Wyeth Wasserman Publications

Please click here for Dr. Wasserman’s Google Scholar page.

  1. Ye, XC, van der Lee, R, Wasserman, WW, Causes Study,, Friedman, JM, Lehman, A et al.. Strabismus in Children With Intellectual Disability: Part of a Broader Motor Control Phenotype?. Pediatr. Neurol. 2019; :. doi: 10.1016/j.pediatrneurol.2019.04.002. PubMed PMID:31492586 .
  2. van Karnebeek, CDM, Ramos, RJ, Wen, XY, Tarailo-Graovac, M, Gleeson, JG, Skrypnyk, C et al.. Bi-allelic GOT2 Mutations Cause a Treatable Malate-Aspartate Shuttle-Related Encephalopathy. Am. J. Hum. Genet. 2019;105 (3):534-548. doi: 10.1016/j.ajhg.2019.07.015. PubMed PMID:31422819 PubMed Central PMC6732527.
  3. Puente-Santamaria, L, Wasserman, WW, Del Peso, L. TFEA.ChIP: A tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets. Bioinformatics. 2019; :. doi: 10.1093/bioinformatics/btz573. PubMed PMID:31347689 .
  4. Milner, AA, Fordyce, JAM, MacPhail-Bartley, I, Wasserman, W, Milner, V, Tutunnikov, I et al.. Controlled Enantioselective Orientation of Chiral Molecules with an Optical Centrifuge. Phys. Rev. Lett. 2019;122 (22):223201. doi: 10.1103/PhysRevLett.122.223201. PubMed PMID:31283279 .
  5. van Kuilenburg, ABP, Tarailo-Graovac, M, Richmond, PA, Drögemöller, BI, Pouladi, MA, Leen, R et al.. Glutaminase Deficiency Caused by Short Tandem Repeat Expansion in GLS. N. Engl. J. Med. 2019;380 (15):1433-1441. doi: 10.1056/NEJMoa1806627. PubMed PMID:30970188 .
  6. Ye, XC, van der Lee, R, Wasserman, WW. Curation and bioinformatic analysis of strabismus genes supports functional heterogeneity and proposes candidate genes with connections to RASopathies. Gene. 2019;697 :213-226. doi: 10.1016/j.gene.2019.02.020. PubMed PMID:30772522 .
  7. Korecki, AJ, Hickmott, JW, Lam, SL, Dreolini, L, Mathelier, A, Baker, O et al.. Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain, Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele. Genetics. 2019;211 (4):1155-1177. doi: 10.1534/genetics.119.301984. PubMed PMID:30765420 PubMed Central PMC6456315.
  8. Johnstone, DL, Al-Shekaili, HH, Tarailo-Graovac, M, Wolf, NI, Ivy, AS, Demarest, S et al.. PLPHP deficiency: clinical, genetic, biochemical, and mechanistic insights. Brain. 2019;142 (3):542-559. doi: 10.1093/brain/awy346. PubMed PMID:30668673 PubMed Central PMC6391652.
  9. Wen, XY, Tarailo-Graovac, M, Brand-Arzamendi, K, Willems, A, Rakic, B, Huijben, K et al.. Sialic acid catabolism by N-acetylneuraminate pyruvate lyase is essential for muscle function. JCI Insight. 2018;3 (24):. doi: 10.1172/jci.insight.122373. PubMed PMID:30568043 PubMed Central PMC6338320.
  10. Matthews, AM, Blydt-Hansen, I, Al-Jabri, B, Andersen, J, Tarailo-Graovac, M, Price, M et al.. Atypical cerebral palsy: genomics analysis enables precision medicine. Genet. Med. 2019;21 (7):1621-1628. doi: 10.1038/s41436-018-0376-y. PubMed PMID:30542205 .
  11. Shi, W, Fornes, O, Wasserman, WW. Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. Bioinformatics. 2019;35 (15):2610-2617. doi: 10.1093/bioinformatics/bty992. PubMed PMID:30541050 PubMed Central PMC6662294.
  12. Lee, JJY, van Karnebeek, CDM, Wasserman, WW. Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics. J Am Med Inform Assoc. 2019;26 (2):124-133. doi: 10.1093/jamia/ocy153. PubMed PMID:30535356 PubMed Central PMC6339516.
