engström PG, Frith MC, Forrest ARR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Yet al., 2006, Genome-wide analysis of mammalian promoter architecture and evolution, NATURE GENETICS, Vol: 38, Pages: 626-635, ISSN: 1061-4036

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• Citations: 974

Gómez-Skarmeta JL, Lenhard B, Becker TS, 2006, New technologies, new findings, and new concepts in the study of vertebate <i>cis</i>-regulatory sequences, DEVELOPMENTAL DYNAMICS, Vol: 235, Pages: 870-885, ISSN: 1058-8388

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• Citations: 36

Engstrom PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, ng EL-CN, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich Let al., 2006, Complex loci in human and mouse genomes, PLOS GENETICS, Vol: 2, Pages: 564-577, ISSN: 1553-7404

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• Citations: 251

Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engstrom PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest ARR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Yet al., 2006, Transcript annotation in FANTOM3:: Mouse gene catalog based on physical cDNAs, PLOS GENETICS, Vol: 2, Pages: 498-503, ISSN: 1553-7404

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• Citations: 133

Andersen M, Lenhard B, Whatling C, Eriksson P, Odeberg Jet al., 2006, Alternative promoter usage of the membrane glycoprotein CD36, BMC MOLECULAR BIOLOGY, Vol: 7, ISSN: 1471-2199

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• Citations: 46

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard Bet al., 2006, A new generation of JASPAR, the open-access repository for transcription factor binding site profiles., Nucleic acids research, Vol: 34

JASPAR is the most complete open-access collection of transcription factor binding site (TFBS) matrices. In this new release, JASPAR grows into a meta-database of collections of TFBS models derived by diverse approaches. We present JASPAR CORE--an expanded version of the original, non-redundant collection of annotated, high-quality matrix-based transcription factor binding profiles, JASPAR FAM--a collection of familial TFBS models and JASPAR phyloFACTS--a set of matrices computationally derived from statistically overrepresented, evolutionarily conserved regulatory region motifs from mammalian genomes. JASPAR phyloFACTS serves as a non-redundant extension to JASPAR CORE, enhancing the overall breadth of JASPAR for promoter sequence analysis. The new release of JASPAR is available at http://jaspar.genereg.net.

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• Citations: 177

Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard Bet al., 2006, A new generation of JASPAR, the open-access repository for transcription factor binding site profiles, NUCLEIC ACIDS RESEARCH, Vol: 34, Pages: D95-D97, ISSN: 0305-1048

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• Citations: 167

Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin Aet al., 2006, Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters, GENOME BIOLOGY, Vol: 7, ISSN: 1474-760X

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• Citations: 85

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, Suzuki H, Carninci P, Hayashizaki Y, Wells C, Frith M, Ravasi T, Pang KC, Hallinan J, Mattick J, Hume DA, Lipovich L, Batalov S, Engström PG, Mizuno Y, Faghihi MA, Sandelin A, Chalk AM, Mottagui-Tabar S, Liang Z, Lenhard B, Wahlestedt Cet al., 2005, Antisense transcription in the mammalian transcriptome, SCIENCE, Vol: 309, Pages: 1564-1566, ISSN: 0036-8075

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• Citations: 1323

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest ARR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato X, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SPT, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Babu MM, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CAM, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishioet al., 2005, The transcriptional landscape of the mammalian genome, SCIENCE, Vol: 309, Pages: 1559-1563, ISSN: 0036-8075

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• Citations: 2699

Ståhlberg N, Merino R, Hernández LH, Fernández-Pérez L, Sandelin A, Engström P, Tollet-Egnell P, Lenhard B, Flores-Morales Aet al., 2005, Exploring hepatic hormone actions using a compilation of gene expression profiles., BMC Physiol, Vol: 5

BACKGROUND: Microarray analysis is attractive within the field of endocrine research because regulation of gene expression is a key mechanism whereby hormones exert their actions. Knowledge discovery and testing of hypothesis based on information-rich expression profiles promise to accelerate discovery of physiologically relevant hormonal mechanisms of action. However, most studies so-far concentrate on the analysis of actions of single hormones and few examples exist that attempt to use compilation of different hormone-regulated expression profiles to gain insight into how hormone act to regulate tissue physiology. This report illustrates how a meta-analysis of multiple transcript profiles obtained from a single tissue, the liver, can be used to evaluate relevant hypothesis and discover novel mechanisms of hormonal action. We have evaluated the differential effects of Growth Hormone (GH) and estrogen in the regulation of hepatic gender differentiated gene expression as well as the involvement of sterol regulatory element-binding proteins (SREBPs) in the hepatic actions of GH and thyroid hormone. RESULTS: Little similarity exists between liver transcript profiles regulated by 17-alpha-ethinylestradiol and those induced by the continuos infusion of bGH. On the other hand, strong correlations were found between both profiles and the female enriched transcript profile. Therefore, estrogens have feminizing effects in male rat liver which are different from those induced by GH. The similarity between bGH and T3 were limited to a small group of genes, most of which are involved in lipogenesis. An in silico promoter analysis of genes rapidly regulated by thyroid hormone predicted the activation of SREBPs by short-term treatment in vivo. It was further demonstrated that proteolytic processing of SREBP1 in the endoplasmic reticulum might contribute to the rapid actions of T3 on these genes. CONCLUSION: This report illustrates how a meta-analysis of multiple transcript profil

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Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt Cet al., 2005, Identification of functional SNPs in the 5-prime flanking sequences of human genes -: art. no. 18, BMC GENOMICS, Vol: 6, ISSN: 1471-2164

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• Citations: 38

Pang KC, Stephen S, Engström PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JSet al., 2005, RNAdb--a comprehensive mammalian noncoding RNA database., Nucleic Acids Res, Vol: 33, Pages: D125-D130

In recent years, there have been increasing numbers of transcripts identified that do not encode proteins, many of which are developmentally regulated and appear to have regulatory functions. Here, we describe the construction of a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes. The database is available at http://research.imb.uq.edu.au/RNAdb and is searchable by many criteria. It includes microRNAs and snoRNAs, but not infrastructural RNAs, such as rRNAs and tRNAs, which are catalogued elsewhere. The database also includes over 1100 putative antisense ncRNAs and almost 20,000 putative ncRNAs identified in high-quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.

