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Items: 1 to 50 of 183

1.

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data.

Freytag S, Tian L, Lönnstedt I, Ng M, Bahlo M.

Version 2. F1000Res. 2018 Aug 15 [revised 2018 Jan 1];7:1297. doi: 10.12688/f1000research.15809.2. eCollection 2018.

2.

Genetic investigation into an increased susceptibility to biliary atresia in an extended New Zealand Māori family.

Cameron-Christie SR, Wilde J, Gray A, Tankard R, Bahlo M, Markie D, Evans HM, Robertson SP.

BMC Med Genomics. 2018 Dec 18;11(1):121. doi: 10.1186/s12920-018-0440-0.

3.

Reanalysis and optimisation of bioinformatic pipelines is critical for mutation detection.

Cowley MJ, Liu YC, Oliver KL, Carvill G, Myers CT, Gayevskiy V, Delatycki M, Vlaskamp DRM, Zhu Y, Mefford H, Buckley MF, Bahlo M, Scheffer IE, Dinger ME, Roscioli T.

Hum Mutat. 2018 Dec 17. doi: 10.1002/humu.23699. [Epub ahead of print]

PMID:
30556619
4.

Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data.

Tankard RM, Bennett MF, Degorski P, Delatycki MB, Lockhart PJ, Bahlo M.

Am J Hum Genet. 2018 Dec 6;103(6):858-873. doi: 10.1016/j.ajhg.2018.10.015. Epub 2018 Nov 29.

PMID:
30503517
5.

dtangle: accurate and robust cell type deconvolution.

Hunt GJ, Freytag S, Bahlo M, Gagnon-Bartsch JA.

Bioinformatics. 2018 Nov 8. doi: 10.1093/bioinformatics/bty926. [Epub ahead of print]

PMID:
30407492
6.

Splice-altering variant in COL11A1 as a cause of nonsyndromic hearing loss DFNA37.

Booth KT, Askew JW, Talebizadeh Z, Huygen PLM, Eudy J, Kenyon J, Hoover D, Hildebrand MS, Smith KR, Bahlo M, Kimberling WJ, Smith RJH, Azaiez H, Smith SD.

Genet Med. 2018 Sep 24. doi: 10.1038/s41436-018-0285-0. [Epub ahead of print]

PMID:
30245514
7.

Evidence of linkage to chromosome 5p13.2-q11.1 in a large inbred family with genetic generalized epilepsy.

Kinay D, Oliver KL, Tüzün E, Damiano JA, Ulusoy C, Andermann E, Hildebrand MS, Bahlo M, Berkovic SF.

Epilepsia. 2018 Aug;59(8):e125-e129. doi: 10.1111/epi.14506. Epub 2018 Jul 4.

PMID:
29974457
8.

Recent advances in the detection of repeat expansions with short-read next-generation sequencing.

Bahlo M, Bennett MF, Degorski P, Tankard RM, Delatycki MB, Lockhart PJ.

F1000Res. 2018 Jun 13;7. pii: F1000 Faculty Rev-736. doi: 10.12688/f1000research.13980.1. eCollection 2018. Review.

9.

Recessive Spondylocarpotarsal Synostosis Syndrome Due to Compound Heterozygosity for Variants in MYH3.

Cameron-Christie SR, Wells CF, Simon M, Wessels M, Tang CZN, Wei W, Takei R, Aarts-Tesselaar C, Sandaradura S, Sillence DO, Cordier MP, Veenstra-Knol HE, Cassina M, Ludkig K, Trevisson E, Bahlo M, Markie DM, Jenkins ZA, Robertson SP.

Am J Hum Genet. 2018 Jun 7;102(6):1115-1125. doi: 10.1016/j.ajhg.2018.04.008. Epub 2018 May 24.

10.

Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens.

Henden L, Lee S, Mueller I, Barry A, Bahlo M.

PLoS Genet. 2018 May 23;14(5):e1007279. doi: 10.1371/journal.pgen.1007279. eCollection 2018 May.

11.

