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    Pennacchio, Len

    TitleBiologist Senior Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/980-3711
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Monti R, Barozzi I, Osterwalder M, Lee E, Kato M, Garvin TH, Plajzer-Frick I, Pickle CS, Akiyama JA, Afzal V, Beerenwinkel N, Dickel DE, Visel A, Pennacchio L. Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb. PLoS Comput Biol. 2017 Aug; 13(8):e1005720. PMID: 28827824.
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      2. Gompers AL, Su-Feher L, Ellegood J, Copping NA, Riyadh MA, Stradleigh TW, Pride MC, Schaffler MD, Wade AA, Catta-Preta R, Zdilar I, Louis S, Kaushik G, Mannion BJ, Plajzer-Frick I, Afzal V, Visel A, Pennacchio L, Dickel DE, Lerch JP, Crawley JN, Zarbalis KS, Silverman JL, Nord AS. Germline Chd8 haploinsufficiency alters brain development in mouse. Nat Neurosci. 2017 Aug; 20(8):1062-1073. PMID: 28671691.
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      3. Anderson CM, Hu J, Thomas R, Gainous TB, Celona B, Sinha T, Dickel DE, Heidt AB, Xu SM, Bruneau BG, Pollard KS, Pennacchio L, Black BL. Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. Development. 2017 Apr 01; 144(7):1235-1241. PMID: 28351867.
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      4. He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio L, Ren B, Ecker JR. Improved regulatory element prediction based on tissue-specific local epigenomic signatures. Proc Natl Acad Sci U S A. 2017 Feb 28; 114(9):E1633-E1640. PMID: 28193886.
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      5. Kvon EZ, Kamneva OK, Melo US, Barozzi I, Osterwalder M, Mannion BJ, Tissières V, Pickle CS, Plajzer-Frick I, Lee EA, Kato M, Garvin TH, Akiyama JA, Afzal V, Lopez-Rios J, Rubin EM, Dickel DE, Pennacchio L, Visel A. Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell. 2016 Oct 20; 167(3):633-642.e11. PMID: 27768887.
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      6. Dickel DE, Barozzi I, Zhu Y, Fukuda-Yuzawa Y, Osterwalder M, Mannion BJ, May D, Spurrell CH, Plajzer-Frick I, Pickle CS, Lee E, Garvin TH, Kato M, Akiyama JA, Afzal V, Lee AY, Gorkin DU, Ren B, Rubin EM, Visel A, Pennacchio L. Genome-wide compendium and functional assessment of in vivo heart enhancers. Nat Commun. 2016 Oct 05; 7:12923. PMID: 27703156.
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      7. Chatterjee S, Kapoor A, Akiyama JA, Auer DR, Lee D, Gabriel S, Berrios C, Pennacchio L, Chakravarti A. Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease. Cell. 2016 Oct 06; 167(2):355-368.e10. PMID: 27693352.
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      8. van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio L, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW. 52 Genetic Loci Influencing Myocardial Mass. J Am Coll Cardiol. 2016 Sep 27; 68(13):1435-1448. PMID: 27659466.
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      9. Hirano A, Shi G, Jones CR, Lipzen A, Pennacchio L, Xu Y, Hallows WC, McMahon T, Yamazaki M, Ptácek LJ, Fu YH. A Cryptochrome 2 mutation yields advanced sleep phase in humans. Elife. 2016 Aug 16; 5. PMID: 27529127.
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      10. Hay D, Hughes JR, Babbs C, Davies JOJ, Graham BJ, Hanssen L, Kassouf MT, Marieke Oudelaar AM, Sharpe JA, Suciu MC, Telenius J, Williams R, Rode C, Li PS, Pennacchio L, Sloane-Stanley JA, Ayyub H, Butler S, Sauka-Spengler T, Gibbons RJ, Smith AJH, Wood WG, Higgs DR. Genetic dissection of the a-globin super-enhancer in vivo. Nat Genet. 2016 Aug; 48(8):895-903. PMID: 27376235.
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      11. Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio L, Roberts RJ. The Epigenomic Landscape of Prokaryotes. PLoS Genet. 2016 Feb; 12(2):e1005854. PMID: 26870957; PMCID: PMC4752239.
      12. Aldiri I, Ajioka I, Xu B, Zhang J, Chen X, Benavente C, Finkelstein D, Johnson D, Akiyama J, Pennacchio L, Dyer MA. Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma. Development. 2015 Dec 01; 142(23):4092-106. PMID: 26628093; PMCID: PMC4712833.
      13. Cordeddu V, Yin JC, Gunnarsson C, Virtanen C, Drunat S, Lepri F, De Luca A, Rossi C, Ciolfi A, Pugh TJ, Bruselles A, Priest JR, Pennacchio L, Lu Z, Danesh A, Quevedo R, Hamid A, Martinelli S, Pantaleoni F, Gnazzo M, Daniele P, Lissewski C, Bocchinfuso G, Stella L, Odent S, Philip N, Faivre L, Vlckova M, Seemanova E, Digilio C, Zenker M, Zampino G, Verloes A, Dallapiccola B, Roberts AE, Cavé H, Gelb BD, Neel BG, Tartaglia M. Activating Mutations Affecting the Dbl Homology Domain of SOS2 Cause Noonan Syndrome. Hum Mutat. 2015 Nov; 36(11):1080-7. PMID: 26173643; PMCID: PMC4604019 [Available on 11/01/16].
      14. Gittelman RM, Hun E, Ay F, Madeoy J, Pennacchio L, Noble WS, Hawkins RD, Akey JM. Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res. 2015 Sep; 25(9):1245-55. PMID: 26104583; PMCID: PMC4561485.
      15. Dogan N, Wu W, Morrissey CS, Chen KB, Stonestrom A, Long M, Keller CA, Cheng Y, Jain D, Visel A, Pennacchio L, 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. PMID: 25984238; PMCID: PMC4432502.
