research-student

Publications

Recent peer-reviewed and book publications (2009/2016)

1. Kasimoglu E, Park SJ, Malek J, Tseng CP, Gunsalus RP. Transcriptional regulation of the proton-translocating ATPase (atpIBEFHAGDC) operon of Escherichia coli: control by cell growth rate. Journal of Bacteriology. 1996;178(19):5563-7. JIP: 3.726

2. 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, et al. Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature. 1999;399(6734):323-9. JIP: 36.104

3. Zhao S, Malek J, Mahairas G, Fu L, Nierman W, Venter JC, et al. Human BAC ends quality assessment and sequence analyses. Genomics. 2000;63(3):321-32. JIP: 3.327

4. Malek JA, Shatsman SY, Akinretoye BA, Gill JE. Degradation of persistent RNA in RNase-containing, high-throughput alkaline lysis DNA preparations. BioTechniques. 2000;29(2):250-2. JIP: 2.550

5. Gaspard R, Dharap S, Malek J, Qi R, Quackenbush J. Optimized growth conditions for direct amplification of cDNA clone inserts from culture. BioTechniques. 2001;31(1):35-6. JIP: 2.550

6. 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, et al. Mouse BAC ends quality assessment and sequence analyses. Genome Research. 2001;11(10):1736-45. JIP: 13.588

7. Malek JA. Abundant protein domains occur in proportion to proteome size. Genome Biology. 2001;2(9):research0039.1-research.5-research.1-research.5. JIP: 6.885

8. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD, Dodson RJ, Umayam L, Brinkac LM, Beanan MJ, Daugherty SC, Deboy TR, Durkin AS, Kolonay JF, Madupu R, Nelson WC, Ayodeji B, Kraul M, Shetty J, Malek J, et al. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proceedings of the National Academy of Sciences of the United States of America. 2002;99(20):13148-53. JIP: 9.771

9. 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, Chatuverdi 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,et al. The genome sequence of the malaria mosquito Anopheles gambiae. Science (New York, NY). 2002;298(5591):129-49. JIP 31.377

10. 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 ,et al. A physical map of the mouse genome. Nature. 2002;418(6899):743-50. JIP: 36.104

11. 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, et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 2002;99(26):16899-903. JIP: 9.771

12. Sidjanin DJ, Miller B, Kijas J, McElwee J, Pillardy J, Malek J, et al. Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17. Genomics. 2003;81(2):138-48. JIP: 3.327

13. Malek JA, Wierzbowski JM, Dasch GA, Eremeva ME, McEwan PJ, McKernan KJ. Annotation of novel proteins utilizing a functional genome shotgun coupled with high-throughput protein interaction mapping. Cold Spring Harbor Symposia on Quantitative Biology. 2003;68:331-4. JIP: n/a

14. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Research. 2004;14(10B):2121-7. JIP: 13.588

15. Seshadri R, Myers GSA, Tettelin H, Eisen JA, Heidelberg JF, Dodson RJ, Davidsen TM, DeBoy RT, Fouts DE, Haft DH, Selengut J, Ren Q, Brinkac LM, Madupu R, Kolonay J, Durkin SA, Daugherty SC, Shetty J, Shvartsbeyn A, Gebregeorgis E, Geer K, Tsegaye G, Malek J, et al. Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proceedings of the National Academy of Sciences of the United States of America. 2004;101(15):5646-51. JIP: 9.771

16. Malek JA, Wierzbowski JM, Tao W, Bosak SA, Saranga DJ, Doucette-Stamm L, et al. Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. Nucleic Acids Research. 2004;32(3):1059-64. JIP: 7.836

17. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, et al. Sequencing genomes from single cells by polymerase cloning. Nat Biotech. 2006;24(6):680-6. JIP: n/a

18. Miller WG, Parker CT, Rubenfield M, Mendz GL, Wösten MMSM, Ussery DW, Stolz JF, Binnewies TT, Hallin PF, Wang G, Malek JA, et al. The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri. PLoS ONE. 2007;2(12). JIP: 4.411

19. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research. 2008;18(7):1051-63. JIP: 13.588

20. Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, et al. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biology. 2009;10(10):R103-R. JIP: 6.885

21. 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, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research. 2009;19(9):1527-41. JIP: 13.588

22. Lis R, Touboul C, Mirshahi P, Ali F, Mathew S, Nolan DJ, Maleki M, Abdalla SA, Raynaud CM, Querleu D, Al-Azwani E, Malek J, et al. Tumor associated mesenchymal stem cells protects ovarian cancer cells from hyperthermia through CXCL12. International Journal of Cancer Journal International Du Cancer. 2011;128(3):715-25. JIP: 4.926

