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ref.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for lixueqi at 2019-04-16 03:19:26 -0700
%% Saved with string encoding Unicode (UTF-8)
@comment{jabref-meta: databaseType:bibtex;}
@inproceedings{yuanrong,
Acmid = {3225134},
Address = {New York, NY, USA},
Articleno = {65},
Author = {Wang, Yuanrong and Li, Xueqi and Zang, Dawei and Tan, Guangming and Sun, Ninghui},
Booktitle = {Proceedings of the 47th International Conference on Parallel Processing},
Date-Added = {2019-04-16 03:12:42 -0700},
Date-Modified = {2019-04-16 03:12:49 -0700},
Doi = {10.1145/3225058.3225134},
Isbn = {978-1-4503-6510-9},
Keywords = {Energy efficiency, Genome alignment, Hardware-acceleration},
Location = {Eugene, OR, USA},
Numpages = {12},
Pages = {65:1--65:12},
Publisher = {ACM},
Series = {ICPP 2018},
Title = {Accelerating FM-index Search for Genomic Data Processing},
Url = {http://doi.acm.org/10.1145/3225058.3225134},
Year = {2018},
Bdsk-Url-1 = {http://doi.acm.org/10.1145/3225058.3225134},
Bdsk-Url-2 = {https://doi.org/10.1145/3225058.3225134}}
@inproceedings{sniper,
Author = {T. E. {Carlson} and W. {Heirmant} and L. {Eeckhout}},
Booktitle = {SC '11: Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2019-04-16 03:11:34 -0700},
Date-Modified = {2019-04-16 03:11:42 -0700},
Doi = {10.1145/2063384.2063454},
Issn = {2167-4329},
Keywords = {cache storage;digital simulation;multiprocessing systems;Sniper;abstraction level exploration;parallel multicore simulation;high-performance computing;core larger numbers;on-chip cache memory;processor architectures;hardware design space;interval simulation;cycle-accurate simulation;one-IPC simulation;core-uncore interactions;multithreaded workloads;16-core system;8-core SMP machine;Multicore processing;Load modeling;Synchronization;Accuracy;Analytical models;Kernel;Interval simulation;interval model;performance modeling;multi-core processor},
Month = {Nov},
Pages = {1-12},
Title = {Sniper: Exploring the level of abstraction for scalable and accurate parallel multi-core simulation},
Year = {2011},
Bdsk-Url-1 = {https://doi.org/10.1145/2063384.2063454}}
@inproceedings{wilkerson2010reducing,
Author = {Wilkerson, Chris and Alameldeen, Alaa R and Chishti, Zeshan and Wu, Wei and Somasekhar, Dinesh and Lu, Shih-lien},
Booktitle = {ACM SIGARCH Computer Architecture News},
Date-Added = {2019-04-16 03:10:19 -0700},
Date-Modified = {2019-04-16 03:10:19 -0700},
Number = {3},
Organization = {ACM},
Pages = {83--93},
Title = {Reducing cache power with low-cost, multi-bit error-correcting codes},
Volume = {38},
Year = {2010}}
@article{HBMbank,
Author = {Sohn, Kyomin and Yun, Won-Joo and Oh, Reum and Oh, Chi-Sung and Seo, Seong-Young and Park, Min-Sang and Shin, Dong-Hak and Jung, Won-Chang and Shin, Sang-Hoon and Ryu, Je-Min and others},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {IEEE Journal of Solid-State Circuits},
Number = {1},
Pages = {250--260},
Publisher = {IEEE},
Title = {A 1.2 V 20 nm 307 GB/s HBM DRAM with at-speed wafer-level IO test scheme and adaptive refresh considering temperature distribution},
Volume = {52},
Year = {2017}}
@inproceedings{loh2013processing,
Author = {Loh, Gabriel H and Jayasena, Nuwan and Oskin, M and Nutter, Mark and Roberts, David and Meswani, Mitesh and Zhang, Dong Ping and Ignatowski, Mike},
Booktitle = {Workshop on Near-Data Processing (WoNDP)},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Title = {A processing in memory taxonomy and a case for studying fixed-function pim},
Year = {2013}}
@inproceedings{yoo2011scalable,
Author = {Yoo, Andy and Baker, Allison H and Pearce, Roger and others},
Booktitle = {Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {63},
Title = {A scalable eigensolver for large scale-free graphs using 2D graph partitioning},
Year = {2011}}
@article{NTX,
Author = {Schuiki, Fabian and Schaffner, Michael and G{\"u}rkaynak, Frank K and Benini, Luca},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {arXiv preprint arXiv:1803.04783},
