Skip to main content
Department of Neurosciences Department of Neurosciences
  1. HOME
  2. Research
  3. Research Programs
  4. Structural Brain Defects
  5. Publications

Publications

Joseph Gleeson, M.D.

  1. CYP2U1 mutations in two Iranian patients with activity induced dystonia, motor regression and spastic paraplegia. Kariminejad A, Schöls L, Schüle R, Tonekaboni SH, Abolhassani A, Fadaee M, Rosti RO, Gleeson JG. Eur J Paediatr Neurol. 2016 Jun 2. pii: S1090-3798(16)30067-8. PMID: 27292318
  2. Molybdenum cofactor and isolated sulphite oxidase deficiencies: Clinical and molecular spectrum among Egyptian patients. Zaki MS, Selim L, El-Bassyouni HT, Isaa MY, Mahmoud I, Ismail S, Girgis M, Sadek AA, Gleeson JG, Abdel Hamid MS. Eur J Paediatr Neurol. 2016 May 30. pii: S1090-3798(16)30065-4. PMID: 27289259
  3. PYCR2 mutations cause a lethal syndrome of microcephaly and failure to thrive. Zaki MS, Bhat G, Sultan T, Issa M, Jung HJ, Dikoglu E, Selim L, Gamal I, Abdel-Hamid MS, Abdel-Salam G, Marin-Valencia I, Gleeson JG. Ann Neurol. 2016 Apr 30. PMID:
  4. Extending the mutation spectrum for Galloway-Mowat syndrome to include homozygous missense mutations in the WDR73 gene. Rosti RO, Dikoglu E, Zaki MS, Abdel-Salam G, Makhseed N, Sese JC, Musaev D, Rosti B, Harbert MJ, Jones MC, Vaux KK, Gleeson JG. Am J Med Genet A. 2016 Apr;170(4):992-8. PMID: 27001912
  5. Mutations in UNC80, Encoding Part of the UNC79-UNC80-NALCN Channel Complex, Cause Autosomal-Recessive Severe Infantile Encephalopathy. Shamseldin HE, Faqeih E, Alasmari A, Zaki MS, Gleeson JG, Alkuraya FS. Am J Hum Genet. 2016 Jan 7;98(1):210-5. PMID: 26708753
  6. TSEN54 gene-related pontocerebellar hypoplasia type 2 presenting with exaggerated startle response: report of two cases in a family. Maraş-Genç H, Uyur-Yalçın E, Rosti RÖ, Gleeson JG, Kara B. Turk J Pediatr. 2015 May-Jun;57(3):286-9. PMID: 26701950
  7. The human gene damage index as a gene-level approach to prioritizing exome variants. Itan Y, Shang L, Boisson B, Patin E, Bolze A, Moncada-Vélez M, Scott E, Ciancanelli MJ, Lafaille FG, Markle JG, Martinez-Barricarte R, de Jong SJ, Kong XF, Nitschke P, Belkadi A, Bustamante J, Puel A, Boisson-Dupuis S, Stenson PD, Gleeson JG, Cooper DN, Quintana-Murci L, Claverie JM, Zhang SY, Abel L, Casanova JL. Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13615-20. PMID: 26483451
  8. Overexpression of KLC2 due to a homozygous deletion in the non-coding region causes SPOAN syndrome. Melo US, Macedo-Souza LI, Figueiredo T, Muotri AR, Gleeson JG, Coux G, Armas P, Calcaterra NB, Kitajima JP, Amorim S, Olávio TR, Griesi-Oliveira K, Coatti GC, Rocha CR, Martins-Pinheiro M, Menck CF, Zaki MS, Kok F, Zatz M, Santos S. Hum Mol Genet. 2015 Dec 15;24(24):6877-85.  PMID: 26385635
  9. Dandy-Walker malformation, genitourinary abnormalities, and intellectual disability in two families. Zaki MS, Masri A, Gregor A, Gleeson JG, Rosti RO. Am J Med Genet A. 2015 Nov;167A(11):2503-7. PMID: 26109232
  10. Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Guemez-Gamboa A, Nguyen LN, Yang H, Zaki MS, Kara M, Ben-Omran T, Akizu N, Rosti RO, Rosti B, Scott E, Schroth J, Copeland B, Vaux KK, Cazenave-Gassiot A, Quek DQ, Wong BH, Tan BC, Wenk MR, Gunel M, Gabriel S, Chi NC, Silver DL, Gleeson JG. Nat Genet. 2015 Jul;47(7):809-13. PMID: 26005868
