Publications

Please see resume for updated publication list

The publications are sorted in chronological order below. For the list of publications related to a particular topic, please see the corresponding research page.

  1. B. Pupacdi, A. Javed, M.J. Zaki and M. Ruchirawat
    NSIT: Novel Sequence Identification Tool
    PLoS One, September 2014 [pubmed]
     
  2. A. Javed*, S. Agrawal, and P.C. Ng* (* corresponding authors)
    Phen-Gen: combining Phenotype and Genotype to analyze rare disorders
    Nature Methods, September 2014 [pubmed, webserver]
     
  3. C.A. Brownstein, A.H. Beggs, N. Homer, B. Merriman, T.W. Yu, K.C. Flannery, E.T. DeChene, M.C. Towne, S.K. Savage, E.N. Price, I.A. Holm, L.J. Luquette, E. Lyon, J. Majzoub, P. Neupert, D. McCallie Jr, P. Szolovits, H.F. Willard, N.J. Mendelsohn, R. Temme, R.S. Finkel, S.W. Yum, L. Medne, S.R. Sunyaev, I. Adzhubey, C.A. Cassa, P.I. de Bakker, H. Duzkale, P. Dworzynski, W. Fairbrother, L. Francioli, B.H. Funke, M.A. Giovanni, R.E. Handsaker, K. Lage, M.S. Lebo, M. Lek, I. Leshchiner, D.G. MacArthur, H.M. McLaughlin, M.F. Murray, T.H. Pers, P.P. Polak, S. Raychaudhuri, H.L. Rehm, R. Soemedi, N.O. Stitziel, S. Vestecka, J. Supper, C. Gugenmus, B. Klocke, A. Hahn, M. Schubach, M. Menzel, S. Biskup, P. Freisinger, M. Deng, M. Braun, S. Perner, R.J. Smith, J.L. Andorf, J. Huang, K. Ryckman, V.C. Sheffield, E.M. Stone, T. Bair, E.A. Black-Ziegelbein, T.A. Braun, B. Darbro, A.P. DeLuca, D.L. Kolbe, T.W. Scheetz, A.E. Shearer, R. Sompallae, K. Wang, A.G. Bassuk, E. Edens, K. Mathews, S.A. Moore, O.A. Shchelochkov, P. Trapane, A. Bossler, C.A. Campbell, J.W. Heusel, A. Kwitek, T. Maga, K. Panzer, T. Wassink, D. Van Daele, H. Azaiez, K. Booth, N. Meyer, M.M. Segal, M.S. Williams, G. Tromp, P. White, D. Corsmeier, S. Fitzgerald-Butt, G. Herman, D. Lamb-Thrush, K.L. McBride, D. Newsom, C.R. Pierson, A.T. Rakowsky, A. Maver A, L. Lovrecic, A. Palandacic, B. Peterlin, A. Torkamani, A. Wedell, M. Huss, A. Alexeyenko, J.M. Lindvall, M. Magnusson, D. Nilsson, H. Stranneheim, F. Taylan, C. Gilissen, A. Hoischen, B. van Bon, H. Yntema H, M. Nelen, W. Zhang, J. Sager, L. Zhang, K. Blair, D. Kural, M. Cariaso, G.G. Lennon, A. Javed, S. Agrawal, P.C. Ng, K.S. Sandhu, S. Krishna, V. Veeramachaneni, O. Isakov, E. Halperin, E. Friedman, N. Shomron, G. Glusman, J.C. Roach, J. Caballero, H.C. Cox, D. Mauldin, S.A. Ament, L. Rowen, D.R. Richards, F.A. San Lucas, M.L. Gonzalez-Garay, C.T. Caskey, Y. Bai, Y. Huang, F. Fang, Y. Zhang, Z. Wang, J. Barrera, J.M. Garcia-Lobo, D. González-Lamuño, J. Llorca, M.C. Rodriguez, I. Varela, M.G. Reese, F.M. De La Vega FM, E. Kiruluta, M. Cargill, R.K. Hart, J.M. Sorenson, G.J. Lyon, D.A. Stevenson, B.E. Bray, B.M. Moore, K. Eilbeck, M. Yandell, H. Zhao, L. Hou, X. Chen, X. Yan, M. Chen, C. Li, C. Yang, M. Gunel, P. Li, Y. Kong, A.C. Alexander, Z.I. Albertyn, K.M. Boycott, D.E. Bulman, P.M. Gordon, A.M. Innes, B.M. Knoppers, J. Majewski, C.R. Marshall, J.S. Parboosingh, S.L. Sawyer, M.E. Samuels, J. Schwartzentruber, I.S. Kohane, D.M. Margulies
    An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results inthe CLARITY Challenge
    Genome Biology, March 2014 [pubmed]
     