Functional analysis of a hypomorphic allele shows that MMP14 catalytic activity is the prime determinant of the Winchester syndrome phenotype.

de Vos IJHM, Tao EY, Ong SLM, Goggi JL, Scerri T, Wilson GR, Low CGM, Wong ASW, Grussu D, Stegmann APA, van Geel M, Janssen R, Amor DJ, Bahlo M, Dunn NR, Carney TJ, Lockhart PJ, Coull BJ, van Steensel MAM.

Hum Mol Genet. 2018 Aug 15;27(16):2775-2788. doi: 10.1093/hmg/ddy168.

12.

De novo and inherited private variants in MAP1B in periventricular nodular heterotopia.

Heinzen EL, O'Neill AC, Zhu X, Allen AS, Bahlo M, Chelly J, Chen MH, Dobyns WB, Freytag S, Guerrini R, Leventer RJ, Poduri A, Robertson SP, Walsh CA, Zhang M; Epi4K Consortium; Epilepsy Phenome/Genome Project.

PLoS Genet. 2018 May 8;14(5):e1007281. doi: 10.1371/journal.pgen.1007281. eCollection 2018 May.

13.

A set of regulatory genes co-expressed in embryonic human brain is implicated in disrupted speech development.

Eising E, Carrion-Castillo A, Vino A, Strand EA, Jakielski KJ, Scerri TS, Hildebrand MS, Webster R, Ma A, Mazoyer B, Francks C, Bahlo M, Scheffer IE, Morgan AT, Shriberg LD, Fisher SE.

Mol Psychiatry. 2018 Feb 20. doi: 10.1038/s41380-018-0020-x. [Epub ahead of print]

PMID:
29463886
14.

Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the Southwest Pacific.

Waltmann A, Koepfli C, Tessier N, Karl S, Fola A, Darcy AW, Wini L, Harrison GLA, Barnadas C, Jennison C, Karunajeewa H, Boyd S, Whittaker M, Kazura J, Bahlo M, Mueller I, Barry AE.

PLoS Negl Trop Dis. 2018 Jan 26;12(1):e0006146. doi: 10.1371/journal.pntd.0006146. eCollection 2018 Jan.

15.

Neuropathology of childhood-onset basal ganglia degeneration caused by mutation of VAC14.

Stutterd C, Diakumis P, Bahlo M, Fanjul Fernandez M, Leventer RJ, Delatycki M, Amor D, Chow CW, Stephenson S, Meisler MH, Mclean C, Lockhart PJ.

Ann Clin Transl Neurol. 2017 Nov 7;4(12):859-864. doi: 10.1002/acn3.487. eCollection 2017 Dec.

16.

Mosaic uniparental disomy results in GM1 gangliosidosis with normal enzyme assay.

Myers KA, Bennett MF, Chow CW, Carden SM, Mandelstam SA, Bahlo M, Scheffer IE.

Am J Med Genet A. 2018 Jan;176(1):230-234. doi: 10.1002/ajmg.a.38549. Epub 2017 Nov 21.

PMID:
29160035
17.

De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures.

Myers CT, Stong N, Mountier EI, Helbig KL, Freytag S, Sullivan JE, Ben Zeev B, Nissenkorn A, Tzadok M, Heimer G, Shinde DN, Rezazadeh A, Regan BM, Oliver KL, Ernst ME, Lippa NC, Mulhern MS, Ren Z, Poduri A, Andrade DM, Bird LM, Bahlo M, Berkovic SF, Lowenstein DH, Scheffer IE, Sadleir LG, Goldstein DB, Mefford HC, Heinzen EL.

Am J Hum Genet. 2017 Oct 5;101(4):516-524. doi: 10.1016/j.ajhg.2017.08.013. Epub 2017 Sep 21.

18.

Familial epilepsy with anterior polymicrogyria as a presentation of COL18A1 mutations.

Corbett MA, Turner SJ, Gardner A, Silver J, Stankovich J, Leventer RJ, Derry CP, Carroll R, Ha T, Scheffer IE, Bahlo M, Jackson GD, Mackey DA, Berkovic SF, Gecz J.