  11. Polo-like kinase 2 regulates angiogenic sprouting and blood vessel development. Yang H, Fang L, Zhan R, Hegarty JM, Ren J, Hsiai TK, Gleeson JG, Miller YI, Trejo J, Chi NC. Dev Biol. 2015 Aug 15;404(2):49-60. PMID: 26004360
  12. Ten new cases further delineate the syndromic intellectual disability phenotype caused by mutations in DYRK1A. Bronicki LM, Redin C, Drunat S, Piton A, Lyons M, Passemard S, Baumann C, Faivre L, Thevenon J, Rivière JB, Isidor B, Gan G, Francannet C, Willems M, Gunel M, Jones JR, Gleeson JG, Mandel JL, Stevenson RE, Friez MJ, Aylsworth AS. Eur J Hum Genet. 2015 Nov;23(11):1482-7. PMID: 25920557
  13. Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction. Akizu N, Cantagrel V, Zaki MS, Al-Gazali L, Wang X, Rosti RO, Dikoglu E, Gelot AB, Rosti B, Vaux KK, Scott EM, Silhavy JL, Schroth J, Copeland B, Schaffer AE, Gordts PL, Esko JD, Buschman MD, Field SJ, Napolitano G, Abdel-Salam GM, Ozgul RK, Sagıroglu MS, Azam M, Ismail S, Aglan M, Selim L, Mahmoud IG, Abdel-Hadi S, Badawy AE, Sadek AA, Mojahedi F, Kayserili H, Masri A, Bastaki L, Temtamy S, Müller U, Desguerre I, Casanova JL, Dursun A, Gunel M, Gabriel SB, de Lonlay P, Gleeson JG. Nat Genet. 2015 May;47(5):528-34.  PMID: 25848753
  14. Novel STAMBP mutation and additional findings in an Arabic family. Faqeih EA, Bastaki L, Rosti RO, Spencer EG, Zada AP, Saleh MA, Um K, Gleeson JG. Am J Med Genet A. 2015 Apr;167A(4):805-9. PMID: 25692795
  15. Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Mishra-Gorur K, Çağlayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüş GT, Nishimura S, Han W, Tu S, Baran B, Gümüş H, Dilber C, Zaki MS, Hossni HA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çağlar C, Çağlar Ç, Dölen D, Baranoski JF, Kumandaş S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi NC, Šestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M. Neuron. 2014 Dec 17;84(6):1226-39. PMID: 25521378
  16. Homozygous mutation of STXBP5L explains an autosomal recessive infantile-onset neurodegenerative disorder. Kumar R, Corbett MA, Smith NJ, Jolly LA, Tan C, Keating DJ, Duffield MD, Utsumi T, Moriya K, Smith KR, Hoischen A, Abbott K, Harbord MG, Compton AG, Woenig JA, Arts P, Kwint M, Wieskamp N, Gijsen S, Veltman JA, Bahlo M, Gleeson JG, Haan E, Gecz J. Hum Mol Genet. 2015 Apr 1;24(7):2000-10. PMID: 25504045
  17. Mutations in FA2H in three Arab families with a clinical spectrum of neurodegeneration and hereditary spastic paraparesis. Zaki MS, Selim L, Mansour L, Mahmoud IG, Fenstermaker AG, Gabriel SB, Gleeson JG. Clin Genet. 2015 Jul;88(1):95-7.  PMID: 25496456
  18. Biallelic truncating mutations in FMN2, encoding the actin-regulatory protein Formin 2, cause nonsyndromic autosomal-recessive intellectual disability. Law R, Dixon-Salazar T, Jerber J, Cai N, Abbasi AA, Zaki MS, Mittal K, Gabriel SB, Rafiq MA, Khan V, Nguyen M, Ali G, Copeland B, Scott E, Vasli N, Mikhailov A, Khan MN, Andrade DM, Ayaz M, Ansar M, Ayub M, Vincent JB, Gleeson JG. Am J Hum Genet. 2014 Dec 4;95(6):721-8.  PMID: 25480035