  4. A. Javed, M. Melé, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky, E. Balanovska, L. Jin, Y. Yang, G. Arunkumar , R.M. Pitchappan, J. Bertranpetit, F. Calafell, L. Parida, and The Genographic Consortium
    Recombination networks as genetic markers: a human variation study of the Old World
    Human Genetics, April 2012 [pubmed]
     
  5. A. Javed, P. Drineas, M.W. Mahoney, and P. Paschou
    Efficient genomewide selection of PCA-correlated tSNPs for genotype imputation
    Annals of Human Genetics, November 2011 [pubmed]
     
  6. M. Melé, A. Javed, M. Pybus, P. Zalloua, M. Haber, D. Comas, M. Netea, O. Balanovsky, E. Balanovska, L. Jin, Y. Yang, R.M. Pitchappan, G. Arunkumar , L. Parida, F. Calafell, J. Bertranpetit, and The Genographic Consortium
    Recombination gives a new insight in the effective population size and the history of the old world human populations
    Molecular Biology and Evolution, October 2011 [pubmed]
     
  7. A. Javed, M. Pybus, M. Melé, F. Utro, J. Bertranpetit, F. Calafell, and L. Parida
    IRiS: Construction of ARG network at genomic scales
    Bioinformatics, July 2011 [pubmed]
     
  8. L. Parida, P.F. Palamara, and A. Javed
    A Minimal Descriptor of an Ancestral Recombinations Graph
    BMC Bioinformatics, APBC, February 2011 [pubmed]
     
  9. M. Melé, A. Javed, M. Pybus, F. Calafell, L. Parida, J. Bertranpetit, and The Genographic Consortium
    A New Method to Reconstruct Recombination Events at a Genomic Scale
    PLoS Computational Biology, November 2010 [pubmed]
     
  10. P. Paschou, J. Lewis, A. Javed, P. Drineas
    Ancestry informative markers for fine-scale individual assignment to worldwide populations
    J Med Genet Dec 2010 [pubmed]
     
  11. A. Javed, and L. Parida
    Recombinomics: Population Genomics from a Recombination Perspective
    Proceedings of C3S2E, May 2010 [ACM DL]
     
  12. L. Parida, A. Javed, M. Melé, F. Calafell, J. Bertranpetit, and The Genographic Consortium
    Minimizing recombinations in consensus networks for phylogeographic studies
    BMC Bioinformatics, APBC, January 2009 [pubmed]
     
  13. L. Parida, A. Javed, M. Melé, and J. Bertranpetit
    A case for Recombinomics
    IBM Technical Report RC24677, August 2008
     
  14. A. Javed and P. Paschou
    Extracting tagging SNPs from Genome-wide Datasets
    Data Mining for Biomedical Informatics, workshop held in conjunction with 7th SIAM Conference on Data Mining, April 2007
     
  15. P. Paschou, M.W. Mahoney, A. Javed, J.R. Kidd, A.J. Pakstis, S. Gu, K.K. Kidd, and P. Drineas
    Intra- and inter-population genotype reconstruction from tagging SNPs
    Genome Research, January 2007 [pubmed]
     
  16. P. Drineas, A. Javed, M. Magdon-Ismail, G. Pandurangan, R.Virrankoski, and A. Savvides
    Distance Matrix Reconstruction from Incomplete Distance Information for Sensor Network Localization
    3rdAnnual IEEE Conference on Sensor, Mesh and Ad Hoc Communications and Networks (SECON), September 2006
     