23. Elmeer K, Sarwath H, Malek J, Baum M, Hamwieh A. New microsatellite markers for assessment of genetic diversity in date palm (Phoenix dactylifera L.). 3 Biotech. 2011;1(2):91-7. JIP: n/a

24. Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh Y, et a Al-Azwani E, Chaluvadi S, Pontaroli A, DeBarry J, Arondel V, Ohlrogge J, Saie I, Suliman-Elmeer K, Bennetzen J, Kruegger R, Malek JA . De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nature Biotechnology. 2011;29(6):521-7. JIP: 31.090

25. Malek JA, Mery E, Mahmoud YA, Al-Azwani EK, Roger L, Huang R, et al. Copy number variation analysis of matched ovarian primary tumors and peritoneal metastasis. PloS One. 2011;6(12):e28561-e. JIP: 4.411

26. Al-Mahmoud ME, Al-Dous EK, Al-Azwani EK, Malek JA. DNA-based assays to distinguish date palm (Arecaceae) gender. American Journal of Botany. 2012;99(1):e7-e10-e7-e. JIP: 3.052

27. Lis R, Touboul C, Raynaud CM, Malek J, Suhre K, Mirshahi M, Rafii A. Mesenchymal cell interaction with ovarian cancer cells triggers pro-metastatic properties. PLoS one [Internet]. 2012 May 30 [cited 2012 Jun 7]; 7(5):e38340 [10 p.]. Available from:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038340.

28. JIP: 4.092

29. Malek J, Martinez A, Eliane M, Raynaud CM, Huang R, Jouve E, Ferron G, Thiery JP, Querleu D, Rafii A. Gene expression analysis of matched ovarian primary tumors and peritoneal metastasis. Journal of translational medicine [Internet]. 2012 Jun 11 [cited 2012 Jul 24]; 10:121 [18 p.]. Available from:http://www.translational-medicine.com/content/10/1/121/abstract. JIP: 3.474

30. Raynaud CM, Maleki M, Lis R, Ahmed B, Al-Azwani I, Malek J, Safadi FF, Rafii A. Comprehensive characterization of mesenchymal stem cells from human placenta and fetal membrane and their response to osteoactivin stimulation. Stem cells international [Internet]. 2012 Mar 30 [cited 2012 Jul 24]; 2012:658356 [13 p.]. Available from: http://www.hindawi.com/journals/sci/2012/658356/.JIP: N/A

31. Rafii A, Halabi NM, Malek JA. High-prevalence and broad spectrum of cell adhesion and extracellular matrix gene pathway mutations in epithelial ovarian cancer. Journal of clinical bioinformatics [Internet]. 2012 Sep 24 [cited 2012 Oct 15]; 2(1):15 [0 p.] [Epub ahead of print]. Available from: http://www.jclinbioinformatics.com/content/2/1/15/abstract. JIP: N/A

32. 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.  Exome sequencing of only seven Qataris identifies potentially deleterious variants in the Qatari population. PLoS One. 2012 7(11):e47614. doi: 10.1371/journal.pone.0047614

33. Shan J, Dsouza SP, Bakhru S, Al-Azwani EK, Ascierto ML, Sastry KS, Bedri S, Kizhakayil D, Aigha II, Malek J, Al-Bozom I, Gehani S, Furtado S, Mathiowitz E, Wang E, Marincola FM, Chouchane L. TNRC9 downregulates BRCA1 expression and promotes breast cancer aggressiveness. Cancer Res. 2013 May 1;73(9):2840-9. doi: 10.1158/0008-5472.CAN-12-4313. Epub 2013 Feb 27. PubMed PMID: 23447579.

34. 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. Longitudinal Study of Recurrent Metastatic Melanoma Cell Lines Underscores the Individuality of Cancer Biology. J Invest Dermatol. 2013 Nov 22. doi: 10.1038/jid.2013.495. [Epub ahead of print] PubMed PMID: 24270663.

35. 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. Exome sequencing identifies potential risk variants for Mendelian disorders at high prevalence in Qatar. Hum Mutat. 2014 Jan;35(1):105-16. doi: 10.1002/humu.22460. Epub 2013 Nov 10. PubMed PMID: 24123366; PubMed Central PMCID: PMC3908915.

