Genomics CoreJoel Malek, MS
Assistant Professor of Genetic Medicine
Director of the Genomics Laboratory
Telephone: +974 4492 8420
Phone: (974) 4492 8321
The genomics core laboratory provides a full range of modern genomics analysis. Projects are conducted in collaboration with investigators to use the right technology for their project. With a suite of the latest high throughput genomics analysis technologies, the Genomics Core is continually implementing or developing applications to answer new questions.
The genomics core laboratory is equipped with the latest genomic analysis equipment including Next Generation DNA Sequencing, Microarrays, High-Throughput Real Time PCR, Liquid Handling Robots, etc. The laboratory is currently implementing an end to end Laboratory Information Management System (LIMS) giving investigators real time access to data and chain of custody information.
Joel A. Malek
I’m the Assistant Professor of Genetic Medicine and Director of the Genomics Laboratory at Weill Cornell Medicine - Qatar (WCM-Q). I received my B.S. in Microbiology and Molecular Genetics from UCLA and my M.S. in Biotechnology from the Johns Hopkins University. Prior to joining WCM-Q, I held positions at the Institute for Genomic Research, Agencourt Bioscience, and Applied Biosystems. I was involved in the Human Genome Project and the development of Next Generation DNA sequencing technologies. My research focuses on the development, application, and data analysis of genomic technologies.
I’m the Manager of the Genomics Core at the Weill Cornell Medicine - Qatar (WCM-Q). Prior to joining WCM-Q, I was a Bioinformatics Project Manager at the National Institutes of Allergy and Infectious Diseases (NIAID) working with NIH researchers on bioinformatics and data analysis projects. Before the NIH, I held positions at the Institute for Genomic research (TIGR) where I participated in the sequencing and finishing of many prokaryotic genomes and contributed to the development of Next Generation sequence data analysis pipeline. My educational background includes a B.S. in Biochemical Pharmacology from the State University of New York at Buffalo, an M.S. in Biotechnology with concentration in Bioinformatics from the Johns Hopkins University, and an Associate’s Certificate in Project Management from George Washington University.
Eman Khalid Al-Azwani
I’m a Biomedical graduate from Qatar University. I have been working as Research Specialist in the Genomics core since Oct 2008. My pervious experience includes working in the Molecular Lab in HMC, where I was involved in developing “a rapid genotyping assay for Cystic Fibrosis Ile1234Val mutation by Real-Time PCR”. Right now I’m working on two technologies: U133 gene expression Microarray and High throughput SNP genotyping using 7900HT-Real-Time PCR and JANUS liquid Handling Robot, for two projects (Type II diabetes and Population genetic structure of people of Qatar). Recently, I started working on Cell culture and ChIP-Chip.
I’m a Research Specialist in the Genomics Core Lab since Oct 2008. Graduated with a Bachelor's Degree in Biomedical Sciences from Qatar University. Previous experience involved conducting a research on the Application of FISH Technique "Fluorescence in Situ Hybridization" in Invasive Breast Cancer Diagnosis.
Since joined WCM-Q, I have been involved in multiple projects including the Date Palm Project, recently published article in Nature Biotechnology on June 2011 issue, De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera), Volume 29 Number 6, pp521 - 527. Moreover my work concentration is on the field of Epigenetics, currently working on Diabetes Epigenetics and Folic Acid Epigenetics.
I am a Bioinformatics Data Analyst of the Genomics Core. I obtained my Bachelor's Degree in Information Science and Engineering from Visveswaraiah University, India. My previous experience was as a software engineer with Hewlett Packard in Bangalore, India. In my experiences here, I've been involved in the deNovo assembly of the Date Palm genome, rnaSeq analysis and whole exome capture analysis of the human genome. My life outside Cornell is filled with music, movies, stitching, crocheting and social networking.
- Whole genome expression profiling
- SNP genotyping
- Copy number variations
- Deep Sequencing
- Gene expression analysis
- Library construction
Recent peer-reviewed and book publications (2009/2010)
- 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. J. Bacteriol 1996;178:5563 – 5567.
- 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;399:323 – 329.
- Zhao S, Malek J, Mahairas G, Fu L, Nierman W, Venter JC, Adams MD. Human BAC Ends Quality Assessment and Sequence Analysis. Genomics 2000;63(3):321-332.
- 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):250-252.
- 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):35-36.
- 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. Mouse BAC Ends Quality Assessment and Sequence Analyses. Genome Res. 2001;11(10):1736-1745.
- Malek JA. Conserved protein domains are maintained in an average ratio to proteome size. Genome Biology 2001; 2(5):research 0039.1-0039.5.
- 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. Proc Natl Acad Sci U S A 2002;99(20):13148-53.
- 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 2002;298(5591):129-49.
- 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 JOEL MALEK, M.S. PUBLICATIONS - 2 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, 743 – 750.
- 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. Proc Natl Acad Sci USA 2002;99(26):16899-903.
- Sidjanin DJ, Miller B, Kijas J, McElwee J, Pillardy J, Malek J, Pai G, Feldblyum T, Fraser C, Acland G, Aguirre G. 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.
