Wyeth Wasserman Publications

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

  1. 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 .
  2. 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.
  3. 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; :. doi: 10.1038/gim.2017.50. PubMed PMID:28471432 .
  4. 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 .
  5. 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 .
  6. 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.
  7. 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 .
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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 .
  18. 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 .
  19. 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.
  20. 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.
  21. 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 .
  22. 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 .
  23. 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 .
  24. 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.
  25. 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.
  26. 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 .
  27. 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):1493-504. doi: 10.1016/j.celrep.2015.10.002. PubMed PMID:26549461 .
  28. 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.
  29. 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 .
  30. 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.
  31. 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.
  32. 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 .
  33. 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.
  34. 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.
  35. Yang, L, Dror, I, Zhou, T, Mathelier, A, Wasserman, WW, Gordân, R et al.. 15 TFBSshape: a motif database for DNA shape features of transcription factor binding sites. J. Biomol. Struct. Dyn. 2015;33 Suppl 1 :9. doi: 10.1080/07391102.2015.1032555. PubMed PMID:26103228 .
  36. 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 .
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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 .
  42. 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 .
  43. 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.
  44. 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 .
  45. 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.
  46. 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 .
  47. 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.
  48. 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.
  49. 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 .
  50. 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.
  51. 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.
  52. 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.
  53. 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 .
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. 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.
  61. 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.
  62. 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.
  63. 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.
  64. 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 .
  65. 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.
  66. 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.
  67. 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.
  68. Cheung, WA, Ouellette, BF, Wasserman, WW. Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity. BMC Med Genomics. 2013;6 Suppl 2 :S3. doi: 10.1186/1755-8794-6-S2-S3. PubMed PMID:23819887 PubMed Central PMC3654871.
  69. Aminkeng, F, Ross, CJ, Rassekh, SR, Brunham, LR, Sistonen, J, Dube, MP et al.. Higher frequency of genetic variants conferring increased risk for ADRs for commonly used drugs treating cancer, AIDS and tuberculosis in persons of African descent. Pharmacogenomics J. 2014;14 (2):160-70. doi: 10.1038/tpj.2013.13. PubMed PMID:23588107 PubMed Central PMC4684079.
  70. Robillard, JM, Whiteley, L, Johnson, TW, Lim, J, Wasserman, WW, Illes, J et al.. Utilizing social media to study information-seeking and ethical issues in gene therapy. J. Med. Internet Res. 2013;15 (3):e44. doi: 10.2196/jmir.2313. PubMed PMID:23470490 PubMed Central PMC3636301.
  71. Visscher, H, Ross, CJ, Rassekh, SR, Sandor, GS, Caron, HN, van Dalen, EC et al.. Validation of variants in SLC28A3 and UGT1A6 as genetic markers predictive of anthracycline-induced cardiotoxicity in children. Pediatr Blood Cancer. 2013;60 (8):1375-81. doi: 10.1002/pbc.24505. PubMed PMID:23441093 .
  72. Cheung, WA, Ouellette, BF, Wasserman, WW. Inferring novel gene-disease associations using Medical Subject Heading Over-representation Profiles. Genome Med. 2012;4 (9):75. doi: 10.1186/gm376. PubMed PMID:23021552 PubMed Central PMC3580445.
  73. Cheung, WA, Ouellette, BF, Wasserman, WW. Quantitative biomedical annotation using medical subject heading over-representation profiles (MeSHOPs). BMC Bioinformatics. 2012;13 :249. doi: 10.1186/1471-2105-13-249. PubMed PMID:23017167 PubMed Central PMC3564935.
  74. Kwon, AT, Arenillas, DJ, Worsley Hunt, R, Wasserman, WW. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. G3 (Bethesda). 2012;2 (9):987-1002. doi: 10.1534/g3.112.003202. PubMed PMID:22973536 PubMed Central PMC3429929.
  75. Shah, SP, Roth, A, Goya, R, Oloumi, A, Ha, G, Zhao, Y et al.. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486 (7403):395-9. doi: 10.1038/nature10933. PubMed PMID:22495314 PubMed Central PMC3863681.