  19. Mutations in ADAR1, IFIH1, and RNASEH2B presenting as spastic paraplegia. Crow YJ, Zaki MS, Abdel-Hamid MS, Abdel-Salam G, Boespflug-Tanguy O, Cordeiro NJ, Gleeson JG, Gowrinathan NR, Laugel V, Renaldo F, Rodriguez D, Livingston JH, Rice GI. Neuropediatrics. 2014 Dec;45(6):386-93. PMID: 25243380
  20. Asparagine synthetase deficiency detected by whole exome sequencing causes congenital microcephaly, epileptic encephalopathy and psychomotor delay. Ben-Salem S, Gleeson JG, Al-Shamsi AM, Islam B, Hertecant J, Ali BR, Al-Gazali L. Metab Brain Dis. 2015 Jun;30(3):687-94.  PMID: 25227173
  21. Focal dysplasia of the cerebral cortex and infantile spasms associated with somatic 1q21.1-q44 duplication including the AKT3 gene. Conti V, Pantaleo M, Barba C, Baroni G, Mei D, Buccoliero AM, Giglio S, Giordano F, Baek ST, Gleeson JG, Guerrini R. Clin Genet. 2015 Sep;88(3):241-7.  PMID: 25091978
  22. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M. EMBO J. 2014 Sep 17;33(18):2020-39. PMID: 25063673
  23. CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration. Schaffer AE, Eggens VR, Caglayan AO, Reuter MS, Scott E, Coufal NG, Silhavy JL, Xue Y, Kayserili H, Yasuno K, Rosti RO, Abdellateef M, Caglar C, Kasher PR, Cazemier JL, Weterman MA, Cantagrel V, Cai N, Zweier C, Altunoglu U, Satkin NB, Aktar F, Tuysuz B, Yalcinkaya C, Caksen H, Bilguvar K, Fu XD, Trotta CR, Gabriel S, Reis A, Gunel M, Baas F, Gleeson JG. Cell. 2014 Apr 24;157(3):651-63. PMID: 24766810
  24. Mutations in CENPE define a novel kinetochore-centromeric mechanism for microcephalic primordial dwarfism. Mirzaa GM, Vitre B, Carpenter G, Abramowicz I, Gleeson JG, Paciorkowski AR, Cleveland DW, Dobyns WB, O'Driscoll M. Hum Genet. 2014 Aug;133(8):1023-39. PMID: 24748105 Free PMC Article
  25. Novel mutation in the fukutin gene in an Egyptian family with Fukuyama congenital muscular dystrophy and microcephaly. Ismail S, Schaffer AE, Rosti RO, Gleeson JG, Zaki MS. Gene. 2014 Apr 15;539(2):279-82. PMID: 24530477
  26. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Novarino G, Fenstermaker AG, Zaki MS, Hofree M, Silhavy JL, Heiberg AD, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al-Aama JY, Abdel-Salam GM, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben-Omran T, Mojahedi F, Mahmoud IG, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al-Allawi N, Bindu PS, Azam M, Gunel M, Caglayan A, Bilguvar K, Tolun A, Issa MY, Schroth J, Spencer EG, Rosti RO, Akizu N, Vaux KK, Johansen A, Koh AA, Megahed H, Durr A, Brice A, Stevanin G, Gabriel SB, Ideker T, Gleeson JG. Science. 2014 Jan 31;343(6170):506-11. PMID: 24482476
  27. The genetic landscape of autism spectrum disorders. Rosti RO, Sadek AA, Vaux KK, Gleeson JG. Dev Med Child Neurol. 2014 Jan;56(1):12-8.  PMID: 24116704
  28. The sacred disease: the puzzling genetics of epileptic disorders. Novarino G, Baek ST, Gleeson JG. Neuron. 2013 Oct 2;80(1):9-11. PMID: 24094099
  29. Virmid: accurate detection of somatic mutations with sample impurity inference. Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Genome Biol. 2013 Aug 29;14(8):R90. PMID: 23987214