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Pang KC, Stephen S, Engström PG, Tajul-Arifin K, Chen WS, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JSet al., 2005, RNAdb -: a comprehensive mammalian noncoding RNA database, NUCLEIC ACIDS RESEARCH, Vol: 33, Pages: D125-D130, ISSN: 0305-1048

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• Citations: 125

Sandelin A, Bailey P, Bruce S, Engström PG, Klos JM, Wasserman WW, Ericson J, Lenhard Bet al., 2004, Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes -: art. no. 99, BMC GENOMICS, Vol: 5, ISSN: 1471-2164

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• Citations: 223

Kemmer D, Faxén M, Hodges E, Lim J, Herzog E, Ljungström E, Lundmark A, Olsen MK, Podowski R, Sonnhammer ELL, Nilsson P, Reimers M, Lenhard B, Roberds SL, Wahlestedt C, Höög C, Agarwal P, Wasserman WWet al., 2004, Exploring the foundation of genomics:: a Northern blot reference set for the comparative analysis of transcript profiling technologies, COMPARATIVE AND FUNCTIONAL GENOMICS, Vol: 5, Pages: 584-595, ISSN: 1531-6912

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• Citations: 1

Katzov H, Bennet AM, Kehoe P, Wiman B, Gatz M, Blennow K, Lenhard B, Pedersen NL, de Faire U, Prince JAet al., 2004, A cladistic model of <i>ACE</i> sequence variation with implications for myocardial infarction, Alzheimer disease and obesity, HUMAN MOLECULAR GENETICS, Vol: 13, Pages: 2647-2657, ISSN: 0964-6906

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• Citations: 43

Sandelin A, Wasserman WW, Lenhard B, 2004, ConSite: web-based prediction of regulatory elements using cross-species comparison, NUCLEIC ACIDS RESEARCH, Vol: 32, Pages: W249-W252, ISSN: 0305-1048

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• Citations: 340

Alkema WBL, Lenhard B, Wasserman WW, 2004, Regulog analysis:: Detection of conserved regulatory networks across bacteria:: Application to <i>Staphylococcus aureus</i>, GENOME RESEARCH, Vol: 14, Pages: 1362-1373, ISSN: 1088-9051

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• Citations: 49

Johansson AM, Katzov H, Lenhard B, Zetterberg H, Feuk L, Johansson B, Bogdanovic N, Andreasen N, Brookes AJ, Pederson NL, Blennow K, Prince JAet al., 2004, Variants of <i>CYP46A1</i> interact with age and <i>APOE</i> to influence csf Aβ42 and phospho-tau levels in Alzheimer's disease, 9th International Conference on Alzheimers Disease and Related Disorders, Publisher: ELSEVIER SCIENCE INC, Pages: S505-S505, ISSN: 0197-4580

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Geijer J, Lenhard B, Merino-Martinez R, Norstedt G, Flores-Morales Aet al., 2004, Grid computing for the analysis of regulatory elements in CO-regulated sets of genes, Parallel Processing Letters, Vol: 14, Pages: 137-150, ISSN: 0129-6264

We describe an initial implementation of a platform for the analysis of gene promoter architecture for sets of genes from human and other higher organisms, using NorduGrid as the Grid Virtual Organization. The procedure leading from a set of co-regulated genes to a set of inferred common regulatory elements involves a number of computationally intensive, but well scalable steps. We show it is feasible to implement a high performance genomic regulatory sequence analysis pipeline on the Grid with minimal modification to the existing computational biology software components. We applied a job binning step to dramatically reduce the overhead for submitting a set of many small jobs to the Grid. Even with simple jobs and a relatively small size of the Grid, we observed up to 25-fold performance improvement over a comparable or more powerful single or dual-CPU platform, Our implementation of biological sequence alignment and transcription factor binding site algorithms on the Grid proves that even simple applications can take advantage of computational resources that adopted this computational paradigm.

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Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia LB, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin LH, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MD, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayash K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano Set al., 2004, Integrative annotation of 21,037 human genes validated by full-length cDNA clones, PLOS BIOLOGY, Vol: 2, Pages: 856-875, ISSN: 1544-9173

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• Citations: 260

Johansson A, Katzov H, Zetterberg H, Feuk L, Johansson B, Bogdanovic N, Andreasen N, Lenhard B, Brookes AJ, Pedersen NL, Blennow K, Prince JAet al., 2004, Variants of <i>CYP46A1</i> may interact with age and <i>APOE</i> to influence CSF Aβ42 levels in Alzheimer's disease, HUMAN GENETICS, Vol: 114, Pages: 581-587, ISSN: 0340-6717

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• Citations: 52

Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard Bet al., 2004, JASPAR:: an open-access database for eukaryotic transcription factor binding profiles, NUCLEIC ACIDS RESEARCH, Vol: 32, Pages: D91-D94, ISSN: 0305-1048

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• Citations: 1212