      16. Alexander JM, Hota SK, He D, Thomas S, Ho L, Pennacchio L, Bruneau BG. Brg1 modulates enhancer activation in mesoderm lineage commitment. Development. 2015 Apr 15; 142(8):1418-30. PMID: 25813539; PMCID: PMC4392595.
      17. Giorgio E, Robyr D, Spielmann M, Ferrero E, Di Gregorio E, Imperiale D, Vaula G, Stamoulis G, Santoni F, Atzori C, Gasparini L, Ferrera D, Canale C, Guipponi M, Pennacchio L, Antonarakis SE, Brussino A, Brusco A. A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). Hum Mol Genet. 2015 Jun 01; 24(11):3143-54. PMID: 25701871; PMCID: PMC4424952.
      18. 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. PMID: 25409826.
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      19. He A, Gu F, Hu Y, Ma Q, Ye LY, Akiyama JA, Visel A, Pennacchio L, Pu WT. Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease. Nat Commun. 2014 Sep 24; 5:4907. PMID: 25249388; PMCID: PMC4236193.
      20. Wu H, Nord AS, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio L, Visel A. Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet. 2014 Sep; 10(9):e1004610. PMID: 25188404; PMCID: PMC4154669.
      21. Ounzain S, Pezzuto I, Micheletti R, Burdet F, Sheta R, Nemir M, Gonzales C, Sarre A, Alexanian M, Blow MJ, May D, Johnson R, Dauvillier J, Pennacchio L, Pedrazzini T. Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease. J Mol Cell Cardiol. 2014 Nov; 76:55-70. PMID: 25149110; PMCID: PMC4445080.
      22. Gordon CT, Attanasio C, Bhatia S, Benko S, Ansari M, Tan TY, Munnich A, Pennacchio L, 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. PMID: 24934569; PMCID: PMC4389788.
      23. Pattabiraman K, Golonzhka O, Lindtner S, Nord AS, Taher L, Hoch R, Silberberg SN, Zhang D, Chen B, Zeng H, Pennacchio L, Puelles L, Visel A, Rubenstein JL. Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex. Neuron. 2014 Jun 04; 82(5):989-1003. PMID: 24814534; PMCID: PMC4104757.
      24. MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio L, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C. Guidelines for investigating causality of sequence variants in human disease. Nature. 2014 Apr 24; 508(7497):469-76. PMID: 24759409; PMCID: PMC4180223.
      25. 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 L. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9. PMID: 24752179; PMCID: PMC4032856.
      26. Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, Plajzer-Frick I, Kirkpatrick A, Göttgens B, Bruneau BG, Visel A, Pennacchio L. Function-based identification of mammalian enhancers using site-specific integration. Nat Methods. 2014 May; 11(5):566-71. PMID: 24658141; PMCID: PMC4008384.
      27. Byrne RT, Klingele AJ, Cabot EL, Schackwitz WS, Martin JA, Martin J, Wang Z, Wood EA, Pennacchio C, Pennacchio L, Perna NT, Battista JR, Cox MM. Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair. Elife. 2014 Mar 04; 3:e01322. PMID: 24596148; PMCID: PMC3939492.
      28. 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 L, 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. PMID: 24442519; PMCID: PMC3990169.
      29. 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 L, Visel A. Rapid and pervasive changes in genome-wide enhancer usage during mammalian development. Cell. 2013 Dec 19; 155(7):1521-31. PMID: 24360275; PMCID: PMC3989111.
      30. 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 L, Visel A. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013 Oct 25; 342(6157):1241006. PMID: 24159046; PMCID: PMC3991470.
      31. 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 L, 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. PMID: 24115316.
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      32. Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N, Black BL, Visel A, Pennacchio L, Collins FS. 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. PMID: 24127591; PMCID: PMC3816444.
      33. Wilkinson AC, Goode DK, Cheng YH, Dickel DE, Foster S, Sendall T, Tijssen MR, Sanchez MJ, Pennacchio L, Kirkpatrick AM, Göttgens B. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses. Biol Open. 2013; 2(11):1229-38. PMID: 24244860; PMCID: PMC3828770.
      34. Dickel DE, Visel A, Pennacchio L. Functional anatomy of distant-acting mammalian enhancers. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1620):20120359. PMID: 23650633; PMCID: PMC3682724.
      35. Chen YJ, Vogt D, Wang Y, Visel A, Silberberg SN, Nicholas CR, Danjo T, Pollack JL, Pennacchio L, 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. PMID: 23658702; PMCID: PMC3641041.
      36. Pennacchio L, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013 04; 14(4):288-95. PMID: 23503198; PMCID: PMC4445073.
      37. Bollmann A, Sedlacek CJ, Norton J, Laanbroek HJ, Suwa Y, Stein LY, Klotz MG, Arp D, Sayavedra-Soto L, Lu M, Bruce D, Detter C, Tapia R, Han J, Woyke T, Lucas SM, Pitluck S, Pennacchio L, Nolan M, Land ML, Huntemann M, Deshpande S, Han C, Chen A, Kyrpides N, Mavromatis K, Markowitz V, Szeto E, Ivanova N, Mikhailova N, Pagani I, Pati A, Peters L, Ovchinnikova G, Goodwin LA. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations. Stand Genomic Sci. 2013; 7(3):469-82. PMID: 24019993; PMCID: PMC3764937.
      38. 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 L, Rubenstein JL. A high-resolution enhancer atlas of the developing telencephalon. Cell. 2013 Feb 14; 152(4):895-908. PMID: 23375746; PMCID: PMC3660042.
      39. McKinsey GL, Lindtner S, Trzcinski B, Visel A, Pennacchio L, 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 09; 77(1):83-98. PMID: 23312518; PMCID: PMC3547499.
      40. Ariza-Cosano A, Visel A, Pennacchio L, 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 Dec 19; 13:713. PMID: 23253453; PMCID: PMC3541358.
      41. Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio L, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QC, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol. 2012 Nov; 196(3):713-25. PMID: 22861491.