- Malek JA, Wierzbowski JM, Dasch GA, Eremeeva ME, Mcewan PJ, McKernan KJ. Annotation of Novel Proteins Utilizing a Functional Genome Shotgun Coupled with High-throughput Protein Interaction Mapping. Cold Spring Harb Symp Quant Biol 2003;68:331-4.
- MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004;14(10B):2121-7.
- Seshadri R, Myers GS, 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. Proc Natl Acad Sci U S A 2004;101(15):5646-51
- Malek JA, Wierzbowski JM, Tao W, Bosak SA, Saranga DJ, Doucette- Stamm L, Smith DR, McEwan PJ, McKernan KJ. Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica. Nucleic Acids Res. 2004; 32(3):1059-64.
- Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol. 2006 May 28.
- 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. The Complete Genome Sequence and Analysis of the Epsilonproteobacterium Arcobacter butzleri. PLoS ONE 2007;2(12):e1358.
- 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 .A highresolution, nucleosome position map of C. elegans reveals a lack of universal JOEL MALEK, M.S.
PUBLICATIONS - 3
sequence-dictated positioning. Genome Res. 2008; 18(7):1051-63.Maccallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol. 2009;10(10):R103.
- 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 Res. 2009;19(9):1527-41.
- 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, Mirshahi M, Rafii A. Tumor associated mesenchymal stem cells protects ovarian cancer cells from hyperthermia through CXCL12. International Journal of Cancer. 2011 Feb 1;128(3):715-25.
- Al-Dous E, George B, Al-Mahmoud M, Al-Jaber M, Wang H, Salameh Y, 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 the date palm (Phoenix dactylifera). Nature Biotechnology. Forthcoming 2011.
The date palm is one of the oldest cultivated trees in the world, with evidence of domestication dating back >5,000 years. The discovery of dates in the tombs of pharaohs and in neolithic sites dating from 7,000 to 8,000 years ago demonstrates the historical significance of the species to human nutrition. Date palm trees are critical to agriculture in many hot and arid regions, and dates are the most important agricultural product of many countries in the Arabian Gulf. Total global production of dates in 2007 was 6.9 million tons (http://faostat.fao.org/ ).
However, date palm biotechnology faces many challenges, including long generation times, the inability to simply distinguish between the many varieties of date palm and the inability to distinguish female from male trees at an early stage. There are >2,000 date varieties with differences in color, flavor, shape, size and ripening time and the genetic component of gender determination is not well understood. Specifically, date palms take 5–8 years after planting to flower, the earliest point at which male and female trees can be distinguished. Especially because date palm orchards, which primarily comprise fruit-bearing female trees, can be rapidly ravished by disease, the ability to quickly replant orchards from seeds or seedlings known to be female would be of great benefit. There are no easily distinguishable sex chromosomes in date palm, despite some cytological evidence that they exist. As biochemical studies have yielded little insight into how to identify the genders of immature plants, the identification of DNA sequences or sequence polymorphisms that are gender specific offers a promising alternative to efficiently determine date palm gender.
In large part owing to its long generation time, there are few genetic resources for date palm. The most extensive is a backcrossing program initiated in California in the 1940s, which required >30 years to generate. To our knowledge, there is no publicly available physical or genetic map for the genome of any date palm, and at the outset of this project only ~100 kbp of nuclear date palm DNA sequences were found in GenBank (http://www.ncbi.nlm.nih.gov/ , March 1, 2009). To provide date palm researchers with the additional resources needed for comprehensive efforts to study and improve this important crop, we used massively parallel sequencing to assemble a draft genome sequence of date palm. Our analysis of nine varieties reveals polymorphisms that should provide an invaluable resource for the date palm community to identify ways to predict plant gender, maintain genetic diversity and improve traits such as fruit quality and ripening time.
Qatar Foundation, 14 April 2009 - ”Researchers Sequence Date Palm Genome”
e-Bulletin, May 2009 Issue1 - "WCM-Q Researchers Unlock Genetic Secrets of Date Palm"
Qatar Chronicle, 2009 - ”WCM-Q Researchers Unlock Genetic Secrets of Date Palm”
The National, 11 Sep 2009 - "Gene tests for female date palm bear fruit"
The Blessed Tree Khalifa International Date Palm Award - volume No.2, Issue No.2 June 2010 - "Second Winner of the First Category (Distinguished Research/ Studies)" Download PDF
Qatar Chronicle 2011 - "WCM-Q Researchers Answer Thousand Year Old Date Palm Question"
The Foundation issue, 31 july 2011 "Date Palm Mystery Unraveled"
QNRF Newsletter - "Gene discovery-From date palm toward human genes"
Nature Biotechnolohy, June 2011 Volume 29 No 6 Front page
Gulf Times, 31 May 2011 - "Qatar experts closer to solving the riddle of date palm gender"
Qatar Tribune, 31 May 2011 - "WCM-Q scholars make breakthrough in date palm research"
The Peninsula, 31 May 2011 - "WCM-Q researchers identify palm gender genome"
Al-Raya, 31 May 2011 - No.10615
Al-Sharq newspaper, 3 June 2011 - No.8387