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Francesc Lopez-Giraldez, PhD, BS

Research Scientist in Genetics; YCGA Associate Director of Bioinformatics, Genetics

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Francesc Lopez-Giraldez, PhD, BS

Research Summary

YCGA Associate Director of Bioinformatics

Coauthors

Selected Publications

  • The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree.Townsend JP, López-Giráldez F, Friedman R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. Journal Of Molecular Evolution 2008, 67: 437-47. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.
  • Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies.Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.
  • The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.Schoch CL, Sung GH, López-Giráldez F, Townsend JP, Miadlikowska J, Hofstetter V, Robbertse B, Matheny PB, Kauff F, Wang Z, Gueidan C, Andrie RM, Trippe K, Ciufetti LM, Wynns A, Fraker E, Hodkinson BP, Bonito G, Groenewald JZ, Arzanlou M, de Hoog GS, Crous PW, Hewitt D, Pfister DH, Peterson K, Gryzenhout M, Wingfield MJ, Aptroot A, Suh SO, Blackwell M, Hillis DM, Griffith GW, Castlebury LA, Rossman AY, Lumbsch HT, Lücking R, Büdel B, Rauhut A, Diederich P, Ertz D, Geiser DM, Hosaka K, Inderbitzin P, Kohlmeyer J, Volkmann-Kohlmeyer B, Mostert L, O'Donnell K, Sipman H, Rogers JD, Shoemaker RA, Sugiyama J, Summerbell RC, Untereiner W, Johnston PR, Stenroos S, Zuccaro A, Dyer PS, Crittenden PD, Cole MS, Hansen K, Trappe JM, Yahr R, Lutzoni F, Spatafora JW. The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits. Systematic Biology 2009, 58: 224-39. PMID: 20525580, DOI: 10.1093/sysbio/syp020.
  • Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships.Townsend JP, Lopez-Giraldez F. Optimal selection of gene and ingroup taxon sampling for resolving phylogenetic relationships. Systematic Biology 2010, 59: 446-57. PMID: 20547780, DOI: 10.1093/sysbio/syq025.
  • LOX: inferring Level Of eXpression from diverse methods of census sequencing.Zhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics (Oxford, England) 2010, 26: 1918-9. PMID: 20538728, PMCID: PMC2905554, DOI: 10.1093/bioinformatics/btq303.
  • Multi-targeted priming for genome-wide gene expression assays.Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.
  • Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data.Wang Z, Nilsson RH, Lopez-Giraldez F, Zhuang WY, Dai YC, Johnston PR, Townsend JP. Tasting soil fungal diversity with earth tongues: phylogenetic test of SATé alignments for environmental ITS data. PloS One 2011, 6: e19039. PMID: 21533038, PMCID: PMC3080880, DOI: 10.1371/journal.pone.0019039.
  • PhyDesign: an online application for profiling phylogenetic informativeness.López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evolutionary Biology 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.
  • RBE controls microRNA164 expression to effect floral organogenesis.Huang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development (Cambridge, England) 2012, 139: 2161-9. PMID: 22573623, DOI: 10.1242/dev.075069.
  • Sex-specific gene expression during asexual development of Neurospora crassa.Wang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology : FG & B 2012, 49: 533-43. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.
  • Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology.Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology : FG & B 2012, 49: 663-73. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.
  • Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets.López-Giráldez F, Moeller AH, Townsend JP. Evaluating phylogenetic informativeness as a predictor of phylogenetic signal for metazoan, fungal, and mammalian phylogenomic data sets. BioMed Research International 2013, 2013: 621604. PMID: 23878813, PMCID: PMC3708382, DOI: 10.1155/2013/621604.
  • Phylogenetic and phylogenomic overview of the Polyporales.Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013, 105: 1350-73. PMID: 23935031, DOI: 10.3852/13-003.
  • Molecular chaperone Hsp110 rescues a vesicle transport defect produced by an ALS-associated mutant SOD1 protein in squid axoplasm.Song Y, Nagy M, Ni W, Tyagi NK, Fenton WA, López-Giráldez F, Overton JD, Horwich AL, Brady ST. Molecular chaperone Hsp110 rescues a vesicle transport defect produced by an ALS-associated mutant SOD1 protein in squid axoplasm. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 5428-33. PMID: 23509252, PMCID: PMC3619309, DOI: 10.1073/pnas.1303279110.
  • Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition.Bahal R, Quijano E, McNeer NA, Liu Y, Bhunia DC, Lopez-Giraldez F, Fields RJ, Saltzman WM, Ly DH, Glazer PM. Single-stranded γPNAs for in vivo site-specific genome editing via Watson-Crick recognition. Current Gene Therapy 2014, 14: 331-42. PMID: 25174576, PMCID: PMC4333085, DOI: 10.2174/1566523214666140825154158.
  • Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa.Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene expression differences among three Neurospora species reveal genes required for sexual reproduction in Neurospora crassa. PloS One 2014, 9: e110398. PMID: 25329823, PMCID: PMC4203796, DOI: 10.1371/journal.pone.0110398.
  • Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa.Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa. Eukaryotic Cell 2014, 13: 154-69. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/EC.00248-13.
  • A locus encompassing the Epstein-Barr virus bglf4 kinase regulates expression of genes encoding viral structural proteins.El-Guindy A, Lopez-Giraldez F, Delecluse HJ, McKenzie J, Miller G. A locus encompassing the Epstein-Barr virus bglf4 kinase regulates expression of genes encoding viral structural proteins. PLoS Pathogens 2014, 10: e1004307. PMID: 25166506, PMCID: PMC4148442, DOI: 10.1371/journal.ppat.1004307.
  • De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies.Homsy J, Zaidi S, Shen Y, Ware JS, Samocha KE, Karczewski KJ, DePalma SR, McKean D, Wakimoto H, Gorham J, Jin SC, Deanfield J, Giardini A, Porter GA, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts AE, Russell MW, Mital S, Newburger JW, Gaynor JW, Breitbart RE, Iossifov I, Ronemus M, Sanders SJ, Kaltman JR, Seidman JG, Brueckner M, Gelb BD, Goldmuntz E, Lifton RP, Seidman CE, Chung WK. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science (New York, N.Y.) 2015, 350: 1262-6. PMID: 26785492, PMCID: PMC4890146, DOI: 10.1126/science.aac9396.
  • The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities.Chong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, Harrell TM, McMillin MJ, Wiszniewski W, Gambin T, Coban Akdemir ZH, Doheny K, Scott AF, Avramopoulos D, Chakravarti A, Hoover-Fong J, Mathews D, Witmer PD, Ling H, Hetrick K, Watkins L, Patterson KE, Reinier F, Blue E, Muzny D, Kircher M, Bilguvar K, López-Giráldez F, Sutton VR, Tabor HK, Leal SM, Gunel M, Mane S, Gibbs RA, Boerwinkle E, Hamosh A, Shendure J, Lupski JR, Lifton RP, Valle D, Nickerson DA, Bamshad MJ. The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and Opportunities. American Journal Of Human Genetics 2015, 97: 199-215. PMID: 26166479, PMCID: PMC4573249, DOI: 10.1016/j.ajhg.2015.06.009.
  • E2F8 as a Novel Therapeutic Target for Lung Cancer.Park SA, Platt J, Lee JW, López-Giráldez F, Herbst RS, Koo JS. E2F8 as a Novel Therapeutic Target for Lung Cancer. Journal Of The National Cancer Institute 2015, 107 PMID: 26089541, PMCID: PMC4651101, DOI: 10.1093/jnci/djv151.
  • The Epstein-Barr Virus Immunoevasins BCRF1 and BPLF1 Are Expressed by a Mechanism Independent of the Canonical Late Pre-initiation Complex.McKenzie J, Lopez-Giraldez F, Delecluse HJ, Walsh A, El-Guindy A. The Epstein-Barr Virus Immunoevasins BCRF1 and BPLF1 Are Expressed by a Mechanism Independent of the Canonical Late Pre-initiation Complex. PLoS Pathogens 2016, 12: e1006008. PMID: 27855219, PMCID: PMC5113994, DOI: 10.1371/journal.ppat.1006008.
  • In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery.Bahal R, Ali McNeer N, Quijano E, Liu Y, Sulkowski P, Turchick A, Lu YC, Bhunia DC, Manna A, Greiner DL, Brehm MA, Cheng CJ, López-Giráldez F, Ricciardi A, Beloor J, Krause DS, Kumar P, Gallagher PG, Braddock DT, Mark Saltzman W, Ly DH, Glazer PM. In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery. Nature Communications 2016, 7: 13304. PMID: 27782131, PMCID: PMC5095181, DOI: 10.1038/ncomms13304.