  30. AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, Morisaki H, Sonmez FM, Celep F, Oraby A, Zaki MS, Al-Baradie R, Faqeih EA, Saleh MA, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, Morisaki T, Holmes EW, Gleeson JG. Cell. 2013 Aug 1;154(3):505-17. PMID: 23911318
  31. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. Cell Rep. 2013 Jul 25;4(2):255-61. PMID: 23871666
  32. Deletion 16p13.11 uncovers NDE1 mutations on the non-deleted homolog and extends the spectrum of severe microcephaly to include fetal brain disruption. Paciorkowski AR, Keppler-Noreuil K, Robinson L, Sullivan C, Sajan S, Christian SL, Bukshpun P, Gabriel SB, Gleeson JG, Sherr EH, Dobyns WB. Am J Med Genet A. 2013 Jul;161A(7):1523-30. PMID: 23704059
  33. Mutations in LAMB1 cause cobblestone brain malformation without muscular or ocular abnormalities. Radmanesh F, Caglayan AO, Silhavy JL, Yilmaz C, Cantagrel V, Omar T, Rosti B, Kaymakcalan H, Gabriel S, Li M, Sestan N, Bilguvar K, Dobyns WB, Zaki MS, Gunel M, Gleeson JG. Am J Hum Genet. 2013 Mar 7;92(3):468-74. PMID: 23472759
  34. Whole-exome sequencing identifies mutated c12orf57 in recessive corpus callosum hypoplasia. Akizu N, Shembesh NM, Ben-Omran T, Bastaki L, Al-Tawari A, Zaki MS, Koul R, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, da Gente G, Li J, Deardorff MA, Conlin LK, Horton MA, Zackai EH, Sherr EH, Gleeson JG. Am J Hum Genet. 2013 Mar 7;92(3):392-400. PMID: 23453666
  35. Alteration of fatty-acid-metabolizing enzymes affects mitochondrial form and function in hereditary spastic paraplegia. Tesson C, Nawara M, Salih MA, Rossignol R, Zaki MS, Al Balwi M, Schule R, Mignot C, Obre E, Bouhouche A, Santorelli FM, Durand CM, Oteyza AC, El-Hachimi KH, Al Drees A, Bouslam N, Lamari F, Elmalik SA, Kabiraj MM, Seidahmed MZ, Esteves T, Gaussen M, Monin ML, Gyapay G, Lechner D, Gonzalez M, Depienne C, Mochel F, Lavie J, Schols L, Lacombe D, Yahyaoui M, Al Abdulkareem I, Zuchner S, Yamashita A, Benomar A, Goizet C, Durr A, Gleeson JG, Darios F, Brice A, Stevanin G. Am J Hum Genet. 2012 Dec 7;91(6):1051-64. PMID: 23176821
  36. A homozygous IER3IP1 mutation causes microcephaly with simplified gyral pattern, epilepsy, and permanent neonatal diabetes syndrome (MEDS). Abdel-Salam GM, Schaffer AE, Zaki MS, Dixon-Salazar T, Mostafa IS, Afifi HH, Gleeson JG. Am J Med Genet A. 2012 Nov;158A(11):2788-96. PMID: 22991235
  37. A missense founder mutation in VLDLR is associated with Dysequilibrium Syndrome without quadrupedal locomotion. Ali BR, Silhavy JL, Gleeson MJ, Gleeson JG, Al-Gazali L. BMC Med Genet. 2012 Sep 14;13:80. PMID: 22973972
  38. Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Novarino G, El-Fishawy P, Kayserili H, Meguid NA, Scott EM, Schroth J, Silhavy JL, Kara M, Khalil RO, Ben-Omran T, Ercan-Sencicek AG, Hashish AF, Sanders SJ, Gupta AR, Hashem HS, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris RA, State MW, Gleeson JG. Science. 2012 Oct 19;338(6105):394-7. PMID: 22956686
  39. Mild paroxysmal kinesigenic dyskinesia caused by PRRT2 missense mutation with reduced penetrance. Friedman J, Olvera J, Silhavy JL, Gabriel SB, Gleeson JG. Neurology. 2012 Aug 28;79(9):946-8. PMID: 22895590
  40. Neurodevelopment and disease. Gleeson JG, Polleux F. Curr Opin Neurobiol. 2012 Oct;22(5):735-6. PMID: 22889697
