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Items: 46

1.

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

Jain C, Dilthey A, Koren S, Aluru S, Phillippy AM.

J Comput Biol. 2018 Apr 30. doi: 10.1089/cmb.2018.0036. [Epub ahead of print]

PMID:
29708767
2.

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.

Pan T, Flick P, Jain C, Liu Y, Aluru S.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Oct 9. doi: 10.1109/TCBB.2017.2760829. [Epub ahead of print]

PMID:
28991750
3.

A greedy alignment-free distance estimator for phylogenetic inference.

Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.

BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238. doi: 10.1186/s12859-017-1658-0.

4.

Efficient detection of viral transmissions with Next-Generation Sequencing data.

Rytsareva I, Campo DS, Zheng Y, Sims S, Thankachan SV, Tetik C, Chirag J, Chockalingam SP, Sue A, Aluru S, Khudyakov Y.

BMC Genomics. 2017 May 24;18(Suppl 4):372. doi: 10.1186/s12864-017-3732-4.

5.

RD26 mediates crosstalk between drought and brassinosteroid signalling pathways.

Ye H, Liu S, Tang B, Chen J, Xie Z, Nolan TM, Jiang H, Guo H, Lin HY, Li L, Wang Y, Tong H, Zhang M, Chu C, Li Z, Aluru M, Aluru S, Schnable PS, Yin Y.

Nat Commun. 2017 Feb 24;8:14573. doi: 10.1038/ncomms14573.

6.

Tear Fluid Protein Changes in Dry Eye Syndrome Associated with Rheumatoid Arthritis: A Proteomic Approach.

Aluru SV, Shweta A, Bhaskar S, Geetha K, Sivakumar RM, Utpal T, Padmanabhan P, Angayarkanni N.

Ocul Surf. 2017 Jan;15(1):112-129. doi: 10.1016/j.jtos.2016.09.005. Epub 2016 Oct 24.

PMID:
27789276
7.

Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.

Chockalingam S, Aluru M, Aluru S.

Microarrays (Basel). 2016 Sep 19;5(3). pii: E23. doi: 10.3390/microarrays5030023.

8.

Molar Incisor Hypomineralization.

Rao MH, Aluru SC, Jayam C, Bandlapalli A, Patel N.

J Contemp Dent Pract. 2016 Jul 1;17(7):609-13. Review.

PMID:
27595731
9.

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.

Liu Y, Loewer M, Aluru S, Schmidt B.

BMC Syst Biol. 2016 Aug 1;10 Suppl 2:47. doi: 10.1186/s12918-016-0300-5.

10.

ALFRED: A Practical Method for Alignment-Free Distance Computation.

Thankachan SV, Chockalingam SP, Liu Y, Apostolico A, Aluru S.

J Comput Biol. 2016 Jun;23(6):452-60. doi: 10.1089/cmb.2015.0217. Epub 2016 May 3.

PMID:
27138275
11.

A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem.

Thankachan SV, Apostolico A, Aluru S.

J Comput Biol. 2016 Jun;23(6):472-82. doi: 10.1089/cmb.2015.0235. Epub 2016 Apr 8.

PMID:
27058840
12.

Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

Roy I, Aluru S.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Jan-Feb;13(1):99-111. doi: 10.1109/TCBB.2015.2430313.

PMID:
26886735
13.

Genetic Diversity and Population Structure of Leishmania infantum from Southeastern France: Evaluation Using Multi-Locus Microsatellite Typing.

Pomares C, Marty P, Bañuls AL, Lemichez E, Pratlong F, Faucher B, Jeddi F, Moore S, Michel G, Aluru S, Piarroux R, Hide M.

PLoS Negl Trop Dis. 2016 Jan 25;10(1):e0004303. doi: 10.1371/journal.pntd.0004303. eCollection 2016 Jan.

14.

In search of perfect reads.

Pal S, Aluru S.

BMC Bioinformatics. 2015;16 Suppl 17:S7. doi: 10.1186/1471-2105-16-S17-S7. Epub 2015 Dec 7.

15.

Guest Editors’ Introduction: Selected Papers from ACM-BCB 2013.

Aluru S, Slonim DK.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):2-3. No abstract available.

PMID:
26605392
16.

Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel® Xeon Phi™ Coprocessor.

Misra S, Pamnany K, Aluru S.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1008-20. doi: 10.1109/TCBB.2015.2415931.