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      42. Martinez RJ, Bruce D, Detter C, Goodwin LA, Han J, Han CS, Held B, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Sobecky PA. Complete genome sequence of Rahnella aquatilis CIP 78.65. J Bacteriol. 2012 Jun; 194(11):3020-1. PMID: 22582378; PMCID: PMC3370627.
      43. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Land M, Chang YJ, Kyrpides NC, Ovchinnikova G, Hauser L, Lapidus A, Yan J, Bowman KS, da Costa MS, Rainey FA, Moe WM. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to "Dehalococcoides" strains. Stand Genomic Sci. 2012 May 25; 6(2):251-64. PMID: 22768368; PMCID: PMC3387798.
      44. Isanapong J, Goodwin L, Bruce D, Chen A, Detter C, Han J, Han CS, Held B, Huntemann M, Ivanova N, Land ML, Mavromatis K, Nolan M, Pati A, Pennacchio L, Pitluck S, Szeto E, Tapia R, Woyke T, Rodrigues JL. High-quality draft genome sequence of the Opitutaceae bacterium strain TAV1, a symbiont of the wood-feeding termite Reticulitermes flavipes. J Bacteriol. 2012 May; 194(10):2744-5. PMID: 22535930; PMCID: PMC3347190.
      45. Martinez RJ, Bruce D, Detter C, Goodwin LA, Han J, Han CS, Held B, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Sobecky PA. Complete genome sequence of Rahnella sp. strain Y9602, a gammaproteobacterium isolate from metal- and radionuclide-contaminated soil. J Bacteriol. 2012 Apr; 194(8):2113-4. PMID: 22461551; PMCID: PMC3318479.
      46. Joshi HJ, Christiansen KM, Fitz J, Cao J, Lipzen A, Martin J, Smith-Moritz AM, Pennacchio L, Schackwitz WS, Weigel D, Heazlewood JL. 1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions. Bioinformatics. 2012 May 15; 28(10):1303-6. PMID: 22451271.
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      47. Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, Ahituv N, Pennacchio L, Shendure J. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol. 2012 Feb 26; 30(3):265-70. PMID: 22371081; PMCID: PMC3402344.
      48. Peng Z, Zhao Z, Nath N, Froula JL, Clum A, Zhang T, Cheng JF, Copeland AC, Pennacchio L, Chen F. Generation of long insert pairs using a Cre-LoxP Inverse PCR approach. PLoS One. 2012; 7(1):e29437. PMID: 22253722; PMCID: PMC3253782.
      49. Schleheck D, Weiss M, Pitluck S, Bruce D, Land ML, Han S, Saunders E, Tapia R, Detter C, Brettin T, Han J, Woyke T, Goodwin L, Pennacchio L, Nolan M, Cook AM, Kjelleberg S, Thomas T. Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T)). Stand Genomic Sci. 2011 Dec 31; 5(3):298-310. PMID: 22675581; PMCID: PMC3368416.
      50. Bini E, Rauschenbach I, Narasingarao P, Starovoytov V, Hauser L, Jeffries CD, Land M, Bruce D, Detter C, Goodwin L, Han S, Held B, Tapia R, Copeland A, Ivanova N, Mikhailova N, Nolan M, Pati A, Pennacchio L, Pitluck S, Woyke T, Häggblom M. Complete genome sequence of Desulfurispirillum indicum strain S5(T). Stand Genomic Sci. 2011 Dec 31; 5(3):371-8. PMID: 22675586; PMCID: PMC3368425.
      51. 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 L, Visel A. Large-scale discovery of enhancers from human heart tissue. Nat Genet. 2011 Dec 04; 44(1):89-93. PMID: 22138689; PMCID: PMC3246570.
      52. Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML, Pawlowski K, Berry AM. Genome sequence of "Candidatus Frankia datiscae" Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata. J Bacteriol. 2011 Dec; 193(24):7017-8. PMID: 22123767; PMCID: PMC3232863.
      53. Marini NJ, Hoffmann TJ, Lammer EJ, Hardin J, Lazaruk K, Stein JB, Gilbert DA, Wright C, Lipzen A, Pennacchio L, Carmichael SL, Witte JS, Shaw GM, Rine J. A genetic signature of spina bifida risk from pathway-informed comprehensive gene-variant analysis. PLoS One. 2011; 6(11):e28408. PMID: 22140583; PMCID: PMC3227667.
      54. Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Land ML, Nesbø CL, Gogarten JP, Noll KM. Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea. J Bacteriol. 2011 Oct; 193(19):5566-7. PMID: 21914881; PMCID: PMC3187421.
      55. Swithers KS, DiPippo JL, Bruce DC, Detter C, Tapia R, Han S, Saunders E, Goodwin LA, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Mikhailova N, Lykidis A, Land ML, Brettin T, Stetter KO, Nelson KE, Gogarten JP, Noll KM. Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores. J Bacteriol. 2011 Oct; 193(20):5869-70. PMID: 21952543; PMCID: PMC3187219.
      56. Osbun N, Li J, O'Driscoll MC, Strominger Z, Wakahiro M, Rider E, Bukshpun P, Boland E, Spurrell CH, Schackwitz W, Pennacchio L, Dobyns WB, Black GC, Sherr EH. Genetic and functional analyses identify DISC1 as a novel callosal agenesis candidate gene. Am J Med Genet A. 2011 Aug; 155A(8):1865-76. PMID: 21739582.
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      58. Klippel B, Lochner A, Bruce DC, Davenport KW, Detter C, Goodwin LA, Han J, Han S, Land ML, Mikhailova N, Nolan M, Pennacchio L, Pitluck S, Tapia R, Woyke T, Wiebusch S, Basner A, Abe F, Horikoshi K, Keller M, Antranikian G. Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5. J Bacteriol. 2011 Sep; 193(17):4547-8. PMID: 21705587; PMCID: PMC3165521.
