SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.

Srinivas Aluru Georgia Institute of Technology, Atlanta, GA, USA Iowa State University, Ames, Iowa, USA New Mexico State University, Las Cruces, NM, USA Syracuse University, NY, USA Indian Institute of Technology, Madras, India http://www.cc.gatech.edu/~saluru/ http://www.ece.iastate.edu/profiles/srinivas-aluru/ https://scholar.google.com/citations?user=YOGOScoAAAAJ https://zbmath.org/authors/?q=ai:aluru.srinivas https://mathscinet.ams.org/mathscinet/MRAuthorID/326381 https://mathgenealogy.org/id.php?id=168180 https://en.wikipedia.org/wiki/Srinivas_Aluru https://orcid.org/0000-0003-4279-469X https://www.wikidata.org/entity/Q44476196 https://id.loc.gov/authorities/names/n99253216 https://www.wikidata.org/entity/Q130970301

Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data. 2025 41 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btaf057 db/journals/bioinformatics/bioinformatics41.html#ChockalingamAA25

Rahul Nihalani Jaroslaw Zola Srinivas Aluru Disambiguating a Soft Metagenomic Clustering. 473-485 2025 32 J. Comput. Biol. 5 https://doi.org/10.1089/cmb.2024.0825 db/journals/jcb/jcb32.html#NihalaniZA25 streams/journals/jcb

Srinivas Aluru Anne Benoit Bora Uçar Efficient and effective methods for variant selection. 9:1-9:10 2025 BCB https://doi.org/10.1145/3765612.3767208 conf/bcb/2025 db/conf/bcb/bcb2025.html#AluruBU25 Srinivas Aluru The Power of Parallelism: Accelerating Discovery in the Biosciences. 419 2025 IPDPS https://doi.org/10.1109/IPDPS64566.2025.00044 conf/ipps/2025 db/conf/ipps/ipdps2025.html#Aluru25 Aranya Banerjee Daniel Gibney Helen Xu 0001 Srinivas Aluru A Work-Optimal Parallel Algorithm for Aligning Sequences to Genome Graphs. 460-471 2025 IPDPS https://doi.org/10.1109/IPDPS64566.2025.00048 conf/ipps/2025 db/conf/ipps/ipdps2025.html#BanerjeeGXA25

Neda Tavakoli Daniel Gibney Srinivas Aluru GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants. 616-637 2024 31 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2024.0601 db/journals/jcb/jcb31.html#TavakoliGA24 streams/journals/jcb

Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru Datasets for evaluating SCEMENT: Scalable and Memory Efficient Integration of Large-scale Single Cell RNA-sequencing Data. 2024 June https://doi.org/10.5281/zenodo.11521688 Zenodo streams/repo/zenodo

Tony C. Pan Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework. 2023 39 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btad373 db/journals/bioinformatics/bioinformatics39.html#PanCAA23

Ankit Srivastava Sriram P. Chockalingam Srinivas Aluru A Parallel Framework for Constraint-Based Bayesian Network Learning via Markov Blanket Discovery. 1699-1715 2023 June 34 IEEE Trans. Parallel Distributed Syst. 6 https://doi.org/10.1109/TPDS.2023.3244135 db/journals/tpds/tpds34.html#SrivastavaCA23

Shruti Shivakumar Jiajia Li 0001 Ramakrishnan Kannan Srinivas Aluru Sparse Symmetric Format for Tucker Decomposition. 1743-1756 2023 June 34 IEEE Trans. Parallel Distributed Syst. 6 https://doi.org/10.1109/TPDS.2023.3263124 db/journals/tpds/tpds34.html#ShivakumarLKA23

Shruti Shivakumar Ilya Amburg Sinan G. Aksoy Jiajia Li 0001 Stephen J. Young Srinivas Aluru Fast Parallel Tensor Times Same Vector for Hypergraphs. 324-334 2023 HiPC https://doi.org/10.1109/HiPC58850.2023.00049 conf/hipc/2023 db/conf/hipc/hipc2023.html#ShivakumarAALYA23

Shruti Shivakumar Ilya Amburg Sinan G. Aksoy Jiajia Li 0001 Stephen J. Young Srinivas Aluru Fast Parallel Tensor Times Same Vector for Hypergraphs. 2023 abs/2311.08595 CoRR https://doi.org/10.48550/arXiv.2311.08595 db/journals/corr/corr2311.html#abs-2311-08595

Maneesha Aluru Harsh Shrivastava 0001 Sriram P. Chockalingam Shruti Shivakumar Srinivas Aluru EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks. 1312-1319 2022 38 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btab829 db/journals/bioinformatics/bioinformatics38.html#AluruSCSA22

Harsh Shrivastava 0001 Xiuwei Zhang 0002 Le Song Srinivas Aluru GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks. 27-44 2022 29 J. Comput. Biol. 1 https://doi.org/10.1089/cmb.2021.0437 db/journals/jcb/jcb29.html#ShrivastavaZSA22

Daniel Gibney Sharma V. Thankachan Srinivas Aluru On the Hardness of Sequence Alignment on De Bruijn Graphs. 1377-1396 2022 29 J. Comput. Biol. 12 https://doi.org/10.1089/cmb.2022.0411 db/journals/jcb/jcb29.html#GibneyTA22

Neda Tavakoli Daniel Gibney Srinivas Aluru Haplotype-aware variant selection for genome graphs. 51:1-51:9 2022 BCB https://doi.org/10.1145/3535508.3545556 conf/bcb/2022 db/conf/bcb/bcb2022.html#TavakoliGA22 Daniel Gibney Sharma V. Thankachan Srinivas Aluru The Complexity of Approximate Pattern Matching on de Bruijn Graphs. 263-278 2022 RECOMB https://doi.org/10.1007/978-3-031-04749-7_16 conf/recomb/2022 db/conf/recomb/recomb2022.html#GibneyTA22 Daniel Gibney Sharma V. Thankachan Srinivas Aluru Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. 17:1-17:16 2022 WABI https://doi.org/10.4230/LIPIcs.WABI.2022.17 conf/wabi/2022 db/conf/wabi/wabi2022.html#GibneyTA22 Donald A. Adjeroh Qi Long Xinghua Mindy Shi Fei Guo 0001 Xiaohua Hu 0001 Srinivas Aluru Giri Narasimhan Jianxin Wang 0001 Mingon Kang Ananda Mondal Jin Liu 0012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022, Las Vegas, NV, USA, December 6-8, 2022 BIBM IEEE 2022 978-1-6654-6819-0 https://doi.org/10.1109/BIBM55620.2022 db/conf/bibm/bibm2022.html

Daniel Gibney Sharma V. Thankachan Srinivas Aluru The Complexity of Approximate Pattern Matching on De Bruijn Graphs. 2022 abs/2201.12454 CoRR https://arxiv.org/abs/2201.12454 db/journals/corr/corr2201.html#abs-2201-12454

Chirag Jain Neda Tavakoli Srinivas Aluru A variant selection framework for genome graphs. 460-467 2021 37 Bioinform. Supplement https://doi.org/10.1093/bioinformatics/btab302 db/journals/bioinformatics/bioinformatics37.html#JainTA21

Haowen Zhang Haoran Li 0015 Chirag Jain Haoyu Cheng Kin Fai Au Heng Li 0002 Srinivas Aluru Real-time mapping of nanopore raw signals. 477-483 2021 37 Bioinform. Supplement https://doi.org/10.1093/bioinformatics/btab264 db/journals/bioinformatics/bioinformatics37.html#ZhangLJCALA21

Srinivas Aluru Editorial: From the New Editor-in-Chief. 2058 2021 18 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2021.3108133 db/journals/tcbb/tcbb18.html#Aluru21

Shruti Shivakumar Jiajia Li 0001 Ramakrishnan Kannan Srinivas Aluru Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors. 193-204 2021 ACDA https://doi.org/10.1137/1.9781611976830.18 conf/acda/2021 db/conf/acda/acda2021.html#ShivakumarLKA21 Ankit Srivastava Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru Parallel construction of module networks. 26 2021 SC https://doi.org/10.1145/3458817.3476207 conf/sc/2021 db/conf/sc/sc2021.html#SrivastavaCAA21

Sriram P. Chockalingam Jodh Pannu Sahar Hooshmand Sharma V. Thankachan Srinivas Aluru An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction. 404 2020 21-S BMC Bioinform. 6 https://doi.org/10.1186/s12859-020-03738-5 https://www.wikidata.org/entity/Q102139976 db/journals/bmcbi/bmcbi21S.html#ChockalingamPHT20

Chirag Jain Haowen Zhang Yu Gao 0001 Srinivas Aluru On the Complexity of Sequence-to-Graph Alignment. 640-654 2020 27 J. Comput. Biol. 4 https://doi.org/10.1089/cmb.2019.0066 https://www.wikidata.org/entity/Q126410529 db/journals/jcb/jcb27.html#JainZGA20

Indranil Roy Ankit Srivastava Matt Grimm Srinivas Aluru Interval stabbing on the Automata Processor. 234-245 2020 135 J. Parallel Distributed Comput. https://doi.org/10.1016/j.jpdc.2018.01.010 db/journals/jpdc/jpdc135.html#RoySGA20

Sriram P. Chockalingam Sharma V. Thankachan Srinivas Aluru Sequential and parallel algorithms for all-pair k-mismatch maximal common substrings. 68-79 2020 144 J. Parallel Distributed Comput. https://doi.org/10.1016/j.jpdc.2020.05.018 db/journals/jpdc/jpdc144.html#ChockalingamTA20

Tony Pan Rahul Nihalani Srinivas Aluru Fast de Bruijn Graph Compaction in Distributed Memory Environments. 136-148 2020 17 IEEE ACM Trans. Comput. Biol. Bioinform. 1 https://doi.org/10.1109/TCBB.2018.2858797 https://www.wikidata.org/entity/Q90720971 db/journals/tcbb/tcbb17.html#PanNA20

Harsh Shrivastava 0001 Xinshi Chen Binghong Chen Guanghui Lan Srinivas Aluru Han Liu 0001 Le Song GLAD: Learning Sparse Graph Recovery. 2020 ICLR https://openreview.net/forum?id=BkxpMTEtPB conf/iclr/2020 db/conf/iclr/iclr2020.html#ShrivastavaCCLA20 Ankit Srivastava Sriram P. Chockalingam Srinivas Aluru A parallel framework for constraint-based bayesian network learning via markov blanket discovery. 7 2020 SC https://doi.org/10.1109/SC41405.2020.00011 https://dl.acm.org/doi/10.5555/3433701.3433710 conf/sc/2020 db/conf/sc/sc2020.html#SrivastavaCA20 Xintao Wu Chris Jermaine Li Xiong 0001 Xiaohua Hu 0001 Olivera Kotevska Siyuan Lu Weija Xu Srinivas Aluru Chengxiang Zhai Eyhab Al-Masri Zhiyuan Chen 0003 Jeff Saltz 0001 2020 IEEE International Conference on Big Data (IEEE BigData 2020), Atlanta, GA, USA, December 10-13, 2020 IEEE BigData IEEE 2020 978-1-7281-6251-5 https://doi.org/10.1109/BigData50022.2020 db/conf/bigdataconf/bigdataconf2020.html

