Ecosyste.ms: Papers

10.1371/journal.pone.0072614

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
Cited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: about 11 years ago

10.1186/1471-2105-15-167

PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Cited by: 4
Author(s): Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh
Software Mentions: 6
Published: over 10 years ago

10.1093/gigascience/giy052

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files
Cited by: 3
Author(s): Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng, Esteban G. Burchard, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes, Fusheng Wang, Zhaohui S. Qin
Software Mentions: 5
Published: over 6 years ago

10.1155/2013/481545

Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies
Cited by: 13
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0201483

HSRA: Hadoop-based spliced read aligner for RNA sequencing data
Cited by: 11
Author(s): Roberto R. Expósito, Jorge González-Domínguez, Juan Touriño
Software Mentions: 5
Published: over 6 years ago

10.1186/1756-0500-4-171

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Cited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: over 13 years ago

10.1186/s12859-018-2019-3

Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2105-13-S17-S22

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
Cited by: 20
Author(s): Mohamed El‐Kalioby, Mohamed Abouelhoda, Jan Walters Kruger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter J. Tonellato
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2164-14-425

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing
Cited by: 47
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith, Thomas Messina, Huiying Fan, Edward P. Jaeger, S. A. Stephens
Software Mentions: 4
Published: almost 12 years ago

10.1155/2013/791051

Streaming Support for Data Intensive Cloud-Based Sequence Analysis
Cited by: 7
Author(s): Shady Issa, Romeo Kienzler, Mohamed El‐Kalioby, Peter J. Tonellato, Dennis P. Wall, Rémy Bruggmann, Mohamed Abouelhoda
Software Mentions: 4
Published: almost 12 years ago

10.3389/fgene.2018.00537

SeqVItA: Sequence Variant Identification and Annotation Platform for Next Generation Sequencing Data
Cited by: 4
Author(s): Prashanthi Dharanipragada, Sampreeth Reddy Seelam, Nita Parekh
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-13-42

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Cited by: 142
Author(s): Konstantinos Krampis, Tim Booth, Brad Chapman, Brijesh K. Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson
Software Mentions: 3
Published: over 12 years ago

10.1186/s13742-015-0058-5

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
Cited by: 15
Author(s): Alexey Siretskiy, T. Sundqvist, Mikhail Voznesenskiy, Ola Spjuth
Software Mentions: 3
Published: over 9 years ago

10.1093/bib/bby051

Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application
Cited by: 103
Author(s): Gaye Lightbody, Valeriia Haberland, Fiona Browne, Laura E. Taggart, Huiru Zheng, Eileen E. Parkes, Jaine K. Blayney
Software Mentions: 3
Published: over 5 years ago

10.3390/s120912606

Efficient Security Mechanisms for mHealth Applications Using Wireless Body Sensor Networks
Cited by: 50
Author(s): Prasan Kumar Sahoo
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0084860

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud
Cited by: 26
Author(s): Konrad J. Karczewski, Guy Haskin Fernald, Martin Ar, M Snyder, Nicholas P. Tatonetti, Joel T. Dudley
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-13-315

CloudMan as a platform for tool, data, and analysis distribution
Cited by: 41
Author(s): Enis Afgan, Brad Chapman, James Taylor
Software Mentions: 3
Published: almost 12 years ago

10.3390/s100605809

Power Consumption Analysis of Operating Systems for Wireless Sensor Networks
Cited by: 43
Author(s): R. Lajara, José Pelegrí-Sebastiá, Juan J. Pérez-Solano
Software Mentions: 3
Published: over 14 years ago

10.1155/2014/859279

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data
Cited by: 10
Author(s): Milan Vukičević, Sandro Radovanović, Miloš Milovanović, Miroslav Minović
Software Mentions: 3
Published: almost 11 years ago

10.1155/2013/730210

Computational and Bioinformatics Frameworks for Next-Generation Whole Exome and Genome Sequencing
Cited by: 45
Author(s): Marisa Dolled‐Filhart, Michael Lee, Chih-wen Ou-Yang, Rajini Haraksingh, Jimmy C. Lin
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2105-11-S12-S1

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
Cited by: 371
Author(s): Ron Taylor
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2105-11-S12-S2