  13. De Souza, RAG, Kosior, N, Thomson, SB, Mathelier, A, Zhang, AW, Bečanović, K et al.. Computational Analysis of Transcriptional Regulation Sites at the HTT Gene Locus. J Huntingtons Dis. 2018;7 (3):223-237. doi: 10.3233/JHD-170272. PubMed PMID:30103339 .
  14. Simpson, EM, Korecki, AJ, Fornes, O, McGill, TJ, Cueva-Vargas, JL, Agostinone, J et al.. New MiniPromoter Ple345 (NEFL) Drives Strong and Specific Expression in Retinal Ganglion Cells of Mouse and Primate Retina. Hum. Gene Ther. 2019;30 (3):257-272. doi: 10.1089/hum.2018.118. PubMed PMID:30062914 PubMed Central PMC6437624.
  15. Fornes, O, Gheorghe, M, Richmond, PA, Arenillas, DJ, Wasserman, WW, Mathelier, A et al.. MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations. Sci Data. 2018;5 :180141. doi: 10.1038/sdata.2018.141. PubMed PMID:30040077 PubMed Central PMC6057437.
  16. Colineau, L, Lambertz, U, Fornes, O, Wasserman, WW, Reiner, NE. c-Myc is a novel Leishmania virulence factor by proxy that targets the host miRNA system and is essential for survival in human macrophages. J. Biol. Chem. 2018;293 (33):12805-12819. doi: 10.1074/jbc.RA118.002462. PubMed PMID:29934305 PubMed Central PMC6102154.
  17. Lecellier, CH, Wasserman, WW, Mathelier, A. Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response. Genetics. 2018;209 (4):1055-1071. doi: 10.1534/genetics.118.301116. PubMed PMID:29871881 PubMed Central PMC6063234.
  18. Li, Y, Shi, W, Wasserman, WW. Genome-wide prediction of cis-regulatory regions using supervised deep learning methods. BMC Bioinformatics. 2018;19 (1):202. doi: 10.1186/s12859-018-2187-1. PubMed PMID:29855387 PubMed Central PMC5984344.
  19. Horvath, GA, Zhao, Y, Tarailo-Graovac, M, Boelman, C, Gill, H, Shyr, C et al.. Gain-of-function KCNJ6 Mutation in a Severe Hyperkinetic Movement Disorder Phenotype. Neuroscience. 2018;384 :152-164. doi: 10.1016/j.neuroscience.2018.05.031. PubMed PMID:29852244 PubMed Central PMC6679957.
  20. Zhang, AW, McPherson, A, Milne, K, Kroeger, DR, Hamilton, PT, Miranda, A et al.. Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell. 2018;173 (7):1755-1769.e22. doi: 10.1016/j.cell.2018.03.073. PubMed PMID:29754820 .
  21. Graham, E, Lee, J, Price, M, Tarailo-Graovac, M, Matthews, A, Engelke, U et al.. Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review. J. Inherit. Metab. Dis. 2018;41 (3):435-445. doi: 10.1007/s10545-018-0139-6. PubMed PMID:29721916 PubMed Central PMC5959954.
  22. van Kuilenburg, ABP, Tarailo-Graovac, M, Meijer, J, Drogemoller, B, Vockley, J, Maurer, D et al.. Genome sequencing reveals a novel genetic mechanism underlying dihydropyrimidine dehydrogenase deficiency: A novel missense variant c.1700G>A and a large intragenic inversion in DPYD spanning intron 8 to intron 12. Hum. Mutat. 2018;39 (7):947-953. doi: 10.1002/humu.23538. PubMed PMID:29691939 .
  23. van Karnebeek, CDM, Wortmann, SB, Tarailo-Graovac, M, Langeveld, M, Ferreira, CR, van de Kamp, JM et al.. The role of the clinician in the multi-omics era: are you ready?. J. Inherit. Metab. Dis. 2018;41 (3):571-582. doi: 10.1007/s10545-017-0128-1. PubMed PMID:29362952 PubMed Central PMC5959952.
  24. Lee, JJY, Gottlieb, MM, Lever, J, Jones, SJM, Blau, N, van Karnebeek, CDM et al.. Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. J. Inherit. Metab. Dis. 2018;41 (3):555-562. doi: 10.1007/s10545-017-0125-4. PubMed PMID:29340838 PubMed Central PMC5959948.