Title = {A Scalable Near-Memory Architecture for Training Deep Neural Networks on Large In-Memory Datasets},
Year = {2018}}
@article{TESSERACT,
Author = {Ahn, Junwhan and Hong, Sungpack and Yoo, Sungjoo and Mutlu, Onur and Choi, Kiyoung},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {ACM SIGARCH Computer Architecture News},
Number = {3},
Pages = {105--117},
Publisher = {ACM},
Title = {A scalable processing-in-memory accelerator for parallel graph processing},
Volume = {43},
Year = {2016}}
@inproceedings{zhu2013accelerating,
Author = {Zhu, Qiuling and Graf, Tobias and Sumbul, H Ekin and Pileggi, Larry and Franchetti, Franz},
Booktitle = {High Performance Extreme Computing Conference (HPEC), 2013 IEEE},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE},
Pages = {1--6},
Title = {Accelerating sparse matrix-matrix multiplication with 3D-stacked logic-in-memory hardware},
Year = {2013}}
@inproceedings{BRO,
Author = {Tang, Wai Teng and Tan, Wen Jun and Ray, Rajarshi and Wong, Yi Wen and Chen, Weiguang and Kuo, Shyh-hao and Goh, Rick Siow Mong and Turner, Stephen John and Wong, Weng-Fai},
Booktitle = {Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {26},
Title = {Accelerating sparse matrix-vector multiplication on GPUs using bit-representation-optimized schemes},
Year = {2013}}
@article{AMB,
Author = {Nagasaka, Yusuke and Nukada, Akira and Matsuoka, Satoshi},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {Procedia Computer Science},
Pages = {131--142},
Publisher = {Elsevier},
Title = {Adaptive multi-level blocking optimization for sparse matrix vector multiplication on GPU},
Volume = {80},
Year = {2016}}
@inproceedings{8675225,
Author = {A. {Basak} and S. {Li} and X. {Hu} and S. M. {Oh} and X. {Xie} and L. {Zhao} and X. {Jiang} and Y. {Xie}},
Booktitle = {2019 IEEE International Symposium on High Performance Computer Architecture (HPCA)},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Doi = {10.1109/HPCA.2019.00051},
Issn = {2378-203X},
Keywords = {Prefetching;Random access memory;Arrays;Parallel processing;Hardware;Benchmark testing;Graph Processing;Workload Characterization;Prefetching},
Month = {Feb},
Pages = {373-386},
Title = {Analysis and Optimization of the Memory Hierarchy for Graph Processing Workloads},
Year = {2019},
Bdsk-Url-1 = {https://doi.org/10.1109/HPCA.2019.00051}}
@inproceedings{sedaghati2015automatic,
Author = {Sedaghati, Naser and Mu, Te and Pouchet, Louis-Noel and Parthasarathy, Srinivasan and Sadayappan, P},
Booktitle = {Proceedings of the 29th ACM on International Conference on Supercomputing},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {99--108},
Title = {Automatic selection of sparse matrix representation on GPUs},
Year = {2015}}
@inproceedings{chen2012cacti,
Author = {Chen, Ke and Li, Sheng and Muralimanohar, Naveen and Ahn, Jung Ho and Brockman, Jay B and Jouppi, Norman P},
Booktitle = {Proceedings of the Conference on Design, Automation and Test in Europe},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {EDA Consortium},
Pages = {33--38},
Title = {CACTI-3DD: Architecture-level modeling for 3D die-stacked DRAM main memory},
Year = {2012}}
@inproceedings{clSpMV,
Author = {Su, Bor-Yiing and Keutzer, Kurt},
Booktitle = {Proceedings of the 26th ACM international conference on Supercomputing},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {353--364},
Title = {clSpMV: A cross-platform OpenCL SpMV framework on GPUs},
Year = {2012}}
@inproceedings{CMP-PIM,
Author = {Angizi, Shaahin and He, Zhezhi and Rakin, Adnan Siraj and Fan, Deliang},
Booktitle = {Proceedings of the 55th Annual Design Automation Conference},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {105},
Title = {CMP-PIM: an energy-efficient comparator-based processing-in-memory neural network accelerator},
Year = {2018}}
@inproceedings{CVR,
Author = {Xie, Biwei and Zhan, Jianfeng and Liu, Xu and Gao, Wanling and Jia, Zhen and He, Xiwen and Zhang, Lixin},
Booktitle = {Proceedings of the 2018 International Symposium on Code Generation and Optimization},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {149--162},