      59. Brown SD, Wall JD, Kucken AM, Gilmour CC, Podar M, Brandt CC, Teshima H, Detter JC, Han CS, Land ML, Lucas S, Han J, Pennacchio L, Nolan M, Pitluck S, Woyke T, Goodwin L, Palumbo AV, Elias DA. Genome sequence of the mercury-methylating and pleomorphic Desulfovibrio africanus Strain Walvis Bay. J Bacteriol. 2011 Aug; 193(15):4037-8. PMID: 21642452; PMCID: PMC3147520.
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      61. 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 L. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet. 2010 Sep; 42(9):806-10. PMID: 20729851; PMCID: PMC3138496.
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      63. Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio L, 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. PMID: 20363979; PMCID: PMC2860159.
      64. Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio L. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature. 2010 Mar 18; 464(7287):409-12. PMID: 20173736; PMCID: PMC2938076.
      65. Cirstea IC, Kutsche K, Dvorsky R, Gremer L, Carta C, Horn D, Roberts AE, Lepri F, Merbitz-Zahradnik T, König R, Kratz CP, Pantaleoni F, Dentici ML, Joshi VA, Kucherlapati RS, Mazzanti L, Mundlos S, Patton MA, Silengo MC, Rossi C, Zampino G, Digilio C, Stuppia L, Seemanova E, Pennacchio L, Gelb BD, Dallapiccola B, Wittinghofer A, Ahmadian MR, Tartaglia M, Zenker M. A restricted spectrum of NRAS mutations causes Noonan syndrome. Nat Genet. 2010 Jan; 42(1):27-9. PMID: 19966803; PMCID: PMC3118669.
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      67. Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proc Natl Acad Sci U S A. 2009 Sep 22; 106(38):16151-6. PMID: 19805272; PMCID: PMC2752593.
      68. Cordeddu V, Di Schiavi E, Pennacchio L, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, Flex E, Lepri F, Bartholdi D, Kutsche K, Ferrero GB, Anichini C, Selicorni A, Rossi C, Tenconi R, Zenker M, Merlo D, Dallapiccola B, Iyengar R, Bazzicalupo P, Gelb BD, Tartaglia M. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet. 2009 Sep; 41(9):1022-6. PMID: 19684605; PMCID: PMC2765465.
      69. Bickel RD, Schackwitz WS, Pennacchio L, Nuzhdin SV, Kopp A. Contrasting patterns of sequence evolution at the functionally redundant bric à brac paralogs in Drosophila melanogaster. J Mol Evol. 2009 Aug; 69(2):194-202. PMID: 19639236; PMCID: PMC2722720.
      70. Bressler J, Fornage M, Hanis CL, Kao WH, Lewis CE, McPherson R, Dent R, Mosley TH, Pennacchio L, Boerwinkle E. The INSIG2 rs7566605 genetic variant does not play a major role in obesity in a sample of 24,722 individuals from four cohorts. BMC Med Genet. 2009 Jun 12; 10:56. PMID: 19523229; PMCID: PMC2706232.
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      72. Slavotinek AM, Moshrefi A, Lopez Jiminez N, Chao R, Mendell A, Shaw GM, Pennacchio L, Bates MD. Sequence variants in the HLX gene at chromosome 1q41-1q42 in patients with diaphragmatic hernia. Clin Genet. 2009 May; 75(5):429-39. PMID: 19459883; PMCID: PMC2874832.
      73. Visel A, Akiyama JA, Shoukry M, Afzal V, Rubin EM, Pennacchio L. Functional autonomy of distant-acting human enhancers. Genomics. 2009 Jun; 93(6):509-13. PMID: 19268701; PMCID: PMC2683195.
      74. Zhang Z, Alpert D, Francis R, Chatterjee B, Yu Q, Tansey T, Sabol SL, Cui C, Bai Y, Koriabine M, Yoshinaga Y, Cheng JF, Chen F, Martin J, Schackwitz W, Gunn TM, Kramer KL, De Jong PJ, Pennacchio L, Lo CW. Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy. Proc Natl Acad Sci U S A. 2009 Mar 03; 106(9):3219-24. PMID: 19218456; PMCID: PMC2651267.
      75. 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 L. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009 Feb 12; 457(7231):854-8. PMID: 19212405; PMCID: PMC2745234.
      76. Merritt WM, Lin YG, Han LY, Kamat AA, Spannuth WA, Schmandt R, Urbauer D, Pennacchio L, Cheng JF, Nick AM, Deavers MT, Mourad-Zeidan A, Wang H, Mueller P, Lenburg ME, Gray JW, Mok S, Birrer MJ, Lopez-Berestein G, Coleman RL, Bar-Eli M, Sood AK. Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med. 2008 Dec 18; 359(25):2641-50. PMID: 19092150; PMCID: PMC2710981.
      77. Calton MA, Ersoy BA, Zhang S, Kane JP, Malloy MJ, Pullinger CR, Bromberg Y, Pennacchio L, Dent R, McPherson R, Ahituv N, Vaisse C. Association of functionally significant Melanocortin-4 but not Melanocortin-3 receptor mutations with severe adult obesity in a large North American case-control study. Hum Mol Genet. 2009 Mar 15; 18(6):1140-7. PMID: 19091795; PMCID: PMC2649015.
      78. Romeo S, Yin W, Kozlitina J, Pennacchio L, Boerwinkle E, Hobbs HH, Cohen JC. Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest. 2009 Jan; 119(1):70-9. PMID: 19075393.
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      79. De Val S, Chi NC, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio L, 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. PMID: 19070576; PMCID: PMC2782666.
      80. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjöblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky Y, Kopelovich L, Papadopoulos N, Pennacchio L, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008 Oct 21; 105(42):16224-9. PMID: 18852474; PMCID: PMC2571022.
      81. 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 L, 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. PMID: 18836445; PMCID: PMC2691688.
      82. Romeo S, Kozlitina J, Xing C, Pertsemlidis A, Cox D, Pennacchio L, Boerwinkle E, Cohen JC, Hobbs HH. Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet. 2008 Dec; 40(12):1461-5. PMID: 18820647; PMCID: PMC2597056.