  41. Diencephalic-mesencephalic junction dysplasia: a novel recessive brain malformation. Zaki MS, Saleem SN, Dobyns WB, Barkovich AJ, Bartsch H, Dale AM, Ashtari M, Akizu N, Gleeson JG, Grijalvo-Perez AM. Brain. 2012 Aug;135(Pt 8):2416-27. PMID: 22822038
  42. Exome sequencing can improve diagnosis and alter patient management. Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. Sci Transl Med. 2012 Jun 13;4(138):138ra78.  PMID: 22700954
  43. A mutation in KIF7 is responsible for the autosomal recessive syndrome of macrocephaly, multiple epiphyseal dysplasia and distinctive facial appearance. Ali BR, Silhavy JL, Akawi NA, Gleeson JG, Al-Gazali L. Orphanet J Rare Dis. 2012 May 15;7:27. PMID: 22587682
  44. Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz-like syndrome. Martinez FJ, Lee JH, Lee JE, Blanco S, Nickerson E, Gabriel S, Frye M, Al-Gazali L, Gleeson JG. J Med Genet. 2012 Jun;49(6):380-5. PMID: 22577224
  45. The very low density lipoprotein receptor-associated pontocerebellar hypoplasia and dysmorphic features in three Turkish patients. Sonmez FM, Gleeson JG, Celep F, Kul S. J Child Neurol. 2013 Mar;28(3):379-83. PMID: 22532556
  46. Mutations in the glycosylphosphatidylinositol gene PIGL cause CHIME syndrome. Ng BG, Hackmann K, Jones MA, Eroshkin AM, He P, Wiliams R, Bhide S, Cantagrel V, Gleeson JG, Paller AS, Schnur RE, Tinschert S, Zunich J, Hegde MR, Freeze HH. Am J Hum Genet. 2012 Apr 6;90(4):685-8. doi: 10.1016/j.ajhg.2012.02.010. Epub 2012 Mar 22. PMID: 22444671
  47. New recessive syndrome of microcephaly, cerebellar hypoplasia, and congenital heart conduction defect. Zaki MS, Salam GM, Saleem SN, Dobyns WB, Issa MY, Sattar S, Gleeson JG. Am J Med Genet A. 2011 Dec;155A(12):3035-41. PMID: 22002884
  48. Faulty initiation of proteoglycan synthesis causes cardiac and joint defects. Baasanjav S, Al-Gazali L, Hashiguchi T, Mizumoto S, Fischer B, Horn D, Seelow D, Ali BR, Aziz SA, Langer R, Saleh AA, Becker C, Nürnberg G, Cantagrel V, Gleeson JG, Gomez D, Michel JB, Stricker S, Lindner TH, Nürnberg P, Sugahara K, Mundlos S, Hoffmann K. Am J Hum Genet. 2011 Jul 15;89(1):15-27. PMID: 21763480
  49. Function follows form: understanding brain function from a genetic perspective. Marín O, Gleeson JG. Curr Opin Genet Dev. 2011 Jun;21(3):237-9. PMID: 21536429
  50. Distinguishing 3 classes of corpus callosal abnormalities in consanguineous families. Hanna RM, Marsh SE, Swistun D, Al-Gazali L, Zaki MS, Abdel-Salam GM, Al-Tawari A, Bastaki L, Kayserili H, Rajab A, Boglárka B, Dietrich RB, Dobyns WB, Truwit CL, Sattar S, Chuang NA, Sherr EH, Gleeson JG. Neurology. 2011 Jan 25;76(4):373-82. PMID: 21263138
  51. SRD5A3 is required for converting polyprenol to dolichol and is mutated in a congenital glycosylation disorder. Cantagrel V, Lefeber DJ, Ng BG, Guan Z, Silhavy JL, Bielas SL, Lehle L, Hombauer H, Adamowicz M, Swiezewska E, De Brouwer AP, Blümel P, Sykut-Cegielska J, Houliston S, Swistun D, Ali BR, Dobyns WB, Babovic-Vuksanovic D, van Bokhoven H, Wevers RA, Raetz CR, Freeze HH, Morava E, Al-Gazali L, Gleeson JG. Cell. 2010 Jul 23;142(2):203-17. PMID: 20637498

Ulrich Mueller, Ph.D.