  76. Yusuf, D, Butland, SL, Swanson, MI, Bolotin, E, Ticoll, A, Cheung, WA et al.. The transcription factor encyclopedia. Genome Biol. 2012;13 (3):R24. doi: 10.1186/gb-2012-13-3-r24. PubMed PMID:22458515 PubMed Central PMC3439975.
  77. Schmouth, JF, Banks, KG, Mathelier, A, Gregory-Evans, CY, Castellarin, M, Holt, RA et al.. Retina restored and brain abnormalities ameliorated by single-copy knock-in of human NR2E1 in null mice. Mol. Cell. Biol. 2012;32 (7):1296-311. doi: 10.1128/MCB.06016-11. PubMed PMID:22290436 PubMed Central PMC3302440.
  78. Kwon, AT, Chou, AY, Arenillas, DJ, Wasserman, WW. Validation of skeletal muscle cis-regulatory module predictions reveals nucleotide composition bias in functional enhancers. PLoS Comput. Biol. 2011;7 (12):e1002256. doi: 10.1371/journal.pcbi.1002256. PubMed PMID:22144875 PubMed Central PMC3228787.
  79. Worsley-Hunt, R, Bernard, V, Wasserman, WW. Identification of cis-regulatory sequence variations in individual genome sequences. Genome Med. 2011;3 (10):65. doi: 10.1186/gm281. PubMed PMID:21989199 PubMed Central PMC3239227.
  80. Vilariño-Güell, C, Wider, C, Ross, OA, Dachsel, JC, Kachergus, JM, Lincoln, SJ et al.. VPS35 mutations in Parkinson disease. Am. J. Hum. Genet. 2011;89 (1):162-7. doi: 10.1016/j.ajhg.2011.06.001. PubMed PMID:21763482 PubMed Central PMC3135796.
  81. Fulton, DL, Denarier, E, Friedman, HC, Wasserman, WW, Peterson, AC. Towards resolving the transcription factor network controlling myelin gene expression. Nucleic Acids Res. 2011;39 (18):7974-91. doi: 10.1093/nar/gkr326. PubMed PMID:21729871 PubMed Central PMC3185407.
  82. Portales-Casamar, E, Evans, A, Wasserman, W, Pavlidis, P. The NeuroDevNet Neuroinformatics Core. Semin Pediatr Neurol. 2011;18 (1):17-20. doi: 10.1016/j.spen.2011.02.001. PubMed PMID:21575836 .
  83. Le Béchec, A, Portales-Casamar, E, Vetter, G, Moes, M, Zindy, PJ, Saumet, A et al.. MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics. 2011;12 :67. doi: 10.1186/1471-2105-12-67. PubMed PMID:21375730 PubMed Central PMC3061897.
  84. Portales-Casamar, E, Swanson, DJ, Liu, L, de Leeuw, CN, Banks, KG, Ho Sui, SJ et al.. A regulatory toolbox of MiniPromoters to drive selective expression in the brain. Proc. Natl. Acad. Sci. U.S.A. 2010;107 (38):16589-94. doi: 10.1073/pnas.1009158107. PubMed PMID:20807748 PubMed Central PMC2944712.
  85. Ross, CJ, Visscher, H, Sistonen, J, Brunham, LR, Pussegoda, K, Loo, TT et al.. The Canadian Pharmacogenomics Network for Drug Safety: a model for safety pharmacology. Thyroid. 2010;20 (7):681-7. doi: 10.1089/thy.2010.1642. PubMed PMID:20578893 .
  86. Malhotra, D, Portales-Casamar, E, Singh, A, Srivastava, S, Arenillas, D, Happel, C et al.. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis. Nucleic Acids Res. 2010;38 (17):5718-34. doi: 10.1093/nar/gkq212. PubMed PMID:20460467 PubMed Central PMC2943601.
  87. Milisavljevic, M, Hearty, T, Wong, TY, Portales-Casamar, E, Simpson, EM, Wasserman, WW et al.. Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies. Mamm. Genome. 2010;21 (5-6):224-30. doi: 10.1007/s00335-010-9258-6. PubMed PMID:20411264 PubMed Central PMC5047758.