  25. O'Byrne, JJ, Tarailo-Graovac, M, Ghani, A, Champion, M, Deshpande, C, Dursun, A et al.. The genotypic and phenotypic spectrum of MTO1 deficiency. Mol. Genet. Metab. 2018;123 (1):28-42. doi: 10.1016/j.ymgme.2017.11.003. PubMed PMID:29331171 PubMed Central PMC5780301.
  26. Horvath, GA, Tarailo-Graovac, M, Bartel, T, Race, S, Van Allen, MI, Blydt-Hansen, I et al.. Improvement of Self-Injury With Dopamine and Serotonin Replacement Therapy in a Patient With a Hemizygous PAK3 Mutation: A New Therapeutic Strategy for Neuropsychiatric Features of an Intellectual Disability Syndrome. J. Child Neurol. 2018;33 (1):106-113. doi: 10.1177/0883073817740443. PubMed PMID:29246092 .
  27. Shyr, C, Tarailo-Graovac, M, Gottlieb, M, Lee, JJ, van Karnebeek, C, Wasserman, WW et al.. Correction to: FLAGS, frequently mutated genes in public exomes. BMC Med Genomics. 2017;10 (1):69. doi: 10.1186/s12920-017-0309-7. PubMed PMID:29187224 PubMed Central PMC5706417.
  28. Khan, A, Fornes, O, Stigliani, A, Gheorghe, M, Castro-Mondragon, JA, van der Lee, R et al.. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018;46 (D1):D1284. doi: 10.1093/nar/gkx1188. PubMed PMID:29161433 PubMed Central PMC5753202.
  29. Khan, A, Fornes, O, Stigliani, A, Gheorghe, M, Castro-Mondragon, JA, van der Lee, R et al.. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 2018;46 (D1):D260-D266. doi: 10.1093/nar/gkx1126. PubMed PMID:29140473 PubMed Central PMC5753243.
  30. Tiana, M, Acosta-Iborra, B, Puente-Santamaría, L, Hernansanz-Agustin, P, Worsley-Hunt, R, Masson, N et al.. The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. Nucleic Acids Res. 2018;46 (1):120-133. doi: 10.1093/nar/gkx951. PubMed PMID:29059365 PubMed Central PMC5758878.
  31. Zarate, YA, Steinraths, M, Matthews, A, Smith, WE, Sun, A, Wilson, LC et al.. Bone health and SATB2-associated syndrome. Clin. Genet. 2018;93 (3):588-594. doi: 10.1111/cge.13121. PubMed PMID:28787087 .
  32. Matthews, AM, Tarailo-Graovac, M, Price, EM, Blydt-Hansen, I, Ghani, A, Drögemöller, BI et al.. A de novo mosaic mutation in SPAST with two novel alternative alleles and chromosomal copy number variant in a boy with spastic paraplegia and autism spectrum disorder. Eur J Med Genet. 2017;60 (10):548-552. doi: 10.1016/j.ejmg.2017.07.015. PubMed PMID:28778789 .
  33. Lee, JJY, Wasserman, WW, Hoffmann, GF, van Karnebeek, CDM, Blau, N. Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. Genet. Med. 2018;20 (1):151-158. doi: 10.1038/gim.2017.108. PubMed PMID:28726811 PubMed Central PMC5763153.
  34. van Karnebeek, CDM, Bonafé, L, Wen, XY, Tarailo-Graovac, M, Balzano, S, Royer-Bertrand, B et al.. Corrigendum: NANS-mediated synthesis of sialic acid is required for brain and skeletal development. Nat. Genet. 2017;49 (6):969. doi: 10.1038/ng0617-969a. PubMed PMID:28546570 .
  35. Lee, JJY, van Karnebeek, CDM, Drögemoller, B, Shyr, C, Tarailo-Graovac, M, Eydoux, P et al.. Further Validation of the SIGMAR1 c.151+1G>T Mutation as Cause of Distal Hereditary Motor Neuropathy. Child Neurol Open. ;3 :2329048X16669912. doi: 10.1177/2329048X16669912. PubMed PMID:28503617 PubMed Central PMC5417346.
  36. Tarailo-Graovac, M, Zhu, JYA, Matthews, A, van Karnebeek, CDM, Wasserman, WW. Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders. Genet. Med. 2017;19 (12):1300-1308. doi: 10.1038/gim.2017.50. PubMed PMID:28471432 PubMed Central PMC5729344.
