Francesc Lopez-Giraldez, PhD, BS
Research Scientist in Genetics; YCGA Associate Director of Bioinformatics, Genetics
Research & Publications
Biography
Research Summary
YCGA Associate Director of Bioinformatics
Coauthors
Selected Publications
- Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in NeurosporaWang Z, Wang Y, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend J. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLOS Genetics 2023, 19: e1011019. PMID: 37934795, PMCID: PMC10684091, DOI: 10.1371/journal.pgen.1011019.
- Origins of lineage‐specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassaWang Z, Wang Y, Kasuga T, Hassler H, Lopez‐Giraldez F, Dong C, Yarden O, Townsend J. Origins of lineage‐specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa. Molecular Ecology 2023 PMID: 37843462, DOI: 10.1111/mec.17168.
- MicroRNA-1 protects the endothelium in acute lung injuryKorde A, Haslip M, Pednekar P, Khan A, Chioccioli M, Mehta S, Lopez-Giraldez F, Bermejo S, Rojas M, Dela Cruz C, Matthay M, Pober J, Pierce R, Takyar S. MicroRNA-1 protects the endothelium in acute lung injury. JCI Insight 2023, 8: e164816. PMID: 37737266, PMCID: PMC10561733, DOI: 10.1172/jci.insight.164816.
- Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cystsKundishora A, Allington G, McGee S, Mekbib K, Gainullin V, Timberlake A, Nelson-Williams C, Kiziltug E, Smith H, Ocken J, Shohfi J, Allocco A, Duy P, Elsamadicy A, Dong W, Zhao S, Wang Y, Qureshi H, DiLuna M, Mane S, Tikhonova I, Fu P, Castaldi C, López-Giráldez F, Knight J, Furey C, Carter B, Haider S, Moreno-De-Luca A, Alper S, Gunel M, Millan F, Lifton R, Torene R, Jin S, Kahle K. Multiomic analyses implicate a neurodevelopmental program in the pathogenesis of cerebral arachnoid cysts. Nature Medicine 2023, 29: 667-678. PMID: 36879130, DOI: 10.1038/s41591-023-02238-2.
- HYDIN Variants Are a Common Cause of Primary Ciliary Dyskinesia in French Canadians.Shapiro A, Sillon G, D'Agostino D, Baret L, López-Giráldez F, Mane S, Leigh M, Davis S, Knowles M, Zariwala M. HYDIN Variants Are a Common Cause of Primary Ciliary Dyskinesia in French Canadians. Annals Of The American Thoracic Society 2023, 20: 140-144. PMID: 36112114, PMCID: PMC9819264, DOI: 10.1513/annalsats.202203-253rl.
- Brain metastatic outgrowth and osimertinib resistance are potentiated by RhoA in EGFR-mutant lung cancerAdua S, Arnal-Estapé A, Zhao M, Qi B, Liu Z, Kravitz C, Hulme H, Strittmatter N, López-Giráldez F, Chande S, Albert A, Melnick M, Hu B, Politi K, Chiang V, Colclough N, Goodwin R, Cross D, Smith P, Nguyen D. Brain metastatic outgrowth and osimertinib resistance are potentiated by RhoA in EGFR-mutant lung cancer. Nature Communications 2022, 13: 7690. PMID: 36509758, PMCID: PMC9744876, DOI: 10.1038/s41467-022-34889-z.
- Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinasZhang H, Li B, Huang Q, López-Giráldez F, Tanaka Y, Lin Q, Mehta S, Wang G, Graham M, Liu X, Park I, Eichmann A, Min W, Zhou J. Mitochondrial dysfunction induces ALK5-SMAD2-mediated hypovascularization and arteriovenous malformations in mouse retinas. Nature Communications 2022, 13: 7637. PMID: 36496409, PMCID: PMC9741628, DOI: 10.1038/s41467-022-35262-w.
- 167 Comprehensive profiling of cancer-associated fibroblasts in CD8+T cell-exclusive non-small cell lung cancer tumor microenvironments using the Nanostring GeoMX® digital spatial profilerCho C, Woodard G, Lopez-Giraldez F, Badri T, Vesely M, Chen L. 167 Comprehensive profiling of cancer-associated fibroblasts in CD8+T cell-exclusive non-small cell lung cancer tumor microenvironments using the Nanostring GeoMX® digital spatial profiler. 2022, a179-a179. DOI: 10.1136/jitc-2022-sitc2022.0167.
- Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloidesGortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. Journal Of Fungi 2022, 8: 854. PMID: 36012842, PMCID: PMC9410309, DOI: 10.3390/jof8080854.
- Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassaWang 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, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.
- Whole-Exome Sequencing of Germline Variants in Non-BRCA Families with Hereditary Breast CancerLiu 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: 1004. PMID: 35625741, PMCID: PMC9138793, DOI: 10.3390/biomedicines10051004.
- Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemiaDong 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, PMCID: PMC9126845, DOI: 10.1016/j.jlr.2022.100209.
- ArhGEF12 activates Rap1A and not RhoA in human dermal microvascular endothelial cells to reduce tumor necrosis factor‐induced leakKhan 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. The FASEB Journal 2022, 36: e22254. PMID: 35294066, PMCID: PMC9103844, DOI: 10.1096/fj.202101873rr.
- The role of SPAG1 in the assembly of axonemal dyneins in human airway epitheliaSmith 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.
- Centers for Mendelian Genomics: A decade of facilitating gene discoveryBaxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Consortium C, Adams M, Aguet F, Akay G, Anderson P, Antonescu C, Arachchi H, Atik M, Austin-Tse C, Babb L, Bacus T, Bahrambeigi V, Balasubramanian S, Bayram Y, Beaudet A, Beck C, Belmont J, Below J, Bilguvar K, Boehm C, Boerwinkle E, Boone P, Bowne S, Brand H, Buckingham K, Byrne A, Calame D, Campbell I, Cao X, Carvalho C, Chander V, Chang J, Chao K, Chinn I, Clarke D, Collins R, Cummings B, Dardas Z, Dawood M, Delano K, DiTroia S, Doddapaneni H, Du H, Du R, Duan R, Eldomery M, Eng C, England E, Evangelista E, Everett S, Fatih J, Felsenfeld A, Francioli L, Frazar C, Fu J, Gamarra E, Gambin T, Gan W, Gandhi M, Ganesh V, Garimella K, Gauthier L, Giroux D, Gonzaga-Jauregui C, Goodrich J, Gordon W, Griffith S, Grochowski C, Gu S, Gudmundsson S, Hall S, Hansen A, Harel T, Harmanci A, Herman I, Hetrick K, Hijazi H, Horike-Pyne M, Hsu E, Hu J, Huang Y, Hurless J, Jahl S, Jarvik G, Jiang Y, Johanson E, Jolly A, Karaca E, Khayat M, Knight J, Kolar J, Kumar S, Lalani S, Laricchia K, Larkin K, Leal S, Lemire G, Lewis R, Li H, Ling H, Lipson R, Liu P, Lovgren A, López-Giráldez F, MacMillan M, Mangilog B, Mano S, Marafi D, Marosy B, Marshall J, Martin R, Marvin C, Mawhinney M, McGee S, McGoldrick D, Mehaffey M, Mekonnen B, Meng X, Mitani T, Miyake C, Mohr D, Morris S, Mullen T, Murdock D, Murugan M, Muzny D, Myers B, Neira J, Nguyen K, Nielsen P, Nudelman N, O’Heir E, O’Leary M, Ongaco C, Orange J, Osei-Owusu I, Paine I, Pais L, Paschall J, Patterson K, Pehlivan D, Pelle B, Penney S, de Acha Chavez J, Pierce-Hoffman E, Poli C, Punetha J, Radhakrishnan A, Richardson M, Rodrigues E, Roote G, Rosenfeld J, Ryke E, Sabo A, Sanchez A, Schrauwen I, Scott D, Sedlazeck F, Serrano J, Shaw C, Shelford T, Shively K, Singer-Berk M, Smith J, Snow H, Snyder G, Solomonson M, Son R, Song X, Stankiewicz P, Stephan T, Sutton V, Sveden A, Sánchez D, Tackett M, Talkowski M, Threlkeld M, Tiao G, Udler M, Vail L, Valivullah Z, Valkanas E, VanNoy G, Wang Q, Wang G, Wang L, Wangler M, Watts N, Weisburd B, Weiss J, Wheeler M, White J, Williamson C, Wilson M, Wiszniewski W, Withers M, Witmer D, Witzgall L, Wohler E, Wojcik M, Wong I, Wood J, Wu N, Xing J, Yang Y, Yi Q, Yuan B, Zeiger J, Zhang C, Zhang P, Zhang Y, Zhang X, Zhang Y, Zhang S, Zoghbi H, van den Veyver I, Rehm H, O’Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genetics In Medicine 2022, 24: 784-797. PMID: 35148959, PMCID: PMC9119004, DOI: 10.1016/j.gim.2021.12.005.