PMID:
26451815
17.

Multilocus microsatellite typing of Leishmania and clinical applications: a review.

Aluru S, Hide M, Michel G, Bañuls AL, Marty P, Pomares C.

Parasite. 2015;22:16. doi: 10.1051/parasite/2015016. Epub 2015 May 5. Review.

18.

Fast and accurate construction of ultra-dense consensus genetic maps using evolution strategy optimization.

Mester D, Ronin Y, Schnable P, Aluru S, Korol A.

PLoS One. 2015 Apr 13;10(4):e0122485. doi: 10.1371/journal.pone.0122485. eCollection 2015.

19.

Local delivery of hyaluronan 0.8% as an adjunct to scaling and root planing in the treatment of chronic periodontitis: A clinical and microbiological study.

Polepalle T, Srinivas M, Swamy N, Aluru S, Chakrapani S, Chowdary BA.

J Indian Soc Periodontol. 2015 Jan-Feb;19(1):37-42. doi: 10.4103/0972-124X.145807.

20.

Mechanisms and networks for brassinosteroid regulated gene expression.

Guo H, Li L, Aluru M, Aluru S, Yin Y.

Curr Opin Plant Biol. 2013 Oct;16(5):545-53. doi: 10.1016/j.pbi.2013.08.002. Epub 2013 Aug 27. Review.

PMID:
23993372
21.

Isolation and characterization of ethanol tolerant yeast strains.

Tikka C, Osuru HP, Atluri N, Raghavulu PC, Yellapu NK, Mannur IS, Prasad UV, Aluru S, K NV, Bhaskar M.

Bioinformation. 2013 Apr 30;9(8):421-5. doi: 10.6026/97320630009421. Print 2013.

22.

Large-scale metagenomic sequence clustering on map-reduce clusters.

Yang X, Zola J, Aluru S.

J Bioinform Comput Biol. 2013 Feb;11(1):1340001. doi: 10.1142/S0219720013400015. Epub 2012 Dec 25.

PMID:
23427983
23.

Lacrimal proline rich 4 (LPRR4) protein in the tear fluid is a potential biomarker of dry eye syndrome.

Aluru SV, Agarwal S, Srinivasan B, Iyer GK, Rajappa SM, Tatu U, Padmanabhan P, Subramanian N, Narayanasamy A.

PLoS One. 2012;7(12):e51979. doi: 10.1371/journal.pone.0051979. Epub 2012 Dec 18.

24.

Reverse engineering and analysis of large genome-scale gene networks.

Aluru M, Zola J, Nettleton D, Aluru S.

Nucleic Acids Res. 2013 Jan 7;41(1):e24. doi: 10.1093/nar/gks904. Epub 2012 Oct 4.

25.

Recent advances in the diagnosis of Mycobacterium tuberculosis.

Anochie PI, Onyeneke EC, Ogu AC, Onyeozirila AC, Aluru S, Onyejepu N, Zhang J, Efere L, Adetunji MA, Sánchez JG.

Germs. 2012 Sep 1;2(3):110-20. doi: 10.11599/germs.2012.1021. eCollection 2012 Sep 1. Review.

26.

Two-phase analysis in consensus genetic mapping.

Ronin Y, Mester D, Minkov D, Belotserkovski R, Jackson BN, Schnable PS, Aluru S, Korol A.

G3 (Bethesda). 2012 May;2(5):537-49. doi: 10.1534/g3.112.002428. Epub 2012 May 1.

27.

A survey of error-correction methods for next-generation sequencing.

Yang X, Chockalingam SP, Aluru S.

Brief Bioinform. 2013 Jan;14(1):56-66. doi: 10.1093/bib/bbs015. Epub 2012 Apr 6. Review.

PMID:
22492192
28.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

29.

A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana.

Yu X, Li L, Zola J, Aluru M, Ye H, Foudree A, Guo H, Anderson S, Aluru S, Liu P, Rodermel S, Yin Y.

Plant J. 2011 Feb;65(4):634-46. doi: 10.1111/j.1365-313X.2010.04449.x. Epub 2011 Jan 10.

30.

Reptile: representative tiling for short read error correction.

Yang X, Dorman KS, Aluru S.

Bioinformatics. 2010 Oct 15;26(20):2526-33. doi: 10.1093/bioinformatics/btq468. Epub 2010 Aug 16.