  37. Coe, RR, McKinnon, ML, Tarailo-Graovac, M, Ross, CJ, Wasserman, WW, Friedman, JM et al.. A case of splenomegaly in CBL syndrome. Eur J Med Genet. 2017;60 (7):374-379. doi: 10.1016/j.ejmg.2017.04.009. PubMed PMID:28414188 .
  38. Tarailo-Graovac, M, Wasserman, WW, Van Karnebeek, CD. Impact of next-generation sequencing on diagnosis and management of neurometabolic disorders: current advances and future perspectives. Expert Rev. Mol. Diagn. 2017;17 (4):307-309. doi: 10.1080/14737159.2017.1293527. PubMed PMID:28277145 .
  39. Seid-Karbasi, P, Ye, XC, Zhang, AW, Gladish, N, Cheng, SY, Rothe, K et al.. CuboCube: Student creation of a cancer genetics e-textbook using open-access software for social learning. PLoS Biol. 2017;15 (3):e2001192. doi: 10.1371/journal.pbio.2001192. PubMed PMID:28267757 PubMed Central PMC5340349.
  40. Armstrong, L, Tarailo-Graovac, M, Sinclair, G, Seath, KI, Wasserman, WW, Ross, CJ et al.. A girl with developmental delay, ataxia, cranial nerve palsies, severe respiratory problems in infancy-Expanding NDST1 syndrome. Am. J. Med. Genet. A. 2017;173 (3):712-715. doi: 10.1002/ajmg.a.37621. PubMed PMID:28211985 .
  41. Tarailo-Graovac, M, Drögemöller, BI, Wasserman, WW, Ross, CJ, van den Ouweland, AM, Darin, N et al.. Identification of a large intronic transposal insertion in SLC17A5 causing sialic acid storage disease. Orphanet J Rare Dis. 2017;12 (1):28. doi: 10.1186/s13023-017-0584-6. PubMed PMID:28187749 PubMed Central PMC5303239.
  42. Bourne, SC, Townsend, KN, Shyr, C, Matthews, A, Lear, SA, Attariwala, R et al.. Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novo OPA3 mutation. Cold Spring Harb Mol Case Stud. 2017;3 (1):a001156. doi: 10.1101/mcs.a001156. PubMed PMID:28050599 PubMed Central PMC5171695.
  43. Chen, CY, Shi, W, Balaton, BP, Matthews, AM, Li, Y, Arenillas, DJ et al.. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses. Sci Rep. 2016;6 :37324. doi: 10.1038/srep37324. PubMed PMID:27857184 PubMed Central PMC5114649.
  44. Roche, O, Deguiz, ML, Tiana, M, Galiana-Ribote, C, Martinez-Alcazar, D, Rey-Serra, C et al.. Identification of non-coding genetic variants in samples from hypoxemic respiratory disease patients that affect the transcriptional response to hypoxia. Nucleic Acids Res. 2016;44 (19):9315-9330. doi: 10.1093/nar/gkw811. PubMed PMID:27625398 PubMed Central PMC5100585.
  45. Hickmott, JW, Chen, CY, Arenillas, DJ, Korecki, AJ, Lam, SL, Molday, LL et al.. PAX6 MiniPromoters drive restricted expression from rAAV in the adult mouse retina. Mol Ther Methods Clin Dev. 2016;3 :16051. doi: 10.1038/mtm.2016.51. PubMed PMID:27556059 PubMed Central PMC4980111.
  46. Mathelier, A, Xin, B, Chiu, TP, Yang, L, Rohs, R, Wasserman, WW et al.. DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. Cell Syst. 2016;3 (3):278-286.e4. doi: 10.1016/j.cels.2016.07.001. PubMed PMID:27546793 PubMed Central PMC5042832.
  47. Shi, W, Fornes, O, Mathelier, A, Wasserman, WW. Evaluating the impact of single nucleotide variants on transcription factor binding. Nucleic Acids Res. 2016;44 (21):10106-10116. doi: 10.1093/nar/gkw691. PubMed PMID:27492288 PubMed Central PMC5137422.
  48. Arenillas, DJ, Forrest, AR, Kawaji, H, Lassmann, T, FANTOM Consortium, Wasserman, WW et al.. CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. Bioinformatics. 2016;32 (18):2858-60. doi: 10.1093/bioinformatics/btw337. PubMed PMID:27334471 PubMed Central PMC5018375.