Eur J Med Genet. 2017 Aug;60(8):437-443. doi: 10.1016/j.ejmg.2017.06.002. Epub 2017 Jun 8.

PMID:
28602933
19.

brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets.

Freytag S, Burgess R, Oliver KL, Bahlo M.

Genome Med. 2017 Jun 8;9(1):55. doi: 10.1186/s13073-017-0444-y.

20.

Genome-wide analyses identify common variants associated with macular telangiectasia type 2.

Scerri TS, Quaglieri A, Cai C, Zernant J, Matsunami N, Baird L, Scheppke L, Bonelli R, Yannuzzi LA, Friedlander M; MacTel Project Consortium, Egan CA, Fruttiger M, Leppert M, Allikmets R, Bahlo M.

Nat Genet. 2017 Apr;49(4):559-567. doi: 10.1038/ng.3799. Epub 2017 Feb 27.

PMID:
28250457
21.

Mutations in DCC cause isolated agenesis of the corpus callosum with incomplete penetrance.

Marsh AP, Heron D, Edwards TJ, Quartier A, Galea C, Nava C, Rastetter A, Moutard ML, Anderson V, Bitoun P, Bunt J, Faudet A, Garel C, Gillies G, Gobius I, Guegan J, Heide S, Keren B, Lesne F, Lukic V, Mandelstam SA, McGillivray G, McIlroy A, Méneret A, Mignot C, Morcom LR, Odent S, Paolino A, Pope K, Riant F, Robinson GA, Spencer-Smith M, Srour M, Stephenson SE, Tankard R, Trouillard O, Welniarz Q, Wood A, Brice A, Rouleau G, Attié-Bitach T, Delatycki MB, Mandel JL, Amor DJ, Roze E, Piton A, Bahlo M, Billette de Villemeur T, Sherr EH, Leventer RJ, Richards LJ, Lockhart PJ, Depienne C.

Nat Genet. 2017 Apr;49(4):511-514. doi: 10.1038/ng.3794. Epub 2017 Feb 27.

22.

SCN1A clinical spectrum includes the self-limited focal epilepsies of childhood.

Kivity S, Oliver KL, Afawi Z, Damiano JA, Arsov T, Bahlo M, Berkovic SF.

Epilepsy Res. 2017 Mar;131:9-14. doi: 10.1016/j.eplepsyres.2017.01.012. Epub 2017 Feb 4.

PMID:
28192756
23.

EIF2S3 Mutations Associated with Severe X-Linked Intellectual Disability Syndrome MEHMO.

Skopkova M, Hennig F, Shin BS, Turner CE, Stanikova D, Brennerova K, Stanik J, Fischer U, Henden L, Müller U, Steinberger D, Leshinsky-Silver E, Bottani A, Kurdiova T, Ukropec J, Nyitrayova O, Kolnikova M, Klimes I, Borck G, Bahlo M, Haas SA, Kim JR, Lotspeich-Cole LE, Gasperikova D, Dever TE, Kalscheuer VM.

Hum Mutat. 2017 Apr;38(4):409-425. doi: 10.1002/humu.23170. Epub 2017 Jan 23.

24.

A SLC39A8 variant causes manganese deficiency, and glycosylation and mitochondrial disorders.

Riley LG, Cowley MJ, Gayevskiy V, Roscioli T, Thorburn DR, Prelog K, Bahlo M, Sue CM, Balasubramaniam S, Christodoulou J.

J Inherit Metab Dis. 2017 Mar;40(2):261-269. doi: 10.1007/s10545-016-0010-6. Epub 2016 Dec 19.

PMID:
27995398
25.

Heterozygous mutations in HSD17B4 cause juvenile peroxisomal D-bifunctional protein deficiency.

Amor DJ, Marsh AP, Storey E, Tankard R, Gillies G, Delatycki MB, Pope K, Bromhead C, Leventer RJ, Bahlo M, Lockhart PJ.

Neurol Genet. 2016 Oct 18;2(6):e114. eCollection 2016 Dec.

26.

Early neuroimaging markers of FOXP2 intragenic deletion.

