Ajay Royyuru  Ajay Royyuru photo         

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IBM Fellow & IBM Distinguished Industry Leader; Chief Science Officer, Healthcare & Life Sciences Research
Thomas J. Watson Research Center, Yorktown Heights, NY USA
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Professional Associations

Professional Associations:  International Society for Computational Biology

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More information:  LinkedIn


What's in a name?

In certain publications my name appears as R. Ajay Kumar.

In certain publications I am listed as an Investigator of The Genographic Consortium.

 

Peer-reviewed publications

  1. Enhancing next-generation sequencing-guided cancer care through cognitive computing.

    Patel NM, Michelini VV, Snell JM, Balu S, Hoyle AP, Parker JS, Hayward MC, Eberhard DA, Salazar AH, McNeillie P, Xu J, Huettner CS, Koyama T, Utro F, Rhrissorrakrai K, Norel R, Bilal E, Royyuru A, Parida L, Earp HS, Grilley-Olson JE, Hayes DN, Harvey SJ, Sharpless NE, Kim WY.
    Oncologist. 23(2):179-85 (2018).

 
  1. Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

    Wrzeszczynski KO, Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Vacic V, Norel R, Bilal E, Bergmann EA, Moore Vogel JL, Bruce JN, Lassman AB, Canoll P, Grommes C, Harvey S, Parida L, Michelini VV, Zody MC, Jobanputra V, Royyuru AK, Darnell RB.
    Neurol Genet. 3(4):e164 (2017).

 
  1. Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity.

    Nagle N, van Oven M, Wilcox S, van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne KN, Wilcox L, Papac L, Cooke K, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ; Genographic Consortium.
    Sci Rep. 7:43041 (2017).

 
  1. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania.

    Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, van Holst Pellekaan S, Schurr TG, McAllister P, Williams L, Kayser M, Mitchell RJ; Genographic Consortium.
    J Hum Genet. 62(3):343-53 (2017).

 
  1. New native South American Y chromosome lineages.

    Jota MS, Lacerda DR, Sandoval JR, Vieira PP, Ohasi D, Santos-Júnior JE, Acosta O, Cuellar C, Revollo S, Paz-Y-Miño C, Fujita R, Vallejo GA, Schurr TG, Tarazona-Santos EM, Pena SDj, Ayub Q, Tyler-Smith C, Santos FR; Genographic Consortium.
    J Hum Genet. 61(7):593-603 (2016).

 
  1. Antiquity and diversity of aboriginal Australian Y-chromosomes.

    Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ; Genographic Consortium.
    Am J Phys Anthropol. 159(3):367-81 (2016).

 
  1. Genetic diversity in the Lesser Antilles and its implications for the settlement of the Caribbean Basin.

    Benn Torres J, Vilar MG, Torres GA, Gaieski JB, Bharath Hernandez R, Browne ZE, Stevenson M, Walters W, Schurr TG; Genographic Consortium.
    PLoS One 10(10):e0139192 (2015).

 
  1. Genome-wide signatures of male-mediated migration shaping the Indian gene pool.

    ArunKumar G, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Pitchappan R; Genographic Consortium.
    J Hum Genet. 60:493-9 (2015).

 
  1. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies.

    Vilar MG, Melendez C, Sanders AB, Walia A, Gaieski JB, Owings AC, Schurr TG; Genographic Consortium.
    Am J Phys Anthropol. 155:352-68 (2014).

 
  1. Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales.

    Bai J, Wang D, Nam SW, Peng H, Bruce R, Gignac L, Brink M, Kratschmer E, Rossnagel S, Waggoner P, Reuter K, Wang C, Astier Y, Balagurusamy V, Luan B, Kwark Y, Joseph E, Guillorn M, Polonsky S, Royyuru A, Papa Rao S, Stolovitzky G.
    Nanoscale 6:8900-6 (2014).

 
  1. Geographic population structure analysis of worldwide human populations infers their biogeographical origins.

    Elhaik E, Tatarinova T, Chebotarev D, Piras IS, Maria Calò C, De Montis A, Atzori M, Marini M, Tofanelli S, Francalacci P, Pagani L, Tyler-Smith C, Xue Y, Cucca F, Schurr TG, Gaieski JB, Melendez C, Vilar MG, Owings AC, Gómez R, Fujita R, Santos FR, Comas D, Balanovsky O, Balanovska E, Zalloua P, Soodyall H, Pitchappan R, Ganeshprasad A, Hammer M, Matisoo-Smith L, Wells RS; Genographic Consortium.
    Nature Communications 5:3513 (2014).

 
  1. Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages.

