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Items: 43

1.

Point-of-care whole-exome sequencing of idiopathic male infertility.

Fakhro KA, Elbardisi H, Arafa M, Robay A, Rodriguez-Flores JL, Al-Shakaki A, Syed N, Mezey JG, Abi Khalil C, Malek JA, Al-Ansari A, Al Said S, Crystal RG.

Genet Med. 2018 Apr 12. doi: 10.1038/gim.2018.10. [Epub ahead of print]

PMID:
29790874
2.

Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population.

Yousri NA, Fakhro KA, Robay A, Rodriguez-Flores JL, Mohney RP, Zeriri H, Odeh T, Kader SA, Aldous EK, Thareja G, Kumar M, Al-Shakaki A, Chidiac OM, Mohamoud YA, Mezey JG, Malek JA, Crystal RG, Suhre K.

Nat Commun. 2018 Jan 23;9(1):333. doi: 10.1038/s41467-017-01972-9.

3.

Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation.

Zaghlool SB, Mook-Kanamori DO, Kader S, Stephan N, Halama A, Engelke R, Sarwath H, Al-Dous EK, Mohamoud YA, Roemisch-Margl W, Adamski J, Kastenmüller G, Friedrich N, Visconti A, Tsai PC, Spector T, Bell JT, Falchi M, Wahl A, Waldenberger M, Peters A, Gieger C, Pezer M, Lauc G, Graumann J, Malek JA, Suhre K.

Hum Mol Genet. 2018 Mar 15;27(6):1106-1121. doi: 10.1093/hmg/ddy006.

4.

Mutation in noncoding RNA RNU12 causes early onset cerebellar ataxia.

Elsaid MF, Chalhoub N, Ben-Omran T, Kumar P, Kamel H, Ibrahim K, Mohamoud Y, Al-Dous E, Al-Azwani I, Malek JA, Suhre K, Ross ME, Aleem AA.

Ann Neurol. 2017 Jan;81(1):68-78. doi: 10.1002/ana.24826.

PMID:
27863452
5.

Correction: Type 2 Diabetes Risk Allele Loci in the Qatari Population.

O'Beirne SL, Salit J, Rodriguez-Flores JL, Staudt MR, Abi Khalil C, Fakhro KA, Robay A, Ramstetter MD, Al-Azwani IK, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Chiuchiolo MJ, Al-Shakaki A, Chidiac O, Gharbiah M, Bener A, Stadler D, Hackett NR, Mezey JG, Crystal RG.

PLoS One. 2016 Aug 23;11(8):e0161910. doi: 10.1371/journal.pone.0161910. eCollection 2016.

6.

The Qatar genome: a population-specific tool for precision medicine in the Middle East.

Fakhro KA, Staudt MR, Ramstetter MD, Robay A, Malek JA, Badii R, Al-Marri AA, Abi Khalil C, Al-Shakaki A, Chidiac O, Stadler D, Zirie M, Jayyousi A, Salit J, Mezey JG, Crystal RG, Rodriguez-Flores JL.

Hum Genome Var. 2016 Jun 30;3:16016. doi: 10.1038/hgv.2016.16. eCollection 2016.

7.

Type 2 Diabetes Risk Allele Loci in the Qatari Population.

O'Beirne SL, Salit J, Rodriguez-Flores JL, Staudt MR, Abi Khalil C, Fakhro KA, Robay A, Ramstetter MD, Al-Azwani IK, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Chiuchiolo MJ, Al-Shakaki A, Chidiac O, Gharbiah M, Bener A, Stadler D, Hackett NR, Mezey JG, Crystal RG.

PLoS One. 2016 Jul 6;11(7):e0156834. doi: 10.1371/journal.pone.0156834. eCollection 2016. Erratum in: PLoS One. 2016;11(8):e0161910.

8.

Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma.

Ahmed I, Karedath T, Andrews SS, Al-Azwani IK, Mohamoud YA, Querleu D, Rafii A, Malek JA.