36. Abou Ziki MD, Strulovici-Barel Y, Hackett NR, Rodriguez-Flores JL, Mezey JG, Salit J, Radisch S, Hollmann C, Chouchane L, Malek J, Zirie MA, Jayyuosi A, Gotto AM Jr, Crystal RG. Prevalence of the apolipoprotein E Arg145Cys dyslipidemia at-risk polymorphism in African-derived populations. Am J Cardiol. 2014 Jan 15;113(2):302-8. doi: 10.1016/j.amjcard.2013.09.021. Epub 2013 Oct 3. PubMed PMID: 24239320; PubMed Central PMCID: PMC3943837.

37. Lis R, Touboul C, Halabi NM, Madduri AS, Querleu D, Mezey J, Malek JA, Suhre K, Rafii A. Mesenchymal cell interaction with ovarian cancer cells induces a background dependent pro-metastatic transcriptomic profile. J Transl Med. 2014 Mar 5;12(1):59. doi: 10.1186/1479-5876-12-59. PubMed PMID: 24597747.

38. Elsaid MF(1), Kamel H, Chalhoub N, Aziz NA, Ibrahim K, Ben-Omran T, George B, Al-Dous E, Mohamoud Y, Malek JA, Ross ME, Aleem AA (2014). Whole genome sequencing identifies a novel occludin mutation in microcephaly with band-like calcification and polymicrogyria that extends the phenotypic spectrum. Am J Med Genet A. 2014 Mar 25. doi: 10.1002/ajmg.a.36485.

39. 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. (2014) Metabolomics of Ramadan fasting: an opportunity for the controlled study of physiological responses to food intake. J Transl Med. 2014 Jun 6;12:161. doi: 10.1186/1479-5876-12-161.

40. 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 (2014). A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genomics. 2014 Apr 15;15:285. doi: 10.1186/1471-2164-15-285

41. Rafii A, Touboul C, Al Thani H, Suhre K, Malek JA. (2014) Where cancer genomics should go next: a clinician's perspective. Hum Mol Genet. 2014 Sep 15;23(R1):R69-75. doi: 10.1093/hmg/ddu234. Epub 2014 May 15.

42. Emerson AI, Andrews S, Ahmed I, Azis T, Malek JA. (2015) K-core decomposition of a protein domain co-occurrence network reveals lower cancer mutation rates for interior cores. Journal of Clinical Bioinformatics 2015, 5:1 (3 March 2015) doi:10.1186/s13336-015-0016-6

43. 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. (2015) A Genome-Wide Survey of Date Palm Cultivars Supports Two Major Subpopulations in Phoenix dactylifera. G3 (Bethesda). May 8;5(7):1429-38. doi: 10.1534/g3.115.018341. PubMed PMID: 25957276; PubMed Central PMCID: PMC4502377.

44. 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. (2015) Copy number variations in the genome of the Qatari population. BMC Genomics. Oct 22;16(1):834. doi: 10.1186/s12864-015-1991-5. PubMed PMID: 26490036; PubMed Central PMCID: PMC4618522

45. 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. (2015) Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat Commun. Nov 9;6:8824. doi: 10.1038/ncomms9824. PubMed PMID: 26549859; PubMed Central PMCID: PMC4667612

46. Diboun I, Mathew S, Al-Rayyashi M, Elrayess M, Torres M, Halama A, Méret M, Mohney RP, Karoly ED, Malek J, Suhre K. (2015) Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition. BMC Plant Biol. Dec 16;15(1):291. doi: 10.1186/s12870-015-0672-5. PubMed PMID: 26674306; PubMed Central PMCID: PMC4681049

47. 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. (2016) Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer. PLoS Genet. 2016 Jan 6;12(1):e1005755. doi: 10.1371/journal.pgen.1005755. eCollection 2016 Jan. Erratum in: PLoS Genet. Feb;12(2):e1005892. PubMed PMID: 26735499; PubMed Central PMCID: PMC4703369.

48. 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. (2016) Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res. Feb;26(2):151-62. doi: 10.1101/gr.191478.115. Epub 2016 Jan 4. PubMed PMID: 26728717; PubMed Central PMCID: PMC4728368

49. 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. (2016) The Qatar genome: a population-specific tool for precision medicine in the Middle East. Hum Genome Var. 2016 Jun 30;3:16016. doi: 10.1038/hgv.2016.16. eCollection 2016. PMID: 27408750 Free PMC Article

50. Ahmed I, Karedath T, Andrews SS, Al-Azwani IK, Ali Mohamoud Y, Querleu D, Rafii A, Malek JA. (2016) Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma. Oncotarget. 2016 Apr 22. doi: 10.18632/oncotarget.8917. [Epub ahead of print]