Title = {CVR: efficient vectorization of SpMV on x86 processors},
Year = {2018}}
@inproceedings{HMCConfig,
Author = {Hadidi, Ramyad and Asgari, Bahar and Mudassar, Burhan Ahmad and Mukhopadhyay, Saibal and Yalamanchili, Sudhakar and Kim, Hyesoon},
Booktitle = {2017 IEEE International Symposium on Workload Characterization (IISWC)},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE},
Pages = {66--75},
Title = {Demystifying the characteristics of 3d-stacked memories: A case study for hybrid memory cube},
Year = {2017}}
@inproceedings{3Dstacking,
Author = {Weis, Christian and Wehn, Norbert and Igor, Loi and Benini, Luca},
Booktitle = {2011 Design, Automation \& Test in Europe},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE},
Pages = {1--6},
Title = {Design space exploration for 3D-stacked DRAMs},
Year = {2011}}
@inproceedings{DRISA,
Author = {Li, Shuangchen and Niu, Dimin and Malladi, Krishna T and Zheng, Hongzhong and Brennan, Bob and Xie, Yuan},
Booktitle = {Proceedings of the 50th Annual IEEE/ACM International Symposium on Microarchitecture},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {288--301},
Title = {Drisa: A dram-based reconfigurable in-situ accelerator},
Year = {2017}}
@inproceedings{CSRAdaptive,
Author = {Greathouse, Joseph L and Daga, Mayank},
Booktitle = {Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE Press},
Pages = {769--780},
Title = {Efficient sparse matrix-vector multiplication on GPUs using the CSR storage format},
Year = {2014}}
@inproceedings{ESB,
Author = {Liu, Xing and Smelyanskiy, Mikhail and Chow, Edmond and Dubey, Pradeep},
Booktitle = {Proceedings of the 27th international ACM conference on International conference on supercomputing},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {ACM},
Pages = {273--282},
Title = {Efficient sparse matrix-vector multiplication on x86-based many-core processors},
Year = {2013}}
@inproceedings{SpMVReRAM,
Author = {B. Feinberg and U. K. R. Vengalam and N. Whitehair and S. Wang and E. Ipek},
Booktitle = {2018 ACM/IEEE 45th Annual International Symposium on Computer Architecture (ISCA)},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Doi = {10.1109/ISCA.2018.00039},
Issn = {2575-713X},
Month = {June},
Pages = {367-382},
Title = {Enabling Scientific Computing on Memristive Accelerators},
Year = {2018},
Bdsk-Url-1 = {https://doi.org/10.1109/ISCA.2018.00039}}
@article{yang2011fast,
Author = {Yang, Xintian and Parthasarathy, Srinivasan and Sadayappan, Ponnuswamy},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {Proceedings of the VLDB Endowment},
Number = {4},
Pages = {231--242},
Publisher = {VLDB Endowment},
Title = {Fast sparse matrix-vector multiplication on GPUs: implications for graph mining},
Volume = {4},
Year = {2011}}
@inproceedings{galal2013fpu,
Author = {Galal, Sameh and Shacham, Ofer and Brunhaver II, John S and Pu, Jing and Vassiliev, Artem and Horowitz, Mark},
Booktitle = {2013 IEEE 21st Symposium on Computer Arithmetic},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE},
Pages = {25--34},
Title = {FPU generator for design space exploration},
Year = {2013}}
@article{GraphH,
Author = {Dai, Guohao and Huang, Tianhao and Chi, Yuze and Zhao, Jishen and Sun, Guangyu and Liu, Yongpan and Wang, Yu and Xie, Yuan and Yang, Huazhong},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Journal = {IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems},
Publisher = {IEEE},
Title = {GraphH: A Processing-in-Memory Architecture for Large-scale Graph Processing},
Year = {2018}}
@inproceedings{GraphP,
Author = {Zhang, Mingxing and Zhuo, Youwei and Wang, Chao and Gao, Mingyu and Wu, Yongwei and Chen, Kang and Kozyrakis, Christos and Qian, Xuehai},
Booktitle = {High Performance Computer Architecture (HPCA), 2018 IEEE International Symposium on},
Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
Organization = {IEEE},
Pages = {544--557},
Title = {GraphP: Reducing Communication for PIM-based Graph Processing with Efficient Data Partition},