    Luan B, Wang C, Royyuru AK, Stolovitzky G.
    Nanotechnology 25:265101 (2014).

 
  1. Molecular Recognition of Metabotropic Glutamate Receptor Type 1 (mGluR1): Synergistic Understanding with Free Energy Perturbation and Linear Response Modeling.

    Kang SG, Das P, McGrane SJ, Martin AJ, Huynh T, Royyuru AK, Taylor AJ, Jones PG, Zhou R.
    J Phys Chem B. 118:6393-404 (2014).

 
  1. Mitochondrial genome sequencing in Mesolithic North East Europe Unearths a new sub-clade within the broadly distributed human haplogroup C1.

    Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JE, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W; The Genographic Consortium.
    PLoS One 9(2):e87612 (2014).

 
  1. From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.

    Clarke AC, Prost S, Stanton JA, White WT, Kaplan ME, Matisoo-Smith EA; The Genographic Consortium.
    BMC Genomics 15:68 (2014).

 
  1. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity.

    Brandt G, Haak W, Adler CJ, Roth C, Szecsenyi-Nagy A, Karimnia S, Moller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nicklisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt KW; The Genographic Consortium.
    Science 342:257-61 (2013).

 
  1. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.

    Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D; The Genographic Consortium.
    PLoS One 8(5):e65441 (2013).

 
  1. The GenoChip: a new tool for genetic anthropology.

    Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R; The Genographic Consortium.
    Genome Biol Evol. 5(5):1021-31 (2013).

 
  1. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.

    Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Jane Adler C, Richards SM, Sarkissian CD, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SY, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A; The Genographic Consortium.
    Nat Commun. 4:1764 (2013).

 
  1. Ancient DNA reveals prehistoric gene-flow from siberia in the complex human population history of North East Europe.

    Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W; The Genographic Consortium.
    PLoS Genet. 9(2):e1003296 (2013).

 
  1. Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations.

    Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA; The Genographic Consortium.
    PLoS One 8(1):e54616 (2013).

 
  1. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system.

    Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R; The Genographic Consortium.
    PLoS One 7(11):e50269 (2012).

 
  1. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements.

    Rebala K, Martinez-Cruz B, Tonjes A, Kovacs P, Stumvoll M, Lindner I, Buttner A, Wichmann HE, Sivakova D, Sotak M, Quintana-Murci L, Szczerkowska Z, Comas D; The Genographic Consortium.
    Eur J Hum Genet. 21(4):415-22 (2013).

 
  1. Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings.

    Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG; The Genographic Consortium.
    PLoS One 7(7):e41803 (2012).

 
  1. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times.

    Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharcabal B, Bauduer F, Comas D, Quintana-Murci L; The Genographic Consortium.
    Am J Hum Genet. 90:486-93 (2012).

 
  1. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations.

    Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG; The Genographic Consortium.
    Proc Natl Acad Sci U S A. 109:8471-6 (2012).

 
  1. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska.

    Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F; The Genographic Consortium.
    Am J Phys Anthropol. 148:422-35 (2012).

 
  1. Mitochondrial origin of the matrilocal Mosuo people in China.

    Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H; The Genographic Consortium.
    Mitochondrial DNA 23:13-9 (2012).

 
  1. Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events.

    Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, Martinez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PA; The Genographic Consortium.
    PLoS One 7(3):e34288 (2012).

 
  1. Industrial Methodology for Process Verification in Research (IMPROVER): Towards Systems Biology Verification.

    Meyer P, Hoeng J, Norel R, Sprengel J, Stolle K, Bonk T, Corthesy S, Royyuru A, Peitsch MC, Rice JJ, Stolovitzky G.
    Bioinformatics 28:1193-201(2012).

 
  1. Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers.

    Martinez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharcabal B, Quintana-Murci L, Comas D; The Genographic Consortium.
    Mol Biol Evol. 29:2211-22 (2012).

 
  1. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times.

    Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharcabal B, Bauduer F, Comas D, Quintana-Murci L; The Genographic Consortium.
    Am J Hum Genet. 90:486-93 (2012).

 
  1. Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas.

    Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H; The Genographic Consortium.
    Ann Hum Genet. 76:92-9 (2012).

 

  1. Modeling mutations of influenza virus with IBM Blue Gene.

    Xia Z, Das P, Huynh T, Royyuru AK, Zhou R.
    IBM J Res & Dev. 55:7:1-11 (2011). doi 10.1147/JRD.2011.2163276
    IEEE Xplore

 
  1. Recombination networks as genetic markers in a human variation study of the Old World.

    Javed A, Mele M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L; The Genographic Consortium.
    Hum Genet. 131:601-13 (2011).