Liégeois FJ, Hildebrand MS, Bonthrone A, Turner SJ, Scheffer IE, Bahlo M, Connelly A, Morgan AT.

Sci Rep. 2016 Oct 13;6:35192. doi: 10.1038/srep35192.

27.

Dominant KCNA2 mutation causes episodic ataxia and pharmacoresponsive epilepsy.

Corbett MA, Bellows ST, Li M, Carroll R, Micallef S, Carvill GL, Myers CT, Howell KB, Maljevic S, Lerche H, Gazina EV, Mefford HC, Bahlo M, Berkovic SF, Petrou S, Scheffer IE, Gecz J.

Neurology. 2016 Nov 8;87(19):1975-1984. Epub 2016 Oct 12.

28.

Diagnosis and misdiagnosis of adult neuronal ceroid lipofuscinosis (Kufs disease).

Berkovic SF, Staropoli JF, Carpenter S, Oliver KL, Kmoch S, Anderson GW, Damiano JA, Hildebrand MS, Sims KB, Cotman SL, Bahlo M, Smith KR, Cadieux-Dion M, Cossette P, Jedličková I, Přistoupilová A, Mole SE; ANCL Gene Discovery Consortium.

Neurology. 2016 Aug 9;87(6):579-84. doi: 10.1212/WNL.0000000000002943. Epub 2016 Jul 13.

29.

Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype.

Alston CL, Compton AG, Formosa LE, Strecker V, Oláhová M, Haack TB, Smet J, Stouffs K, Diakumis P, Ciara E, Cassiman D, Romain N, Yarham JW, He L, De Paepe B, Vanlander AV, Seneca S, Feichtinger RG, Płoski R, Rokicki D, Pronicka E, Haller RG, Van Hove JL, Bahlo M, Mayr JA, Van Coster R, Prokisch H, Wittig I, Ryan MT, Thorburn DR, Taylor RW.

Am J Hum Genet. 2016 Jul 7;99(1):217-27. doi: 10.1016/j.ajhg.2016.05.021. Epub 2016 Jun 30.

30.

Identity by descent fine mapping of familial adult myoclonus epilepsy (FAME) to 2p11.2-2q11.2.

Henden L, Freytag S, Afawi Z, Baldassari S, Berkovic SF, Bisulli F, Canafoglia L, Casari G, Crompton DE, Depienne C, Gecz J, Guerrini R, Helbig I, Hirsch E, Keren B, Klein KM, Labauge P, LeGuern E, Licchetta L, Mei D, Nava C, Pippucci T, Rudolf G, Scheffer IE, Striano P, Tinuper P, Zara F, Corbett M, Bahlo M.

Hum Genet. 2016 Oct;135(10):1117-25. doi: 10.1007/s00439-016-1700-8. Epub 2016 Jul 1.

PMID:
27368338
31.

Evaluation of non-coding variation in GLUT1 deficiency.

Liu YC, Lee JW, Bellows ST, Damiano JA, Mullen SA, Berkovic SF, Bahlo M, Scheffer IE, Hildebrand MS; Clinical Group.

Dev Med Child Neurol. 2016 Dec;58(12):1295-1302. doi: 10.1111/dmcn.13163. Epub 2016 Jun 6.

32.

XIBD: software for inferring pairwise identity by descent on the X chromosome.

Henden L, Wakeham D, Bahlo M.

Bioinformatics. 2016 Aug 1;32(15):2389-91. doi: 10.1093/bioinformatics/btw124. Epub 2016 Mar 21.

PMID:
27153693
33.

ALPK3-deficient cardiomyocytes generated from patient-derived induced pluripotent stem cells and mutant human embryonic stem cells display abnormal calcium handling and establish that ALPK3 deficiency underlies familial cardiomyopathy.

Phelan DG, Anderson DJ, Howden SE, Wong RC, Hickey PF, Pope K, Wilson GR, Pébay A, Davis AM, Petrou S, Elefanty AG, Stanley EG, James PA, Macciocca I, Bahlo M, Cheung MM, Amor DJ, Elliott DA, Lockhart PJ.