- Macrophage IL-1β promotes arteriogenesis by autocrine STAT3- and NF-κB-mediated transcription of pro-angiogenic VEGF-AMantsounga 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.
- CCM3 Loss-Induced Lymphatic Defect Is Mediated by the Augmented VEGFR3-ERK1/2 SignalingQin 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.
- DIAPH1 Variants in Non–East Asian Patients With Sporadic Moyamoya DiseaseKundishora 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.
- Tumor necrosis factor‐induced ArhGEF10 selectively activates RhoB contributing to human microvascular endothelial cell tight junction disruptionKhan 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. The FASEB Journal 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 MiceHwang 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.
- The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassaHerold I, Zolti A, Garduño-Rosales M, Wang Z, López-Giráldez F, Mouriño-Pérez R, Townsend J, Ulitsky I, Yarden O. The GUL-1 Protein Binds Multiple RNAs Involved in Cell Wall Remodeling and Affects the MAK-1 Pathway in Neurospora crassa. Frontiers In Fungal Biology 2021, 2: 672696. PMID: 37744127, PMCID: PMC10512220, DOI: 10.3389/ffunb.2021.672696.
- Insulin-stimulated endoproteolytic TUG cleavage links energy expenditure with glucose uptakeHabtemichael 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.
- Author Correction: Mutations disrupting neuritogenesis genes confer risk for cerebral palsyJin 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: 412-412. PMID: 33432185, DOI: 10.1038/s41588-021-00780-8.
- Comparative genomics within and across Bilaterians illuminates the evolutionary history of ALK and LTK proto-oncogene origination and diversificationDornburg 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 2020, 13: evaa228-. PMID: 33196781, PMCID: PMC7851593, DOI: 10.1093/gbe/evaa228.
- Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndromeDyment DA, O'Donnell‐Luria A, Agrawal PB, Akdemir Z, Aleck KA, Antaki D, Sharhan H, Au P, 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 B, 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, 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, Consortium C, Genomics C, 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 2020, 185: 119-133. PMID: 33098347, PMCID: PMC8197629, DOI: 10.1002/ajmg.a.61926.
- Mutations disrupting neuritogenesis genes confer risk for cerebral palsyJin 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. Mutations disrupting neuritogenesis genes confer risk for cerebral palsy. Nature Genetics 2020, 52: 1046-1056. PMID: 32989326, PMCID: PMC9148538, DOI: 10.1038/s41588-020-0695-1.
- Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal NeuralgiaDong 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.
- Congenital Heart Defects Due to TAF1 Missense VariantsMorton 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.
- Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin RepairShook 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.
- Tumor progression and chromatin landscape of lung cancer are regulated by the lineage factor GATA6Arnal-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.
- Differential functional roles of fibroblasts and pericytes in the formation of tissue-engineered microvascular networks in vitroKosyakova 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.
- PD-1H (VISTA)–mediated suppression of autoimmunity in systemic and cutaneous lupus erythematosusHan 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.
- Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosumWang 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: e02119-19. PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mbio.02119-19.
- Progenitor-derived human endothelial cells evade alloimmunity by CRISPR/Cas9-mediated complete ablation of MHC expressionMerola 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.
- MA17.01 Cell Lineage and Chromatin Landscape of Lung Cancer Are Controlled by GATA6Estapé A, Cai W, Albert A, López-Giráldez F, Zhao M, Stevens L, Patel K, Nguyen D. MA17.01 Cell Lineage and Chromatin Landscape of Lung Cancer Are Controlled by GATA6. Journal Of Thoracic Oncology 2019, 14: s317. DOI: 10.1016/j.jtho.2019.08.637.
- Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancyTal 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.
- The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylationRyu H, Su D, Wilson‐Eisele N, 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.
- A multigene phylogeny toward a new phylogenetic classification of LeotiomycetesJohnston 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 BlockadeCasadevall 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: po.18.00335. PMID: 32914041, PMCID: PMC7450962, DOI: 10.1200/po.18.00335.
- Implication of DNA repair genes in Lynch-like syndromeXicola 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.
- Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassaWang 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: e00192-19. PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mbio.00192-19.
- Distinct adaptive mechanisms drive recovery from aneuploidy caused by loss of the Ulp2 SUMO proteaseRyu 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 MalformationDuran 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 2018, 101: 429-443.e4. PMID: 30578106, PMCID: PMC10292091, DOI: 10.1016/j.neuron.2018.11.041.
- Myofibroblast proliferation and heterogeneity are supported by macrophages during skin repairShook 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 2018, 362 PMID: 30467144, PMCID: PMC6684198, DOI: 10.1126/science.aar2971.
- De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital HydrocephalusFurey 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.
- In utero nanoparticle delivery for site-specific genome editingRicciardi 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.
- Targeted protein unfolding uncovers a Golgi-specific transcriptional stress responseSerebrenik 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.
- Interferon-γ converts human microvascular pericytes into negative regulators of alloimmunity through induction of indoleamine 2,3-dioxygenase 1Liu 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: e97881. PMID: 29515027, PMCID: PMC5922286, DOI: 10.1172/jci.insight.97881.
- Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic LeptospiraAdhikarla 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.
- Identification of Intrinsic Axon Growth Modulators for Intact CNS Neurons after InjuryFink 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.
- The Epstein-Barr Virus Immunoevasins BCRF1 and BPLF1 Are Expressed by a Mechanism Independent of the Canonical Late Pre-initiation ComplexMcKenzie 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 deliveryBahal 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.
- De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomaliesHomsy 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 2015, 350: 1262-1266. PMID: 26785492, PMCID: PMC4890146, DOI: 10.1126/science.aac9396.
- Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani populationShahzad M, Campos J, Tariq N, Serrano C, Yousaf R, Jiménez‐Cervantes C, Yousaf S, Waryah YM, Dad HA, Blue EM, Sobreira N, López‐Giráldez F, Genomics U, Kausar T, Ali M, Waryah AM, Riazuddin S, Shaikh RS, García‐Borrón J, Ahmed ZM. Identification and functional characterization of natural human melanocortin 1 receptor mutant alleles in Pakistani population. Pigment Cell & Melanoma Research 2015, 28: 730-735. PMID: 26197705, PMCID: PMC4609612, DOI: 10.1111/pcmr.12400.
- The Genetic Basis of Mendelian Phenotypes: Discoveries, Challenges, and OpportunitiesChong JX, Buckingham KJ, Jhangiani SN, Boehm C, Sobreira N, Smith JD, Harrell TM, McMillin MJ, Wiszniewski W, Gambin T, Akdemir Z, 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, Genomics C, 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.
- Microarray analysis of neonatal rat anteroventral periventricular transcriptomes identifies the proapoptotic Cugbp2 gene as sex-specific and regulated by estradiolDel 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: 312-322. PMID: 26166732, DOI: 10.1016/j.neuroscience.2015.07.008.
- E2F8 as a Novel Therapeutic Target for Lung CancerPark 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.
- Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassaLehr 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.
- A Locus Encompassing the Epstein-Barr Virus bglf4 Kinase Regulates Expression of Genes Encoding Viral Structural ProteinsEl-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.
- The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noiseSu Z, Wang Z, López-Giráldez F, Townsend J. The impact of incorporating molecular evolutionary model into predictions of phylogenetic signal and noise. Frontiers In Ecology And Evolution 2014, 2: 11. DOI: 10.3389/fevo.2014.00011.
- 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.
- Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassaWang 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. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.
- Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic DogsThalmann 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 K, 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 2013, 342: 871-874. PMID: 24233726, DOI: 10.1126/science.1243650.
- Phylogenetic and phylogenomic overview of the PolyporalesBinder 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: 1350-1373. PMID: 23935031, DOI: 10.3852/13-003.
- Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data SetsLópez-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.
- Molecular chaperone Hsp110 rescues a vesicle transport defect produced by an ALS-associated mutant SOD1 protein in squid axoplasmSong 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: 5428-5433. PMID: 23509252, PMCID: PMC3619309, DOI: 10.1073/pnas.1303279110.
- Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecologySikhakolli 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 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.
- Sex-specific gene expression during asexual development of Neurospora crassaWang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology 2012, 49: 533-543. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.