  49. Tarailo-Graovac, M, Shyr, C, Ross, CJ, Horvath, GA, Salvarinova, R, Ye, XC et al.. Exome Sequencing and the Management of Neurometabolic Disorders. N. Engl. J. Med. 2016;374 (23):2246-55. doi: 10.1056/NEJMoa1515792. PubMed PMID:27276562 PubMed Central PMC4983272.
  50. van Karnebeek, CD, Bonafé, L, Wen, XY, Tarailo-Graovac, M, Balzano, S, Royer-Bertrand, B et al.. NANS-mediated synthesis of sialic acid is required for brain and skeletal development. Nat. Genet. 2016;48 (7):777-84. doi: 10.1038/ng.3578. PubMed PMID:27213289 .
  51. Klein, S, Dieterich, LC, Mathelier, A, Chong, C, Sliwa-Primorac, A, Hong, YK et al.. DeepCAGE transcriptomics identify HOXD10 as a transcription factor regulating lymphatic endothelial responses to VEGF-C. J. Cell. Sci. 2016;129 (13):2573-85. doi: 10.1242/jcs.186767. PubMed PMID:27199372 .
  52. de Leeuw, CN, Korecki, AJ, Berry, GE, Hickmott, JW, Lam, SL, Lengyell, TC et al.. rAAV-compatible MiniPromoters for restricted expression in the brain and eye. Mol Brain. 2016;9 (1):52. doi: 10.1186/s13041-016-0232-4. PubMed PMID:27164903 PubMed Central PMC4862195.
  53. Anastasio, N, Tarailo-Graovac, M, Al-Khalifah, R, Legault, L, Drogemoller, B, Ross, CJ et al.. Mitochondrial Complex III Deficiency with Ketoacidosis and Hyperglycemia Mimicking Neonatal Diabetes. JIMD Rep. 2017;31 :57-62. doi: 10.1007/8904_2016_557. PubMed PMID:27074787 PubMed Central PMC5388639.
  54. Santra, S, Cameron, JM, Shyr, C, Zhang, L, Drögemöller, B, Ross, CJ et al.. Cytosolic phosphoenolpyruvate carboxykinase deficiency presenting with acute liver failure following gastroenteritis. Mol. Genet. Metab. 2016;118 (1):21-7. doi: 10.1016/j.ymgme.2016.03.001. PubMed PMID:26971250 .
  55. De Souza, RA, Islam, SA, McEwen, LM, Mathelier, A, Hill, A, Mah, SM et al.. DNA methylation profiling in human Huntington's disease brain. Hum. Mol. Genet. 2016;25 (10):2013-2030. doi: 10.1093/hmg/ddw076. PubMed PMID:26953320 .
  56. Li, Y, Chen, CY, Wasserman, WW. Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters. J. Comput. Biol. 2016;23 (5):322-36. doi: 10.1089/cmb.2015.0189. PubMed PMID:26799292 .
  57. Hurst, LD, Ghanbarian, AT, Forrest, AR, FANTOM consortium, Huminiecki, L. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome. PLoS Biol. 2015;13 (12):e1002315. doi: 10.1371/journal.pbio.1002315. PubMed PMID:26685068 PubMed Central PMC4686125.
  58. Carbajo, D, Magi, S, Itoh, M, Kawaji, H, Lassmann, T, Arner, E et al.. Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PLoS ONE. 2015;10 (12):e0144176. doi: 10.1371/journal.pone.0144176. PubMed PMID:26658111 PubMed Central PMC4682858.
  59. Horvath, GA, Demos, M, Shyr, C, Matthews, A, Zhang, L, Race, S et al.. Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?. Mol. Genet. Metab. 2016;117 (1):42-8. doi: 10.1016/j.ymgme.2015.11.008. PubMed PMID:26647175 .
  60. Dieterich, LC, Klein, S, Mathelier, A, Sliwa-Primorac, A, Ma, Q, Hong, YK et al.. DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium. Cell Rep. 2015;13 (7):1493-1504. doi: 10.1016/j.celrep.2015.10.002. PubMed PMID:26549461 .
  61. Mathelier, A, Fornes, O, Arenillas, DJ, Chen, CY, Denay, G, Lee, J et al.. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2016;44 (D1):D110-5. doi: 10.1093/nar/gkv1176. PubMed PMID:26531826 PubMed Central PMC4702842.