Oncotarget. 2016 Jun 14;7(24):36366-36381. doi: 10.18632/oncotarget.8917.

9.

Correction: Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.

Halabi NM, Martinez A, Al-Farsi H, Mery E, Puydenus L, Pujol P, Khalak HG, McLurcan C, Ferron G, Querleu D, Al-Azwani I, Al-Dous E, Mohamoud YA, Malek JA, Rafii A.

PLoS Genet. 2016 Feb 18;12(2):e1005892. doi: 10.1371/journal.pgen.1005892. eCollection 2016 Feb. No abstract available.

10.

Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer.

Halabi NM, Martinez A, Al-Farsi H, Mery E, Puydenus L, Pujol P, Khalak HG, McLurcan C, Ferron G, Querleu D, Al-Azwani I, Al-Dous E, Mohamoud YA, Malek JA, Rafii A.

PLoS Genet. 2016 Jan 6;12(1):e1005755. doi: 10.1371/journal.pgen.1005755. eCollection 2016 Jan. Erratum in: PLoS Genet. 2016 Feb;12(2):e1005892.

11.

Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations.

Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG.

Genome Res. 2016 Feb;26(2):151-62. doi: 10.1101/gr.191478.115. Epub 2016 Jan 4.

12.

Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.

Hazzouri KM, Flowers JM, Visser HJ, Khierallah HS, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD.

Nat Commun. 2015 Nov 9;6:8824. doi: 10.1038/ncomms9824.

13.

Copy number variations in the genome of the Qatari population.

Fakhro KA, Yousri NA, Rodriguez-Flores JL, Robay A, Staudt MR, Agosto-Perez F, Salit J, Malek JA, Suhre K, Jayyousi A, Zirie M, Stadler D, Mezey JG, Crystal RG.

BMC Genomics. 2015 Oct 22;16:834. doi: 10.1186/s12864-015-1991-5.

14.

A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera.

Mathew LS, Seidel MA, George B, Mathew S, Spannagl M, Haberer G, Torres MF, Al-Dous EK, Al-Azwani EK, Diboun I, Krueger RR, Mayer KF, Mohamoud YA, Suhre K, Malek JA.

G3 (Bethesda). 2015 May 8;5(7):1429-38. doi: 10.1534/g3.115.018341.

15.

K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores.

Emerson AI, Andrews S, Ahmed I, Azis TK, Malek JA.

J Clin Bioinforma. 2015 Mar 3;5:1. doi: 10.1186/s13336-015-0016-6. eCollection 2015.

16.

Metabolomics of Ramadan fasting: an opportunity for the controlled study of physiological responses to food intake.

Mathew S, Krug S, Skurk T, Halama A, Stank A, Artati A, Prehn C, Malek JA, Kastenmüller G, Römisch-Margl W, Adamski J, Hauner H, Suhre K.

J Transl Med. 2014 Jun 6;12:161. doi: 10.1186/1479-5876-12-161.

17.

Where cancer genomics should go next: a clinician's perspective.

Rafii A, Touboul C, Al Thani H, Suhre K, Malek JA.

Hum Mol Genet. 2014 Sep 15;23(R1):R69-75. doi: 10.1093/hmg/ddu234. Epub 2014 May 15. Review.

PMID:
24833724
18.

A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms.

Mathew LS, Spannagl M, Al-Malki A, George B, Torres MF, Al-Dous EK, Al-Azwani EK, Hussein E, Mathew S, Mayer KF, Mohamoud YA, Suhre K, Malek JA.

BMC Genomics. 2014 Apr 15;15:285. doi: 10.1186/1471-2164-15-285.

19.

Whole genome sequencing identifies a novel occludin mutation in microcephaly with band-like calcification and polymicrogyria that extends the phenotypic spectrum.

Elsaid MF, Kamel H, Chalhoub N, Aziz NA, Ibrahim K, Ben-Omran T, George B, Al-Dous E, Mohamoud Y, Malek JA, Ross ME, Aleem AA.

