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    22833 Publications
    3073 Total Profiles
    24 Edited Profiles

    Visel, Axel

    TitleBiologist Staff Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentGenomics
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone510/495-2301

       Bibliographic 
       Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can sign in to make corrections and additions, or contact us for help.
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      1. Lupiáñez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, Horn D, Kayserili H, Opitz JM, Laxova R, Santos-Simarro F, Gilbert-Dussardier B, Wittler L, Borschiwer M, Haas SA, Osterwalder M, Franke M, Timmermann B, Hecht J, Spielmann M, Visel A, Mundlos S. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015 May 21; 161(5):1012-25.
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      2. Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio LA, Weiss MJ, Blobel GA, Hardison RC. Occupancy by key transcription factors is a more accurate predictor of enhancer activity than histone modifications or chromatin accessibility. Epigenetics Chromatin. 2015; 8:16.
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      3. Lidral AC, Liu H, Bullard SA, Bonde G, Machida J, Visel A, Uribe LM, Li X, Amendt B, Cornell RA. A single nucleotide polymorphism associated with isolated cleft lip and palate, thyroid cancer and hypothyroidism alters the activity of an oral epithelium and thyroid enhancer near FOXE1. Hum Mol Genet. 2015 Jul 15; 24(14):3895-907.
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      4. Nord AS, Pattabiraman K, Visel A, Rubenstein JL. Genomic perspectives of transcriptional regulation in forebrain development. Neuron. 2015 Jan 7; 85(1):27-47.
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      5. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20; 515(7527):371-5.
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      6. Osterwalder M, Speziale D, Shoukry M, Mohan R, Ivanek R, Kohler M, Beisel C, Wen X, Scales SJ, Christoffels VM, Visel A, Lopez-Rios J, Zeller R. HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme. Dev Cell. 2014 Nov 10; 31(3):345-57.
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      7. He A, Gu F, Hu Y, Ma Q, Yi Ye L, Akiyama JA, Visel A, Pennacchio LA, Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014; 5:4907.
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      8. Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet. 2014 Sep; 10(9):e1004610.
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      9. Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, Tan TY, Munnich A, Pennacchio LA, Abadie V, Temple IK, Goldenberg A, van Heyningen V, Amiel J, FitzPatrick D, Kleinjan DA, Visel A, Lyonnet S. Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence. Hum Mutat. 2014 Aug; 35(8):1011-20.
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      10. Shi W, Moon CD, Leahy SC, Kang D, Froula J, Kittelmann S, Fan C, Deutsch S, Gagic D, Seedorf H, Kelly WJ, Atua R, Sang C, Soni P, Li D, Pinares-Patiño CS, McEwan JC, Janssen PH, Chen F, Visel A, Wang Z, Attwood GT, Rubin EM. Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. Genome Res. 2014 Sep; 24(9):1517-25.
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      11. Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, Visel A, Woyke T, Kyrpides NC, Rubin EM. Stop codon reassignments in the wild. Science. 2014 May 23; 344(6186):909-13.
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      12. Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio LA, Puelles L, Visel A, Rubenstein JL. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron. 2014 Jun 4; 82(5):989-1003.
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      13. Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, Bernstein BE, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9.
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      14. Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, Plajzer-Frick I, Kirkpatrick A, Göttgens B, Bruneau BG, Visel A, Pennacchio LA. Function-based identification of mammalian enhancers using site-specific integration. Nat Methods. 2014 May; 11(5):566-71.
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      15. Eckler MJ, Larkin KA, McKenna WL, Katzman S, Guo C, Roque R, Visel A, Rubenstein JL, Chen B. Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex. Neural Dev. 2014; 9(1):6.
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      16. Fakhouri WD, Rahimov F, Attanasio C, Kouwenhoven EN, Ferreira De Lima RL, Felix TM, Nitschke L, Huver D, Barrons J, Kousa YA, Leslie E, Pennacchio LA, Van Bokhoven H, Visel A, Zhou H, Murray JC, Schutte BC. An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects. Hum Mol Genet. 2014 May 15; 23(10):2711-20.