Year = {2018}}
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Year = {2003}}
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Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
Date-Modified = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Date-Added = {2019-04-16 03:10:09 -0700},
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Title = {TOP-PIM: throughput-oriented programmable processing in memory},
Year = {2014}}
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Pages = {107--118},
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Volume = {49},
Year = {2014}}
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Date-Added = {2019-04-16 03:10:02 -0700},
Date-Modified = {2019-04-16 03:10:02 -0700},
Organization = {IEEE},
Pages = {380--392},
Title = {Neurocube: A programmable digital neuromorphic architecture with high-density 3D memory},
Year = {2016}}
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Date-Modified = {2019-04-16 01:02:12 -0700},
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Title = {A map of human genome variation from population-scale sequencing},
Volume = {467},
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Date-Added = {2019-04-16 01:02:12 -0700},
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Title = {Accelerating data-intensive genome analysis in the cloud},
Year = {2013}}
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Author = {M. Carneiro},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Institution = {Broad Institute},
Source = {https://hpc.mssm.edu/files/Carneiro_ workshop.pdf},
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Year = {2013}}
@article{massie2013adam,
Author = {Massie, Matt and Nothaft, Frank and Hartl, Christopher and Kozanitis, Christos and Schumacher, Andr{\'e} and Joseph, Anthony D and Patterson, David A},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {University of California, Berkeley Technical Report, No. UCB/EECS-2013},
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@techreport{Massie:EECS-2013-207,
Abstract = {Current genomics data formats and processing pipelines are not designed to scale well to large datasets. The current Sequence/Binary Alignment/Map (SAM/BAM) formats were intended for single node processing. There have been attempts to adapt BAM to distributed computing environments, but they see limited scalability past eight nodes. Additionally, due to the lack of an explicit data schema, there are well known incompatibilities between libraries that implement SAM/BAM/Variant Call Format (VCF) data access.
To address these problems, we introduce ADAM, a set of formats, APIs, and processing stage implementations for genomic data. ADAM is fully open source under the Apache 2 license, and is implemented on top of Avro and Parquet for data storage. Our reference pipeline is implemented on top of Spark, a high performance in-memory map-reduce system. This combination provides the following advantages:
1) Avro provides explicit data schema access in C/C++/C#, Java/Scala, Python, php, and Ruby;
2) Parquet allows access by database systems like Impala and Shark; and
3) Spark improves performance through in-memory caching and reducing disk I/O.
In addition to improving the format's cross-platform portability, these changes lead to significant performance improvements. On a single node, we are able to speedup sort and duplicate marking by 2×. More importantly, on a 250 Gigabyte (GB) high (60×) coverage human genome, this system achieves a 50× speedup on a 100 node computing cluster (see Table 1), fulfilling the promise of scalability of ADAM.
The ADAM format provides explicit schemas for read and reference oriented (pileup) sequence data, variants, and genotypes. As the schemas are implemented in Apache Avro---a cross-platform/language serialization format---they eliminate the need for the development of language-specific libraries for format decoding/encoding, which eliminates the possibility of library incompatibilities.