Indranil Roy Ankit Srivastava Matt Grimm Marziyeh Nourian Michela Becchi Srinivas Aluru Evaluating High Performance Pattern Matching on the Automata Processor. 1201-1212 2019 68 IEEE Trans. Computers 8 https://doi.org/10.1109/TC.2019.2901466 https://www.wikidata.org/entity/Q128322860 db/journals/tc/tc68.html#RoySGNBA19

Tony Pan Patrick Flick Chirag Jain Yongchao Liu 0004 Srinivas Aluru Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. 1117-1131 2019 16 IEEE ACM Trans. Comput. Biol. Bioinform. 4 https://doi.org/10.1109/TCBB.2017.2760829 https://www.wikidata.org/entity/Q42696360 db/journals/tcbb/tcbb16.html#PanFJLA19

Nagakishore Jammula Srinivas Aluru ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets. 447-456 2019 BCB https://doi.org/10.1145/3307339.3342171 conf/bcb/2019 db/conf/bcb/bcb2019.html#JammulaA19 Md. Vasimuddin Sanchit Misra Heng Li 0002 Srinivas Aluru Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 314-324 2019 IPDPS https://doi.org/10.1109/IPDPS.2019.00041 conf/ipps/2019 db/conf/ipps/ipdps2019.html#VasimuddinMLA19 Chirag Jain Sanchit Misra Haowen Zhang Alexander T. Dilthey Srinivas Aluru Accelerating Sequence Alignment to Graphs. 451-461 2019 IPDPS https://doi.org/10.1109/IPDPS.2019.00055 conf/ipps/2019 db/conf/ipps/ipdps2019.html#JainMZDA19 Chirag Jain Haowen Zhang Yu Gao 0001 Srinivas Aluru On the Complexity of Sequence to Graph Alignment. 85-100 2019 RECOMB https://doi.org/10.1007/978-3-030-17083-7_6 conf/recomb/2019 db/conf/recomb/recomb2019.html#JainZGA19 Patrick Flick Srinivas Aluru Distributed enhanced suffix arrays: efficient algorithms for construction and querying. 72:1-72:17 2019 SC https://doi.org/10.1145/3295500.3356211 https://www.wikidata.org/entity/Q130884819 conf/sc/2019 db/conf/sc/sc2019.html#FlickA19 Chirag Jain Haowen Zhang Alexander T. Dilthey Srinivas Aluru Validating Paired-End Read Alignments in Sequence Graphs. 17:1-17:13 2019 WABI https://doi.org/10.4230/LIPIcs.WABI.2019.17 conf/wabi/2019 db/conf/wabi/wabi2019.html#JainZDA19

Harsh Shrivastava 0001 Xinshi Chen Binghong Chen Guanghui Lan Srinivas Aluru Le Song GLAD: Learning Sparse Graph Recovery. 2019 abs/1906.00271 CoRR http://arxiv.org/abs/1906.00271 db/journals/corr/corr1906.html#abs-1906-00271

Harsh Shrivastava 0001 Eugene Bart Bob Price Hanjun Dai Bo Dai 0001 Srinivas Aluru Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. 2019 abs/1906.00291 CoRR http://arxiv.org/abs/1906.00291 db/journals/corr/corr1906.html#abs-1906-00291

Md. Vasimuddin Sanchit Misra Heng Li 0002 Srinivas Aluru Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 abs/1907.12931 CoRR http://arxiv.org/abs/1907.12931 db/journals/corr/corr1907.html#abs-1907-12931

Chirag Jain Sergey Koren Alexander T. Dilthey Adam M. Phillippy Srinivas Aluru A fast adaptive algorithm for computing whole-genome homology maps. i748-i756 2018 34 Bioinform. 17 https://doi.org/10.1093/bioinformatics/bty597 https://www.wikidata.org/entity/Q58757825 db/journals/bioinformatics/bioinformatics34.html#JainKDPA18

Rosario I. Corona Sanjana Sudarshan Srinivas Aluru Jun-tao Guo An SVM-based method for assessment of transcription factor-DNA complex models. 49-57 2018 19-S BMC Bioinform. 20 https://doi.org/10.1186/s12859-018-2538-y https://www.wikidata.org/entity/Q60937551 db/journals/bmcbi/bmcbi19S.html#CoronaSAG18

Chirag Jain Alexander T. Dilthey Sergey Koren Srinivas Aluru Adam M. Phillippy A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. 766-779 2018 25 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2018.0036 https://www.wikidata.org/entity/Q63649589 db/journals/jcb/jcb25.html#JainDKAP18

Sanchit Misra Tony C. Pan Kanak Mahadik George Powley Priya N. Vaidya Md. Vasimuddin Srinivas Aluru Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis. 3:1-3:14 2018 PACT https://doi.org/10.1145/3243176.3243197 conf/IEEEpact/2018 db/conf/IEEEpact/pact2018.html#MisraPMPVVA18 Sahar Hooshmand Paniz Abedin Daniel Gibney Srinivas Aluru Sharma V. Thankachan Faster Computation of Genome Mappability. 537 2018 BCB https://doi.org/10.1145/3233547.3233645 conf/bcb/2018 db/conf/bcb/bcb2018.html#HooshmandAGAT18 Jodh Pannu Sriram P. Chockalingam Sharma V. Thankachan Srinivas Aluru An Alignment-free Heuristic for Fast Sequence Comparisons with Applications to Phylogeny Reconstruction. 540 2018 BCB https://doi.org/10.1145/3233547.3233648 conf/bcb/2018 db/conf/bcb/bcb2018.html#PannuCTA18 Sahar Hooshmand Paniz Abedin Daniel Gibney Srinivas Aluru Sharma V. Thankachan Faster Computation of Genome Mappability with one Mismatch. 1 2018 ICCABS https://doi.org/10.1109/ICCABS.2018.8541897 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2018.8541897 conf/iccabs/2018 db/conf/iccabs/iccabs2018.html#HooshmandAGAT18 Md. Vasimuddin Sriram P. Chockalingam Srinivas Aluru A Parallel Algorithm for Bayesian Network Inference Using Arithmetic Circuits. 34-43 2018 IPDPS https://doi.org/10.1109/IPDPS.2018.00014 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2018.00014 conf/ipps/2018 db/conf/ipps/ipdps2018.html#VasimuddinCA18 Srinivas Aluru David A. Bader Paul Medvedev Introduction to HiCOMB 2018. 226 2018 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2018.00044 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2018.00044 conf/ipps/2018w db/conf/ipps/ipdps2018w.html#AluruBM18 Harsh Shrivastava 0001 Eugene Bart Bob Price Hanjun Dai Bo Dai 0001 Srinivas Aluru Cooperative neural networks (CoNN): Exploiting prior independence structure for improved classification. 4130-4140 2018 NeurIPS https://proceedings.neurips.cc/paper/2018/hash/051928341be67dcba03f0e04104d9047-Abstract.html http://papers.nips.cc/paper/7667-cooperative-neural-networks-conn-exploiting-prior-independence-structure-for-improved-classification conf/nips/2018 db/conf/nips/nips2018.html#ShrivastavaBPDD18 Sharma V. Thankachan Chaitanya Aluru Sriram P. Chockalingam Srinivas Aluru Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. 211-224 2018 RECOMB https://doi.org/10.1007/978-3-319-89929-9_14 conf/recomb/2018 db/conf/recomb/recomb2018.html#ThankachanACA18 Tony C. Pan Sanchit Misra Srinivas Aluru Optimizing high performance distributed memory parallel hash tables for DNA k-mer counting. 11:1-11:13 2018 SC http://dl.acm.org/citation.cfm?id=3291671 conf/sc/2018 db/conf/sc/sc2018.html#PanMA18 Srinivas Aluru Ananth Kalyanaraman Debajyoti Bera Kishore Kothapalli David Abramson 0001 Ilkay Altintas Sanjukta Bhowmick Madhu Govindaraju Smruti Ranjan Sarangi Sushil K. Prasad Steven Bogaerts Vikas Saxena Sanjay Goel 2018 Eleventh International Conference on Contemporary Computing, IC3 2018, Noida, India, August 2-4, 2018 IC3 IEEE Computer Society 2018 978-1-5386-6834-4 978-1-5386-6835-1 https://ieeexplore.ieee.org/xpl/conhome/8509799/proceeding https://www.computer.org/csdl/proceedings/ic3/2018/6834/00/index.html db/conf/ic3/ic3-2018.html

Sharma V. Thankachan Sriram P. Chockalingam Yongchao Liu 0004 Ambujam Krishnan Srinivas Aluru A greedy alignment-free distance estimator for phylogenetic inference. 238:1-238:8 2017 18 BMC Bioinform. 8 https://doi.org/10.1186/s12859-017-1658-0 https://www.wikidata.org/entity/Q33802269 db/journals/bmcbi/bmcbi18S.html#ThankachanCLKA17

Patrick Flick Chirag Jain Tony Pan Srinivas Aluru Reprint of "A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications". 54-65 2017 70 Parallel Comput. https://doi.org/10.1016/j.parco.2017.09.002 db/journals/pc/pc70.html#FlickJPA17

Chirag Jain Patrick Flick Tony Pan Oded Green Srinivas Aluru An Adaptive Parallel Algorithm for Computing Connected Components. 2428-2439 2017 28 IEEE Trans. Parallel Distributed Syst. 9 https://doi.org/10.1109/TPDS.2017.2672739 http://doi.ieeecomputersociety.org/10.1109/TPDS.2017.2672739 db/journals/tpds/tpds28.html#JainFPGA17