  1. Cadherin 2/4 signaling via PTP1B and catenins is crucial for nucleokinesis during radial neuronal migration in the neocortex. Martinez-Garay I, Gil-Sanz C, Franco SJ, Espinosa A, Molnár Z, Mueller U. Development. 2016 Jun 15;143(12):2121-34.  PMID: 27151949
  2. A New Chapter in the Life of Cajal's Short-Axon Neurons: Separation of Interneuron Siblings after Birth. Gil-Sanz C, Müller U. Neuron. 2015 Sep 2;87(5):909-11.  PMID: 26335637
  3. Lineage Tracing Using Cux2-Cre and Cux2-CreERT2 Mice. Gil-Sanz C, Espinosa A, Fregoso SP, Bluske KK, Cunningham CL, Martinez-Garay I, Zeng H, Franco SJ, Müller U. Neuron. 2015 May 20;86(4):1091-9. PMID: 25996136
  4. Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction. Akizu N, Cantagrel V, Zaki MS, Al-Gazali L, Wang X, Rosti RO, Dikoglu E, Gelot AB, Rosti B, Vaux KK, Scott EM, Silhavy JL, Schroth J, Copeland B, Schaffer AE, Gordts PL, Esko JD, Buschman MD, Field SJ, Napolitano G, Abdel-Salam GM, Ozgul RK, Sagıroglu MS, Azam M, Ismail S, Aglan M, Selim L, Mahmoud IG, Abdel-Hadi S, Badawy AE, Sadek AA, Mojahedi F, Kayserili H, Masri A, Bastaki L, Temtamy S, Müller U, Desguerre I, Casanova JL, Dursun A, Gunel M, Gabriel SB, de Lonlay P, Gleeson JG. Nat Genet. 2015 May;47(5):528-34. PMID: 25848753
  5. Specification of excitatory neurons in the developing cerebral cortex: progenitor diversity and environmental influences. Costa MR, Müller U. Front Cell Neurosci. 2015 Jan 12;8:449. PMID: 25628534
  6. MACF1 regulates the migration of pyramidal neurons via microtubule dynamics and GSK-3 signaling. Ka M, Jung EM, Mueller U, Kim WY. Dev Biol. 2014 Nov 1;395(1):4-18. PMID: 25224226
  7. Proliferative defects and formation of a double cortex in mice lacking Mltt4 and Cdh2 in the dorsal telencephalon. Gil-Sanz C, Landeira B, Ramos C, Costa MR, Müller U. J Neurosci. 2014 Aug 6;34(32):10475-87. PMID: 25100583
  8. Lineage origins of GABAergic versus glutamatergic neurons in the neocortex. Marín O, Müller U. Curr Opin Neurobiol. 2014 Jun;26:132-41. PMID: 24549207
  9. Dab1 is required for synaptic plasticity and associative learning. Trotter J, Lee GH, Kazdoba TM, Crowell B, Domogauer J, Mahoney HM, Franco SJ, Müller U, Weeber EJ, D'Arcangelo G. J Neurosci. 2013 Sep 25;33(39):15652-68. PMID: 24068831
  10. Cajal-Retzius cells instruct neuronal migration by coincidence signaling between secreted and contact-dependent guidance cues. Gil-Sanz C, Franco SJ, Martinez-Garay I, Espinosa A, Harkins-Perry S, Müller U. Neuron. 2013 Aug 7;79(3):461-77.  PMID: 23931996
  11. Shaping our minds: stem and progenitor cell diversity in the mammalian neocortex. Franco SJ, Müller U. Neuron. 2013 Jan 9;77(1):19-34. PMID: 23312513
  12. Fate-restricted neural progenitors in the mammalian cerebral cortex. Franco SJ, Gil-Sanz C, Martinez-Garay I, Espinosa A, Harkins-Perry SR, Ramos C, Müller U. Science. 2012 Aug 10;337(6095):746-9. PMID: 22879516
  13. Extracellular matrix functions during neuronal migration and lamination in the mammalian central nervous system. Franco SJ, Müller U. Dev Neurobiol. 2011 Nov;71(11):889-900. PMID: 21739613
  14. Reelin regulates cadherin function via Dab1/Rap1 to control neuronal migration and lamination in the neocortex. Franco SJ, Martinez-Garay I, Gil-Sanz C, Harkins-Perry SR, Müller U. Neuron. 2011 Feb 10;69(3):482-97. PMID: 21315259
  15. Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis. Arnold CN, Xia Y, Lin P, Ross C, Schwander M, Smart NG, Müller U, Beutler B. Genetics. 2011 Mar;187(3):633-41. PMID: 21196518
  16. Extracellular matrix: functions in the nervous system. Barros CS, Franco SJ, Müller U. Cold Spring Harb Perspect Biol. 2011 Jan 1;3(1):a005108. PMID: 21123393

Neil Chi, M.D., Ph.D.

  1. Coordinating cardiomyocyte interactions to direct ventricular chamber morphogenesis. Han P, Bloomekatz J, Ren J, Zhang R, Grinstein JD, Zhao L, Burns CG, Burns CE, Anderson RM, Chi NC. Nature. 2016 Jun 29;534(7609):700-4. PMID: 27357797
  2. 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation. Lee J, Fei P, Packard RR, Kang H, Xu H, Baek KI, Jen N, Chen J, Yen H, Kuo CC, Chi NC, Ho CM, Li R, Hsiai TK. J Clin Invest. 2016 May 2;126(5):1679-90. doi: 10.1172/JCI83496. Epub 2016 Mar 28.