 
  1. Genetic ancestry and indigenous heritage in a Native American descendant community in Bermuda.

    Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG; The Genographic Consortium.
    Am J Phys Anthropol. 146:392-405(2011).

 

  1. A new subhaplogroup of native American Y-Chromosomes from the Andes.

    Jota MS, Lacerda DR, Sandoval JR, Vieira PP, Santos-Lopes SS, Bisso-Machado R, Paixão-Cortes VR, Revollo S, Paz-Y-Miño C, Fujita R, Salzano FM, Bonatto SL, Bortolini MC, Santos FR; and The Genographic Consortium.
    Am J Phys Anthropol. 146:553-9 (2011).
    PubMed

 

  1. Human Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes.

    Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H; The Genographic Consortium.
    PLoS One 6(8):e24282 (2011).
    PubMed

 

  1. Verification of systems biology research in the age of collaborative competition.

    Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.
    Nature Biotech. 29:811-5 (2011).
    PubMed

 
  1. Recombination gives a new insight in the effective population size and the history of the Old World human populations.

    Mele M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan R, Arunkumar G, Parida L, Calafell F, Bertranpetit J; The Genographic Consortium.
    Mol Biol Evol. 29:25-30 (2011).

 
  1. Parallel evolution of genes and languages in the Caucasus region.

    Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya O, Romanov A, Zakharova T, Soria Hernanz DF, Zalloua P, Koshel S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E; The Genographic Consortium.
    Mol Biol Evol. 28:2905-20 (2011).

 
  1. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4.

    Yan S, Wang CC, Li H, Li SL, Jin L; The Genographic Consortium.
    Eur J Hum Genet. 19:1013-5(2011).

 
  1. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes.

    Martinez-Cruz B, Ziegle J, Sanz P, Sotelo G, Anglada R, Plaza S, Comas D; The Genographic Consortium.
    Investig Genet. 2:13(2011).

 
  1. Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan.

    Yang K, Zheng H, Qin Z, Lu Y, Farina SE, Li S, Jin L, Li D, Li H; The Genographic Consortium.
    J Hum Genet. 56:253-6 (2011).

 

  1. A new method to reconstruct recombination events at a genomic scale.

    Mele M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J; Genographic Consortium Members.
    PLoS Comput Biol. 6:e1001010 (2010).
    PubMed

 
  1. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon.

    Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA; The Genographic Consortium.
    Eur J Hum Genet. 19:333-40 (2011).

 

  1. Ancient DNA from European early neolithic farmers reveals their near eastern affinities.

    Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CS, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A; and Members of The Genographic Consortium.
    PLoS Biol. 8:e1000536 (2010).
    PubMed

 
  1. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum.

    Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H; and The Genographic Consortium.
    Am J Phys Anthropol. 143:555-69 (2010).

 
  1. Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts.

    Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG; Genographic Project Consortium.
    Am J Phys Anthropol. 142:579-89 (2010).

 
  1. Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast.

    El-Sibai M, Platt DE, Haber M, Xue Y, Youhanna SC, Wells RS, Izaabel H, Sanyoura MF, Harmanani H, Bonab MA, Behbehani J, Hashwa F, Tyler-Smith C, Zalloua PA; Genographic Consortium.
    Ann Hum Genet. 73:568-81 (2009).

 

  1. Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.

    Das P, Li J, Royyuru AK, Zhou R.
    J Comput Chem. 30:1654-63 (2009).
    PubMed

 

  1. Minimizing recombinations in consensus networks for phylogeographic studies.

    Parida L, Javed A, Melé M, Calafell F, Bertranpetit J; Genographic Consortium.
    BMC Bioinformatics 10:S72 (2009).
    PubMed

 

  1. Single mutation induced H3N2 hemagglutinin antibody neutralization: a free energy perturbation study.

    Zhou R, Das P, Royyuru AK.
    J Phys Chem B. 112:15813-20 (2008).
    PubMed

 

  1. Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean.

    Zalloua PA, Platt DE, El Sibai M, Khalife J, Makhoul N, Haber M, Xue Y, Izaabel H, Bosch E, Adams SM, Arroyo E, López-Parra AM, Aler M, Picornell A, Ramon M, Jobling MA, Comas D, Bertranpetit J, Wells RS, Tyler-Smith C; Genographic Consortium.
    Am J Hum Genet. 83:633-42 (2008).
    PubMed

 

  1. Estimating the ancestral recombinations graph (ARG) as compatible networks of SNP patterns.

    Parida L, Melé M, Calafell F, Bertranpetit J; Genographic Consortium.
    J Comput Biol. 15:1133-54 (2008).
    PubMed

 

  1. Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification.