A key feature of ADAM is that any application that implements the ADAM schema is compatible with ADAM. This is important, as it prevents applications from being locked into a specific tool or pattern. The ADAM stack is inspired by the ``narrow waist'' of the Internet Protocol (IP) suite (see Figure 2). We consider the explicit use of a schema in this format to be the greatest contribution of the ADAM stack.
In addition to the advantages outlined above, ADAM eliminates the file headers in modern genomics formats. All header information is available inside of each individual record. The variant and genotype formats also demonstrate two significant improvements. First, these formats are co-designed so that variant data can be seamlessly calculated from a given collection of sample genotypes. Secondly, these formats are designed to flexibly accommodate annotations without cluttering the core variant/genotype schema. In addition to the benefits described above, ADAM files are up to 25% smaller on disk than compressed BAM files without losing any information.
The ADAM processing pipeline uses Spark as a compute engine and Parquet for data access. Spark is an in-memory MapReduce framework which minimizes I/O accesses. We chose Parquet for data storage as it is an open-source columnar store that is designed for distribution across multiple computers with high compression. Additionally, Parquet sup- ports efficient methods (predicates and projections) for accessing only a specific segment or fields of a file, which can provide significant (2-10×) additional speedup for genomics data access patterns.},
Author = {Massie, Matt and Nothaft, Frank and Hartl, Christopher and Kozanitis, Christos and Schumacher, Andr{\'e} and Joseph, Anthony D. and Patterson, David A.},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Institution = {EECS Department, University of California, Berkeley},
Month = {Dec},
Number = {UCB/EECS-2013-207},
Title = {ADAM: Genomics Formats and Processing Patterns for Cloud Scale Computing},
Url = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.html},
Year = {2013},
Bdsk-Url-1 = {http://www.eecs.berkeley.edu/Pubs/TechRpts/2013/EECS-2013-207.html}}
@url{amazon,
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Title = {Amazon Elastic Compute Cloud (Amazon EC2)},
Urldate = {http://aws.amazon.com/ec2}}
@article{Jiang2008An,
Author = {Jiang, K. and Thorsen, O. and Peters, A. and Smith, B. and Sosa, C. P.},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {IEEE Transactions on Parallel & Distributed Systems},
Number = {1},
Pages = {15-23},
Title = {An Efficient Parallel Implementation of the Hidden Markov Methods for Genomic Sequence-Search on a Massively Parallel System},
Volume = {19},
Year = {2008}}
@article{Brownstein2014,
Abstract = {There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance.},
Author = {Brownstein, Catherine A. and Beggs, Alan H. and Homer, Nils and Merriman, Barry and Yu, Timothy W. and Flannery, Katherine C. and DeChene, Elizabeth T. and Towne, Meghan C. and Savage, Sarah K. and Price, Emily N. and Holm, Ingrid A. and Luquette, Lovelace J. and Lyon, Elaine and Majzoub, Joseph and Neupert, Peter and McCallie Jr, David and Szolovits, Peter and Willard, Huntington F. and Mendelsohn, Nancy J. and Temme, Renee and Finkel, Richard S. and Yum, Sabrina W. and Medne, Livija and Sunyaev, Shamil R. and Adzhubey, Ivan and Cassa, Christopher A. and de Bakker, Paul IW and Duzkale, Hatice and Dworzy{\'{n}}ski, Piotr and Fairbrother, William and Francioli, Laurent and Funke, Birgit H. and Giovanni, Monica A. and Handsaker, Robert E. and Lage, Kasper and Lebo, Matthew S. and Lek, Monkol and Leshchiner, Ignaty and MacArthur, Daniel G. and McLaughlin, Heather M. and Murray, Michael F. and Pers, Tune H. and Polak, Paz P. and