Am J Med Genet A. 2014 Jun;164A(6):1614-7. doi: 10.1002/ajmg.a.36485. Epub 2014 Mar 25. No abstract available.

PMID:
24668585
20.

Mesenchymal cell interaction with ovarian cancer cells induces a background dependent pro-metastatic transcriptomic profile.

Lis R, Touboul C, Halabi NM, Madduri AS, Querleu D, Mezey J, Malek JA, Suhre K, Rafii A.

J Transl Med. 2014 Mar 5;12:59. doi: 10.1186/1479-5876-12-59.

21.

Longitudinal study of recurrent metastatic melanoma cell lines underscores the individuality of cancer biology.

Pos Z, Spivey TL, Liu H, Sommariva M, Chen J, Wunderlich JR, Parisi G, Tomei S, Ayotte BD, Stroncek DF, Malek JA, Robbins PF, Rivoltini L, Maio M, Chouchane L, Wang E, Marincola FM.

J Invest Dermatol. 2014 May;134(5):1389-1396. doi: 10.1038/jid.2013.495. Epub 2013 Nov 22.

22.

Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar.

Rodriguez-Flores JL, Fakhro K, Hackett NR, Salit J, Fuller J, Agosto-Perez F, Gharbiah M, Malek JA, Zirie M, Jayyousi A, Badii R, Al-Nabet Al-Marri A, Chouchane L, Stadler DJ, Mezey JG, Crystal RG.

Hum Mutat. 2014 Jan;35(1):105-16. doi: 10.1002/humu.22460. Epub 2013 Nov 10.

23.

Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population.

Rodriguez-Flores JL, Fuller J, Hackett NR, Salit J, Malek JA, Al-Dous E, Chouchane L, Zirie M, Jayoussi A, Mahmoud MA, Crystal RG, Mezey JG.

PLoS One. 2012;7(11):e47614. doi: 10.1371/journal.pone.0047614. Epub 2012 Nov 6.

24.

High-prevalence and broad spectrum of Cell Adhesion and Extracellular Matrix gene pathway mutations in epithelial ovarian cancer.

Rafii A, Halabi NM, Malek JA.

J Clin Bioinforma. 2012 Sep 24;2(1):15. doi: 10.1186/2043-9113-2-15.

25.

Gene expression analysis of matched ovarian primary tumors and peritoneal metastasis.

Malek JA, Martinez A, Mery E, Ferron G, Huang R, Raynaud C, Jouve E, Thiery JP, Querleu D, Rafii A.

J Transl Med. 2012 Jun 11;10:121. doi: 10.1186/1479-5876-10-121.

26.

Mesenchymal cell interaction with ovarian cancer cells triggers pro-metastatic properties.

Lis R, Touboul C, Raynaud CM, Malek JA, Suhre K, Mirshahi M, Rafii A.

PLoS One. 2012;7(5):e38340. doi: 10.1371/journal.pone.0038340. Epub 2012 May 30.

27.

DNA-based assays to distinguish date palm (Arecaceae) gender.

Al-Mahmoud ME, Al-Dous EK, Al-Azwani EK, Malek JA.

Am J Bot. 2012 Jan;99(1):e7-10. doi: 10.3732/ajb.1100425. Epub 2011 Dec 27.

28.

Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis.

Malek JA, Mery E, Mahmoud YA, Al-Azwani EK, Roger L, Huang R, Jouve E, Lis R, Thiery JP, Querleu D, Rafii A.

PLoS One. 2011;6(12):e28561. doi: 10.1371/journal.pone.0028561. Epub 2011 Dec 14.

29.

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera).

Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J, Arondel V, Ohlrogge J, Saie IJ, Suliman-Elmeer KM, Bennetzen JL, Kruegger RR, Malek JA.

Nat Biotechnol. 2011 May 29;29(6):521-7. doi: 10.1038/nbt.1860.

PMID:
21623354
30.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP.

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109. Epub 2009 Jun 22.

31.

Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM.

Genome Res. 2008 Oct;18(10):1638-42. doi: 10.1101/gr.077776.108. Epub 2008 Sep 4.