  17. A. Javed and A. Khokhar
    Frequent Pattern Mining on Message Passing Multiprocessor Systems
    Distributed and Parallel Databases-An International Journal (DAPD), November 2004. [ACM portal]
     
  18. A. Javed and A. Khokhar
    Scalable Parallel Algorithm for Mining Frequent Patterns on Message Passing Parallel Systems
    ISCA Parallel and Distributed Computing Systems, (PDCS), August 2003
     

Consortium Publications

  1. G. Brandt, W. Haak, C.J. Adler, C. Roth, A. Szécsényi-Nagy, S. Karimnia, S. Möller-Rieker, H. Meller, R. Ganslmeier, S. Friederich, V. Dresely, N. Nicklisch, J.K. Pickrell, F. Sirocko, D. Reich, A. Cooper, K.W. Alt, and The Genographic Consortium, Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity, Science, October 2013 [pubmed]
     
  2. P. Brotherton, W. Haak, J. Templeton, G. Brandt, J. Soubrier, C. Jane Adler, S.M. Richards, C.D. Sarkissian, R. Ganslmeier, S. Friederich, V. Dresely, M. van Oven, R. Kenyon, M.B. Van der Hoek, J. Korlach, K. Luong, S.Y. Ho, L. Quintana-Murci, D.M. Behar, H. Meller, K.W. Alt, A. Cooper, and The Genographic Consortium, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans, Nat Commun., April 2013 [pubmed]
     
  3. K. Rebala K, B. Martínez-Cruz, A. Tönjes, P. Kovacs, M. Stumvoll, I. Lindner, A. Büttner, H.E. Wichmann, D. Siváková, M. Soták, L. Quintana-Murci, Z. Szczerkowska, D. Comas, and The Genographic Consortium, Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements, Eur J Hum Genet. April 2013 [pubmed]
     
  4. D.A. Badro, B. Douaihy, M. Haber, S.C. Youhanna, A. Salloum, M. Ghassibe-Sabbagh, B. Johnsrud, G. Khazen, E. Matisoo-Smith, D.F. Soria-Hernanz, R.S. Wells, C. Tyler-Smith, D.E. Platt, P.A. Zalloua, and The Genographic Consortium, Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations, PLoS One, January 2013 [pubmed]
     
  5. G. Arunkumar, D.F. Soria-Hernanz, V.J. Kavitha, V.S. Arun, A. Syama, K.S. Ashokan, K.T. Gandhirajan, K. Vijayakumar, M. Narayanan, M. Jayalakshmi, J.S. Ziegle, A.K. Royyuru, L. Parida, R.S. Wells, C. Renfrew, T.G. Schurr, C.T. Smith, D.E. Platt, R. Pitchappan, and The Genographic Consortium, Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system, PLoS One, November 2012 [pubmed]
     
  6. B. Martínez-Cruz, M. Ioana, F. Calafell, L.R. Arauna, P. Sanz P, R. Ionescu, S. Boengiu, L. Kalaydjieva, H. Pamjav, H. Makukh, T. Plantinga, J.W. van der Meer, D. Comas, M.G. Netea, and The Genographic Consortium, Y-chromosome analysis in individuals bearing the Basarab name of the first dynasty of Wallachian kings, PLoS One, July 2012 [pubmed]
     
  7. T.G. Schurr, M.C. Dulik, A.C. Owings, S.I. Zhadanov, J.B. Gaieski, M.G. Vilar, J. Ramos, M.B. Moss, F. Natkong F, and The Genographic Consortium, Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska, Am J Phys Anthropol. Jul 2012[pubmed]
     
  8. M.C. Dulik, A.C. Owings, J.B. Gaieski, M.G. Vilar, A. Andre, C. Lennie C, M.A. Mackenzie, I. Kritsch, S. Snowshoe, R. Wright, J. Martin, N. Gibson, T.D. Andrews, T.G. Schurr, and The Genographic Consortium, Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations, Proc Natl Acad Sci May 2012 [pubmed]
     