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      17. Nord AS, Blow MJ, Attanasio C, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Rubenstein JL, Rubin EM, Pennacchio LA, Visel A. Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development. Cell. 2013 Dec 19; 155(7):1521-31.
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      18. Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R, Phouanenavong S, Akiyama JA, Shoukry M, Afzal V, Rubin EM, FitzPatrick DR, Ren B, Hallgrímsson B, Pennacchio LA, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013 Oct 25; 342(6157):1241006.
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      19. Sanchez-Castro M, Gordon CT, Petit F, Nord AS, Callier P, Andrieux J, Guérin P, Pichon O, David A, Abadie V, Bonnet D, Visel A, Pennacchio LA, Amiel J, Lyonnet S, Le Caignec C. Congenital Heart Defects in Patients with Deletions Upstream of SOX9. Hum Mutat. 2013 Dec; 34(12):1628-31.
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      20. Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A. 2013 Oct 29; 110(44):17921-6.
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      21. Gross SM, Martin JA, Simpson J, Abraham-Juarez MJ, Wang Z, Visel A. De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. BMC Genomics. 2013; 14:563.
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      22. Dickel DE, Visel A, Pennacchio LA. Functional anatomy of distant-acting mammalian enhancers. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1620):20120359.
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      23. Chen YJ, Vogt D, Wang Y, Visel A, Silberberg SN, Nicholas CR, Danjo T, Pollack JL, Pennacchio LA, Anderson S, Sasai Y, Baraban SC, Kriegstein AR, Alvarez-Buylla A, Rubenstein JL. Use of "MGE enhancers" for labeling and selection of embryonic stem cell-derived medial ganglionic eminence (MGE) progenitors and neurons. PLoS One. 2013; 8(5):e61956.
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      24. Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14; 152(4):895-908.
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      25. McKinsey GL, Lindtner S, Trzcinski B, Visel A, Pennacchio LA, Huylebroeck D, Higashi Y, Rubenstein JL. Dlx1&2-dependent expression of Zfhx1b (Sip1, Zeb2) regulates the fate switch between cortical and striatal interneurons. Neuron. 2013 Jan 9; 77(1):83-98.
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      26. Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, Bessa J. Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics. 2012; 13:713.
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      27. May D, Blow MJ, Kaplan T, McCulley DJ, Jensen BC, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Afzal V, Simpson PC, Rubin EM, Black BL, Bristow J, Pennacchio LA, Visel A. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2012 Jan; 44(1):89-93.
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      28. Hochheiser H, Aronow BJ, Artinger K, Beaty TH, Brinkley JF, Chai Y, Clouthier D, Cunningham ML, Dixon M, Donahue LR, Fraser SE, Hallgrimsson B, Iwata J, Klein O, Marazita ML, Murray JC, Murray S, de Villena FP, Postlethwait J, Potter S, Shapiro L, Spritz R, Visel A, Weinberg SM, Trainor PA. The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev Biol. 2011 Jul 15; 355(2):175-82.
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      29. Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science. 2011 Jan 28; 331(6016):463-7.
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      30. Fort A, Fish RJ, Attanasio C, Dosch R, Visel A, Neerman-Arbez M. A liver enhancer in the fibrinogen gene cluster. Blood. 2011 Jan 6; 117(1):276-82.
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      31. Blow MJ, McCulley DJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Bristow J, Ren B, Black BL, Rubin EM, Visel A, Pennacchio LA. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010 Sep; 42(9):806-10.
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      32. Pennacchio LA, Visel A. Limits of sequence and functional conservation. Nat Genet. 2010 Jul; 42(7):557-8.
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      33. Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 2010 May; 20(5):565-77.
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      34. Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature. 2010 Mar 18; 464(7287):409-12.
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      35. Visel A, Rubin EM, Pennacchio LA. Genomic views of distant-acting enhancers. Nature. 2009 Sep 10; 461(7261):199-205.