  62. Li, Y, Chen, CY, Kaye, AM, Wasserman, WW. The identification of cis-regulatory elements: A review from a machine learning perspective. BioSystems. 2015;138 :6-17. doi: 10.1016/j.biosystems.2015.10.002. PubMed PMID:26499213 .
  63. Langlois, S, Tarailo-Graovac, M, Sayson, B, Drögemöller, B, Swenerton, A, Ross, CJ et al.. De novo dominant variants affecting the motor domain of KIF1A are a cause of PEHO syndrome. Eur. J. Hum. Genet. 2016;24 (6):949-53. doi: 10.1038/ejhg.2015.217. PubMed PMID:26486474 PubMed Central PMC4867456.
  64. Jiménez-Triana, CA, Castelán-Martínez, OD, Rivas-Ruiz, R, Jiménez-Méndez, R, Medina, A, Clark, P et al.. Cisplatin Nephrotoxicity and Longitudinal Growth in Children With Solid Tumors: A Retrospective Cohort Study. Medicine (Baltimore). 2015;94 (34):e1413. doi: 10.1097/MD.0000000000001413. PubMed PMID:26313789 PubMed Central PMC4602918.
  65. Visscher, H, Rassekh, SR, Sandor, GS, Caron, HN, van Dalen, EC, Kremer, LC et al.. Genetic variants in SLC22A17 and SLC22A7 are associated with anthracycline-induced cardiotoxicity in children. Pharmacogenomics. 2015;16 (10):1065-76. doi: 10.2217/pgs.15.61. PubMed PMID:26230641 .
  66. Schmouth, JF, Arenillas, D, Corso-Díaz, X, Xie, YY, Bohacec, S, Banks, KG et al.. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development. BMC Genomics. 2015;16 :545. doi: 10.1186/s12864-015-1770-3. PubMed PMID:26204903 PubMed Central PMC4512088.
  67. Shyr, C, Kushniruk, A, van Karnebeek, CD, Wasserman, WW. Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors. J Am Med Inform Assoc. 2016;23 (2):257-68. doi: 10.1093/jamia/ocv053. PubMed PMID:26117142 PubMed Central PMC4784553.
  68. Bečanović, K, Nørremølle, A, Neal, SJ, Kay, C, Collins, JA, Arenillas, D et al.. A SNP in the HTT promoter alters NF-κB binding and is a bidirectional genetic modifier of Huntington disease. Nat. Neurosci. 2015;18 (6):807-16. doi: 10.1038/nn.4014. PubMed PMID:25938884 .
  69. Mathelier, A, Lefebvre, C, Zhang, AW, Arenillas, DJ, Ding, J, Wasserman, WW et al.. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biol. 2015;16 :84. doi: 10.1186/s13059-015-0648-7. PubMed PMID:25903198 PubMed Central PMC4467049.
  70. Sirrs, S, van Karnebeek, CD, Peng, X, Shyr, C, Tarailo-Graovac, M, Mandal, R et al.. Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms. Orphanet J Rare Dis. 2015;10 :38. doi: 10.1186/s13023-015-0248-3. PubMed PMID:25885783 PubMed Central PMC4423390.
  71. Tarailo-Graovac, M, Sinclair, G, Stockler-Ipsiroglu, S, Van Allen, M, Rozmus, J, Shyr, C et al.. The genotypic and phenotypic spectrum of PIGA deficiency. Orphanet J Rare Dis. 2015;10 :23. doi: 10.1186/s13023-015-0243-8. PubMed PMID:25885527 PubMed Central PMC4348372.
  72. Yoshihara, M, Ohmiya, H, Hara, S, Kawasaki, S, FANTOM consortium, Hayashizaki, Y et al.. Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PLoS ONE. 2015;10 (3):e0117581. doi: 10.1371/journal.pone.0117581. PubMed PMID:25807145 PubMed Central PMC4373821.
  73. Gottlieb, MM, Arenillas, DJ, Maithripala, S, Maurer, ZD, Tarailo Graovac, M, Armstrong, L et al.. GeneYenta: a phenotype-based rare disease case matching tool based on online dating algorithms for the acceleration of exome interpretation. Hum. Mutat. 2015;36 (4):432-8. doi: 10.1002/humu.22772. PubMed PMID:25703386 .