Nagakishore Jammula Sriram P. Chockalingam Srinivas Aluru Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. 417-424 2017 BCB https://doi.org/10.1145/3107411.3107491 conf/bcb/2017 db/conf/bcb/bcb2017.html#JammulaCA17 Sriram P. Chockalingam Maneesha Aluru Hongqing Guo Yanhai Yin Srinivas Aluru Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. 480-490 2017 BCB https://doi.org/10.1145/3107411.3107428 conf/bcb/2017 db/conf/bcb/bcb2017.html#ChockalingamAGY17 Rosario I. Corona Sanjana Sudarshan Jun-tao Guo Srinivas Aluru Confidence assessment of protein-DNA complex models. 9-15 2017 BIBM https://doi.org/10.1109/BIBM.2017.8217617 https://doi.ieeecomputersociety.org/10.1109/BIBM.2017.8217617 conf/bibm/2017 db/conf/bibm/bibm2017.html#CoronaSGA17 Rahul Nihalani Sriram P. Chockalingam Shaowei Zhu 0001 Vijay V. Vazirani Srinivas Aluru Probabilistic estimation of overlap graphs for large sequence datasets. 247-252 2017 BIBM https://doi.org/10.1109/BIBM.2017.8217657 https://doi.ieeecomputersociety.org/10.1109/BIBM.2017.8217657 conf/bibm/2017 db/conf/bibm/bibm2017.html#NihalaniCZVA17 Md. Vasimuddin Srinivas Aluru Parallel Exact Dynamic Bayesian Network Structure Learning with Application to Gene Networks. 42-51 2017 HiPC https://doi.org/10.1109/HiPC.2017.00015 https://doi.ieeecomputersociety.org/10.1109/HiPC.2017.00015 conf/hipc/2017 db/conf/hipc/hipc2017.html#VasimuddinA17 Patrick Flick Srinivas Aluru Parallel Construction of Suffix Trees and the All-Nearest-Smaller-Values Problem. 12-21 2017 IPDPS https://doi.org/10.1109/IPDPS.2017.62 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2017.62 conf/ipps/2017 db/conf/ipps/ipdps2017.html#FlickA17 Chirag Jain Alexander T. Dilthey Sergey Koren Srinivas Aluru Adam M. Phillippy A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. 66-81 2017 RECOMB https://doi.org/10.1007/978-3-319-56970-3_5 conf/recomb/2017 db/conf/recomb/recomb2017.html#JainDKAP17 Vijay Raghavan 0001 Srinivas Aluru George Karypis Lucio Miele Xindong Wu 0001 2017 IEEE International Conference on Data Mining, ICDM 2017, New Orleans, LA, USA, November 18-21, 2017 ICDM IEEE Computer Society 2017 978-1-5386-3835-4 https://ieeexplore.ieee.org/xpl/conhome/8211002/proceeding https://www.computer.org/csdl/proceedings/icdm/2017/3835/00/index.html db/conf/icdm/icdm2017.html Raju Gottumukkala Xia Ning Guozhu Dong Vijay Raghavan 0001 Srinivas Aluru George Karypis Lucio Miele Xindong Wu 0001 2017 IEEE International Conference on Data Mining Workshops, ICDM Workshops 2017, New Orleans, LA, USA, November 18-21, 2017 ICDM Workshops IEEE Computer Society 2017 978-1-5386-3800-2 https://ieeexplore.ieee.org/xpl/conhome/8211022/proceeding https://www.computer.org/csdl/proceedings/icdmw/2017/3800/00/index.html db/conf/icdm/icdm2017w.html

Yongchao Liu 0004 Tony Pan Oded Green Srinivas Aluru Parallelized Kendall's Tau Coefficient Computation via SIMD Vectorized Sorting On Many-Integrated-Core Processors. 2017 abs/1704.03767 CoRR http://arxiv.org/abs/1704.03767 db/journals/corr/corr1704.html#LiuPGA17

Yongchao Liu 0004 Martin Loewer Srinivas Aluru Bertil Schmidt SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations. 47 2016 10 BMC Syst. Biol. S-2 https://doi.org/10.1186/s12918-016-0300-5 https://www.wikidata.org/entity/Q36094606 db/journals/bmcsb/bmcsb10S.html#LiuLAS16

Sharma V. Thankachan Sriram P. Chockalingam Yongchao Liu 0004 Alberto Apostolico Srinivas Aluru ALFRED: A Practical Method for Alignment-Free Distance Computation. 452-460 2016 23 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2015.0217 https://www.wikidata.org/entity/Q50654640 db/journals/jcb/jcb23.html#ThankachanCLAA16

Sharma V. Thankachan Alberto Apostolico Srinivas Aluru A Provably Efficient Algorithm for the k-Mismatch Average Common Substring Problem. 472-482 2016 23 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2015.0235 https://www.wikidata.org/entity/Q45922687 db/journals/jcb/jcb23.html#ThankachanAA16

Indranil Roy Srinivas Aluru Discovering Motifs in Biological Sequences Using the Micron Automata Processor. 99-111 2016 13 IEEE ACM Trans. Comput. Biol. Bioinform. 1 https://doi.org/10.1109/TCBB.2015.2430313 https://doi.ieeecomputersociety.org/10.1109/TCBB.2015.2430313 https://dl.acm.org/doi/10.1109/TCBB.2015.2430313 https://www.wikidata.org/entity/Q50711093 db/journals/tcbb/tcbb13.html#RoyA16

Rahul Nihalani Srinivas Aluru Effective Utilization of Paired Reads to Improve Length and Accuracy of Contigs in Genome Assembly. 355-363 2016 BCB https://doi.org/10.1145/2975167.2975204 conf/bcb/2016 db/conf/bcb/bcb2016.html#NihalaniA16 Tony Pan Patrick Flick Chirag Jain Yongchao Liu 0004 Srinivas Aluru Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems. 422-433 2016 BCB https://doi.org/10.1145/2975167.2975211 conf/bcb/2016 db/conf/bcb/bcb2016.html#PanFJLA16 Srinivas Aluru Genomes Galore: Big Data Challenges in the Life Sciences. 1 2016 HiPC https://doi.org/10.1109/HiPC.2016.010 https://doi.ieeecomputersociety.org/10.1109/HiPC.2016.010 conf/hipc/2016 db/conf/hipc/hipc2016.html#Aluru16 Indranil Roy Ankit Srivastava Srinivas Aluru Programming Techniques for the Automata Processor. 205-210 2016 ICPP https://doi.org/10.1109/ICPP.2016.30 https://doi.ieeecomputersociety.org/10.1109/ICPP.2016.30 conf/icpp/2016 db/conf/icpp/icpp2016.html#RoySA16 Indranil Roy Nagakishore Jammula Srinivas Aluru Algorithmic Techniques for Solving Graph Problems on the Automata Processor. 283-292 2016 IPDPS https://doi.org/10.1109/IPDPS.2016.116 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2016.116 conf/ipps/2016 db/conf/ipps/ipdps2016.html#RoyJA16 Srinivas Aluru David A. Bader Ananth Kalyanaraman Jaroslaw Zola HiCOMB Introduction and Committees. 407 2016 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2016.228 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2016.228 conf/ipps/2016w db/conf/ipps/ipdps2016w.html#AluruBKZ16 Vipin Sachdeva Srinivas Aluru David A. Bader A Memory and Time Scalable Parallelization of the Reptile Error-Correction Code. 453-462 2016 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2016.59 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2016.59 conf/ipps/2016w db/conf/ipps/ipdps2016w.html#SachdevaAB16 Indranil Roy Ankit Srivastava Marziyeh Nourian Michela Becchi Srinivas Aluru High Performance Pattern Matching Using the Automata Processor. 1123-1132 2016 IPDPS https://doi.org/10.1109/IPDPS.2016.94 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2016.94 conf/ipps/2016 db/conf/ipps/ipdps2016.html#RoySNBA16 Sharma V. Thankachan Sriram P. Chockalingam Srinivas Aluru An Efficient Algorithm for Finding All Pairs k-Mismatch Maximal Common Substrings. 3-14 2016 ISBRA https://doi.org/10.1007/978-3-319-38782-6_1 conf/isbra/2016 db/conf/isbra/isbra2016.html#ThankachanCA16 Yongchao Liu 0004 Tony Pan Srinivas Aluru Parallel Pairwise Correlation Computation on Intel Xeon Phi Clusters. 141-149 2016 SBAC-PAD https://doi.org/10.1109/SBAC-PAD.2016.26 https://doi.ieeecomputersociety.org/10.1109/SBAC-PAD.2016.26 conf/sbac-pad/2016 db/conf/sbac-pad/sbac-pad2016.html#LiuPA16 Indranil Roy Ankit Srivastava Matt Grimm Srinivas Aluru Parallel Interval Stabbing on the Automata Processor. 10-17 2016 IA3@SC https://doi.org/10.1109/IA3.2016.008 https://doi.ieeecomputersociety.org/10.1109/IA3.2016.008 http://dl.acm.org/citation.cfm?id=3018846 conf/sc/2016ia3 db/conf/sc/ia3-2016.html#RoySGA16 Sriram P. Chockalingam Sharma V. Thankachan Srinivas Aluru A parallel algorithm for finding all pairs k-mismatch maximal common substrings. 784-794 2016 SC https://doi.org/10.1109/SC.2016.66 https://doi.ieeecomputersociety.org/10.1109/SC.2016.66 http://dl.acm.org/citation.cfm?id=3014994 conf/sc/2016 db/conf/sc/sc2016.html#ChockalingamTA16 Srinivas Aluru Text Indexing. 2226-2231 2016 Encyclopedia of Algorithms https://doi.org/10.1007/978-1-4939-2864-4_422 db/reference/algo/algo2016.html#Aluru16

Yongchao Liu 0004 Srinivas Aluru LightScan: Faster Scan Primitive on CUDA Compatible Manycore Processors. 2016 abs/1604.04815 CoRR http://arxiv.org/abs/1604.04815 db/journals/corr/corr1604.html#LiuA16

Yongchao Liu 0004 Tony Pan Srinivas Aluru Parallel Pairwise Correlation Computation On Intel Xeon Phi Clusters. 2016 abs/1605.01584 CoRR http://arxiv.org/abs/1605.01584 db/journals/corr/corr1605.html#LiuPA16

Chirag Jain Patrick Flick Tony Pan Oded Green Srinivas Aluru An Adaptive Parallel Algorithm for Computing Connectivity. 2016 abs/1607.06156 CoRR http://arxiv.org/abs/1607.06156 db/journals/corr/corr1607.html#JainFPGA16

Soumitra Pal 0001 Srinivas Aluru In search of perfect reads. S7 2015 December 16 BMC Bioinform. S17 https://doi.org/10.1186/1471-2105-16-s17-s7 https://www.wikidata.org/entity/Q35872180 db/journals/bmcbi/bmcbi16S.html#PalA15

Srinivas Aluru Yogesh Simmhan Editorial: Scalable Systems for Big Data Management and Analytics. 1-2 2015 79-80 J. Parallel Distributed Comput. https://doi.org/10.1016/j.jpdc.2015.05.001 db/journals/jpdc/jpdc79.html#AluruS15