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      36. Avraham O, Hadas Y, Vald L, Zisman S, Schejter A, Visel A, Klar A. Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1. Neural Dev. 2009; 4:21.
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      37. Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio LA. Functional autonomy of distant-acting human enhancers. Genomics. 2009 Jun; 93(6):509-13.
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      38. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12; 457(7231):854-8.
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      39. De Val S, Chi NC, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio LA, Dubchak I, Krieg PA, Stainier DY, Black BL. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell. 2008 Dec 12; 135(6):1053-64.
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      40. Rahimov F, Marazita ML, Visel A, Cooper ME, Hitchler MJ, Rubini M, Domann FE, Govil M, Christensen K, Bille C, Melbye M, Jugessur A, Lie RT, Wilcox AJ, Fitzpatrick DR, Green ED, Mossey PA, Little J, Steegers-Theunissen RP, Pennacchio LA, Schutte BC, Murray JC. Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet. 2008 Nov; 40(11):1341-7.
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      41. Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio LA, Rubin EM, Noonan JP. Human-specific gain of function in a developmental enhancer. Science. 2008 Sep 5; 321(5894):1346-50.
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      42. Moldrich RX, Lainé J, Visel A, Beart PM, Laffaire J, Rossier J, Potier MC. Transmembrane protein 50b (C21orf4), a candidate for Down syndrome neurophenotypes, encodes an intracellular membrane protein expressed in the rodent brain. Neuroscience. 2008 Jul 17; 154(4):1255-66.
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      43. Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio LA. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet. 2008 Feb; 40(2):158-60.
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      44. Visel A, Carson J, Oldekamp J, Warnecke M, Jakubcakova V, Zhou X, Shaw CA, Alvarez-Bolado G, Eichele G. Regulatory pathway analysis by high-throughput in situ hybridization. PLoS Genet. 2007 Oct; 3(10):1867-83.
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      45. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio LA, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007 Sep; 5(9):e234.
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      46. Visel A, Bristow J, Pennacchio LA. Enhancer identification through comparative genomics. Semin Cell Dev Biol. 2007 Feb; 18(1):140-52.
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      47. Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, Jones AR. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007 Jan 11; 445(7124):168-76.
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      48. Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan; 35(Database issue):D88-92.
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      49. Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23; 444(7118):499-502.
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      50. Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive analysis of the expression patterns of the adenylate cyclase gene family in the developing and adult mouse brain. J Comp Neurol. 2006 Jun 10; 496(5):684-97.
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      51. Yaylaoglu MB, Titmus A, Visel A, Alvarez-Bolado G, Thaller C, Eichele G. Comprehensive expression atlas of fibroblast growth factors and their receptors generated by a novel robotic in situ hybridization platform. Dev Dyn. 2005 Oct; 234(2):371-86.
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      52. Plas DT, Visel A, Gonzalez E, She WC, Crair MC. Adenylate Cyclase 1 dependent refinement of retinotopic maps in the mouse. Vision Res. 2004 Dec; 44(28):3357-64.
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      53. Schumacher S, Laass K, Kant S, Shi Y, Visel A, Gruber AD, Kotlyarov A, Gaestel M. Scaffolding by ERK3 regulates MK5 in development. EMBO J. 2004 Dec 8; 23(24):4770-9.
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      54. Danilova N, Visel A, Willett CE, Steiner LA. Expression of the winged helix/forkhead gene, foxn4, during zebrafish development. Brain Res Dev Brain Res. 2004 Oct 15; 153(1):115-9.
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      55. Visel A, Thaller C, Eichele G. GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D552-6.
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      56. Herzig U, Cadenas C, Sieckmann F, Sierralta W, Thaller C, Visel A, Eichele G. Development of high-throughput tools to unravel the complexity of gene expression patterns in the mammalian brain. Novartis Found Symp. 2001; 239:129-46; discussion 146-59.
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