Lenhard Group - Selected Publications

  • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, Han JH, Hashimoto T, Hide W, Hofmann O, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, Ogawa C, Teasdale RD, Tegnér J, Lenhard B, Teichmann SA, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Hume DA, Ideker T, Hayashizaki Y (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell, 140(5):744-52.


  • Soler E*, Andrieu-Soler C, de Boer E, Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van IJcken W, Hou J, Steinhoff C, Rijkers E, Lenhard B*, Grosveld F (2010). The Genome-Wide Dynamics of the Binding of Ldb1 Complexes during Erythroid Differentiation. Genes Dev., 24(3):277-89.


  • Dong X*, Akalin A, Sharma Y, Lenhard B (2010). Translog, a web browser for studying the expression divergence of homologous genes. BMC Bioinformatics, 11 Suppl 1:S59 (APBC 2010 conference paper).


  • Ragvin A, Moro E, Fredman D, Navratilova P, Drivenes , Engström PG, Alonso ME, de la Calle Mustienes E, Gomez-Skarmeta JL, Tavares MJ, Casares F, Manzanares M, van Heyningen V, Molven A, Njølstad PR, Argenton F, Lenhard B*, Becker TS* (2010). Long-range Gene Regulation links Genomic Type 2 Diabetes and Obesity risk regions to HHEX, SOX4 and IRX3. Proc. Natl. Acad. Sci. USA, 107(2):775-80.


  • Navratilova P, Fredman D, Lenhard B, Becker TS (2010). Regulatory divergence of the duplicated chromosomal loci sox11a/b by subpartitioning and sequence evolution of enhancers in zebrafish. Mol. Gen. Genomics, 283(2):171-84.


  • Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B* (2010). Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res., 38(4):1071-85.


  • Portales-Casamar E1, Thongjuea S1, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B*, Wasserman WW*, Sandelin A* (2010). JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 38(Database Issue):D105-10.


  • Roider H, Lenhard B, Kanhere A, Haas S, Vingron M (2009). CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses. Nucleic Acids Res., 37:6305-10.


  • Dong X, Fredman D, Lenhard B* (2009). Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 10:R86.


  • Bessa J, Tena JT, de la Calle-Mustienes E, Fernandes-Minan A, Naranjo S, Fernandez A, Montoliu L, Akalin A, Lenhard B, Casares F, Gomez-Skarmeta JL (2009). Zebrafish Enhancer Detection (ZED) vector: a new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Dev. Dyn. 238(9):2409-17.


  • Akalin A, Fredman D, Arner E, Dong X, Bryne JC, Suzuki H, Daub CO, Hayashizaki Y, Lenhard B* (2009). Transcriptional features of genomic regulatory blocks. Genome Biol. 10(4):R38.


  • Suzuki H, Forrest A, van Nimwegen E, .., Akalin A,, Engström PG,, Fredman D, , Lenhard B, Sheng Y,, Hayashizaki Y, Hume DA [150 author total] (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. 41(5):553-62.


  • Navratilova P, Fredman D, Hawkins TA, Turner K, Lenhard B, Becker TS (2009). Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev Biol. 327(2):526-40.


  • Engström PG, Fredman D, Lenhard B* (2008). Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol. 9(2):R34.


  • Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW (2008). Gene characterization index: assessing the depth of gene annotation. PLoS ONE 3(1):e1440.


  • Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, , Lenhard B, , Imanishi T, Gojobori T. (2008). The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res. 32:D793-9.


  • Bryne JC, Valen E, Tang MHE, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B*, Sandelin A* (2008). JASPAR, the open access database of transcription factor binding profiles: new content and tools in the 2008 update. Nucleic Acids Res. 32:D102-6


  • Andersen M, Engström PG, Lithwick S, Arenillas D, Eriksson P, Lenhard B, Wasserman WW, Odeberg J (2008). In silico detection of sequence variations modifying transcriptional regulation. PLoS Comp. Biol. 4:e5.


  • Engström PG, Ho Sui SJ, Drivenes Ø, Becker TS, Lenhard B* (2007). Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 17:1898-908


  • Fredman D, Engström PG, Lenhard B * (2009). Web-based tools and approaches to study long-range gene regulation in Metazoa. Review. Brief. Funct. Genomics Proteomic. 8(4):231-242


  • Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS (2007). Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Review. Genome Biol. 8(Suppl 1):S4


  • Becker TS1, Lenhard B1 (2007). The Random vs. Fragile Breakage Models of Chromosome Evolution: A Matter of Resolution. Review. Mol. Genet. Genomics 278:487-91


  • Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, 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 Y (2006). Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet. , 2:e47.