32.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM.

Genome Res. 2008 Jul;18(7):1051-63. doi: 10.1101/gr.076463.108. Epub 2008 May 13.

33.

The complete genome sequence and analysis of the epsilonproteobacterium Arcobacter butzleri.

Miller WG, Parker CT, Rubenfield M, Mendz GL, Wösten MM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, Rogosin A, Stanker LH, Mandrell RE.

PLoS One. 2007 Dec 26;2(12):e1358.

34.

Gene expression profiling studies on Caenorhabditis elegans dystrophin mutants dys-1(cx-35) and dys-1(cx18).

Towers PR, Lescure P, Baban D, Malek JA, Duarte J, Jones E, Davies KE, Ségalat L, Sattelle DB.

Genomics. 2006 Nov;88(5):642-9. Epub 2006 Sep 7.

35.

Annotation of novel proteins utilizing a functional genome shotgun coupled with high-throughput protein interaction mapping.

Malek JA, Wierzbowski JM, Dasch GA, Eremeva ME, McEwan PJ, McKernan KJ.

Cold Spring Harb Symp Quant Biol. 2003;68:331-4. No abstract available.

PMID:
15338634
36.

Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica.

Malek JA, Wierzbowski JM, Tao W, Bosak SA, Saranga DJ, Doucette-Stamm L, Smith DR, McEwan PJ, McKernan KJ.

Nucleic Acids Res. 2004 Feb 10;32(3):1059-64. Print 2004.

37.

Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.

Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madan A, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA; Mammalian Gene Collection Program Team.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

38.

The genome sequence of the malaria mosquito Anopheles gambiae.

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL.

Science. 2002 Oct 4;298(5591):129-49.

39.

A physical map of the mouse genome.

Gregory SG, Sekhon M, Schein J, Zhao S, Osoegawa K, Scott CE, Evans RS, Burridge PW, Cox TV, Fox CA, Hutton RD, Mullenger IR, Phillips KJ, Smith J, Stalker J, Threadgold GJ, Birney E, Wylie K, Chinwalla A, Wallis J, Hillier L, Carter J, Gaige T, Jaeger S, Kremitzki C, Layman D, Maas J, McGrane R, Mead K, Walker R, Jones S, Smith M, Asano J, Bosdet I, Chan S, Chittaranjan S, Chiu R, Fjell C, Fuhrmann D, Girn N, Gray C, Guin R, Hsiao L, Krzywinski M, Kutsche R, Lee SS, Mathewson C, McLeavy C, Messervier S, Ness S, Pandoh P, Prabhu AL, Saeedi P, Smailus D, Spence L, Stott J, Taylor S, Terpstra W, Tsai M, Vardy J, Wye N, Yang G, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Shvartsbeyn A, Gebregeorgis E, Krol M, Russell D, Overton L, Malek JA, Holmes M, Heaney M, Shetty J, Feldblyum T, Nierman WC, Catanese JJ, Hubbard T, Waterston RH, Rogers J, de Jong PJ, Fraser CM, Marra M, McPherson JD, Bentley DR.

Nature. 2002 Aug 15;418(6899):743-50. Epub 2002 Aug 4.

PMID:
12181558
40.

Mouse BAC ends quality assessment and sequence analyses.

Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA, Feldblyum T, Nierman WC, Fraser CM.

Genome Res. 2001 Oct;11(10):1736-45. Erratum in: Genome Res 2001 Nov;11(11):1968.

41.

Abundant protein domains occur in proportion to proteome size.

Malek JA.

Genome Biol. 2001;2(9):RESEARCH0039. Epub 2001 Aug 24.

42.

Degradation of persistent RNA in RNase-containing, high-throughput alkaline lysis DNA preparations.

Malek JA, Shatsman SY, Akinretoye BA, Gill JE.

Biotechniques. 2000 Aug;29(2):250-2. No abstract available.

PMID:
10948425
43.

Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM.

Nature. 1999 May 27;399(6734):323-9.

PMID:
10360571

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