Sai Kiranmayee Samudrala Jaroslaw Zola Srinivas Aluru Baskar Ganapathysubramanian Parallel Framework for Dimensionality Reduction of Large-Scale Datasets. 180214:1-180214:12 2015 2015 Sci. Program. https://doi.org/10.1155/2015/180214 https://www.wikidata.org/entity/Q59120489 db/journals/sp/sp2015.html#SamudralaZAG15

Srinivas Aluru Donna K. Slonim Guest Editors' Introduction: Selected Papers from ACM-BCB 2013. 2-3 2015 12 IEEE ACM Trans. Comput. Biol. Bioinform. 1 https://doi.org/10.1109/TCBB.2015.2389551 https://doi.ieeecomputersociety.org/10.1109/TCBB.2015.2389551 https://dl.acm.org/doi/10.1109/TCBB.2015.2389551 https://www.wikidata.org/entity/Q86800396 db/journals/tcbb/tcbb12.html#AluruS15

Sanchit Misra Kiran Pamnany Srinivas Aluru Parallel Mutual Information Based Construction of Genome-Scale Networks on the Intel®Xeon Phi™ Coprocessor. 1008-1020 2015 12 IEEE ACM Trans. Comput. Biol. Bioinform. 5 https://doi.org/10.1109/TCBB.2015.2415931 https://doi.ieeecomputersociety.org/10.1109/TCBB.2015.2415931 https://dl.acm.org/doi/10.1109/TCBB.2015.2415931 https://www.wikidata.org/entity/Q40448924 db/journals/tcbb/tcbb12.html#MisraPA15

Srinivas Aluru Parallel machine learning approaches for reverse engineering genome-scale networks. 3 2015 BIBM https://doi.org/10.1109/BIBM.2015.7359646 https://doi.ieeecomputersociety.org/10.1109/BIBM.2015.7359646 conf/bibm/2015 db/conf/bibm/bibm2015.html#Aluru15 Yongchao Liu 0004 Martin Loewer Srinivas Aluru Bertil Schmidt SNVSniffer: An integrated caller for germline and somatic SNVs based on Bayesian models. 83-90 2015 BIBM https://doi.org/10.1109/BIBM.2015.7359659 https://doi.ieeecomputersociety.org/10.1109/BIBM.2015.7359659 conf/bibm/2015 db/conf/bibm/bibm2015.html#LiuLAS15 Srinivas Aluru Big data in life sciences and public health. 25 2015 HiPC Workshops https://doi.org/10.1109/HiPCW.2015.32 https://doi.ieeecomputersociety.org/10.1109/HiPCW.2015.32 conf/hipc/2015w db/conf/hipc/hipc2015w.html#Aluru15 Nagakishore Jammula Sriram P. Chockalingam Srinivas Aluru Parallel Read Error Correction for Big Genomic Datasets. 446-455 2015 HiPC https://doi.org/10.1109/HiPC.2015.47 https://doi.ieeecomputersociety.org/10.1109/HiPC.2015.47 conf/hipc/2015 db/conf/hipc/hipc2015.html#JammulaCA15 Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru Information Theory Based Genome-Scale Gene Networks Construction Using MapReduce. 464-473 2015 HiPC https://doi.org/10.1109/HiPC.2015.29 https://doi.ieeecomputersociety.org/10.1109/HiPC.2015.29 conf/hipc/2015 db/conf/hipc/hipc2015.html#ChockalingamAA15 Inna Rytsareva Seth Sims Sriram P. Chockalingam Srinivas Aluru David S. Campo Cansu Tetik Sharma V. Thankachan Yury Khudyakov Yueli Zheng Chirag Jain Amanda Sue Efficient detection of viral transmission with threshold-based methods. 1-6 2015 ICCABS https://doi.org/10.1109/ICCABS.2015.7344723 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2015.7344723 conf/iccabs/2015 db/conf/iccabs/iccabs2015.html#RytsarevaSCACTT15 Sharma V. Thankachan Sriram P. Chockalingam Yongchao Liu 0004 Ambujam Krishnan Srinivas Aluru A greedy alignment-free distance estimator for phylogenetic inference (extended abstract). 1 2015 ICCABS https://doi.org/10.1109/ICCABS.2015.7344711 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2015.7344711 conf/iccabs/2015 db/conf/iccabs/iccabs2015.html#ThankachanCLKA15 Sanguthevar Rajasekaran Srinivas Aluru David A. Bader HiCOMB Introduction and Committees. 329-330 2015 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2015.160 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2015.160 conf/ipps/2015w db/conf/ipps/ipdps2015w.html#RajasekaranAB15 Srinivas Aluru Alberto Apostolico Sharma V. Thankachan Efficient Alignment Free Sequence Comparison with Bounded Mismatches. 1-12 2015 RECOMB https://doi.org/10.1007/978-3-319-16706-0_1 conf/recomb/2015 db/conf/recomb/recomb2015.html#AluruAT15 Patrick Flick Chirag Jain Tony Pan Srinivas Aluru A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications. 15:1-15:11 2015 SC https://doi.org/10.1145/2807591.2807619 conf/sc/2015 db/conf/sc/sc2015.html#FlickJPA15 Patrick Flick Srinivas Aluru Parallel distributed memory construction of suffix and longest common prefix arrays. 16:1-16:10 2015 SC https://doi.org/10.1145/2807591.2807609 conf/sc/2015 db/conf/sc/sc2015.html#FlickA15 Kiran Pamnany Sanchit Misra Md. Vasimuddin Xing Liu Edmond Chow Srinivas Aluru Dtree: Dynamic Task Scheduling at Petascale. 122-138 2015 ISC https://doi.org/10.1007/978-3-319-20119-1_10 conf/supercomputer/2015 db/conf/supercomputer/isc2015.html#PamnanyMVLCA15

Srinivas Aluru Nagakishore Jammula A Review of Hardware Acceleration for Computational Genomics. 19-30 2014 31 IEEE Des. Test 1 https://doi.org/10.1109/MDAT.2013.2293757 db/journals/dt/dt31.html#AluruJ14

Soumitra Pal 0001 Srinivas Aluru In search of perfect reads. 1-2 2014 ICCABS https://doi.org/10.1109/ICCABS.2014.6863919 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2014.6863919 conf/iccabs/2014 db/conf/iccabs/iccabs2014.html#PalA14 Sanchit Misra Kiran Pamnany Srinivas Aluru Parallel Mutual Information Based Construction of Whole-Genome Networks on the Intel (R) Xeon Phi (TM) Coprocessor. 241-250 2014 IPDPS https://doi.org/10.1109/IPDPS.2014.35 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2014.35 conf/ipps/2014 db/conf/ipps/ipdps2014.html#MisraPA14 Indranil Roy Srinivas Aluru Finding Motifs in Biological Sequences Using the Micron Automata Processor. 415-424 2014 IPDPS https://doi.org/10.1109/IPDPS.2014.51 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2014.51 conf/ipps/2014 db/conf/ipps/ipdps2014.html#RoyA14 Alba Cristina Magalhaes Alves de Melo Srinivas Aluru David A. Bader HiCOMB Introduction and Committees. 497-498 2014 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2014.212 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2014.212 conf/ipps/2014w db/conf/ipps/ipdps2014w.html#MeloAB14 Sanchit Misra Md. Vasimuddin Kiran Pamnany Sriram P. Chockalingam Yong Dong Min Xie Maneesha R. Aluru Srinivas Aluru Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks. 461-472 2014 SC https://doi.org/10.1109/SC.2014.43 https://doi.ieeecomputersociety.org/10.1109/SC.2014.43 conf/sc/2014 db/conf/sc/sc2014.html#MisraVPCDXAA14

Yetian Chen Jin Tian 0001 Olga Nikolova Srinivas Aluru A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks. 2014 abs/1408.1664 CoRR http://arxiv.org/abs/1408.1664 db/journals/corr/corr1408.html#ChenTNA14

Xiao Yang 0019 Sriram P. Chockalingam Srinivas Aluru A survey of error-correction methods for next-generation sequencing. 56-66 2013 14 Briefings Bioinform. 1 https://doi.org/10.1093/bib/bbs015 https://www.wikidata.org/entity/Q38001613 db/journals/bib/bib14.html#YangCA13

Xiao Yang 0019 Jaroslaw Zola Srinivas Aluru Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters. 2013 11 J. Bioinform. Comput. Biol. 1 https://doi.org/10.1142/S0219720013400015 https://www.wikidata.org/entity/Q51253797 db/journals/jbcb/jbcb11.html#YangZA13

Olga Nikolova Jaroslaw Zola Srinivas Aluru Parallel globally optimal structure learning of Bayesian networks. 1039-1048 2013 73 J. Parallel Distributed Comput. 8 https://doi.org/10.1016/j.jpdc.2013.04.001 db/journals/jpdc/jpdc73.html#NikolovaZA13

Abhinav Sarje Srinivas Aluru All-pairs computations on many-core graphics processors. 79-93 2013 39 Parallel Comput. 2 https://doi.org/10.1016/j.parco.2013.01.002 db/journals/pc/pc39.html#SarjeA13

Srinivas Aluru Large-scale metagenomic clustering via quasi clique enumeration and read assignment ambiguity resolution. 1 2013 ICCABS https://doi.org/10.1109/ICCABS.2013.6629239 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2013.6629239 conf/iccabs/2013 db/conf/iccabs/iccabs2013.html#Aluru13 Jaroslaw Zola David A. Bader Srinivas Aluru HiCOMB Introduction. 499-500 2013 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2013.285 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2013.285 conf/ipps/2013w db/conf/ipps/ipdps2013w.html#ZolaBA13 Srinivas Aluru Invited: Reverse engineering whole-genome networks. 1 2012 ICCABS https://doi.org/10.1109/ICCABS.2012.6182618 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2012.6182618 conf/iccabs/2012 db/conf/iccabs/iccabs2012.html#Aluru12 Srinivas Aluru Workshop: Taxonomic clustering of large-scale metagnomic data. 1 2012 ICCABS https://doi.org/10.1109/ICCABS.2012.6182667 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2012.6182667 conf/iccabs/2012 db/conf/iccabs/iccabs2012.html#Aluru12a Ankit Shah Sriram P. Chockalingam Srinivas Aluru A Parallel Algorithm for Spectrum-based Short Read Error Correction. 60-70 2012 IPDPS https://doi.org/10.1109/IPDPS.2012.16 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2012.16 conf/ipps/2012 db/conf/ipps/ipdps2012.html#ShahCA12 Mark J. Clement Quinn Snell Srinivas Aluru David A. Bader HiCOMB Introduction. 663-664 2012 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2012.338 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2012.338 conf/ipps/2012w db/conf/ipps/ipdps2012w.html#ClementSAB12 Olga Nikolova Srinivas Aluru Parallel Bayesian network structure learning with application to gene networks. 63 2012 SC https://doi.org/10.1109/SC.2012.90 https://doi.ieeecomputersociety.org/10.1109/SC.2012.90 http://dl.acm.org/citation.cfm?id=2389082 conf/sc/2012 db/conf/sc/sc2012.html#NikolovaA12 Xiao Yang 0019 Florian Sikora Guillaume Blin Sylvie Hamel Romeo Rizzi Srinivas Aluru An Algorithmic View on Multi-Related-Segments: A Unifying Model for Approximate Common Interval. 319-329 2012 TAMC https://doi.org/10.1007/978-3-642-29952-0_33 https://www.wikidata.org/entity/Q60704248 conf/tamc/2012 db/conf/tamc/tamc2012.html#YangSBHRA12