  74. Mathelier, A, Shi, W, Wasserman, WW. Identification of altered cis-regulatory elements in human disease. Trends Genet. 2015;31 (2):67-76. doi: 10.1016/j.tig.2014.12.003. PubMed PMID:25637093 .
  75. Janer, A, van Karnebeek, CD, Sasarman, F, Antonicka, H, Al Ghamdi, M, Shyr, C et al.. RMND1 deficiency associated with neonatal lactic acidosis, infantile onset renal failure, deafness, and multiorgan involvement. Eur. J. Hum. Genet. 2015;23 (10):1301-7. doi: 10.1038/ejhg.2014.293. PubMed PMID:25604853 PubMed Central PMC4592087.
  76. Liang, C, FANTOM Consortium, Forrest, AR, Wagner, GP. The statistical geometry of transcriptome divergence in cell-type evolution and cancer. Nat Commun. 2015;6 :6066. doi: 10.1038/ncomms7066. PubMed PMID:25585899 .
  77. Shyr, C, Tarailo-Graovac, M, Gottlieb, M, Lee, JJ, van Karnebeek, C, Wasserman, WW et al.. FLAGS, frequently mutated genes in public exomes. BMC Med Genomics. 2014;7 :64. doi: 10.1186/s12920-014-0064-y. PubMed PMID:25466818 PubMed Central PMC4267152.
  78. Salvarinova, R, Ye, CX, Rossi, A, Biancheri, R, Roland, EH, Pavlidis, P et al.. Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities. Neurogenetics. 2015;16 (2):145-9. doi: 10.1007/s10048-014-0432-y. PubMed PMID:25432320 .
  79. Stockler, S, Corvera, S, Lambright, D, Fogarty, K, Nosova, E, Leonard, D et al.. Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking. Orphanet J Rare Dis. 2014;9 :141. doi: 10.1186/s13023-014-0141-5. PubMed PMID:25233840 PubMed Central PMC4177245.
  80. Worsley Hunt, R, Wasserman, WW. Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets. Genome Biol. 2014;15 (7):412. doi: 10.1186/s13059-014-0412-4. PubMed PMID:25070602 PubMed Central PMC4165360.
  81. Armstrong, L, Biancheri, R, Shyr, C, Rossi, A, Sinclair, G, Ross, CJ et al.. AIMP1 deficiency presents as a cortical neurodegenerative disease with infantile onset. Neurogenetics. 2014;15 (3):157-9. doi: 10.1007/s10048-014-0411-3. PubMed PMID:24958424 .
  82. Hasegawa, Y, Tang, D, Takahashi, N, Hayashizaki, Y, Forrest, AR, FANTOM Consortium et al.. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep. 2014;4 :5228. doi: 10.1038/srep05228. PubMed PMID:24957798 PubMed Central PMC4067614.
  83. Worsley Hunt, R, Mathelier, A, Del Peso, L, Wasserman, WW. Improving analysis of transcription factor binding sites within ChIP-Seq data based on topological motif enrichment. BMC Genomics. 2014;15 :472. doi: 10.1186/1471-2164-15-472. PubMed PMID:24927817 PubMed Central PMC4082612.
  84. Chen, CY, Chang, IS, Hsiung, CA, Wasserman, WW. On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med Genomics. 2014;7 :34. doi: 10.1186/1755-8794-7-34. PubMed PMID:24920305 PubMed Central PMC4066296.
  85. Shyr, C, Kushniruk, A, Wasserman, WW. Usability study of clinical exome analysis software: top lessons learned and recommendations. J Biomed Inform. 2014;51 :129-36. doi: 10.1016/j.jbi.2014.05.004. PubMed PMID:24860971 .
  86. de Leeuw, CN, Dyka, FM, Boye, SL, Laprise, S, Zhou, M, Chou, AY et al.. Targeted CNS Delivery Using Human MiniPromoters and Demonstrated Compatibility with Adeno-Associated Viral Vectors. Mol Ther Methods Clin Dev. 2014;1 :5. doi: 10.1038/mtm.2013.5. PubMed PMID:24761428 PubMed Central PMC3992516.
  87. Morikawa, H, Ohkura, N, Vandenbon, A, Itoh, M, Nagao-Sato, S, Kawaji, H et al.. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc. Natl. Acad. Sci. U.S.A. 2014;111 (14):5289-94. doi: 10.1073/pnas.1312717110. PubMed PMID:24706905 PubMed Central PMC3986152.