  88. Portales-Casamar, E, Thongjuea, S, Kwon, AT, Arenillas, D, Zhao, X, Valen, E et al.. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010;38 (Database issue):D105-10. doi: 10.1093/nar/gkp950. PubMed PMID:19906716 PubMed Central PMC2808906.
  89. Ross, CJ, Katzov-Eckert, H, Dubé, MP, Brooks, B, Rassekh, SR, Barhdadi, A et al.. Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy. Nat. Genet. 2009;41 (12):1345-9. doi: 10.1038/ng.478. PubMed PMID:19898482 .
  90. Fulton, DL, Sundararajan, S, Badis, G, Hughes, TR, Wasserman, WW, Roach, JC et al.. TFCat: the curated catalog of mouse and human transcription factors. Genome Biol. 2009;10 (3):R29. doi: 10.1186/gb-2009-10-3-r29. PubMed PMID:19284633 PubMed Central PMC2691000.
  91. Portales-Casamar, E, Arenillas, D, Lim, J, Swanson, MI, Jiang, S, McCallum, A et al.. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res. 2009;37 (Database issue):D54-60. doi: 10.1093/nar/gkn783. PubMed PMID:18971253 PubMed Central PMC2686574.
  92. Saumet, A, Vetter, G, Bouttier, M, Portales-Casamar, E, Wasserman, WW, Maurin, T et al.. Transcriptional repression of microRNA genes by PML-RARA increases expression of key cancer proteins in acute promyelocytic leukemia. Blood. 2009;113 (2):412-21. doi: 10.1182/blood-2008-05-158139. PubMed PMID:18941112 .
  93. Brumm, J, Conibear, E, Wasserman, WW, Bryan, J. Discovery and expansion of gene modules by seeking isolated groups in a random graph process. PLoS ONE. 2008;3 (10):e3358. doi: 10.1371/journal.pone.0003358. PubMed PMID:18843375 PubMed Central PMC2559867.
  94. Kemmer, D, Faxén, M, Hodges, E, Lim, J, Herzog, E, Ljungström, E et al.. Exploring the foundation of genomics: a northern blot reference set for the comparative analysis of transcript profiling technologies. Comp. Funct. Genomics. 2004;5 (8):584-95. doi: 10.1002/cfg.443. PubMed PMID:18629180 PubMed Central PMC2447472.
  95. D'Souza, CA, Chopra, V, Varhol, R, Xie, YY, Bohacec, S, Zhao, Y et al.. Identification of a set of genes showing regionally enriched expression in the mouse brain. BMC Neurosci. 2008;9 :66. doi: 10.1186/1471-2202-9-66. PubMed PMID:18625066 PubMed Central PMC2483290.
  96. Astanehe, A, Arenillas, D, Wasserman, WW, Leung, PC, Dunn, SE, Davies, BR et al.. Mechanisms underlying p53 regulation of PIK3CA transcription in ovarian surface epithelium and in ovarian cancer. J. Cell. Sci. 2008;121 (Pt 5):664-74. doi: 10.1242/jcs.013029. PubMed PMID:18270270 .
  97. Marks, VD, Ho Sui, SJ, Erasmus, D, van der Merwe, GK, Brumm, J, Wasserman, WW et al.. Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res. 2008;8 (1):35-52. doi: 10.1111/j.1567-1364.2007.00338.x. PubMed PMID:18215224 PubMed Central PMC5065349.
  98. Kemmer, D, Podowski, RM, Yusuf, D, Brumm, J, Cheung, W, Wahlestedt, C et al.. Gene characterization index: assessing the depth of gene annotation. PLoS ONE. 2008;3 (1):e1440. doi: 10.1371/journal.pone.0001440. PubMed PMID:18213364 PubMed Central PMC2194620.
  99. Andersen, MC, Engström, PG, Lithwick, S, Arenillas, D, Eriksson, P, Lenhard, B et al.. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol. 2008;4 (1):e5. doi: 10.1371/journal.pcbi.0040005. PubMed PMID:18208319 PubMed Central PMC2211530.
  100. Griffith, OL, Montgomery, SB, Bernier, B, Chu, B, Kasaian, K, Aerts, S et al.. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008;36 (Database issue):D107-13. doi: 10.1093/nar/gkm967. PubMed PMID:18006570 PubMed Central PMC2239002.
Search PubMed