Xiao Yang 0019 Srinivas Aluru Karin S. Dorman Repeat-aware modeling and correction of short read errors. S52 2011 12 BMC Bioinform. S-1 https://doi.org/10.1186/1471-2105-12-S1-S52 https://www.wikidata.org/entity/Q33827058 db/journals/bmcbi/bmcbi12S.html#YangAD11

Abhinav Sarje Jaroslaw Zola Srinivas Aluru Accelerating Pairwise Computations on Cell Processors. 69-77 2011 22 IEEE Trans. Parallel Distributed Syst. 1 https://doi.org/10.1109/TPDS.2010.65 http://doi.ieeecomputersociety.org/10.1109/TPDS.2010.65 db/journals/tpds/tpds22.html#SarjeZA11

Aditya Varma Abhiram Ranade Srinivas Aluru An improved maximum likelihood formulation for accurate genome assembly. 165-170 2011 ICCABS https://doi.org/10.1109/ICCABS.2011.5729873 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2011.5729873 conf/iccabs/2011 db/conf/iccabs/iccabs2011.html#VarmaRA11 Xiao Yang 0019 Karin S. Dorman Srinivas Aluru Workshop: Flexible read decomposition for improved short read error correction. 277 2011 ICCABS https://doi.org/10.1109/ICCABS.2011.5729931 https://doi.ieeecomputersociety.org/10.1109/ICCABS.2011.5729931 conf/iccabs/2011 db/conf/iccabs/iccabs2011.html#YangDA11 Olga Nikolova Srinivas Aluru Parallel Discovery of Direct Causal Relations and Markov Boundaries with Applications to Gene Networks. 512-521 2011 ICPP https://doi.org/10.1109/ICPP.2011.49 https://doi.ieeecomputersociety.org/10.1109/ICPP.2011.49 conf/icpp/2011 db/conf/icpp/icpp2011.html#NikolovaA11 Ananth Kalyanaraman Srinivas Aluru David A. Bader HiCOMB Introduction. 426-427 2011 IPDPS Workshops https://doi.org/10.1109/IPDPS.2011.398 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2011.398 conf/ipps/2011w db/conf/ipps/ipdps2011w.html#KalyanaramanAB11 Xiao Yang 0019 Jaroslaw Zola Srinivas Aluru Parallel Metagenomic Sequence Clustering Via Sketching and Maximal Quasi-clique Enumeration on Map-Reduce Clouds. 1223-1233 2011 IPDPS https://doi.org/10.1109/IPDPS.2011.116 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2011.116 conf/ipps/2011 db/conf/ipps/ipdps2011.html#YangZA11 Srinivas Aluru Sanghamitra Bandyopadhyay Ümit V. Çatalyürek Devdatt P. Dubhashi Phillip H. Jones Manish Parashar Bertil Schmidt Contemporary Computing - 4th International Conference, IC3 2011, Noida, India, August 8-10, 2011. Proceedings 168 2011 Springer https://doi.org/10.1007/978-3-642-22606-9 978-3-642-22605-2 Communications in Computer and Information Science IC3 db/conf/ic3/ic3-2011.html Srinivas Aluru Bioinformatics. 134-136 2011 Encyclopedia of Parallel Computing https://doi.org/10.1007/978-0-387-09766-4_110 reference/parallel/2011 db/reference/parallel/parallel2011.html#Aluru11 Jaroslaw Zola Srinivas Aluru Systems Biology, Network Inference in. 1997-2002 2011 Encyclopedia of Parallel Computing https://doi.org/10.1007/978-0-387-09766-4_466 reference/parallel/2011 db/reference/parallel/parallel2011.html#ZolaAA11

Xiao Yang 0019 Karin S. Dorman Srinivas Aluru Reptile: representative tiling for short read error correction. 2526-2533 2010 26 Bioinform. 20 https://doi.org/10.1093/bioinformatics/btq468 https://www.wikidata.org/entity/Q48184458 db/journals/bioinformatics/bioinformatics26.html#YangDA10

André Wehe Wen-Chieh Chang 0002 Oliver Eulenstein Srinivas Aluru A scalable parallelization of the gene duplication problem. 237-244 2010 70 J. Parallel Distributed Comput. 3 https://doi.org/10.1016/j.jpdc.2009.09.010 db/journals/jpdc/jpdc70.html#WeheCEA10

Jaroslaw Zola Maneesha Aluru Abhinav Sarje Srinivas Aluru Parallel Information-Theory-Based Construction of Genome-Wide Gene Regulatory Networks. 1721-1733 2010 21 IEEE Trans. Parallel Distributed Syst. 12 https://doi.org/10.1109/TPDS.2010.59 http://doi.ieeecomputersociety.org/10.1109/TPDS.2010.59 db/journals/tpds/tpds21.html#ZolaASA10

Xiao Yang 0019 Srinivas Aluru An Improved Model for Gene Cluster Inference. 190-195 2010 BICoB conf/bicob/2010 db/conf/bicob/bicob2010.html#YangA10 William Sarje Srinivas Aluru A MapReduce Style Framework for Computations on Trees. 343-352 2010 ICPP https://doi.org/10.1109/ICPP.2010.42 https://doi.ieeecomputersociety.org/10.1109/ICPP.2010.42 conf/icpp/2010 db/conf/icpp/icpp2010.html#SarjeA10 Benjamin G. Jackson Matthew Regennitter Xiao Yang 0019 Patrick S. Schnable Srinivas Aluru Parallel de novo assembly of large genomes from high-throughput short reads. 1-10 2010 IPDPS https://doi.org/10.1109/IPDPS.2010.5470397 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2010.5470397 conf/ipps/2010 db/conf/ipps/ipdps2010.html#JacksonRYSA10 George Karypis Srinivas Aluru David A. Bader Message from the workshop chairs. 1-2 2010 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2010.5470902 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2010.5470902 conf/ipps/2010w db/conf/ipps/ipdps2010w.html#KarypisAB10 Abhinav Sarje Srinivas Aluru Parallel applications employing pairwise computations on emerging architectures. 1-4 2010 IPDPS Workshops https://doi.org/10.1109/IPDPSW.2010.5470805 https://doi.ieeecomputersociety.org/10.1109/IPDPSW.2010.5470805 conf/ipps/2010w db/conf/ipps/ipdps2010w.html#SarjeA10 Abhinav Sarje Jaroslaw Zola Srinivas Aluru Pairwise Computations on the Cell Processor. 297-327 2010 Scientific Computing with Multicore and Accelerators https://doi.org/10.1201/b10376-22 books/tf/10/KBD2010 db/books/collections/KBD2010.html#SarjeZA10

Benjamin G. Jackson Patrick S. Schnable Srinivas Aluru Parallel short sequence assembly of transcriptomes. 2009 10 BMC Bioinform. S-1 https://doi.org/10.1186/1471-2105-10-S1-S14 https://www.wikidata.org/entity/Q33407750 db/journals/bmcbi/bmcbi10S.html#JacksonSA09

Abhinav Sarje Srinivas Aluru Parallel Genomic Alignments on the Cell Broadband Engine. 1600-1610 2009 20 IEEE Trans. Parallel Distributed Syst. 11 https://doi.org/10.1109/TPDS.2008.254 http://doi.ieeecomputersociety.org/10.1109/TPDS.2008.254 db/journals/tpds/tpds20.html#SarjeA09

Benjamin G. Jackson Patrick S. Schnable Srinivas Aluru Assembly of Large Genomes from Paired Short Reads. 30-43 2009 BICoB https://doi.org/10.1007/978-3-642-00727-9_5 conf/bicob/2009 db/conf/bicob/bicob2009.html#JacksonSA09 Olga Nikolova Jaroslaw Zola Srinivas Aluru A parallel algorithm for exact Bayesian network inference. 342-349 2009 HiPC https://doi.org/10.1109/HIPC.2009.5433194 https://doi.ieeecomputersociety.org/10.1109/HIPC.2009.5433194 conf/hipc/2009 db/conf/hipc/hipc2009.html#NikolovaZA09 Jaroslaw Zola Abhinav Sarje Srinivas Aluru Constructing Gene Regulatory Networks on Clusters of Cell Processors. 108-115 2009 ICPP https://doi.org/10.1109/ICPP.2009.35 https://doi.ieeecomputersociety.org/10.1109/ICPP.2009.35 conf/icpp/2009 db/conf/icpp/icpp2009.html#ZolaSA09 Melapudi Vikram Andrew Baczewzki Balasubramaniam Shanker Srinivas Aluru Parallel accelerated cartesian expansions for particle dynamics simulations. 1-11 2009 IPDPS https://doi.org/10.1109/IPDPS.2009.5161038 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2009.5161038 conf/ipps/2009 db/conf/ipps/ipdps2009.html#VikramBSA09 Sanjay Ranka Srinivas Aluru Rajkumar Buyya Yeh-Ching Chung Sumeet Dua Ananth Grama Sandeep K. S. Gupta Rajeev Kumar Vir V. Phoha Contemporary Computing - Second International Conference, IC3 2009, Noida, India, August 17-19, 2009. Proceedings 40 2009 https://doi.org/10.1007/978-3-642-03547-0 978-3-642-03546-3 Communications in Computer and Information Science Springer IC3 db/conf/ic3/ic3-2009.html

David A. Bader Srinivas Aluru High-performance computational biology. 613-615 2008 34 Parallel Comput. 11 https://doi.org/10.1016/j.parco.2008.10.001 https://www.wikidata.org/entity/Q43203294 db/journals/pc/pc34.html#BaderA08

Michael Ott 0001 Jaroslaw Zola Srinivas Aluru Andrew D. Johnson Daniel Janies Alexandros Stamatakis Large-scale phylogenetic analysis on current HPC architectures. 255-270 2008 16 Sci. Program. 2-3 https://doi.org/10.3233/SPR-2008-0247 db/journals/sp/sp16.html#OttZAJJS08