  • Engström PG, Suzuki H, Ninomiya N, Akalin A, Sessa L, Lavorgna G, Brozzi A, Luzi L, Tan SL, Yang L, Kunarso G, Ng EL, Batalov S, Wahlestedt C, Kai C, Kawai J, Carninci P, Hayashizaki Y, Wells C, Bajic VB, Orlando V, Reid JF, Lenhard B, Lipovich L (2006). Complex Loci in human and mouse genomes. PLoS Genet., 2(4):e62. Epub 2006 Apr 28.


  • Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, 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 Y (2006). Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet., 38(6):626-35. Epub 2006 Apr 28.


  • Andersen M, Lenhard B, Whatling C, Eriksson P, Odeberg J (2006). Alternative promoter usage of the membrane glycoprotein CD36. BMC Mol Biol., 7(1):8.


  • Gómez-Skarmeta JL, Lenhard B and Becker TS (2006). New technologies, new findings and new concepts in the study of vertebrate cis-regulatory sequences. Review Dev Dyn. 235:870-885.


  • Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B (2006). A new generation of JASPAR, the open-access repository for transcription factor binding site profiles., Nucleic Acids Res., 1;34(Database issue):D95-7.


  • Stahlberg N, Merino R, Hernandez LH, Fernandez-Perez L, Sandelin A, Engström PG, Tollet-Egnell P, Lenhard B, Flores-Morales A (2005). Exploring hepatic hormone actions using a compilation of gene expression profiles. BMC Physiol., 13;5(1):8.


  • Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engström PG, Lenhard B, Wasserman WW, Wahlestedt C (2005). Identification of functional SNPs in the 5-prime flanking sequences of human genes. BMC Genomics., 17;6(1):18.


  • Pang KC, Stephen S, Engstrom PG, Tajul-Arifin K, Chen W, Wahlestedt C, Lenhard B, Hayashizaki Y, Mattick JS (2005). RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res., 1;33(Database issue):D125-30.


  • Sandelin A, Bailey P, Bruce S, Engström P, Klos JM, Wasserman WW, Ericson J, Lenhard B (2004). Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics, 5:99.


  • Katzov H, Bennet AM, Kehoe P, Wiman B, Gatz M, Blennow K, Lenhard B, Pedersen NL, de Faire U, Prince JA (2004). A cladistic model of ACE sequence variation with implications for myocardial infarction, Alzheimer disease and obesity. Hum Mol Genet., 1;13(21):2647-57. Epub 2004 Sep 14.


  • Imanishi T, Itoh T, Suzuki Y, ....., Lenhard B, ...., Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S [158 authors total] (2004). Integrative annotation of 23,149 human genes validated by full-length cDNA clones. PLoS Biol., 2:856-75. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.


  • Johansson A, Katzov H, Zetterberg H, Feuk L, Johansson B, Bogdanovic N, Andreasen N, Lenhard B, Brookes AJ, Pedersen NL, Blennow K, Prince JA (2004). Variants of CYP46A1 may interact with age and APOE to influence CSF Abeta42 levels in Alzheimer's disease. Hum Genet., 114(6):581-7. Epub 2004 Mar 18.


  • Sandelin A, Wasserman WW, Lenhard B (2004). ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res., 32:W249-52.


  • Alkema WA, Lenhard B, Wasserman WW (2004). Regulog analysis: detection of conserved regulatory networks across bacteria. Genome Res., 14:1362-73.


  • Sandelin A, Alkema W, Engström P, Wasserman WW, Lenhard B (2004). JASPAR: An Open-Access Database for Eukaryotic Transcription Factor Binding Profiles. Nucleic Acids Res.32: D91-4.


  • Sandelin A, Hoglund A, Lenhard B, Wasserman WW (2003). Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct Integr Genomics., 3(3):125-34. Epub 2003 Jun 25.


  • Lenhard B, Wahlestedt C, Wasserman WW (2003). GeneLynx mouse: integrated portal to the mouse genome. Genome Res., 13(6B):1501-4.


  • Lenhard B, Sandelin A, Mendoza L, Engström P., Jareborg N, Wasserman WW (2003). Identification of conserved regulatory regions by comparative genome analysis. J Biol., 2:13


  • Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato, ..., Lenhard B, ..., Lander ES, Rogers J, Birney E, Hayashizaki Y [150 authors total] (2002). Analysis of the Mouse Transcriptome Based Upon Functional Annotation of 60770 full-length cDNAs. Nature, 420:563-73.


  • Lenhard B, Wasserman WW (2002). TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics, 18:1135-6.


  • Lenhard B, Hayes WS, Wasserman WW (2001). GeneLynx: a gene-centric portal to the human genome. Genome Res., 11:2151-7.

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