    Rosset S, Wells RS, Soria-Hernanz DF, Tyler-Smith C, Royyuru AK, Behar DM; Genographic Consortium.
    Genetics 180:1511-24 (2008).
    PubMed

 

  1. A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals.

    Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS; Genographic Consortium.
    Hum Mutat 29:1387-91 (2008).
    PubMed

 

  1. The dawn of human matrilineal diversity.

    Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S; Genographic Consortium.
    Am J Hum Genet. 82:1130-40 (2008).
    PubMed

 

  1. Y-chromosomal diversity in Lebanon is structured by recent historical events.

    Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C; Genographic Consortium.
    Am J Hum Genet. 82:873-82 (2008).
    PubMed

 

  1. Massively parallel molecular dynamics simulations of lysozyme unfolding.

    Zhou R, Eleftheriou M, Hon C-C, Germain R, Royyuru AK, Berne BJ.
    IBM J Res Dev. 52:19-30 (2008).

 
  1. Pinghua population as an exception of Han Chinese's coherent genetic structure.

    Gan RJ, Pan SL, Mustavich LF, Qin ZD, Cai XY, Qian J, Liu CW, Peng JH, Li SL, Xu JS, Jin L, Li H; Genographic Project Consortium.
    J Hum Genet. 53:303-13 (2008).

 

  1. The Genographic Project public participation mitochondrial DNA database.

    Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS; Genographic Consortium.
    PLoS Genet. 3:1083-1095 (2007).
    PubMed

 

  1. Destruction of long-range interactions by a single mutation in lysozyme.

    Zhou R, Eleftheriou M, Royyuru AK, Berne BJ.
    Proc Natl Acad Sci USA 104:5824-9 (2007).
    PubMed

 

  1. Thermal denaturing of mutant lysozyme with both the OPLSAA and the CHARMM force fields.

    Eleftheriou M, Germain RS, Royyuru AK, Zhou R.
    J Am Chem Soc. 128:13388-95 (2006).
    PubMed

 

  1. Preface; Special Issue on Blue Gene.

    Guest Editors: Chiu GL-T, Gupta M, Royyuru AK.
    IBM J Res Dev. 49:191-3 (2005).

 
  1. Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins

    Zhou R, Royyuru A, Athma P, Suits F, Silverman BD.
    Int J Bioinf Res Apps. 2:161-76 (2006).

 

  1. Spatial profiling of protein hydrophobicity: native vs. decoy structures.

    Zhou R, Silverman BD, Royyuru AK, Athma P.
    Proteins 52:561-72 (2003).
    PubMed

 
  1. Principles of mucin architecture: structural studies on synthetic glycopeptides bearing clustered mono-, di-, tri-, and hexasaccharide glycodomains.

    Coltart DM, Royyuru AK, Williams LJ, Glunz PW, Sames D, Kuduk SD, Schwarz JB, Chen XT, Danishefsky SJ, Live DH.
    J Am Chem Soc. 124:9833-44 (2002).

 

  1. Blue Gene: A vision for protein science using a petaflop supercomputer.

    Allen F, et al., Royyuru A, et al.
    IBM Systems J. 40:310-27 (2001).

 
  1. Systematic and fully automated identification of protein sequence patterns.

    Hart RK, Royyuru AK, Stolovitzky G, Califano A.
    J Comput Biol. 7:585-600 (2000).

 
  1. New features and enhancements in the X-PLOR computer program.

    Badger J, Kumar RA, Yip P, Szalma S.
    Proteins 35:25-33 (1999).

 

  1. Probing cell-surface architecture through synthesis: an NMR-determined structural motif for tumor-associated mucins.

    Live DH, Williams LJ, Kuduk SD, Schwarz JB, Glunz PW, Chen XT, Sames D, Kumar RA, Danishefsky SJ.
    Proc Natl Acad Sci USA 96:3489-93 (1999).
    PubMed

 
  1. Structure, recognition and adaptive binding in RNA aptamer complexes.

    Patel DJ, Suri AK, Jiang F, Jiang L, Fan P, Kumar RA, Nonin S.
    J Mol Biol. 272:645-64 (1997).

 
  1. Solution structure of the calicheamicin γ1I-DNA complex.

    Kumar RA, Ikemoto N, Patel DJ.
    J Mol Biol. 265:187-201 (1997).

 
  1. Solution structure of the esperamicin A1-DNA complex.

    Kumar RA, Ikemoto N, Patel DJ.
    J Mol Biol. 265:173-186 (1997).

 

  1. Conformational influences of glycosylation of a peptide: a possible model for the effect of glycosylation on the rate of protein folding.