  9. J.B. Gaieski, A.C. Owings, M.G. Vilar, M.C. Dulik, D.F. Gaieski, R.M. Gittelman, J. Lindo, L. Gau, T.G. Schurr, and The Genographic Consortium, Genetic ancestry and indigenous heritage in a Native American Descendant Community in Bermuda, American Journal of Physical Anthropology, November 2011 [pubmed]
     
  10. O. Balanovsky, K. Dibirova, A. Dybo, O. Mudrak, S. Frolova, E. Pocheshkhova, M. Haber, D. Platt, T. Schurr, W. Haak, M. Kuznetsova, M. Radzhabov, O. Balaganskaya, A. Romanov, T. Zakharova, D.F. Soria Hernanz, P. Zalloua, S. Koshel, M. Ruhlen, C. Renfrew, R.S. Wells, C. Tyler-Smith, E. Balanovska, and The Genographic Consortium, Parallel Evolution of Genes and Languages in the Caucasus Region, Molecular Biology and Evolution, October 2011 [pubmed]
     
  11. M.S. Jota, D.R. Lacerda, J.R. Sandoval, P.P. Vieira, S.S. Santos-Lopes, R. Bisso-Machado, V.R. Paixão-Cortes, S. Revollo S, C. Paz-Y-Miño, R. Fujita, F.M. Salzano, S.L. Bonatto, M.C. Bortolini, F.R. Santos, and The Genographic Consortium, A new subhaplogroup of native American Y-Chromosomes from the Andes, American Journal of Physical Anthropology, September 2011 [pubmed]
     
  12. S. Yan, C.C. Wang, H. Li, S.L. Li, L. Jin, and The Genographic Consortium, An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4, European Journal of Human Genetics, September 2011 [pubmed]
     
  13. B. Martínez-Cruz, J. Ziegle, P. Sanz, G. Sotelo, R. Anglada, S. Plaza, D. Comas, and The Genographic Consortium, Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes, Investigative Genetics, May 2011 [pubmed]
     
  14. M. Haber, D.E. Platt, D.A. Badro, Y. Xue, M. El-Sibai, M.A. Bonab, S.C. Youhanna, S. Saade, D.F. Soria-Hernanz, A. Royyuru, R.S. Wells, C. Tyler-Smith, P.A. Zalloua and The Genographic Consortium, Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon, Eur J Hum Genet March 2011 [pubmed]
     
  15. K. Yang, H. Zheng, Z. Qin, Y. Lu, S.E. Farina, S. Li, L. Jin, D. Li, H. Li, and The Genographic Consortium, Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan, Journal of Human Genetics March 2011 [pubmed]
     
  16. X. Cai, Z. Qin, B. Wen, S. Xu, Y. Wang, Y. Lu, L. Wei, C. Wang, S. Li, X. Huang, L. Jin, H. Li, and The Genographic Consortium, Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes, PLoS One, August 2011 [pubmed]
     
  17. C.J. Adler, W. Haak, D. Donlon, A. Cooper, and The Genographic Consortium, Survival and recovery of DNA from ancient teeth and bones, Journal of Archaeological Science, May 2011
     
  18. Z. Qin, Y. Yang, L. Kang, S. Yan, K. Cho, X. Cai, Y. Lu, H. Zheng, D. Zhu, D. Fei, S. Li, L. Jin, H. Li and The Genographic Consortium A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum, Am J Phys Anthropol Dec 2010 [pubmed]
     
  19. W. Haak, O. Balanovsky, J.J. Sanchez, S. Koshel, V. Zaporozhchenko, C.J. Adler, C.S. Der Sarkissian, G. Brandt, C. Schwarz, N. Nicklisch, V. Dresely, B. Fritsch, E. Balanovska, R. Villems, H. Meller, K.W. Alt, A. Cooper and The Genographic Consortium Ancient DNA from European early neolithic farmers reveals their near eastern affinities, PLOS Biol. Nov 2010 [pubmed]