- RBE controls microRNA164 expression to effect floral organogenesisHuang T, López-Giráldez F, Townsend JP, Irish VF. RBE controls microRNA164 expression to effect floral organogenesis. Development 2012, 139: 2161-2169. PMID: 22573623, DOI: 10.1242/dev.075069.
- Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great ApesFarré 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.
- PhyDesign: an online application for profiling phylogenetic informativenessLópez-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.
- Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS DataWang 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.
- Multi-targeted priming for genome-wide gene expression assaysAdomas 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.
- LOX: inferring Level Of eXpression from diverse methods of census sequencingZhang Z, López-Giráldez F, Townsend JP. LOX: inferring Level Of eXpression from diverse methods of census sequencing. Bioinformatics 2010, 26: 1918-1919. PMID: 20538728, PMCID: PMC2905554, DOI: 10.1093/bioinformatics/btq303.
- Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic RelationshipsTownsend JP, Lopez-Giraldez F. Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships. Systematic Biology 2010, 59: 446-457. PMID: 20547780, DOI: 10.1093/sysbio/syq025.
- First generation microarray-system for identification of primate species subject to bushmeat tradeRönn A, Andrés O, López-Giráldez F, Johnsson-Glans C, Verschoor E, Domingo-Roura X, Bruford M, Syvänen A, Bosch M. First generation microarray-system for identification of primate species subject to bushmeat trade. Endangered Species Research 2009, 9: 133-142. DOI: 10.3354/esr00191.
- The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological TraitsSchoch 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, 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: 224-239. PMID: 20525580, DOI: 10.1093/sysbio/syp020.
- Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using PhylogeniesOtto 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 Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate TreeTownsend 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: 437-447. PMID: 18696029, DOI: 10.1007/s00239-008-9142-0.
- RPS4Ygene family evolution in primatesAndrés O, Kellermann T, López-Giráldez F, Rozas J, Domingo-Roura X, Bosch M. RPS4Ygene family evolution in primates. BMC Ecology And Evolution 2008, 8: 142. PMID: 18477388, PMCID: PMC2397393, DOI: 10.1186/1471-2148-8-142.
- High Incidence of Nonslippage Mechanisms Generating Variability and Complexity in Eurasian Badger MicrosatellitesLópez-Giráldez F, Marmi J, Domingo-Roura X. High Incidence of Nonslippage Mechanisms Generating Variability and Complexity in Eurasian Badger Microsatellites. Journal Of Heredity 2007, 98: 620-628. PMID: 17728273, DOI: 10.1093/jhered/esm068.
- Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEsLópez-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.
- Mitochondrial DNA reveals a strong phylogeographic structure in the badger across EurasiaMARMI 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: 1007-1020. PMID: 16599963, DOI: 10.1111/j.1365-294x.2006.02747.x.
- Badger hair in shaving brushes comes from protected Eurasian badgersDomingo-Roura X, Marmi J, Ferrando A, López-Giráldez F, Macdonald D, Jansman H. Badger hair in shaving brushes comes from protected Eurasian badgers. Biological Conservation 2006, 128: 425-430. DOI: 10.1016/j.biocon.2005.08.013.
- Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivoresDOMINGO-ROURA X, LÓPEZ-GIRÁLDEZ F, SAEKI M, MARMI J. Phylogenetic inference and comparative evolution of a complex microsatellite and its flanking regions in carnivores. Genetics Research 2005, 85: 223-233. PMID: 16174341, DOI: 10.1017/s0016672305007512.
- Genetic distinction of American and European mink (Mustela vison and M. lutreola) and European polecat (M. putorius) hair samples by detection of a species‐specific SINE and a RFLP assayLópez‐Giráldez F, Gómez‐Moliner B, Marmi J, Domingo‐Roura X. Genetic distinction of American and European mink (Mustela vison and M. lutreola) and European polecat (M. putorius) hair samples by detection of a species‐specific SINE and a RFLP assay. Journal Of Zoology 2005, 265: 405-410. DOI: 10.1017/s0952836905006497.
- Phylogeny, evolutionary history and taxonomy of the Mustelidae based on sequences of the cytochrome b gene and a complex repetitive flanking regionMarmi J, López‐Giráldez J, Domingo‐Roura X. Phylogeny, evolutionary history and taxonomy of the Mustelidae based on sequences of the cytochrome b gene and a complex repetitive flanking region. Zoologica Scripta 2004, 33: 481-499. DOI: 10.1111/j.0300-3256.2004.00165.x.