    Live DH, Kumar RA, Beebe X, Danishefsky SJ.
    Proc Natl Acad Sci USA 93:12759-61 (1996).
    PubMed

 
  1. RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex.

    Jiang F, Fiala R, Live D, Kumar RA, Patel DJ.
    Biochemistry 35:13250-66 (1996).

 
  1. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex.

    Jiang F, Kumar RA, Jones RA, Patel DJ.
    Nature 382:183-6 (1996).

 

  1. Solution structure of a DNA quadruplex containing the fragile X syndrome triplet repeat.

    Kettani A, Kumar RA, Patel DJ.
    J Mol Biol. 254:638-56 (1995).
    PubMed

 

  1. Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex.

    Ye X, Kumar RA, Patel DJ.
    Chem Biol. 2:827-40 (1995).
    PubMed

 

  1. Calicheamicin-DNA complexes: warhead alignment and saccharide recognition of the minor groove.

    Ikemoto N, Kumar RA, Ling TT, Ellestad GA, Danishefsky SJ, Patel DJ.
    Proc Natl Acad Sci USA 92:10506-10 (1995).
    PubMed

 
  1. Distance geometry in NMR determination of solution conformation of nucleic acids: application of d-ACCGTTAACGGT.

    Radha PK, Nibedita R, Kumar RA, Hosur RV.
    Methods Enzymol. 261:73-89 (1995).

 
  1. Esperamicin A1 intercalates into duplex DNA from the minor groove.

    Ikemoto N, Kumar RA, Dedon PC, Danishefsky SJ, Patel DJ.
    J Am Chem Soc. 116:9387-8 (1994).

 
  1. Solution structure of GCCAAT recognition motif by 2D NMR, spectral simulation, molecular modeling, and distance geometry calculations.

    Nibedita R, Kumar RA, Majumdar A, Hosur RV, Govil G, Majumder K, Chauhan VS.
    Biochemistry 32:9053-64 (1993).

 
  1. Optimization of interatomic angle geometry in torsion angle space.

    Kumar RA
    J Biomol NMR 2:519-26 (1992).

 
  1. Quantitative comparison of experimental and simulated NOE intensities: correlation with accuracy of oligonucleotide structure determination.

    Nibedita R, Kumar RA, Majumdar A, Hosur RV.
    J Biomol NMR 2:477-84 (1992).

 
  1. Simulation of NOESY spectra of DNA segments: a new scaling procedure for iterative comparison of calculated and experimental NOE intensities.

    Nibedita R, Kumar RA, Majumdar A, Hosur RV.
    J Biomol NMR 2:467-76 (1992).

 
  1. Torsion angle approach to nucleic acid distance geometry: TANDY.

    Kumar RA, Hosur RV, Govil G.
    J Biomol NMR 1:363-78 (1991).

 

  1. NMR recipe for sequencing short DNA fragments.

    Kumar RA, Majumdar A, Hosur RV.
    Curr Sci. 59:1256-9 (1990).
    Archive

 

  1. Role of microenvironment in recognition of DNA by nonintercalating ligands.

    Royyuru AK, Mrigank, Kalia A, Kothekar V.
    Curr Sci. 56:805-10 (1987).
    Archive

 

  1. Theoretical study of conformational flexibility of distamycin-A analog and its binding to DNA.

    Royyuru AK, Mrigank, Kalia A, Kothekar V.
    Curr Sci. 56:581-4 (1987).
    Archive

 
  1. Theoretical study on binding of Hoechst 33258 with oligonucleotides.

    Gopalakrishna K, Kalia A, Royyuru AK, Mrigank, Atreyi M, Rao MV, Kothekar V.
    FEBS Lett. 215:95-9 (1987).

 
  1. Sequence-specific recognition of DNA by lac-repressor headpiece.

    Kalia A, Royyuru AK, Mrigank, Kothekar V.
    Int J Quant Chem. 30:185-94 (1986).

 
  1. Influence of local excitations in DNA conformation on binding of nonintercalating antitumor antibiotic in the minor groove.

    Kothekar V, Mrigank, Royyuru AK, Kalia A.
    Int J Quant Chem. 30:175-83 (1986).

 
  1. Energetics of interaction of oligopeptide (lac 53-57) with DNA base sequences and origin of sequence-specific recognition.

    Kalia A, Royyuru AK, Mrigank, Kothekar V.
    FEBS Lett. 195:48-52 (1986).

 
  1. Origin of sequence-specific recognition of DNA by non-intercalating anti-tumor antibiotics.

    Mrigank, Royyuru AK, Kothekar V.
    FEBS Lett. 195:203-8 (1986).