      83. Alvarez Retuerto AI, Cantor RM, Gleeson JG, Ustaszewska A, Schackwitz WS, Pennacchio L, Geschwind DH. Association of common variants in the Joubert syndrome gene (AHI1) with autism. Hum Mol Genet. 2008 Dec 15; 17(24):3887-96. PMID: 18782849; PMCID: PMC2638573.
      84. Prabhakar S, Visel A, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Morrison H, Fitzpatrick DR, Afzal V, Pennacchio L, Rubin EM, Noonan JP. Human-specific gain of function in a developmental enhancer. Science. 2008 Sep 05; 321(5894):1346-50. PMID: 18772437; PMCID: PMC2658639.
      85. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio L, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008 Jun 19; 453(7198):1064-71. PMID: 18563158.
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      86. Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio L, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008 Jul; 18(7):1100-11. PMID: 18562680; PMCID: PMC2493399.
      87. Nowak M, Helleboid-Chapman A, Jakel H, Moitrot E, Rommens C, Pennacchio L, Fruchart-Najib J, Fruchart JC. Glucose regulates the expression of the apolipoprotein A5 gene. J Mol Biol. 2008 Jul 25; 380(5):789-98. PMID: 18572192.
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      88. Visel A, Prabhakar S, Akiyama JA, Shoukry M, Lewis KD, Holt A, Plajzer-Frick I, Afzal V, Rubin EM, Pennacchio L. Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet. 2008 Feb; 40(2):158-60. PMID: 18176564; PMCID: PMC2647775.
      89. Ahituv N, Akiyama J, Chapman-Helleboid A, Fruchart J, Pennacchio L. In vivo characterization of human APOA5 haplotypes. Genomics. 2007 Dec; 90(6):674-9. PMID: 17936576.
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      90. Costford SR, Kavaslar N, Ahituv N, Chaudhry SN, Schackwitz WS, Dent R, Pennacchio L, McPherson R, Harper ME. Gain-of-function R225W mutation in human AMPKgamma(3) causing increased glycogen and decreased triglyceride in skeletal muscle. PLoS One. 2007 Sep 19; 2(9):e903. PMID: 17878938; PMCID: PMC1964808.
      91. Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio L, Rubin EM. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007 Sep; 5(9):e234. PMID: 17803355; PMCID: PMC1964772.
      92. Pandit B, Sarkozy A, Pennacchio L, Carta C, Oishi K, Martinelli S, Pogna EA, Schackwitz W, Ustaszewska A, Landstrom A, Bos JM, Ommen SR, Esposito G, Lepri F, Faul C, Mundel P, López Siguero JP, Tenconi R, Selicorni A, Rossi C, Mazzanti L, Torrente I, Marino B, Digilio MC, Zampino G, Ackerman MJ, Dallapiccola B, Tartaglia M, Gelb BD. Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet. 2007 Aug; 39(8):1007-12. PMID: 17603483.
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      93. Bleyl SB, Moshrefi A, Shaw GM, Saijoh Y, Schoenwolf GC, Pennacchio L, Slavotinek AM. Candidate genes for congenital diaphragmatic hernia from animal models: sequencing of FOG2 and PDGFRalpha reveals rare variants in diaphragmatic hernia patients. Eur J Hum Genet. 2007 Sep; 15(9):950-8. PMID: 17568391.
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      94. McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio L, Tybjaerg-Hansen A, Folsom AR, Boerwinkle E, Hobbs HH, Cohen JC. A common allele on chromosome 9 associated with coronary heart disease. Science. 2007 Jun 08; 316(5830):1488-91. PMID: 17478681; PMCID: PMC2711874.
      95. Kryukov GV, Pennacchio L, Sunyaev SR. Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet. 2007 Apr; 80(4):727-39. PMID: 17357078; PMCID: PMC1852724.
      96. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio L. Medical sequencing at the extremes of human body mass. Am J Hum Genet. 2007 Apr; 80(4):779-91. PMID: 17357083; PMCID: PMC1852707.
      97. Romeo S, Pennacchio L, Fu Y, Boerwinkle E, Tybjaerg-Hansen A, Hobbs HH, Cohen JC. Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet. 2007 Apr; 39(4):513-6. PMID: 17322881; PMCID: PMC2762948.
      98. Pennacchio L, Loots GG, Nobrega MA, Ovcharenko I. Predicting tissue-specific enhancers in the human genome. Genome Res. 2007 Feb; 17(2):201-11. PMID: 17210927; PMCID: PMC1781352.
      99. Visel A, Bristow J, Pennacchio L. Enhancer identification through comparative genomics. Semin Cell Dev Biol. 2007 Feb; 18(1):140-52. PMID: 17276707; PMCID: PMC1855162.
      100. Cheng JF, Priest JR, Pennacchio L. Comparative genomics: a tool to functionally annotate human DNA. Methods Mol Biol. 2007; 366:229-51. PMID: 17568128.
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      101. Tartaglia M, Pennacchio L, Zhao C, Yadav KK, Fodale V, Sarkozy A, Pandit B, Oishi K, Martinelli S, Schackwitz W, Ustaszewska A, Martin J, Bristow J, Carta C, Lepri F, Neri C, Vasta I, Gibson K, Curry CJ, Siguero JP, Digilio MC, Zampino G, Dallapiccola B, Bar-Sagi D, Gelb BD. Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet. 2007 Jan; 39(1):75-9. PMID: 17143282.
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      102. Visel A, Minovitsky S, Dubchak I, Pennacchio L. VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan; 35(Database issue):D88-92. PMID: 17130149; PMCID: PMC1716724.
      103. Pennacchio L, 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. PMID: 17086198.
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      104. Wood LD, Calhoun ES, Silliman N, Ptak J, Szabo S, Powell SM, Riggins GJ, Wang TL, Yan H, Gazdar A, Kern SE, Pennacchio L, Kinzler KW, Vogelstein B, Velculescu VE. Somatic mutations of GUCY2F, EPHA3, and NTRK3 in human cancers. Hum Mutat. 2006 Oct; 27(10):1060-1. PMID: 16941478.