  • Identification of Intrinsic Axon Growth Modulators for Intact CNS Neurons after Injury.Fink KL, López-Giráldez F, Kim IJ, Strittmatter SM, Cafferty WB. Identification of Intrinsic Axon Growth Modulators for Intact CNS Neurons after Injury. Cell Reports 2017, 18: 2687-2701. PMID: 28297672, PMCID: PMC5389739, DOI: 10.1016/j.celrep.2017.02.058.
  • Interferon-γ converts human microvascular pericytes into negative regulators of alloimmunity through induction of indoleamine 2,3-dioxygenase 1.Liu R, Merola J, Manes TD, Qin L, Tietjen GT, López-Giráldez F, Broecker V, Fang C, Xie C, Chen PM, Kirkiles-Smith NC, Jane-Wit D, Pober JS. Interferon-γ converts human microvascular pericytes into negative regulators of alloimmunity through induction of indoleamine 2,3-dioxygenase 1. JCI Insight 2018, 3 PMID: 29515027, PMCID: PMC5922286, DOI: 10.1172/jci.insight.97881.
  • Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response.Serebrenik YV, Hellerschmied D, Toure M, López-Giráldez F, Brookner D, Crews CM. Targeted protein unfolding uncovers a Golgi-specific transcriptional stress response. Molecular Biology Of The Cell 2018, 29: 1284-1298. PMID: 29851555, PMCID: PMC5994893, DOI: 10.1091/mbc.E17-11-0693.
  • In utero nanoparticle delivery for site-specific genome editing.Ricciardi AS, Bahal R, Farrelly JS, Quijano E, Bianchi AH, Luks VL, Putman R, López-Giráldez F, Coşkun S, Song E, Liu Y, Hsieh WC, Ly DH, Stitelman DH, Glazer PM, Saltzman WM. In utero nanoparticle delivery for site-specific genome editing. Nature Communications 2018, 9: 2481. PMID: 29946143, PMCID: PMC6018676, DOI: 10.1038/s41467-018-04894-2.
  • De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus.Furey CG, Choi J, Jin SC, Zeng X, Timberlake AT, Nelson-Williams C, Mansuri MS, Lu Q, Duran D, Panchagnula S, Allocco A, Karimy JK, Khanna A, Gaillard JR, DeSpenza T, Antwi P, Loring E, Butler WE, Smith ER, Warf BC, Strahle JM, Limbrick DD, Storm PB, Heuer G, Jackson EM, Iskandar BJ, Johnston JM, Tikhonova I, Castaldi C, López-Giráldez F, Bjornson RD, Knight JR, Bilguvar K, Mane S, Alper SL, Haider S, Guclu B, Bayri Y, Sahin Y, Apuzzo MLJ, Duncan CC, DiLuna ML, Günel M, Lifton RP, Kahle KT. De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus. Neuron 2018, 99: 302-314.e4. PMID: 29983323, PMCID: PMC7839075, DOI: 10.1016/j.neuron.2018.06.019.
  • Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair.Shook BA, Wasko RR, Rivera-Gonzalez GC, Salazar-Gatzimas E, López-Giráldez F, Dash BC, Muñoz-Rojas AR, Aultman KD, Zwick RK, Lei V, Arbiser JL, Miller-Jensen K, Clark DA, Hsia HC, Horsley V. Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repair. Science (New York, N.Y.) 2018, 362 PMID: 30467144, PMCID: PMC6684198, DOI: 10.1126/science.aar2971.
  • Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease.Ryu HY, López-Giráldez F, Knight J, Hwang SS, Renner C, Kreft SG, Hochstrasser M. Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO protease. Nature Communications 2018, 9: 5417. PMID: 30575729, PMCID: PMC6303320, DOI: 10.1038/s41467-018-07836-0.
  • Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation.Duran D, Zeng X, Jin SC, Choi J, Nelson-Williams C, Yatsula B, Gaillard J, Furey CG, Lu Q, Timberlake AT, Dong W, Sorscher MA, Loring E, Klein J, Allocco A, Hunt A, Conine S, Karimy JK, Youngblood MW, Zhang J, DiLuna ML, Matouk CC, Mane S, Tikhonova IR, Castaldi C, López-Giráldez F, Knight J, Haider S, Soban M, Alper SL, Komiyama M, Ducruet AF, Zabramski JM, Dardik A, Walcott BP, Stapleton CJ, Aagaard-Kienitz B, Rodesch G, Jackson E, Smith ER, Orbach DB, Berenstein A, Bilguvar K, Vikkula M, Gunel M, Lifton RP, Kahle KT. Mutations in Chromatin Modifier and Ephrin Signaling Genes in Vein of Galen Malformation. Neuron 2019, 101: 429-443.e4. PMID: 30578106, DOI: 10.1016/j.neuron.2018.11.041.
  • Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa.Wang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP. Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio 2019, 10 PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mBio.00192-19.
  • Implication of DNA repair genes in Lynch-like syndrome.Xicola RM, Clark JR, Carroll T, Alvikas J, Marwaha P, Regan MR, Lopez-Giraldez F, Choi J, Emmadi R, Alagiozian-Angelova V, Kupfer SS, Ellis NA, Llor X. Implication of DNA repair genes in Lynch-like syndrome. Familial Cancer 2019, 18: 331-342. PMID: 30989425, PMCID: PMC6561810, DOI: 10.1007/s10689-019-00128-6.
  • The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation.Ryu HY, Su D, Wilson-Eisele NR, Zhao D, López-Giráldez F, Hochstrasser M. The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation. The EMBO Journal 2019, 38: e102003. PMID: 31313851, PMCID: PMC6694223, DOI: 10.15252/embj.2019102003.
  • Progenitor-derived human endothelial cells evade alloimmunity by CRISPR/Cas9-mediated complete ablation of MHC expression.Merola J, Reschke M, Pierce RW, Qin L, Spindler S, Baltazar T, Manes TD, Lopez-Giraldez F, Li G, Bracaglia LG, Xie C, Kirkiles-Smith N, Saltzman WM, Tietjen GT, Tellides G, Pober JS. Progenitor-derived human endothelial cells evade alloimmunity by CRISPR/Cas9-mediated complete ablation of MHC expression. JCI Insight 2019, 4 PMID: 31527312, PMCID: PMC6824302, DOI: 10.1172/jci.insight.129739.
  • Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy.Tal R, Shaikh S, Pallavi P, Tal A, López-Giráldez F, Lyu F, Fang YY, Chinchanikar S, Liu Y, Kliman HJ, Alderman M, Pluchino N, Kayani J, Mamillapalli R, Krause DS, Taylor HS. Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy. PLoS Biology 2019, 17: e3000421. PMID: 31513564, PMCID: PMC6742226, DOI: 10.1371/journal.pbio.3000421.
  • Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum.Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio 2019, 10 PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mBio.02119-19.
  • PD-1H (VISTA)-mediated suppression of autoimmunity in systemic and cutaneous lupus erythematosus.Han X, Vesely MD, Yang W, Sanmamed MF, Badri T, Alawa J, López-Giráldez F, Gaule P, Lee SW, Zhang JP, Nie X, Nassar A, Boto A, Flies DB, Zheng L, Kim TK, Moeckel GW, McNiff JM, Chen L. PD-1H (VISTA)-mediated suppression of autoimmunity in systemic and cutaneous lupus erythematosus. Science Translational Medicine 2019, 11 PMID: 31826980, DOI: 10.1126/scitranslmed.aax1159.
  • Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro.Kosyakova N, Kao DD, Figetakis M, López-Giráldez F, Spindler S, Graham M, James KJ, Won Shin J, Liu X, Tietjen GT, Pober JS, Chang WG. Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitro. NPJ Regenerative Medicine 2020, 5: 1. PMID: 31934351, PMCID: PMC6944695, DOI: 10.1038/s41536-019-0086-3.
  • Tumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6.Arnal-Estapé A, Cai WL, Albert AE, Zhao M, Stevens LE, López-Giráldez F, Patel KD, Tyagi S, Schmitt EM, Westbrook TF, Nguyen DX. Tumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6. Oncogene 2020, 39: 3726-3737. PMID: 32157212, PMCID: PMC7190573, DOI: 10.1038/s41388-020-1246-z.
  • Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair.Shook BA, Wasko RR, Mano O, Rutenberg-Schoenberg M, Rudolph MC, Zirak B, Rivera-Gonzalez GC, López-Giráldez F, Zarini S, Rezza A, Clark DA, Rendl M, Rosenblum MD, Gerstein MB, Horsley V. Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair. Cell Stem Cell 2020, 26: 880-895.e6. PMID: 32302523, PMCID: PMC7853423, DOI: 10.1016/j.stem.2020.03.013.
  • Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores.Domingo-Roura X, López-Giráldez F, Saeki M, Marmi J. Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores. Genetical Research 2005, 85: 223-33. PMID: 16174341, DOI: 10.1017/S0016672305007512.
  • Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia.Marmi J, López-Giráldez F, Macdonald DW, Calafell F, Zholnerovskaya E, Domingo-Roura X. Mitochondrial DNA reveals a strong phylogeographic structure in the badger across Eurasia. Molecular Ecology 2006, 15: 1007-20. PMID: 16599963, DOI: 10.1111/j.1365-294X.2006.02747.x.
  • Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs.López-Giráldez F, Andrés O, Domingo-Roura X, Bosch M. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs. BMC Genomics 2006, 7: 269. PMID: 17059596, PMCID: PMC1634856, DOI: 10.1186/1471-2164-7-269.
  • High incidence of nonslippage mechanisms generating variability and complexity in eurasian badger microsatellites.López-Giráldez F, Marmi J, Domingo-Roura X. High incidence of nonslippage mechanisms generating variability and complexity in eurasian badger microsatellites. The Journal Of Heredity 2007, 98: 620-8. PMID: 17728273, DOI: 10.1093/jhered/esm068.
  • RPS4Y gene family evolution in primates.Andrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Y gene family evolution in primates. BMC Evolutionary Biology 2008, 8: 142. PMID: 18477388, PMCID: PMC2397393, DOI: 10.1186/1471-2148-8-142.
  • Assessing the role of tandem repeats in shaping the genomic architecture of great apes.Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PloS One 2011, 6: e27239. PMID: 22076140, PMCID: PMC3208591, DOI: 10.1371/journal.pone.0027239.
  • Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs.Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli KP, Leonard JA, Meyer M, Krause J, Pääbo S, Green RE, Wayne RK. Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs. Science (New York, N.Y.) 2013, 342: 871-4. PMID: 24233726, DOI: 10.1126/science.1243650.
  • Microarray analysis of neonatal rat anteroventral periventricular transcriptomes identifies the proapoptotic Cugbp2 gene as sex-specific and regulated by estradiol.Del Pino Sans J, Krishnan S, Aggison LK, Adams HL, Shrikant MM, López-Giráldez F, Petersen SL. Microarray analysis of neonatal rat anteroventral periventricular transcriptomes identifies the proapoptotic Cugbp2 gene as sex-specific and regulated by estradiol. Neuroscience 2015, 303: 312-22. PMID: 26166732, DOI: 10.1016/j.neuroscience.2015.07.008.
  • Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani population.Shahzad M, Sires Campos J, Tariq N, Herraiz Serrano C, Yousaf R, Jiménez-Cervantes C, Yousaf S, Waryah YM, Dad HA, Blue EM, Sobreira N, López-Giráldez F, Kausar T, Ali M, Waryah AM, Riazuddin S, Shaikh RS, García-Borrón JC, Ahmed ZM. Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani population. Pigment Cell & Melanoma Research 2015, 28: 730-5. PMID: 26197705, PMCID: PMC4609612, DOI: 10.1111/pcmr.12400.
  • Congenital Heart Defects Due to TAF1 Missense Variants.Morton SU, Agarwal R, Madden JA, Genetti CA, Brownstein CA, López-Giráldez F, Choi J, Seidman CE, Seidman JG, Lyon GJ, Agrawal PB. Congenital Heart Defects Due to TAF1 Missense Variants. Circulation. Genomic And Precision Medicine 2020, 13: e002843. PMID: 32396742, PMCID: PMC7329268, DOI: 10.1161/CIRCGEN.119.002843.
  • Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira.Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 45. PMID: 29600195, PMCID: PMC5863495, DOI: 10.3389/fcimb.2018.00045.