PMID:
20834037
31.

The B73 maize genome: complexity, diversity, and dynamics.

Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK.

Science. 2009 Nov 20;326(5956):1112-5. doi: 10.1126/science.1178534. Erratum in: Science. 2012 Aug 31;337(6098):1040.

32.

Detailed analysis of a contiguous 22-Mb region of the maize genome.

Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, Nagel DH, Collura K, Kudrna D, Currie J, Lin J, Kim H, Angelova A, Scara G, Wissotski M, Golser W, Courtney L, Kruchowski S, Graves TA, Rock SM, Adams S, Fulton LA, Fronick C, Courtney W, Kramer M, Spiegel L, Nascimento L, Kalyanaraman A, Chaparro C, Deragon JM, Miguel PS, Jiang N, Wessler SR, Green PJ, Yu Y, Schwartz DC, Meyers BC, Bennetzen JL, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK, Wing RA.

PLoS Genet. 2009 Nov;5(11):e1000728. doi: 10.1371/journal.pgen.1000728. Epub 2009 Nov 20.

33.

Guest Editors' Introduction, Special Issue on High-Performance Computational Biology.

Bader DA, Aluru S.

Parallel Comput. 2008 Nov;34(11):613-615. No abstract available.

34.

Parallel short sequence assembly of transcriptomes.

Jackson BG, Schnable PS, Aluru S.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S14. doi: 10.1186/1471-2105-10-S1-S14.

35.

Consensus genetic maps as median orders from inconsistent sources.

Jackson BN, Schnable PS, Aluru S.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):161-71. doi: 10.1109/TCBB.2007.70221.

PMID:
18451426
36.

Turning repeats to advantage: scaffolding genomic contigs using LTR retrotransposons.

Kalyanaraman A, Aluru S, Schnable PS.

Comput Syst Bioinformatics Conf. 2006:167-78.

37.

Nearly identical paralogs: implications for maize (Zea mays L.) genome evolution.

Emrich SJ, Li L, Wen TJ, Yandeau-Nelson MD, Fu Y, Guo L, Chou HH, Aluru S, Ashlock DA, Schnable PS.

Genetics. 2007 Jan;175(1):429-39. Epub 2006 Nov 16.

38.

Efficient algorithms and software for detection of full-length LTR retrotransposons.

Kalyanaraman A, Aluru S.

J Bioinform Comput Biol. 2006 Apr;4(2):197-216.

PMID:
16819780
39.

Space-conserving optimal DNA-protein alignment.

Ko P, Narayanan M, Kalyanaraman A, Aluru S.

Proc IEEE Comput Syst Bioinform Conf. 2004:80-8.

PMID:
16448002
40.

Efficient algorithms and software for detection of full-length LTR retrotransposons.

Kalyanaraman A, Aluru S.

Proc IEEE Comput Syst Bioinform Conf. 2005:56-64.

PMID:
16447962
41.

Consensus genetic maps: a graph theoretic approach.

Jackson BN, Aluru S, Schnable PS.

Proc IEEE Comput Syst Bioinform Conf. 2005:35-43.

PMID:
16447960
42.

Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes.

Fu Y, Emrich SJ, Guo L, Wen TJ, Ashlock DA, Aluru S, Schnable PS.

Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12282-7. Epub 2005 Aug 15.

43.

A survey of SL1-spliced transcripts from the root-lesion nematode Pratylenchus penetrans.

Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, Aluru S, Clifton SW, Bird DM, Baum TJ, McCarter JP.

Mol Genet Genomics. 2004 Sep;272(2):138-48. Epub 2004 Aug 28.

PMID:
15338281
44.

A strategy for assembling the maize (Zea mays L.) genome.

Emrich SJ, Aluru S, Fu Y, Wen TJ, Narayanan M, Guo L, Ashlock DA, Schnable PS.

Bioinformatics. 2004 Jan 22;20(2):140-7.

PMID:
14734303
45.

PCAP: a whole-genome assembly program.

Huang X, Wang J, Aluru S, Yang SP, Hillier L.

Genome Res. 2003 Sep;13(9):2164-70.

46.

Efficient clustering of large EST data sets on parallel computers.

Kalyanaraman A, Aluru S, Kothari S, Brendel V.

Nucleic Acids Res. 2003 Jun 1;31(11):2963-74.

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