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      105. Sevenich L, Pennacchio L, Peters C, Reinheckel T. Human cathepsin L rescues the neurodegeneration and lethality in cathepsin B/L double-deficient mice. Biol Chem. 2006 Jul; 387(7):885-91. PMID: 16913838.
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      106. Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio L. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 2006 Jul; 16(7):855-63. PMID: 16769978; PMCID: PMC1484452.
      107. Slavotinek AM, Moshrefi A, Davis R, Leeth E, Schaeffer GB, Burchard GE, Shaw GM, James B, Ptacek L, Pennacchio L. Array comparative genomic hybridization in patients with congenital diaphragmatic hernia: mapping of four CDH-critical regions and sequencing of candidate genes at 15q26.1-15q26.2. Eur J Hum Genet. 2006 Sep; 14(9):999-1008. PMID: 16736036.
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      108. Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Collier JM, Hébert S, Doelle H, Dent R, Pennacchio L, McPherson R. A PYY Q62P variant linked to human obesity. Hum Mol Genet. 2006 Feb 01; 15(3):387-91. PMID: 16368708.
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      109. Shah N, Teplitsky MV, Minovitsky S, Pennacchio L, Hugenholtz P, Hamann B, Dubchak IL. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005 Dec 08; 6:292. PMID: 16336665; PMCID: PMC1325058.
      110. Marçais C, Verges B, Charrière S, Pruneta V, Merlin M, Billon S, Perrot L, Drai J, Sassolas A, Pennacchio L, Fruchart-Najib J, Fruchart JC, Durlach V, Moulin P. Apoa5 Q139X truncation predisposes to late-onset hyperchylomicronemia due to lipoprotein lipase impairment. J Clin Invest. 2005 Oct; 115(10):2862-9. PMID: 16200213; PMCID: PMC1236672.
      111. Grosskopf I, Baroukh N, Lee SJ, Kamari Y, Harats D, Rubin EM, Pennacchio L, Cooper AD. Apolipoprotein A-V deficiency results in marked hypertriglyceridemia attributable to decreased lipolysis of triglyceride-rich lipoproteins and removal of their remnants. Arterioscler Thromb Vasc Biol. 2005 Dec; 25(12):2573-9. PMID: 16166565.
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      112. Swarbrick MM, Waldenmaier B, Pennacchio L, Lind DL, Cavazos MM, Geller F, Merriman R, Ustaszewska A, Malloy M, Scherag A, Hsueh WC, Rief W, Mauvais-Jarvis F, Pullinger CR, Kane JP, Dent R, McPherson R, Kwok PY, Hinney A, Hebebrand J, Vaisse C. Lack of support for the association between GAD2 polymorphisms and severe human obesity. PLoS Biol. 2005 Sep; 3(9):e315. PMID: 16122350; PMCID: PMC1193520.
      113. Poulin F, Nobrega MA, Plajzer-Frick I, Holt A, Afzal V, Rubin EM, Pennacchio L. In vivo characterization of a vertebrate ultraconserved enhancer. Genomics. 2005 Jun; 85(6):774-81. PMID: 15885503.
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      114. Weng L, Kavaslar N, Ustaszewska A, Doelle H, Schackwitz W, Hébert S, Cohen JC, McPherson R, Pennacchio L. Lack of MEF2A mutations in coronary artery disease. J Clin Invest. 2005 Apr; 115(4):1016-20. PMID: 15841183; PMCID: PMC1070426.
      115. Genoux A, Dehondt H, Helleboid-Chapman A, Duhem C, Hum DW, Martin G, Pennacchio L, Staels B, Fruchart-Najib J, Fruchart JC. Transcriptional regulation of apolipoprotein A5 gene expression by the nuclear receptor RORalpha. Arterioscler Thromb Vasc Biol. 2005 Jun; 25(6):1186-92. PMID: 15790933.
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      116. Merkel M, Loeffler B, Kluger M, Fabig N, Geppert G, Pennacchio L, Laatsch A, Heeren J. Apolipoprotein AV accelerates plasma hydrolysis of triglyceride-rich lipoproteins by interaction with proteoglycan-bound lipoprotein lipase. J Biol Chem. 2005 Jun 03; 280(22):21553-60. PMID: 15774484.
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      117. Nowak M, Helleboid-Chapman A, Jakel H, Martin G, Duran-Sandoval D, Staels B, Rubin EM, Pennacchio L, Taskinen MR, Fruchart-Najib J, Fruchart JC. Insulin-mediated down-regulation of apolipoprotein A5 gene expression through the phosphatidylinositol 3-kinase pathway: role of upstream stimulatory factor. Mol Cell Biol. 2005 Feb; 25(4):1537-48. PMID: 15684402; PMCID: PMC548024.
      118. Baroukh N, Ahituv N, Chang J, Shoukry M, Afzal V, Rubin EM, Pennacchio L. Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene. Mamm Genome. 2005 Feb; 16(2):91-5. PMID: 15859353.
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      119. Urbich C, Heeschen C, Aicher A, Sasaki K, Bruhl T, Farhadi MR, Vajkoczy P, Hofmann WK, Peters C, Pennacchio L, Abolmaali ND, Chavakis E, Reinheckel T, Zeiher AM, Dimmeler S. Cathepsin L is required for endothelial progenitor cell-induced neovascularization. Nat Med. 2005 Feb; 11(2):206-13. PMID: 15665831.
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      120. Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio L. The sequence and analysis of duplication-rich human chromosome 16. Nature. 2004 Dec 23; 432(7020):988-94. PMID: 15616553.
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      121. Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio L, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. The DNA sequence and comparative analysis of human chromosome 5. Nature. 2004 Sep 16; 431(7006):268-74. PMID: 15372022.
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      122. Jakel H, Nowak M, Moitrot E, Dehondt H, Hum DW, Pennacchio L, Fruchart-Najib J, Fruchart JC. The liver X receptor ligand T0901317 down-regulates APOA5 gene expression through activation of SREBP-1c. J Biol Chem. 2004 Oct 29; 279(44):45462-9. PMID: 15317819.