Benjamin G. Jackson Patrick S. Schnable Srinivas Aluru Consensus Genetic Maps as Median Orders from Inconsistent Sources. 161-171 2008 5 IEEE ACM Trans. Comput. Biol. Bioinform. 2 https://doi.org/10.1109/TCBB.2007.70221 https://doi.ieeecomputersociety.org/10.1109/TCBB.2007.70221 https://dl.acm.org/doi/10.1109/TCBB.2007.70221 https://www.wikidata.org/entity/Q47735477 db/journals/tcbb/tcbb5.html#JacksonSA08

Jaroslaw Zola Maneesha Aluru Srinivas Aluru Parallel Information Theory Based Construction of Gene Regulatory Networks. 336-349 2008 HiPC https://doi.org/10.1007/978-3-540-89894-8_31 conf/hipc/2008 db/conf/hipc/hipc2008.html#ZolaAA08 Sudip Seal Michael Moody Anna Ceguerra Simon P. Ringer Krishna Rajan Srinivas Aluru Tracking Nanostructural Evolution in Alloys: Large-Scale Analysis of Atom Probe Tomography Data on Blue Gene/L. 338-345 2008 ICPP https://doi.org/10.1109/ICPP.2008.73 https://doi.ieeecomputersociety.org/10.1109/ICPP.2008.73 conf/icpp/2008 db/conf/icpp/icpp2008.html#SealMCRRA08 Benjamin G. Jackson Srinivas Aluru Parallel Construction of Bidirected String Graphs for Genome Assembly. 346-353 2008 ICPP https://doi.org/10.1109/ICPP.2008.70 https://doi.ieeecomputersociety.org/10.1109/ICPP.2008.70 conf/icpp/2008 db/conf/icpp/icpp2008.html#JacksonA08 Andrew Janowczyk Sharat Chandran Srinivas Aluru Fast, Processor-Cardinality Agnostic PRNG with a Tracking Application. 171-178 2008 ICVGIP https://doi.org/10.1109/ICVGIP.2008.90 https://doi.ieeecomputersociety.org/10.1109/ICVGIP.2008.90 conf/icvgip/2008 db/conf/icvgip/icvgip2008.html#JanowczykCA08 Abhinav Sarje Srinivas Aluru Parallel biological sequence alignments on the Cell Broadband Engine. 1-11 2008 IPDPS https://doi.org/10.1109/IPDPS.2008.4536328 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2008.4536328 conf/ipps/2008 db/conf/ipps/ipdps2008.html#SarjeA08 Srinivas Aluru Text Indexing. 2008 Encyclopedia of Algorithms https://doi.org/10.1007/978-0-387-30162-4_422 reference/algo/2008 db/reference/algo/algo2008.html#Aluru08

Anantharaman Kalyanaraman Scott J. Emrich Patrick S. Schnable Srinivas Aluru Assembling genomes on large-scale parallel computers. 1240-1255 2007 67 J. Parallel Distributed Comput. 12 https://doi.org/10.1016/j.jpdc.2007.05.014 db/journals/jpdc/jpdc67.html#KalyanaramanESA07

Jaroslaw Zola Xiao Yang 0019 Adrian Rospondek Srinivas Aluru PARALLEL-TCOFFEE: A parallel multiple sequence aligner. 248-253 2007 conf/ISCApdcs/2007 PDCS db/conf/ISCApdcs/ISCApdcs2007.html#ZolaYRA07 Scott J. Emrich Anantharaman Kalyanaraman Srinivas Aluru Massively parallel expressed sequence tag clustering. 254-261 2007 conf/ISCApdcs/2007 PDCS db/conf/ISCApdcs/ISCApdcs2007.html#EmrichKA07 Srinivas Aluru The Combinatorics of Sequencing the Corn Genome. 1 2007 conf/cocoon/2007 COCOON https://doi.org/10.1007/978-3-540-73545-8_1 db/conf/cocoon/cocoon2007.html#Aluru07 Srinivas Aluru David A. Bader Anantharaman Kalyanaraman Symposium Evening Tutorial: High-performance Computing Methods for Computational Genomics. 13 2007 conf/ipps/2007 IPDPS https://doi.org/10.1109/IPDPS.2007.370203 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2007.370203 db/conf/ipps/ipdps2007.html#AluruBK07 Michael Ott 0001 Jaroslaw Zola Alexandros Stamatakis Srinivas Aluru Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L. 4 2007 SC https://doi.org/10.1145/1362622.1362628 conf/sc/2007 db/conf/sc/sc2007.html#OttZSA07 Pang Ko Srinivas Aluru Optimal Self-adjusting Trees for Dynamic String Data in Secondary Storage. 184-194 2007 conf/spire/2007 SPIRE https://doi.org/10.1007/978-3-540-75530-2_17 db/conf/spire/spire2007.html#KoA07 Srinivas Aluru Manish Parashar Ramamurthy Badrinath Viktor K. Prasanna High Performance Computing - HiPC 2007, 14th International Conference, Goa, India, December 18-21, 2007, Proceedings HiPC Lecture Notes in Computer Science 4873 Springer 2007 978-3-540-77219-4 https://doi.org/10.1007/978-3-540-77220-0 db/conf/hipc/hipc2007.html Srinivas Aluru Sudip Seal Spatial Domain Decomposition Methods in Parallel Scientific Computing. 2007 Handbook of Parallel Computing https://doi.org/10.1201/9781420011296.ch44 reference/crc/2007pc db/reference/crc/pc2007.html#AluruS07

Anantharaman Kalyanaraman Srinivas Aluru Efficient Algorithms and Software for Detection of Full-length Ltr Retrotransposons. 197-216 2006 4 J. Bioinform. Comput. Biol. 2 https://doi.org/10.1142/S021972000600203X https://www.wikidata.org/entity/Q51168785 db/journals/jbcb/jbcb4.html#KalyanaramanA06

Srinivas Aluru Nancy M. Amato David A. Bader Editorial: Special Section on High-Performance Computational Biology. 737-739 2006 17 IEEE Trans. Parallel Distributed Syst. 8 https://doi.org/10.1109/TPDS.2006.102 http://doi.ieeecomputersociety.org/10.1109/TPDS.2006.102 db/journals/tpds/tpds17.html#AluruAB06

Sudip Seal Srinivas Aluru Communication-aware Parallel Domain Decomposition using Space Filling Curves. 159-164 2006 conf/ISCApdcs/2006 PDCS db/conf/ISCApdcs/ISCApdcs2006.html#SealA06 Pang Ko Srinivas Aluru Obtaining Provably Good Performance from Suffix Trees in Secondary Storage. 72-83 2006 conf/cpm/2006 CPM https://doi.org/10.1007/11780441_8 db/conf/cpm/cpm2006.html#KoA06 Srikanta Tirthapura Sudip Seal Srinivas Aluru A Formal Analysis of Space Filling Curves for Parallel Domain Decomposition. 505-512 2006 conf/icpp/2006 ICPP https://doi.org/10.1109/ICPP.2006.7 https://doi.ieeecomputersociety.org/10.1109/ICPP.2006.7 https://www.wikidata.org/entity/Q60148601 db/conf/icpp/icpp2006.html#TirthapuraSA06 Anantharaman Kalyanaraman Scott J. Emrich Patrick S. Schnable Srinivas Aluru Assembling genomes on large-scale parallel computers. 2006 conf/ipps/2006 IPDPS https://doi.org/10.1109/IPDPS.2006.1639259 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2006.1639259 db/conf/ipps/ipdps2006.html#KalyanaramanESA06 Srinivas Aluru David A. Bader Anantharaman Kalyanaraman M11 - High-performance computing methods for computational genomics. 225 2006 conf/sc/2006 SC https://doi.org/10.1145/1188455.1188689 db/conf/sc/sc2006.html#AluruBK06 Srinivas Aluru Bioinformatics. 657-695 2006 Handbook of Nature-Inspired and Innovative Computing https://doi.org/10.1007/0-387-27705-6_21 books/daglib/0014828 db/books/daglib/0014828.html#Aluru06 Srinivas Aluru Nancy M. Amato David A. Bader Suchindra Bhandarkar Laxmikant V. Kalé Dan C. Marinescu Parallel Computational Biology. 357-378 2006 Parallel Processing for Scientific Computing https://doi.org/10.1137/1.9780898718133.ch19 books/siam/06/HRS2006 db/books/collections/HRS2006.html#AluruABBKM06

Sudip Seal Srikanth Komarina Srinivas Aluru An optimal hierarchical clustering algorithm for gene expression data. 143-147 2005 93 Inf. Process. Lett. 3 https://doi.org/10.1016/j.ipl.2004.11.001 db/journals/ipl/ipl93.html#SealKA05

Pang Ko Srinivas Aluru Space efficient linear time construction of suffix arrays. 143-156 2005 3 J. Discrete Algorithms 2-4 https://doi.org/10.1016/j.jda.2004.08.002 db/journals/jda/jda3.html#KoA05

Fatih Erdogan Sevilgen Srinivas Aluru Natsuhiko Futamura Parallel algorithms for tree accumulations. 85-93 2005 65 J. Parallel Distributed Comput. 1 https://doi.org/10.1016/j.jpdc.2004.09.001 db/journals/jpdc/jpdc65.html#SevilgenAF05

Bhanu Hariharan Srinivas Aluru Efficient parallel algorithms and software for compressed octrees with applications to hierarchical methods. 311-331 2005 31 Parallel Comput. 3-4 https://doi.org/10.1016/j.parco.2004.12.007 db/journals/pc/pc31.html#HariharanA05

Rama Sangireddy Natsuhiko Futamura Srinivas Aluru Arun K. Somani Scalable, memory efficient, high-speed IP lookup algorithms. 802-812 2005 13 IEEE/ACM Trans. Netw. 4 https://doi.org/10.1109/TNET.2005.852878 db/journals/ton/ton13.html#SangireddyFAS05

Zhenhui Shen Srinivas Aluru Srikanta Tirthapura Indexing for Subscription Covering in Publish-Subscribe Systems. 328-333 2005 conf/ISCApdcs/2005 PDCS db/conf/ISCApdcs/ISCApdcs2005.html#ShenAT05 Benjamin G. Jackson Srinivas Aluru Patrick S. Schnable Consensus Genetic Maps: A Graph Theoretic Approach. 35-43 2005 conf/csb/2005 CSB https://doi.org/10.1109/CSB.2005.26 https://doi.ieeecomputersociety.org/10.1109/CSB.2005.26 https://www.wikidata.org/entity/Q42679155 db/conf/csb/csb2005.html#JacksonAS05 Anantharaman Kalyanaraman Srinivas Aluru Efficient Algorithms and Software for Detection of Full-Length LTR Retrotransposons. 56-64 2005 conf/csb/2005 CSB https://doi.org/10.1109/CSB.2005.31 https://doi.ieeecomputersociety.org/10.1109/CSB.2005.31 https://www.wikidata.org/entity/Q51279077 db/conf/csb/csb2005.html#KalyanaramanA05