Eur Heart J. 2016 Sep 1;37(33):2586-90. doi: 10.1093/eurheartj/ehw160. Epub 2016 Apr 22.

PMID:
27106955
34.

In silico prioritization based on coexpression can aid epileptic encephalopathy gene discovery.

Oliver KL, Lukic V, Freytag S, Scheffer IE, Berkovic SF, Bahlo M.

Neurol Genet. 2016 Jan 14;2(1):e51. doi: 10.1212/NXG.0000000000000051. eCollection 2016 Feb.

35.

Complete callosal agenesis, pontocerebellar hypoplasia, and axonal neuropathy due to AMPD2 loss.

Marsh AP, Lukic V, Pope K, Bromhead C, Tankard R, Ryan MM, Yiu EM, Sim JC, Delatycki MB, Amor DJ, McGillivray G, Sherr EH, Bahlo M, Leventer RJ, Lockhart PJ.

Neurol Genet. 2015 Jul 16;1(2):e16. doi: 10.1212/NXG.0000000000000014. eCollection 2015 Aug.

36.

Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections.

Mofiz E, Seemann T, Bahlo M, Holt D, Currie BJ, Fischer K, Papenfuss AT.

PLoS Negl Trop Dis. 2016 Feb 12;10(2):e0004384. doi: 10.1371/journal.pntd.0004384. eCollection 2016 Feb.

37.

Multiplex families with epilepsy: Success of clinical and molecular genetic characterization.

Afawi Z, Oliver KL, Kivity S, Mazarib A, Blatt I, Neufeld MY, Helbig KL, Goldberg-Stern H, Misk AJ, Straussberg R, Walid S, Mahajnah M, Lerman-Sagie T, Ben-Zeev B, Kahana E, Masalha R, Kramer U, Ekstein D, Shorer Z, Wallace RH, Mangelsdorf M, MacPherson JN, Carvill GL, Mefford HC, Jackson GD, Scheffer IE, Bahlo M, Gecz J, Heron SE, Corbett M, Mulley JC, Dibbens LM, Korczyn AD, Berkovic SF.

Neurology. 2016 Feb 23;86(8):713-22. doi: 10.1212/WNL.0000000000002404. Epub 2016 Jan 22.

38.

Structurally conserved erythrocyte-binding domain in Plasmodium provides a versatile scaffold for alternate receptor engagement.

Gruszczyk J, Lim NT, Arnott A, He WQ, Nguitragool W, Roobsoong W, Mok YF, Murphy JM, Smith KR, Lee S, Bahlo M, Mueller I, Barry AE, Tham WH.

Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E191-200. doi: 10.1073/pnas.1516512113. Epub 2015 Dec 29.

39.

Systematic noise degrades gene co-expression signals but can be corrected.

Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M.

BMC Bioinformatics. 2015 Sep 24;16:309. doi: 10.1186/s12859-015-0745-3.

40.

PRIMA1 mutation: a new cause of nocturnal frontal lobe epilepsy.

Hildebrand MS, Tankard R, Gazina EV, Damiano JA, Lawrence KM, Dahl HH, Regan BM, Shearer AE, Smith RJ, Marini C, Guerrini R, Labate A, Gambardella A, Tinuper P, Lichetta L, Baldassari S, Bisulli F, Pippucci T, Scheffer IE, Reid CA, Petrou S, Bahlo M, Berkovic SF.

Ann Clin Transl Neurol. 2015 Aug;2(8):821-30. doi: 10.1002/acn3.224. Epub 2015 Jul 3.

41.

Familial cortical dysplasia caused by mutation in the mammalian target of rapamycin regulator NPRL3.

Sim JC, Scerri T, Fanjul-Fernández M, Riseley JR, Gillies G, Pope K, van Roozendaal H, Heng JI, Mandelstam SA, McGillivray G, MacGregor D, Kannan L, Maixner W, Harvey AS, Amor DJ, Delatycki MB, Crino PB, Bahlo M, Lockhart PJ, Leventer RJ.

Ann Neurol. 2016 Jan;79(1):132-7. doi: 10.1002/ana.24502. Epub 2015 Dec 12.