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      123. Fruchart-Najib J, Baugé E, Niculescu LS, Pham T, Thomas B, Rommens C, Majd Z, Brewer B, Pennacchio L, Fruchart JC. Mechanism of triglyceride lowering in mice expressing human apolipoprotein A5. Biochem Biophys Res Commun. 2004 Jun 25; 319(2):397-404. PMID: 15178420.
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      124. Olivier M, Wang X, Cole R, Gau B, Kim J, Rubin EM, Pennacchio L. Haplotype analysis of the apolipoprotein gene cluster on human chromosome 11. Genomics. 2004 May; 83(5):912-23. PMID: 15081120; PMCID: PMC2771640.
      125. Baroukh N, Bauge E, Akiyama J, Chang J, Afzal V, Fruchart JC, Rubin EM, Fruchart-Najib J, Pennacchio L. Analysis of apolipoprotein A5, c3, and plasma triglyceride concentrations in genetically engineered mice. Arterioscler Thromb Vasc Biol. 2004 Jul; 24(7):1297-302. PMID: 15117734.
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      126. Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio L, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM. The DNA sequence and biology of human chromosome 19. Nature. 2004 Apr 01; 428(6982):529-35. PMID: 15057824.
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      127. Wang QF, Liu X, O'Connell J, Peng Z, Krauss RM, Rainwater DL, VandeBerg JL, Rubin EM, Cheng JF, Pennacchio L. Haplotypes in the APOA1-C3-A4-A5 gene cluster affect plasma lipids in both humans and baboons. Hum Mol Genet. 2004 May 15; 13(10):1049-56. PMID: 15044382.
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      128. Shah N, Couronne O, Pennacchio L, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics. 2004 Mar 22; 20(5):636-43. PMID: 15033870.
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      129. Zheng P, Pennacchio L, Le Goff W, Rubin EM, Smith JD. Identification of a novel enhancer of brain expression near the apoE gene cluster by comparative genomics. Biochim Biophys Acta. 2004 Jan 05; 1676(1):41-50. PMID: 14732489.
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      130. Nobrega MA, Pennacchio L. Comparative genomic analysis as a tool for biological discovery. J Physiol. 2004 Jan 01; 554(Pt 1):31-9. PMID: 14678488; PMCID: PMC1664741.
      131. Eichenbaum-Voline S, Olivier M, Jones EL, Naoumova RP, Jones B, Gau B, Patel HN, Seed M, Betteridge DJ, Galton DJ, Rubin EM, Scott J, Shoulders CC, Pennacchio L. Linkage and association between distinct variants of the APOA1/C3/A4/A5 gene cluster and familial combined hyperlipidemia. Arterioscler Thromb Vasc Biol. 2004 Jan; 24(1):167-74. PMID: 14551155; PMCID: PMC2773540.
      132. Houseweart MK, Pennacchio L, Vilaythong A, Peters C, Noebels JL, Myers RM. Cathepsin B but not cathepsins L or S contributes to the pathogenesis of Unverricht-Lundborg progressive myoclonus epilepsy (EPM1). J Neurobiol. 2003 Sep 15; 56(4):315-27. PMID: 12918016.
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      133. Cheng JF, Pennacchio L. Comparative and functional analysis of cardiovascular-related genes. Pharmacogenomics. 2003 Sep; 4(5):571-82. PMID: 12943465.
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      134. Pennacchio L. Insights from human/mouse genome comparisons. Mamm Genome. 2003 Jul; 14(7):429-36. PMID: 12925891.
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      135. Wong WM, Hawe E, Li LK, Miller GJ, Nicaud V, Pennacchio L, Humphries SE, Talmud PJ. Apolipoprotein AIV gene variant S347 is associated with increased risk of coronary heart disease and lower plasma apolipoprotein AIV levels. Circ Res. 2003 May 16; 92(9):969-75. PMID: 12676816.
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      136. Pennacchio L, Rubin EM. Comparative genomic tools and databases: providing insights into the human genome. J Clin Invest. 2003 Apr; 111(8):1099-106. PMID: 12697725; PMCID: PMC152942.
      137. Vu-Dac N, Gervois P, Jakel H, Nowak M, Bauge E, Dehondt H, Staels B, Pennacchio L, Rubin EM, Fruchart-Najib J, Fruchart JC. Apolipoprotein A5, a crucial determinant of plasma triglyceride levels, is highly responsive to peroxisome proliferator-activated receptor alpha activators. J Biol Chem. 2003 May 16; 278(20):17982-5. PMID: 12637506.
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      138. Pennacchio L, Baroukh N, Rubin EM. Human-mouse comparative genomics: successes and failures to reveal functional regions of the human genome. Cold Spring Harb Symp Quant Biol. 2003; 68:303-9. PMID: 15338630.
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      139. Pennacchio L, Rubin EM. Apolipoprotein A5, a newly identified gene that affects plasma triglyceride levels in humans and mice. Arterioscler Thromb Vasc Biol. 2003 Apr 01; 23(4):529-34. PMID: 12615678.
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      140. Shannon P, Pennacchio L, Houseweart MK, Minassian BA, Myers RM. Neuropathological changes in a mouse model of progressive myoclonus epilepsy: cystatin B deficiency and Unverricht-Lundborg disease. J Neuropathol Exp Neurol. 2002 Dec; 61(12):1085-91. PMID: 12484571.
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      141. Pennacchio L, Olivier M, Hubacek JA, Krauss RM, Rubin EM, Cohen JC. Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels. Hum Mol Genet. 2002 Nov 15; 11(24):3031-8. PMID: 12417524.
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      142. Talmud PJ, Hawe E, Martin S, Olivier M, Miller GJ, Rubin EM, Pennacchio L, Humphries SE. Relative contribution of variation within the APOC3/A4/A5 gene cluster in determining plasma triglycerides. Hum Mol Genet. 2002 Nov 15; 11(24):3039-46. PMID: 12417525.