  3. Myocardium and BMP signaling are required for endocardial differentiation. Palencia-Desai S, Rost MS, Schumacher JA, Ton QV, Craig MP, Baltrunaite K, Koenig AL, Wang J, Poss KD, Chi NC, Stainier DY, Sumanas S. Development. 2015 Jul 1;142(13):2304-15. PMID: 26092845
  4. Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Guemez-Gamboa A, Nguyen LN, Yang H, Zaki MS, Kara M, Ben-Omran T, Akizu N, Rosti RO, Rosti B, Scott E, Schroth J, Copeland B, Vaux KK, Cazenave-Gassiot A, Quek DQ, Wong BH, Tan BC, Wenk MR, Gunel M, Gabriel S, Chi NC, Silver DL, Gleeson JG. Nat Genet. 2015 Jul;47(7):809-13.  PMID: 26005868
  5. Polo-like kinase 2 regulates angiogenic sprouting and blood vessel development. Yang H, Fang L, Zhan R, Hegarty JM, Ren J, Hsiai TK, Gleeson JG, Miller YI, Trejo J, Chi NC. Dev Biol. 2015 Aug 15;404(2):49-60.  PMID: 26004360
  6. Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED. Stem Cells. 2015 Jul;33(7):2343-50. PMID: 25826782
  7. Notch signaling regulates venous arterialization during zebrafish fin regeneration. Kametani Y, Chi NC, Stainier DY, Takada S. Genes Cells. 2015 May;20(5):427-38. PMID: 25810153
  8. Integrative analysis of haplotype-resolved epigenomes across human tissues. Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. Nature. 2015 Feb 19;518(7539):350-4. PMID: 25693566
  9. Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Mishra-Gorur K, Çağlayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüş GT, Nishimura S, Han W, Tu S, Baran B, Gümüş H, Dilber C, Zaki MS, Hossni HA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çağlar C, Çağlar Ç, Dölen D, Baranoski JF, Kumandaş S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi NC, Šestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M. Neuron. 2014 Dec 17;84(6):1226-39. PMID: 25521378
  10. The atypical Rho GTPase, RhoU, regulates cell-adhesion molecules during cardiac morphogenesis. Dickover M, Hegarty JM, Ly K, Lopez D, Yang H, Zhang R, Tedeschi N, Hsiai TK, Chi NC. Dev Biol. 2014 May 15;389(2):182-91. PMID: 24607366
  11. Zebrafish cardiac injury and regeneration models: a noninvasive and invasive in vivo model of cardiac regeneration. Dickover MS, Zhang R, Han P, Chi NC. Methods Mol Biol. 2013;1037:463-73. PMID: 24029953
  12. Efficient generation of human iPSCs by a synthetic self-replicative RNA. Yoshioka N, Gros E, Li HR, Kumar S, Deacon DC, Maron C, Muotri AR, Chi NC, Fu XD, Yu BD, Dowdy SF. Cell Stem Cell. 2013 Aug 1;13(2):246-54. PMID: 23910086
  13. In vivo cardiac reprogramming contributes to zebrafish heart regeneration. Zhang R, Han P, Yang H, Ouyang K, Lee D, Lin YF, Ocorr K, Kang G, Chen J, Stainier DY, Yelon D, Chi NC. Nature. 2013 Jun 27;498(7455):497-501. PMID: 23783515
  14. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. Cell. 2013 May 23;153(5):1134-48. PMID: 23664764
  15. UBIAD1-mediated vitamin K2 synthesis is required for vascular endothelial cell survival and development. Hegarty JM, Yang H, Chi NC. Development. 2013 Apr;140(8):1713-9. PMID: 23533172
  16. Zebrafish models in cardiac development and congenital heart birth defects. Tu S, Chi NC. Differentiation. 2012 Jul;84(1):4-16. PMID: 22704690
  17. Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis. Amigo JD, Yu M, Troadec MB, Gwynn B, Cooney JD, Lambert AJ, Chi NC, Weiss MJ, Peters LL, Kaplan J, Cantor AB, Paw BH. Mol Cell Biol. 2011 Apr;31(7):1344-56. PMID: 21248200

Kelly Frazer, Ph.D.