Raychaudhuri, Soumya and Rehm, Heidi L. and Soemedi, Rachel and Stitziel, Nathan O. and Vestecka, Sara and Supper, Jochen and Gugenmus, Claudia and Klocke, Bernward and Hahn, Alexander and Schubach, Max and Menzel, Mortiz and Biskup, Saskia and Freisinger, Peter and Deng, Mario and Braun, Martin and Perner, Sven and Smith, Richard JH and Andorf, Janeen L. and Huang, Jian and Ryckman, Kelli and Sheffield, Val C. and Stone, Edwin M. and Bair, Thomas and Black-Ziegelbein, E. Ann and Braun, Terry A. and Darbro, Benjamin and DeLuca, Adam P. and Kolbe, Diana L. and Scheetz, Todd E. and Shearer, Aiden E. and Sompallae, Rama and Wang, Kai and Bassuk, Alexander G. and Edens, Erik and Mathews, Katherine and Moore, Steven A. and Shchelochkov, Oleg A. and Trapane, Pamela and Bossler, Aaron and Campbell, Colleen A. and Heusel, Jonathan W. and Kwitek, Anne and Maga, Tara and Panzer, Karin and Wassink, Thomas and Van Daele, Douglas and Azaiez, Hela and Booth, Kevin and Meyer, Nic and Segal, Michael M. and Williams, Marc S. and Tromp, Gerard and White, Peter and Corsmeier, Donald and Fitzgerald-Butt, Sara and Herman, Gail and Lamb-Thrush, Devon and McBride, Kim L. and Newsom, David and Pierson, Christopher R. and Rakowsky, Alexander T. and Maver, Ale{\v{s}} and Lovre{\v{c}}i{\'{c}}, Luca and Palanda{\v{c}}i{\'{c}}, Anja and Peterlin, Borut and Torkamani, Ali and Wedell, Anna and Huss, Mikael and Alexeyenko, Andrey and Lindvall, Jessica M. and Magnusson, M{\aa}ns and Nilsson, Daniel and Stranneheim, Henrik and Taylan, Fulya and Gilissen, Christian and Hoischen, Alexander and van Bon, Bregje and Yntema, Helger and Nelen, Marcel and Zhang, Weidong and Sager, Jason and Zhang, Lu and Blair, Kathryn and Kural, Deniz and Cariaso, Michael and Lennon, Greg G. and Javed, Asif and Agrawal, Saloni and Ng, Pauline C. and Sandhu, Komal S. and Krishna, Shuba and Veeramachaneni, Vamsi and Isakov, Ofer and Halperin, Eran and Friedman, Eitan and Shomron, Noam and Glusman, Gustavo and Roach, Jared C. and Caballero, Juan and Cox, Hannah C. and Mauldin, Denise and Ament, Seth A. and Rowen, Lee and Richards, Daniel R. and Lucas, F. Anthony San and Gonzalez-Garay, Manuel L. and Caskey, C. Thomas and Bai, Yu and Huang, Ying and Fang, Fang and Zhang, Yan and Wang, Zhengyuan and Barrera, Jorge and Garcia-Lobo, Juan M. and Gonz{\'a}lez-Lamu{\~{n}}o, Domingo and Llorca, Javier and Rodriguez, Maria C. and Varela, Ignacio and Reese, Martin G. and De La Vega, Francisco M. and Kiruluta, Edward and Cargill, Michele and Hart, Reece K. and Sorenson, Jon M. and Lyon, Gholson J. and Stevenson, David A. and Bray, Bruce E. and Moore, Barry M. and Eilbeck, Karen and Yandell, Mark and Zhao, Hongyu and Hou, Lin and Chen, Xiaowei and Yan, Xiting and Chen, Mengjie and Li, Cong and Yang, Can and Gunel, Murat and Li, Peining and Kong, Yong and Alexander, Austin C. and Albertyn, Zayed I. and Boycott, Kym M. and Bulman, Dennis E. and Gordon, Paul MK and Innes, A. Micheil and Knoppers, Bartha M. and Majewski, Jacek and Marshall, Christian R. and Parboosingh, Jillian S. and Sawyer, Sarah L. and Samuels, Mark E. and Schwartzentruber, Jeremy and Kohane, Isaac S. and Margulies, David M.},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Doi = {10.1186/gb-2014-15-3-r53},
Issn = {1465-6906},
Journal = {Genome Biology},
Number = {3},
Pages = {1--18},
Title = {An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge},
Url = {http://dx.doi.org/10.1186/gb-2014-15-3-r53},
Volume = {15},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1186/gb-2014-15-3-r53}}
@url{Hadoop,
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Title = {Apache Software Foundation project home page},
Urldate = {http://hadoop.apache.org/}}
@article{klus2012barracuda,