  88. Arner, E, Forrest, AR, Ehrlund, A, Mejhert, N, Itoh, M, Kawaji, H et al.. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS ONE. 2014;9 (3):e80274. doi: 10.1371/journal.pone.0080274. PubMed PMID:24676332 PubMed Central PMC3968011.
  89. FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest, AR, Kawaji, H, Rehli, M, Baillie, JK, de Hoon, MJ et al.. A promoter-level mammalian expression atlas. Nature. 2014;507 (7493):462-70. doi: 10.1038/nature13182. PubMed PMID:24670764 PubMed Central PMC4529748.
  90. Andersson, R, Gebhard, C, Miguel-Escalada, I, Hoof, I, Bornholdt, J, Boyd, M et al.. An atlas of active enhancers across human cell types and tissues. Nature. 2014;507 (7493):455-461. doi: 10.1038/nature12787. PubMed PMID:24670763 PubMed Central PMC5215096.
  91. Ye, XC, Pegado, V, Patel, MS, Wasserman, WW. Strabismus genetics across a spectrum of eye misalignment disorders. Clin. Genet. 2014;86 (2):103-11. doi: 10.1111/cge.12367. PubMed PMID:24579652 PubMed Central PMC4233980.
  92. van Karnebeek, CD, Sly, WS, Ross, CJ, Salvarinova, R, Yaplito-Lee, J, Santra, S et al.. Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. Am. J. Hum. Genet. 2014;94 (3):453-61. doi: 10.1016/j.ajhg.2014.01.006. PubMed PMID:24530203 PubMed Central PMC3951944.
  93. Vilariño-Güell, C, Rajput, A, Milnerwood, AJ, Shah, B, Szu-Tu, C, Trinh, J et al.. DNAJC13 mutations in Parkinson disease. Hum. Mol. Genet. 2014;23 (7):1794-801. doi: 10.1093/hmg/ddt570. PubMed PMID:24218364 PubMed Central PMC3999380.
  94. Yang, L, Zhou, T, Dror, I, Mathelier, A, Wasserman, WW, Gordân, R et al.. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res. 2014;42 (Database issue):D148-55. doi: 10.1093/nar/gkt1087. PubMed PMID:24214955 PubMed Central PMC3964943.
  95. Mathelier, A, Zhao, X, Zhang, AW, Parcy, F, Worsley-Hunt, R, Arenillas, DJ et al.. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42 (Database issue):D142-7. doi: 10.1093/nar/gkt997. PubMed PMID:24194598 PubMed Central PMC3965086.
  96. Cotton, AM, Chen, CY, Lam, LL, Wasserman, WW, Kobor, MS, Brown, CJ et al.. Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains. Hum. Mol. Genet. 2014;23 (5):1211-23. doi: 10.1093/hmg/ddt513. PubMed PMID:24158853 PubMed Central PMC4051349.
  97. Filges, I, Nosova, E, Bruder, E, Tercanli, S, Townsend, K, Gibson, WT et al.. Exome sequencing identifies mutations in KIF14 as a novel cause of an autosomal recessive lethal fetal ciliopathy phenotype. Clin. Genet. 2014;86 (3):220-8. doi: 10.1111/cge.12301. PubMed PMID:24128419 .
  98. Schmouth, JF, Castellarin, M, Laprise, S, Banks, KG, Bonaguro, RJ, McInerny, SC et al.. Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice. BMC Biol. 2013;11 :106. doi: 10.1186/1741-7007-11-106. PubMed PMID:24124870 PubMed Central PMC4015596.
  99. Mathelier, A, Wasserman, WW. The next generation of transcription factor binding site prediction. PLoS Comput. Biol. 2013;9 (9):e1003214. doi: 10.1371/journal.pcbi.1003214. PubMed PMID:24039567 PubMed Central PMC3764009.
  100. Ye, XC, Ng, I, Seid-Karbasi, P, Imam, T, Lee, CE, Chen, SY et al.. Portal for Families Overcoming Neurodevelopmental Disorders (PFOND): Implementation of a Software Framework for Facilitated Community Website Creation by Nontechnical Volunteers. JMIR Res Protoc. 2013;2 (2):e25. doi: 10.2196/resprot.2675. PubMed PMID:23920006 PubMed Central PMC3742411.
Search PubMed