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      143. Pennacchio L, Olivier M, Hubacek JA, Cohen JC, Cox DR, Fruchart JC, Krauss RM, Rubin EM. An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science. 2001 Oct 05; 294(5540):169-73. PMID: 11588264.
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      144. Lieuallen K, Pennacchio L, Park M, Myers RM, Lennon GG. Cystatin B-deficient mice have increased expression of apoptosis and glial activation genes. Hum Mol Genet. 2001 Sep 01; 10(18):1867-71. PMID: 11555622.
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      145. Pennacchio L, Rubin EM. Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001 Feb; 2(2):100-9. PMID: 11253049.
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      146. Serratosa JM, Gardiner RM, Lehesjoki AE, Pennacchio L, Myers RM. The molecular genetic bases of the progressive myoclonus epilepsies. Adv Neurol. 1999; 79:383-98. PMID: 10514828.
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      147. Pennacchio L, Bouley DM, Higgins KM, Scott MP, Noebels JL, Myers RM. Progressive ataxia, myoclonic epilepsy and cerebellar apoptosis in cystatin B-deficient mice. Nat Genet. 1998 Nov; 20(3):251-8. PMID: 9806543.
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      148. Prange CK, Pennacchio L, Lieuallen K, Fan W, Lennon GG. Characterization of the human neurocan gene, CSPG3. Gene. 1998 Oct 23; 221(2):199-205. PMID: 9795216.
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      149. Virtaneva K, D'Amato E, Miao J, Koskiniemi M, Norio R, Avanzini G, Franceschetti S, Michelucci R, Tassinari CA, Omer S, Pennacchio L, Myers RM, Dieguez-Lucena JL, Krahe R, de la Chapelle A, Lehesjoki AE. Unstable minisatellite expansion causing recessively inherited myoclonus epilepsy, EPM1. Nat Genet. 1997 Apr; 15(4):393-6. PMID: 9090386.
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      150. Pennacchio L, Myers RM. Isolation and characterization of the mouse cystatin B gene. Genome Res. 1996 Nov; 6(11):1103-9. PMID: 8938434.
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      151. Pennacchio L, Lehesjoki AE, Stone NE, Willour VL, Virtaneva K, Miao J, D'Amato E, Ramirez L, Faham M, Koskiniemi M, Warrington JA, Norio R, de la Chapelle A, Cox DR, Myers RM. Mutations in the gene encoding cystatin B in progressive myoclonus epilepsy (EPM1) Science. 1996 Mar 22; 271(5256):1731-4. PMID: 8596935.
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      152. Stone NE, Fan JB, Willour V, Pennacchio L, Warrington JA, Hu A, de la Chapelle A, Lehesjoki AE, Cox DR, Myers RM. Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene. Genome Res. 1996 Mar; 6(3):218-25. PMID: 8963899.
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      153. Pennacchio L, Bergmann A, Fukushima A, Okubo K, Salemi A, Lennon GG. Structure, sequence and location of the UQCRFS1 gene for the human Rieske Fe-S protein. Gene. 1995 Apr 03; 155(2):207-11. PMID: 7721092.
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      154. Yacoub M, Pennacchio L, Ross D, McDonald L. Replacement of mitral valve in active infective endocarditis. Br Heart J. 1972 Jul; 34(7):758-60. PMID: 5041445; PMCID: PMC458533.
      155. Pennacchio L, Mele G. [Intermediate form between acute leukemia with promyelocytic basophils and systemic mastocytosis]. Minerva Med. 1971 Oct 17; 62(78):3747-59. PMID: 5286162.
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      156. Pennacchio L, Mele G. [Systemic mastocytosis as an evolutive phase of mast cell pathology. Review and anatomo-clinical case]. Minerva Med. 1970 Feb 14; 61(13):565-81. PMID: 4906751.
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      157. Pennacchio L, Orlandini M. [Immunoglobulin diseases. (Basis of modern immunology. Clinical contribution. Bing-Neel syndrome)]. Policlinico Prat. 1969 Mar 31; 76(13):401-22. PMID: 4097396.
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      158. Pennacchio L. [Prevention of viral hepatitis caused by inoculation, as a social problem]. Epatologia. 1966 Jul-Aug; 12(4):632-6. PMID: 5990206.
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      163. PENNACCHIO L. [Probable etiology of a case of eosinophilic pleurisy]. Policlinico Prat. 1957 Sep 30; 64(39):1405-10. PMID: 13494230.
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      164. PENNACCHIO L. [Isolated myocarditis as an idiopathic disease and as a syndrome]. Minerva Med. 1957 Aug 04; 48(61-62):2547-56. PMID: 13483247.
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      170. PENNACCHIO L. [A serious case of diencephalic-pituitary cacnexia caused by a toxemic tubercular state and cured by streptomycin]. Policlinico Prat. 1953 Feb 23; 60(8):261-73. PMID: 13073511.
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      171. PENNACCHIO L. [Observations on two cases of cardiac aneurysm]. Policlinico Prat. 1953 Jan 19; 60(3):80-92. PMID: 13073498.
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      172. PENNACCHIO L, GAMMARROTA V. [Anatomo-biometric study of right ventricular hypertrophy in pulmonary tuberculosis]. Lotta Tuberc. 1952 Dec; 22(12):1036-56. PMID: 13053906.
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      173. PENNACCHIO L, GAMMARROTA V, DE NUNTIIS S. [Milking of the lung according to Morelli, in the treatment of caverns resistant to normal pneumothoracic collapse therapy]. Lotta Tuberc. 1952 Nov; 22(11):830-46. PMID: 13053882.
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      174. PENNACCHIO L, MAESTRINI D. [Comment on a new theory of cardiac insufficiency]. Policlinico Prat. 1952 Sep 15; 59(37):1223-4. PMID: 13026471.
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      175. PENNACCHIO L. [So-called rhythm of the coronary sinus; clinical and electrocardiographic studies]. Clin Nuova Rass Prog Med Int. 1952 Feb 16; 14(7-10):201-7. PMID: 13106963.
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