Author = {Klus, Petr and Lam, Simon and Lyberg, Dag and Cheung, Ming S and Pullan, Graham and McFarlane, Ian and Yeo, Giles SH and Lam, Brian YH},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {BMC research notes},
Number = {1},
Pages = {27},
Publisher = {BioMed Central Ltd},
Title = {BarraCUDA-a fast short read sequence aligner using graphics processing units},
Volume = {5},
Year = {2012}}
@inproceedings{Kovatch:2015ka,
Address = {New York, New York, USA},
Author = {Kovatch, Patricia and Costa, Anthony and Giles, Zachary and Fluder, Eugene and Cho, Hyung Min and Mazurkova, Svetlana},
Booktitle = {the International Conference for High Performance Computing, Networking, Storage and Analysis},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Pages = {1--12},
Publisher = {ACM Press},
Title = {{Big omics data experience}},
Year = {2015}}
@article{Tan:2006ji,
Author = {Tan, Guangming and Feng, Shengzhong and Sun, Ninghui},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {SC},
Pages = {78},
Title = {{Biology - Locality and parallelism optimization for dynamic programming algorithm in bioinformatics.}},
Year = {2006}}
@article{Crick1970Central,
Author = {Crick, Francis},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {Nature 1970 Vol. 227 pp. 561-63},
Number = {5258},
Pages = {561-563},
Title = {Central Dogma of Molecular Biology. Nature 1970;227(August):561--3},
Volume = {227},
Year = {1970}}
@article{Kelly2015,
Abstract = {While advances in genome sequencing technology make population-scale genomics a possibility, current approaches for analysis of these data rely upon parallelization strategies that have limited scalability, complex implementation and lack reproducibility. Churchill, a balanced regional parallelization strategy, overcomes these challenges, fully automating the multiple steps required to go from raw sequencing reads to variant discovery. Through implementation of novel deterministic parallelization techniques, Churchill allows computationally efficient analysis of a high-depth whole genome sample in less than two hours. The method is highly scalable, enabling full analysis of the 1000 Genomes raw sequence dataset in a week using cloud resources. http://churchill.nchri.org/ .},
Author = {Kelly, Benjamin J. and Fitch, James R. and Hu, Yangqiu and Corsmeier, Donald J. and Zhong, Huachun and Wetzel, Amy N. and Nordquist, Russell D. and Newsom, David L. and White, Peter},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Doi = {10.1186/s13059-014-0577-x},
Issn = {1465-6906},
Journal = {Genome Biology},
Number = {1},
Pages = {1--14},
Title = {Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics},
Url = {http://dx.doi.org/10.1186/s13059-014-0577-x},
Volume = {16},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1186/s13059-014-0577-x}}
@article{Garber:2011ci,
Author = {Garber, Manuel and Grabherr, Manfred G and Guttman, Mitchell and Trapnell, Cole},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {Nature Methods},
Month = jun,
Number = {6},
Pages = {469--477},
Title = {{Computational methods for transcriptome annotation and quantification using RNA-seq}},
Volume = {8},
Year = {2011}}
@inproceedings{qadeer2013convolution,
Author = {Qadeer, Wajahat and Hameed, Rehan and Shacham, Ofer and Venkatesan, Preethi and Kozyrakis, Christos and Horowitz, Mark A},
Booktitle = {ACM SIGARCH Computer Architecture News},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Number = {3},
Organization = {ACM},
Pages = {24--35},
Title = {Convolution engine: balancing efficiency \& flexibility in specialized computing},
Volume = {41},
Year = {2013}}
@article{Lin2010Coordinating,
Author = {Lin, Heshan and Ma, Xiaosong and Feng, Wuchun and Samatova, Nagiza F.},
Date-Added = {2019-04-16 01:02:12 -0700},
Date-Modified = {2019-04-16 01:02:12 -0700},
Journal = {IEEE Transactions on Parallel & Distributed Systems},
Number = {4},