Scott J. Emrich Srinivas Aluru Yan Fu Tsui-Jung Wen Mahesh Narayanan Ling Guo Daniel A. Ashlock Patrick S. Schnable A strategy for assembling the maize (Zea mays L.) genome. 140-147 2004 20 Bioinform. 2 https://doi.org/10.1093/bioinformatics/bth017 https://www.wikidata.org/entity/Q44735634 db/journals/bioinformatics/bioinformatics20.html#EmrichAFWNGAS04

David A. Bader Srinivas Aluru Special Issue: High Performance Computational Biology. 817-821 2004 16 Concurr. Pract. Exp. 9 https://doi.org/10.1002/cpe.865 db/journals/concurrency/concurrency16.html#BaderA04

Stjepan Rajko Srinivas Aluru Space and Time Optimal Parallel Sequence Alignments. 1070-1081 2004 15 IEEE Trans. Parallel Distributed Syst. 12 https://doi.org/10.1109/TPDS.2004.86 http://doi.ieeecomputersociety.org/10.1109/TPDS.2004.86 db/journals/tpds/tpds15.html#RajkoA04

Pang Ko Mahesh Narayanan Anantharaman Kalyanaraman Srinivas Aluru Space-Conserving Optimal DNA-Protein Alignment . 80-88 2004 conf/csb/2004 CSB https://doi.org/10.1109/CSB.2004.1332420 https://doi.ieeecomputersociety.org/10.1109/CSB.2004.1332420 https://www.wikidata.org/entity/Q51279063 db/conf/csb/csb2004.html#KoNKA04 Srinivas Aluru Fatih Erdogan Sevilgen Efficient Methods for Database Storage and Retrieval Using Space-Filling Curves. 503-512 https://doi.org/10.1007/978-3-540-30182-0_51 2004 conf/iscis/2004 ISCIS db/conf/iscis/iscis2004.html#AluruS04 Meng-Shiou Wu Ricky A. Kendall Srinivas Aluru A tunable collective communication framework on a cluster of SMPS. 56-63 2004 conf/pdcn/2004 Parallel and Distributed Computing and Networks db/conf/pdcn/pdcn2004.html#WuKA04 Srinivas Aluru Quadtrees and Octrees. 2004 Handbook of Data Structures and Applications https://doi.org/10.1201/9781420035179.ch19 reference/crc/2004dsa db/reference/crc/dsa2004.html#Aluru04 Srinivas Aluru Suffix Trees and Suffix Arrays. 2004 Handbook of Data Structures and Applications https://doi.org/10.1201/9781420035179.ch29 reference/crc/2004dsa db/reference/crc/dsa2004.html#Aluru04a

Srinivas Aluru Natsuhiko Futamura Kishan Mehrotra Parallel biological sequence comparison using prefix computations. 264-272 2003 63 J. Parallel Distributed Comput. 3 https://doi.org/10.1016/S0743-7315(03)00010-8 db/journals/jpdc/jpdc63.html#AluruFM03

Srinivas Aluru David A. Bader Guest Editor's Introduction: Special issue on high-performance computational biology. 671-673 2003 63 J. Parallel Distributed Comput. 7-8 https://doi.org/10.1016/S0743-7315(03)00128-X db/journals/jpdc/jpdc63.html#AluruB03

Natsuhiko Futamura Srinivas Aluru Xiaoqiu Huang 0001 Parallel Syntenic Alignments. 689-703 2003 13 Parallel Process. Lett. 4 https://doi.org/10.1142/S0129626403001604 db/journals/ppl/ppl13.html#FutamuraAH03

Anantharaman Kalyanaraman Srinivas Aluru Volker Brendel Suresh C. Kothari Space and time efficient parallel algorithms and software for EST clustering. 1209-1221 2003 14 IEEE Trans. Parallel Distributed Syst. 12 https://doi.org/10.1109/TPDS.2003.1255634 db/journals/tpds/tpds14.html#KalyanaramanABK03

Pang Ko Srinivas Aluru Space Efficient Linear Time Construction of Suffix Arrays. 200-210 2003 conf/cpm/2003 CPM https://doi.org/10.1007/3-540-44888-8_15 db/conf/cpm/cpm2003.html#KoA03 Srinivas Aluru Computational biology on parallel computers. 3370-3377 2003 ECC https://doi.org/10.23919/ECC.2003.7086561 conf/eucc/2003 db/conf/eucc/eucc2003.html#Aluru03 Natsuhiko Futamura Rama Sangireddy Srinivas Aluru Arun K. Somani Scalable, memory efficient, high-speed lookup and update algorithms for IP routing. 257-263 2003 ICCCN https://doi.org/10.1109/ICCCN.2003.1284179 conf/icccn/2003 db/conf/icccn/icccn2003.html#FutamuraSAS03 Stjepan Rajko Srinivas Aluru Space and Time Optimal Parallel Sequence Alignments. 39-47 2003 conf/icpp/2003 ICPP https://doi.org/10.1109/ICPP.2003.1240564 https://doi.ieeecomputersociety.org/10.1109/ICPP.2003.1240564 db/conf/icpp/icpp2003.html#RajkoA03

Natsuhiko Futamura Srinivas Aluru Desh Ranjan Bhanu Hariharan Efficient Parallel Algorithms for Solvent Accessible Surface Area of Proteins. 544-555 2002 13 IEEE Trans. Parallel Distributed Syst. 6 https://doi.org/10.1109/TPDS.2002.1011399 http://doi.ieeecomputersociety.org/10.1109/TPDS.2002.1011399 db/journals/tpds/tpds13.html#FutamuraARH02

Meng-Shiou Wu Srinivas Aluru Ricky A. Kendall Mixed Mode Matrix Multiplication. 195- 2002 conf/cluster/2002 CLUSTER https://doi.org/10.1109/CLUSTR.2002.1137747 https://doi.ieeecomputersociety.org/10.1109/CLUSTR.2002.1137747 db/conf/cluster/cluster2002.html#WuAK02 Natsuhiko Futamura Srinivas Aluru Xiaoqiu Huang 0001 Parallel Syntenic Alignments. 420-430 2002 conf/hipc/2002 HiPC https://doi.org/10.1007/3-540-36265-7_40 db/conf/hipc/hipc2002.html#FutamuraAH02 Anantharaman Kalyanaraman Srinivas Aluru Suresh C. Kothari Space and Time Efficient Parallel Algorithms and Software for EST Clustering. 331-342 2002 conf/icpp/2002 ICPP https://doi.org/10.1109/ICPP.2002.1040889 https://doi.ieeecomputersociety.org/10.1109/ICPP.2002.1040889 db/conf/icpp/icpp2002.html#KalyanaramanAK02 David A. Bader Srinivas Aluru Workshop Introduction. 2002 conf/ipps/2002 IPDPS https://doi.ieeecomputersociety.org/10.1109/IPDPS.2002.10028 db/conf/ipps/ipdps2002.html#BaderA02 Anantharaman Kalyanaraman Srinivas Aluru Suresh C. Kothari Parallel EST Clustering. 2002 conf/ipps/2002 IPDPS https://doi.org/10.1109/IPDPS.2002.1016587 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2002.1016587 db/conf/ipps/ipdps2002.html#KalyanaramanAK02 Bhanu Hariharan Srinivas Aluru Balasubramaniam Shanker A scalable parallel fast multipole method for analysis of scattering from perfect electrically conducting surfaces. 16:1-16:17 2002 conf/sc/2002 SC https://doi.org/10.1109/SC.2002.10012 https://doi.ieeecomputersociety.org/10.1109/SC.2002.10012 http://dl.acm.org/citation.cfm?id=762813 db/conf/sc/sc2002.html#HariharanAS02 Bhanu Hariharan Srinivas Aluru Efficient Parallel Algorithms and Software for Compressed Octrees with Applications to Hierarchical Methods. 125-136 2001 conf/hipc/2001 HiPC https://doi.org/10.1007/3-540-45307-5_12 db/conf/hipc/hipc2001.html#HariharanA01

Ibraheem Al-Furaih Srinivas Aluru Sanjay Goil Sanjay Ranka Parallel Construction of Multidimensional Binary Search Trees. 136-148 2000 11 IEEE Trans. Parallel Distributed Syst. 2 https://doi.org/10.1109/71.841750 http://doi.ieeecomputersociety.org/10.1109/71.841750 db/journals/tpds/tpds11.html#Al-furaihAGR00

Fatih Erdogan Sevilgen Natsuhiko Futamura Srinivas Aluru A Provably Optimal, Distribution-Independent Parallel Fast Multipole Method. 77-84 2000 conf/ipps/2000 IPDPS https://doi.org/10.1109/IPDPS.2000.845967 https://doi.ieeecomputersociety.org/10.1109/IPDPS.2000.845967 db/conf/ipps/ipdps2000.html#SevilgenFA00 Srinivas Aluru Fatih Erdogan Sevilgen Dynamic Compressed Hypertoctrees with Application to the N-Body Problem. 21-33 https://doi.org/10.1007/3-540-46691-6_2 1999 conf/fsttcs/1999 FSTTCS db/conf/fsttcs/fsttcs99.html#AluruS99 Srinivas Aluru Desh Ranjan Natsuhiko Futamura A Parallel Monte Carlo Algorithm for Protein Accessible Surface Area Computation. 339-348 1999 conf/hipc/1999 HiPC db/conf/hipc/hipc1999.html#AluruRF99 https://doi.org/10.1007/978-3-540-46642-0_49 Srinivas Aluru Natsuhiko Futamura Kishan Mehrotra Parallel Biological Sequence Comparison Using Prefix Computations. 653-659 1999 conf/ipps/1999 IPPS/SPDP https://doi.org/10.1109/IPPS.1999.760546 https://doi.ieeecomputersociety.org/10.1109/IPPS.1999.760546 db/conf/ipps/ipps1999.html#AluruFM99 Srinivas Aluru Songrit Maneewongvatana A Practical Parallel Algorithm for Line Segment Visibility. 1676-1682 1999 conf/pdpta/1999 PDPTA db/conf/pdpta/pdpta1999-3.html#AluruM99 Fatih Erdogan Sevilgen Srinivas Aluru A Unifying Data Structure for Hierarchical Methods. 24 1999 SC https://doi.org/10.1145/331532.331556 https://doi.ieeecomputersociety.org/10.1109/SC.1999.10056 conf/sc/1999 db/conf/sc/sc1999.html#SevilgenA99