  1. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal. Holm F, Hellqvist E, Mason CN, Ali SA, Delos-Santos N, Barrett CL, Chun HJ, Minden MD, Moore RA, Marra MA, Runza V, Frazer KA, Sadarangani A, Jamieson CH. Proc Natl Acad Sci U S A. 2015 Dec 15;112(50):15444-9. PMID: 26621726
  2. Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED. Stem Cells. 2015 Jul;33(7):2343-50.  PMID: 25826782
  3. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Smith EN, Jepsen K, Khosroheidari M, Rassenti LZ, D'Antonio M, Ghia EM, Carson DA, Jamieson CH, Kipps TJ, Frazer KA. Genome Biol. 2014 Aug 7;15(8):420. PMID: 25103687
  4. MiningABs: mining associated biomarkers across multi-connected gene expression datasets. Cheng CP, DeBoever C, Frazer KA, Liu YC, Tseng VS. BMC Bioinformatics. 2014 Jun 8;15:173. doi: 10.1186/1471-2105-15-173. PMID: 24909518
  5. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. Carson AR, Smith EN, Matsui H, Brækkan SK, Jepsen K, Hansen JB, Frazer KA. BMC Bioinformatics. 2014 May 2;15:125. PMID: 24884706
  6. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Genome Biol. 2014 Feb 20;15(2):R36. PMID: 24555826
  7. Genetic ancestry of participants in the National Children's Study. Smith EN, Jepsen K, Arias AD, Shepard PJ, Chambers CD, Frazer KA. Genome Biol. 2014 Feb 3;15(2):R22. PMID: 24490717
  8. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Am J Hum Genet. 2013 Sep 5;93(3):452-62. PMID: 23954164
  9. Implementing genomic medicine in the clinic: the future is here. Manolio TA, Chisholm RL, Ozenberger B, Roden DM, Williams MS, Wilson R, Bick D, Bottinger EP, Brilliant MH, Eng C, Frazer KA, Korf B, Ledbetter DH, Lupski JR, Marsh C, Mrazek D, Murray MF, O'Donnell PH, Rader DJ, Relling MV, Shuldiner AR, Valle D, Weinshilboum R, Green ED, Ginsburg GS. Genet Med. 2013 Apr;15(4):258-67. PMID: 23306799
  10. Decoding the human genome. Frazer KA. Genome Res. 2012 Sep;22(9):1599-601.  PMID: 22955971

Vineet Bafna, Ph.D.

  1. InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Patel A, Edge P, Selvaraj S, Bansal V, Bafna V. Nucleic Acids Res. 2016 Apr 21. pii: gkw281. PMID: 27105843
  2. A global reference for human genetic variation. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. Nature. 2015 Oct 1;526(7571):68-74. PMID: 26432245
  3. Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. PLoS Genet. 2015 Sep 24;11(9):e1005527. PMID: 26402243
  4. Reconstructing breakage fusion bridge architectures using noisy copy numbers. Zakov S, Bafna V. J Comput Biol. 2015 Jun;22(6):577-94. PMID: 26020441
  5. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Mol Cell Proteomics. 2014 Nov;13(11):3184-98. PMID: 25060758
  6. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. Genome Biol. 2014 Jun 30;15(6):R88.  PMID: 24980144
  7. Inferring gene ontologies from pairwise similarity data. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Bioinformatics. 2014 Jun 15;30(12):i34-42. PMID: 24932003
  8. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Am J Hum Genet. 2013 Sep 5;93(3):452-62. PMID: 23954164
  9. Learning natural selection from the site frequency spectrum. Ronen R, Udpa N, Halperin E, Bafna V. Genetics. 2013 Sep;195(1):181-93. PMID: 23770700
  10. Evaluating genome architecture of a complex region via generalized bipartite matching. Lo C, Kim S, Zakov S, Bafna V. BMC Bioinformatics. 2013;14 Suppl 5:S13. PMID: 23734567
  11. Using Genome Query Language to uncover genetic variation. Kozanitis C, Heiberg A, Varghese G, Bafna V. Bioinformatics. 2014 Jan 1;30(1):1-8. PMID: 23751181
  12. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Kim S, Jeong K, Bafna V. Bioinformatics. 2013 Apr 15;29(8):1076-7.  PMID: 23413434
  13. Exome sequencing can improve diagnosis and alter patient management. Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. Sci Transl Med. 2012 Jun 13;4(138):138ra78. PMID: 22700954
  14. iDASH: integrating data for analysis, anonymization, and sharing. Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, Kim H, Kim J, Matheny ME, Resnic FS, Vinterbo SA; iDASH team. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):196-201. PMID: 22081224
  15. The variant call format and VCFtools. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Bioinformatics. 2011 Aug 1;27(15):2156-8. PMID: 21653522