  • A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes.Johnston PR, Quijada L, Smith CA, Baral HO, Hosoya T, Baschien C, Pärtel K, Zhuang WY, Haelewaters D, Park D, Carl S, López-Giráldez F, Wang Z, Townsend JP. A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus 2019, 10: 1. PMID: 32647610, PMCID: PMC7325659, DOI: 10.1186/s43008-019-0002-x.
  • Genomic and Immune Profiling of a Patient With Triple-Negative Breast Cancer That Progressed During Neoadjuvant Chemotherapy Plus PD-L1 Blockade.Casadevall D, Li X, Powles RL, Wali VB, Buza N, Pelekanou V, Dhawan A, Foldi J, Szekely B, Lopez-Giraldez F, Hatzis C, Pusztai L. Genomic and Immune Profiling of a Patient With Triple-Negative Breast Cancer That Progressed During Neoadjuvant Chemotherapy Plus PD-L1 Blockade. JCO Precision Oncology 2019, 3 PMID: 32914041, PMCID: PMC7450962, DOI: 10.1200/PO.18.00335.
  • Mutations disrupting neuritogenesis genes confer risk for cerebral palsy.Jin SC, Lewis SA, Bakhtiari S, Zeng X, Sierant MC, Shetty S, Nordlie SM, Elie A, Corbett MA, Norton BY, van Eyk CL, Haider S, Guida BS, Magee H, Liu J, Pastore S, Vincent JB, Brunstrom-Hernandez J, Papavasileiou A, Fahey MC, Berry JG, Harper K, Zhou C, Zhang J, Li B, Heim J, Webber DL, Frank MSB, Xia L, Xu Y, Zhu D, Zhang B, Sheth AH, Knight JR, Castaldi C, Tikhonova IR, López-Giráldez F, Keren B, Whalen S, Buratti J, Doummar D, Cho M, Retterer K, Millan F, Wang Y, Waugh JL, Rodan L, Cohen JS, Fatemi A, Lin AE, Phillips JP, Feyma T, MacLennan SC, Vaughan S, Crompton KE, Reid SM, Reddihough DS, Shang Q, Gao C, Novak I, Badawi N, Wilson YA, McIntyre SJ, Mane SM, Wang X, Amor DJ, Zarnescu DC, Lu Q, Xing Q, Zhu C, Bilguvar K, Padilla-Lopez S, Lifton RP, Gecz J, MacLennan AH, Kruer MC. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature Genetics 2020, 52: 1046-1056. PMID: 32989326, DOI: 10.1038/s41588-020-0695-1.
  • Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia.Dong W, Jin SC, Allocco A, Zeng X, Sheth AH, Panchagnula S, Castonguay A, Lorenzo LÉ, Islam B, Brindle G, Bachand K, Hu J, Sularz A, Gaillard J, Choi J, Dunbar A, Nelson-Williams C, Kiziltug E, Furey CG, Conine S, Duy PQ, Kundishora AJ, Loring E, Li B, Lu Q, Zhou G, Liu W, Li X, Sierant MC, Mane S, Castaldi C, López-Giráldez F, Knight JR, Sekula RF, Simard JM, Eskandar EN, Gottschalk C, Moliterno J, Günel M, Gerrard JL, Dib-Hajj S, Waxman SG, Barker FG, Alper SL, Chahine M, Haider S, De Koninck Y, Lifton RP, Kahle KT. Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia. IScience 2020, 23: 101552. PMID: 33083721, PMCID: PMC7554653, DOI: 10.1016/j.isci.2020.101552.
  • Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome.Dyment DA, O'Donnell-Luria A, Agrawal PB, Coban Akdemir Z, Aleck KA, Antaki D, Al Sharhan H, Au PB, Aydin H, Beggs AH, Bilguvar K, Boerwinkle E, Brand H, Brownstein CA, Buyske S, Chodirker B, Choi J, Chudley AE, Clericuzio CL, Cox GF, Curry C, de Boer E, de Vries BBA, Dunn K, Dutmer CM, England EM, Fahrner JA, Geckinli BB, Genetti CA, Gezdirici A, Gibson WT, Gleeson JG, Greenberg CR, Hall A, Hamosh A, Hartley T, Jhangiani SN, Karaca E, Kernohan K, Lauzon JL, Lewis MES, Lowry RB, López-Giráldez F, Matise TC, McEvoy-Venneri J, McInnes B, Mhanni A, Garcia Minaur S, Moilanen J, Nguyen A, Nowaczyk MJM, Posey JE, Õunap K, Pehlivan D, Pajusalu S, Penney LS, Poterba T, Prontera P, Doriqui MJR, Sawyer SL, Sobreira N, Stanley V, Torun D, Wargowski D, Witmer PD, Wong I, Xing J, Zaki MS, Zhang Y, Boycott KM, Bamshad MJ, Nickerson DA, Blue EE, Innes AM. Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. American Journal Of Medical Genetics. Part A 2021, 185: 119-133. PMID: 33098347, PMCID: PMC8197629, DOI: 10.1002/ajmg.a.61926.
  • Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification.Dornburg A, Wang Z, Wang J, Mo ES, Lopez-Giraldez F, Townsend JP. Comparative Genomics within and across Bilaterians Illuminates the Evolutionary History of ALK and LTK Proto-Oncogene Origination and Diversification. Genome Biology And Evolution 2021, 13 PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.
  • Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsy.Jin SC, Lewis SA, Bakhtiari S, Zeng X, Sierant MC, Shetty S, Nordlie SM, Elie A, Corbett MA, Norton BY, van Eyk CL, Haider S, Guida BS, Magee H, Liu J, Pastore S, Vincent JB, Brunstrom-Hernandez J, Papavasileiou A, Fahey MC, Berry JG, Harper K, Zhou C, Zhang J, Li B, Zhao H, Heim J, Webber DL, Frank MSB, Xia L, Xu Y, Zhu D, Zhang B, Sheth AH, Knight JR, Castaldi C, Tikhonova IR, López-Giráldez F, Keren B, Whalen S, Buratti J, Doummar D, Cho M, Retterer K, Millan F, Wang Y, Waugh JL, Rodan L, Cohen JS, Fatemi A, Lin AE, Phillips JP, Feyma T, MacLennan SC, Vaughan S, Crompton KE, Reid SM, Reddihough DS, Shang Q, Gao C, Novak I, Badawi N, Wilson YA, McIntyre SJ, Mane SM, Wang X, Amor DJ, Zarnescu DC, Lu Q, Xing Q, Zhu C, Bilguvar K, Padilla-Lopez S, Lifton RP, Gecz J, MacLennan AH, Kruer MC. Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature Genetics 2021, 53: 412. PMID: 33432185, DOI: 10.1038/s41588-021-00780-8.
  • Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptake.Habtemichael EN, Li DT, Camporez JP, Westergaard XO, Sales CI, Liu X, López-Giráldez F, DeVries SG, Li H, Ruiz DM, Wang KY, Sayal BS, González Zapata S, Dann P, Brown SN, Hirabara S, Vatner DF, Goedeke L, Philbrick W, Shulman GI, Bogan JS. Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptake. Nature Metabolism 2021, 3: 378-393. PMID: 33686286, PMCID: PMC7990718, DOI: 10.1038/s42255-021-00359-x.
  • Tumor necrosis factor-induced ArhGEF10 selectively activates RhoB contributing to human microvascular endothelial cell tight junction disruption.Khan A, Ni W, Lopez-Giraldez F, Kluger MS, Pober JS, Pierce RW. Tumor necrosis factor-induced ArhGEF10 selectively activates RhoB contributing to human microvascular endothelial cell tight junction disruption. FASEB Journal : Official Publication Of The Federation Of American Societies For Experimental Biology 2021, 35: e21627. PMID: 33948992, PMCID: PMC9026622, DOI: 10.1096/fj.202002783RR.
  • Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice.Hwang JY, Nawaz S, Choi J, Wang H, Hussain S, Nawaz M, Lopez-Giraldez F, Jeong K, Dong W, Oh JN, Bilguvar K, Mane S, Lee CK, Bystroff C, Lifton RP, Ahmad W, Chung JJ. Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice. Frontiers In Cell And Developmental Biology 2021, 9: 662903. PMID: 33968937, PMCID: PMC8103034, DOI: 10.3389/fcell.2021.662903.
  • DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease.Kundishora AJ, Peters ST, Pinard A, Duran D, Panchagnula S, Barak T, Miyagishima DF, Dong W, Smith H, Ocken J, Dunbar A, Nelson-Williams C, Haider S, Walker RL, Li B, Zhao H, Thumkeo D, Marlier A, Duy PQ, Diab NS, Reeves BC, Robert SM, Sujijantarat N, Stratman AN, Chen YH, Zhao S, Roszko I, Lu Q, Zhang B, Mane S, Castaldi C, López-Giráldez F, Knight JR, Bamshad MJ, Nickerson DA, Geschwind DH, Chen SL, Storm PB, Diluna ML, Matouk CC, Orbach DB, Alper SL, Smith ER, Lifton RP, Gunel M, Milewicz DM, Jin SC, Kahle KT. DIAPH1 Variants in Non-East Asian Patients With Sporadic Moyamoya Disease. JAMA Neurology 2021, 78: 993-1003. PMID: 34125151, PMCID: PMC8204259, DOI: 10.1001/jamaneurol.2021.1681.
  • CCM3 Loss-Induced Lymphatic Defect Is Mediated by the Augmented VEGFR3-ERK1/2 Signaling.Qin L, Zhang H, Li B, Jiang Q, Lopez F, Min W, Zhou JH. CCM3 Loss-Induced Lymphatic Defect Is Mediated by the Augmented VEGFR3-ERK1/2 Signaling. Arteriosclerosis, Thrombosis, And Vascular Biology 2021, 41: 2943-2960. PMID: 34670407, PMCID: PMC8613000, DOI: 10.1161/ATVBAHA.121.316707.
  • Macrophage IL-1β promotes arteriogenesis by autocrine STAT3- and NF-κB-mediated transcription of pro-angiogenic VEGF-A.Mantsounga CS, Lee C, Neverson J, Sharma S, Healy A, Berus JM, Parry C, Ceneri NM, López-Giráldez F, Chun HJ, Lu Q, Sellke F, Choudhary G, Morrison AR. Macrophage IL-1β promotes arteriogenesis by autocrine STAT3- and NF-κB-mediated transcription of pro-angiogenic VEGF-A. Cell Reports 2022, 38: 110309. PMID: 35108537, PMCID: PMC8865931, DOI: 10.1016/j.celrep.2022.110309.
  • The role of SPAG1 in the assembly of axonemal dyneins in human airway epithelia.Smith AJ, Bustamante-Marin XM, Yin W, Sears PR, Herring LE, Dicheva NN, López-Giráldez F, Mane S, Tarran R, Leigh MW, Knowles MR, Zariwala MA, Ostrowski LE. The role of SPAG1 in the assembly of axonemal dyneins in human airway epithelia. Journal Of Cell Science 2022, 135 PMID: 35178554, PMCID: PMC8995097, DOI: 10.1242/jcs.259512.
  • ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor-induced leak.Khan A, Ni W, Baltazar T, Lopez-Giraldez F, Pober JS, Pierce RW. ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor-induced leak. FASEB Journal : Official Publication Of The Federation Of American Societies For Experimental Biology 2022, 36: e22254. PMID: 35294066, PMCID: PMC9103844, DOI: 10.1096/fj.202101873RR.
  • Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia.Dong W, Wong KHY, Liu Y, Levy-Sakin M, Hung WC, Li M, Li B, Jin SC, Choi J, Lopez-Giraldez F, Vaka D, Poon A, Chu C, Lao R, Balamir M, Movsesyan I, Malloy MJ, Zhao H, Kwok PY, Kane JP, Lifton RP, Pullinger CR. Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia. Journal Of Lipid Research 2022, 63: 100209. PMID: 35460704, DOI: 10.1016/j.jlr.2022.100209.
  • Whole-Exome Sequencing of Germline Variants in Non-BRCA Families with Hereditary Breast Cancer.Liu Y, Helgadottir HT, Kharaziha P, Choi J, López-Giráldez F, Mane SM, Höiom V, Juhlin CC, Larsson C, Bajalica-Lagercrantz S. Whole-Exome Sequencing of Germline Variants in Non-BRCA Families with Hereditary Breast Cancer. Biomedicines 2022, 10 PMID: 35625741, DOI: 10.3390/biomedicines10051004.
  • Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa.Wang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, e0023222. PMID: 35638725, DOI: 10.1128/msystems.00232-22.
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