Srinivas Aluru John L. Gustafson Gurpur M. Prabhu Fatih Erdogan Sevilgen Distribution-Independent Hierarchical Algorithms for the N-body Problem. 303-323 1998 12 J. Supercomput. 4 https://doi.org/10.1023/A:1008047806690 db/journals/tjs/tjs12.html#AluruGPS98

Srinivas Aluru Lagged Fibonacci Random Number Generators for Distributed Memory Parallel Computers. 1-12 1997 45 J. Parallel Distributed Comput. 1 db/journals/jpdc/jpdc45.html#Aluru97 https://doi.org/10.1006/jpdc.1997.1363

Ibraheem Al-Furaih Srinivas Aluru Sanjay Goil Sanjay Ranka Practical Algorithms for Selection on Coarse-Grained Parallel Computers. 813-824 https://doi.org/10.1109/71.605768 http://doi.ieeecomputersociety.org/10.1109/71.605768 1997 8 IEEE Trans. Parallel Distributed Syst. 8 db/journals/tpds/tpds8.html#Al-furiahAGR97

Srinivas Aluru Fatih Erdogan Sevilgen Parallel domain decomposition and load balancing using space-filling curves. 230-235 1997 HiPC https://doi.org/10.1109/HIPC.1997.634498 https://doi.ieeecomputersociety.org/10.1109/HIPC.1997.634498 conf/hipc/1997 db/conf/hipc/hipc1997.html#AluruS97

Srinivas Aluru Greengard's N-Body Algorithm is not Order N. 773-776 1996 17 SIAM J. Sci. Comput. 3 https://doi.org/10.1137/S1064827593272031 db/journals/siamsc/siamsc17.html#Aluru96

John L. Gustafson Srinivas Aluru Massively Parallel Searching for Better Algorithms or How to Do a Cross Product with Five Multiplications. 203-217 1996 5 Sci. Program. 3 https://doi.org/10.1155/1996/284218 http://content.iospress.com/articles/scientific-programming/spr5-3-03 https://www.wikidata.org/entity/Q114070598 db/journals/sp/sp5.html#GustafsonA96

Srinivas Aluru Parallel Additive Lagged Fibonacci Random Number Generators. 102-108 1996 conf/ics/1996 International Conference on Supercomputing https://doi.org/10.1145/237578.237591 db/conf/ics/ics1996.html#Aluru96 Ibraheem Al-Furaih Srinivas Aluru Sanjay Goil Sanjay Ranka Parallel Construction of Multidimensional Binary Search Trees. 205-212 1996 conf/ics/1996 International Conference on Supercomputing https://doi.org/10.1145/237578.237605 db/conf/ics/ics1996.html#Al-FuraihAGR96 Ibraheem Al-Furaih Srinivas Aluru Sanjay Goil Sanjay Ranka Practical Algorithms for Selection on Coarse-Grained Parallel Computers. 309-313 1996 conf/ipps/1996 IPPS https://doi.org/10.1109/IPPS.1996.508074 https://doi.ieeecomputersociety.org/10.1109/IPPS.1996.508074 db/conf/ipps/ipps1996.html#Al-FuraihAGR96 Srinivas Aluru Songrit Maneewongvatana Practical Paralle1 Algorithm for Constructing Line Arrangements. 125-135 1996 conf/pdpta/1996 PDPTA db/conf/pdpta/pdpta1996.html#AluruM96 Sanjay Goil Srinivas Aluru Sanjay Ranka Concatenated parallelism: a technique for efficient parallel divide and conquer. 488-495 1996 SPDP https://doi.org/10.1109/SPDP.1996.570373 https://doi.ieeecomputersociety.org/10.1109/SPDP.1996.570373 conf/spdp/1996 db/conf/spdp/spdp96.html#GoilAR96 Srinivas Aluru Properties of Binomial Coefficients and Implications to Parallelizing Lagged Fibonacci Random Number Generators. 25-28 1995 conf/icpp/1995-3 ICPP (3) db/conf/icpp/icpp1995-3.html#Aluru95 Srinivas Aluru Distribution-independent hierarchical N-body methods. 1994 Iowa State University, Ames, USA https://dr.lib.iastate.edu/handle/20.500.12876/63845 https://hdl.handle.net/20.500.12876/63845 https://doi.org/10.31274/rtd-180813-11599 https://www.base-search.net/Record/e3b7a0056ee20225d9e057fe6439ffffedca284338adb7a47d18f14f9d7278cc base-search.net (ftiowastateuniv:oai:dr.lib.iastate.edu:20.500.12876/63845) Srinivas Aluru Gurpur M. Prabhu John L. Gustafson Truly distribution-independent algorithms for the N-body problem. 420-428 1994 conf/sc/1994 SC https://doi.org/10.1109/SUPERC.1994.344305 https://doi.ieeecomputersociety.org/10.1109/SUPERC.1994.344305 http://dl.acm.org/citation.cfm?id=602844 db/conf/sc/sc1994.html#AluruPG94 Srinivas Aluru John L. Gustafson A Massively Parallel Optimizer for Expression Evaluation. 97-106 1993 conf/ics/1993 International Conference on Supercomputing https://doi.org/10.1145/165939.165960 db/conf/ics/ics1993.html#AluruG93 Srinivas Aluru John L. Gustafson Subtle Issues of SIMD Tree Search. 49-56 1993 conf/parco/1993 PARCO db/conf/parco/parco1993.html#AluruG93

Srinivas Aluru Gurpur M. Prabhu John L. Gustafson A random number generator for parallel computers. 839-847 1992 18 Parallel Comput. 8 db/journals/pc/pc18.html#AluruPG92 https://doi.org/10.1016/0167-8191(92)90030-B

Paniz Abedin David Abramson 0001 Donald A. Adjeroh Sinan G. Aksoy Ibraheem Al-Furaih Eyhab Al-Masri Ilkay Altintas Chaitanya Aluru Maneesha AluruManeesha R. Aluru Nancy M. Amato Ilya Amburg M. Mondal AnandaAnanda Mondal Alberto Apostolico Dan AshlockDaniel A. Ashlock Kin Fai Au Andrew Baczewzki David A. Bader Ramamurthy Badrinath Sanghamitra Bandyopadhyay Aranya Banerjee Eugene Bart Michela Becchi Anne Benoit Debajyoti Bera Suchindra Bhandarkar Sanjukta Bhowmick Guillaume Blin Steven Bogaerts Volker Brendel Rajkumar Buyya David S. Campo Ümit V. Çatalyürek Anna Ceguerra Sharat Chandran Wen-Chieh Chang 0002 Binghong Chen Xinshi Chen Yetian Chen Zhiyuan Chen 0003 Haoyu Cheng Sriram P. Chockalingam Edmond Chow Yeh-Ching Chung Mark J. Clement Rosario I. Corona Bo Dai 0001 Hanjun Dai Alexander T. Dilthey Guozhu Dong Yong Dong Karin S. Dorman Sumeet Dua Devdatt P. Dubhashi Scott J. Emrich Oliver Eulenstein Patrick Flick Yan Fu Natsuhiko Futamura Baskar Ganapathysubramanian Yu Gao 0001 Daniel Gibney Sanjay Goel Sanjay Goil Raju N. GottumukkalaRaju Gottumukkala Madhu Govindaraju Ananth Grama Oded Green Matt Grimm Fei Guo 0001 Hongqing Guo Jun-tao Guo Ling Guo Sandeep K. S. Gupta John L. Gustafson Sylvie Hamel Bhanu Hariharan Sahar Hooshmand Xiaohua Hu 0001 Xiaoqiu Huang 0001 Benjamin G. Jackson Chirag Jain Nagakishore Jammula Daniel Janies Andrew Janowczyk Chris Jermaine Andrew D. Johnson Phillip H. Jones Laxmikant V. Kalé Anantharaman KalyanaramanAnanth Kalyanaraman Mingon Kang Ramakrishnan Kannan George Karypis Ricky A. Kendall Yuri KhudyakovYury Khudyakov Pang Ko Srikanth Komarina Sergey Koren Olivera Kotevska Kishore Kothapalli Suresh C. Kothari Ambujam Krishnan Rajeev Kumar Guanghui Lan Haoran Li 0015 Heng Li 0002 Jiajia Li 0001 Han Liu 0001 Jin Liu 0012 Xing Liu Yongchao Liu 0004 Martin Loewer Qi Long Siyuan Lu Kanak Mahadik Songrit Maneewongvatana Dan C. Marinescu Paul Medvedev Kishan G. MehrotraKishan Mehrotra Alba Cristina Magalhaes Alves de Melo Lucio Miele Sanchit Misra Michael Moody Giri Narasimhan Mahesh Narayanan Rahul Nihalani Olga Nikolova Xia Ning Marziyeh Nourian Michael Ott 0001 Soumitra Pal 0001 Kiran Pamnany Tony PanTony C. Pan Jodh Pannu Manish Parashar Adam M. Phillippy Vir V. Phoha George Powley Gurpur M. Prabhu Sushil K. Prasad Viktor K. Prasanna Bob Price Vijay Raghavan 0001 Krishna Rajan Sanguthevar Rajasekaran Stjepan Rajko Abhiram G. RanadeAbhiram Ranade Desh Ranjan Sanjay Ranka Matthew Regennitter Simon P. Ringer Romeo Rizzi Adrian Rospondek Indranil Roy Inna Rytsareva Vipin Sachdeva Jeffrey S. SaltzJeff Saltz 0001 Sai Kiranmayee Samudrala Rama Sangireddy Smruti R. SarangiSmruti Ranjan Sarangi Abhinav Sarje William Sarje Vikas Saxena Bertil Schmidt Patrick S. Schnable Sudip K. SealSudip Seal Fatih Erdogan Sevilgen Ankit Shah Balasubramaniam Shanker Zhenhui Shen Xinghua ShiXinghua Mindy Shi Shruti Shivakumar Harsh Shrivastava 0001 Florian Sikora Yogesh L. SimmhanYogesh Simmhan Seth Sims Donna K. Slonim Quinn Snell Arun K. Somani Le Song Ankit Srivastava Alexandros Stamatakis Sanjana Sudarshan Amanda Sue Neda Tavakoli Cansu Tetik Sharma V. Thankachan Jin Tian 0001 Srikanta Tirthapura Bora Uçar Priya N. Vaidya Aditya Varma Md. Vasimuddin Vijay V. Vazirani Melapudi Vikram Jianxin Wang 0001 André Wehe Tsui-Jung Wen Meng-Shiou Wu Xindong Wu 0001 Xintao Wu Min Xie Li Xiong 0001 Helen Xu 0001 Weija Xu Xiao Yang 0019 Yanhai Yin Stephen J. Young ChengXiang ZhaiChengxiang Zhai Haowen Zhang Xiuwei Zhang 0002 Yueli Zheng Shaowei Zhu 0001 Jaroslaw Zola