PMID:
26285051
42.

GNE myopathy in Roma patients homozygous for the p.I618T founder mutation.

Chamova T, Guergueltcheva V, Gospodinova M, Krause S, Cirak S, Kaprelyan A, Angelova L, Mihaylova V, Bichev S, Chandler D, Naydenov E, Grudkova M, Djukmedzhiev P, Voit T, Pogoryelova O, Lochmüller H, Goebel HH, Bahlo M, Kalaydjieva L, Tournev I.

Neuromuscul Disord. 2015 Sep;25(9):713-8. doi: 10.1016/j.nmd.2015.07.004. Epub 2015 Jul 13.

PMID:
26231298
43.

Cpipe: a shared variant detection pipeline designed for diagnostic settings.

Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.

Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x. eCollection 2015.

44.

Myoclonic occipital photosensitive epilepsy with dystonia (MOPED): A familial epilepsy syndrome.

Sadleir LG, Paterson S, Smith KR, Redshaw N, Ranta A, Kalnins R, Berkovic SF, Bahlo M, Hildebrand MS, Scheffer IE.

Epilepsy Res. 2015 Aug;114:98-105. doi: 10.1016/j.eplepsyres.2015.04.014. Epub 2015 May 5.

PMID:
26088892
45.

High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA.

Chandrananda D, Thorne NP, Bahlo M.

BMC Med Genomics. 2015 Jun 17;8:29. doi: 10.1186/s12920-015-0107-z.

46.

Familial cortical dysplasia type IIA caused by a germline mutation in DEPDC5.

Scerri T, Riseley JR, Gillies G, Pope K, Burgess R, Mandelstam SA, Dibbens L, Chow CW, Maixner W, Harvey AS, Jackson GD, Amor DJ, Delatycki MB, Crino PB, Berkovic SF, Scheffer IE, Bahlo M, Lockhart PJ, Leventer RJ.

Ann Clin Transl Neurol. 2015 May;2(5):575-80. doi: 10.1002/acn3.191. Epub 2015 Mar 12.

47.

Mutation of the nuclear lamin gene LMNB2 in progressive myoclonus epilepsy with early ataxia.

Damiano JA, Afawi Z, Bahlo M, Mauermann M, Misk A, Arsov T, Oliver KL, Dahl HH, Shearer AE, Smith RJ, Hall NE, Mahmood K, Leventer RJ, Scheffer IE, Muona M, Lehesjoki AE, Korczyn AD, Herrmann H, Berkovic SF, Hildebrand MS.

Hum Mol Genet. 2015 Aug 15;24(16):4483-90. doi: 10.1093/hmg/ddv171. Epub 2015 May 7.

48.

Identical by descent L1CAM mutation in two apparently unrelated families with intellectual disability without L1 syndrome.

Shaw M, Yap TY, Henden L, Bahlo M, Gardner A, Kalscheuer VM, Haan E, Christie L, Hackett A, Gecz J.

Eur J Med Genet. 2015 Jun-Jul;58(6-7):364-8. doi: 10.1016/j.ejmg.2015.04.004. Epub 2015 Apr 28.

PMID:
25934484
49.

Hemispheric cortical dysplasia secondary to a mosaic somatic mutation in MTOR.

Leventer RJ, Scerri T, Marsh AP, Pope K, Gillies G, Maixner W, MacGregor D, Harvey AS, Delatycki MB, Amor DJ, Crino P, Bahlo M, Lockhart PJ.

Neurology. 2015 May 19;84(20):2029-32. doi: 10.1212/WNL.0000000000001594. Epub 2015 Apr 15.

50.

Plasmodium vivax populations are more genetically diverse and less structured than sympatric Plasmodium falciparum populations.

Jennison C, Arnott A, Tessier N, Tavul L, Koepfli C, Felger I, Siba PM, Reeder JC, Bahlo M, Mueller I, Barry AE.

PLoS Negl Trop Dis. 2015 Apr 15;9(4):e0003634. doi: 10.1371/journal.pntd.0003634. eCollection 2015 Apr.

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