SeqWare Query Engine: storing and searching sequence data in the cloud
Cited by: 79
Author(s): Brian D. O’Connor, Barry Merriman, Stanley F. Nelson
Software Mentions: 2
Published: almost 14 years ago

10.1186/1471-2164-13-S6-S19

Atlas2 Cloud: a framework for personal genome analysis in the cloud
Cited by: 42
Author(s): Uday S. Evani, Danny Challis, Jian Yu, Andrew Jackson, Sameer Paithankar, Matthew N. Bainbridge, Adinarayana Jakkamsetti, Peter Pham, Cristian Coarfa, Aleksandar Milosavljevic, Fuli Yu
Software Mentions: 2
Published: about 12 years ago

10.1186/1756-0381-7-22

Applications of the MapReduce programming framework to clinical big data analysis: current landscape and future trends
Cited by: 108
Author(s): Emad A. Mohammed, Behrouz H. Far, Christopher Naugler
Software Mentions: 2
Published: about 10 years ago

10.1093/bioinformatics/btt422

DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments
Cited by: 1
Author(s): Chiao‐Feng Lin, Otto Valladares, Daniel Micah Childress, Egor Klevak, Evan Geller, Yi‐Ting Hwang, Ellen Tsai, Gerard D. Schellenberg, Li-San Wang
Software Mentions: 2
Published: over 11 years ago

10.1155/2018/7501042

Parallel MapReduce: Maximizing Cloud Resource Utilization and Performance Improvement Using Parallel Execution Strategies
Cited by: 2
Author(s): Ahmed Abdulhakim Al-Absi, Najeeb Abbas Al-Sammarraie, Wael M. S. Yafooz, Dae-Ki Kang
Software Mentions: 2
Published: about 6 years ago

10.1155/2013/185679

Enabling Large-Scale Biomedical Analysis in the Cloud
Cited by: 15
Author(s): Yen-Ting Lin, Chin-Sheng Yu, Yen-Jen Lin
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0075402

Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data
Cited by: 53
Author(s): Shunichi Kosugi, Satoshi Natsume, Kentaro Yoshida, Dan MacLean, Liliana Cano, Sophien Kamoun, Ryohei Terauchi
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0052249

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
Cited by: 406
Author(s): Haibin Xu, Xiang Luo, Jun Qian, Xiaohui Pang, Jingyuan Song, Guang‐Rui Qian, Jinhui Chen, Shilin Chen
Software Mentions: 2
Published: almost 12 years ago

10.1155/2015/549026

G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS
Cited by: 2
Author(s): Rongdong Hu, Guangming Liu, Jingfei Jiang, Lixin Wang
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.csbj.2017.07.004

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges
Cited by: 49
Author(s): Zekun Yin, Haidong Lan, Guangming Tan, Ming–Wei Lu, Athanasios V. Vasilakos, Weiguo Liu
Software Mentions: 2
Published: almost 8 years ago

10.3390/s100402919

Adaptive-Compression Based Congestion Control Technique for Wireless Sensor Networks
Cited by: 60
Author(s): Joahyoung Lee, Inhwa Jung
Software Mentions: 2
Published: over 14 years ago

10.3390/s90100281

A Localized Coverage Preserving Protocol for Wireless Sensor Networks
Cited by: 25
Author(s): Yuheng Liu, Jiexin Pu, Shuo Zhang, Yunlu Liu, Xiong Zhang
Software Mentions: 2
Published: almost 16 years ago

10.3390/s141120562

Wireless Sensor Networks for Heritage Object Deformation Detection and Tracking Algorithm
Cited by: 3
Author(s): Zhijun Xie, Guangyan Huang, Roozbeh Zarei, Jing He, Yanchun Zhang, Hongwu Ye
Software Mentions: 2
Published: about 10 years ago

10.1155/2013/439681

Implementation of a Parallel Protein Structure Alignment Service on Cloud
Cited by: 24
Author(s): Che Lun Hung, Yaw Ling Lin
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pcbi.1006144

Cloud computing applications for biomedical science: A perspective
Cited by: 55
Author(s): Vivek Navale, Philip E. Bourne
Software Mentions: 1
Published: over 6 years ago

10.1155/2015/807407

Long Read Alignment with Parallel MapReduce Cloud Platform
Cited by: 8
Author(s): Ahmed Abdulhakim Al-Absi, Dae-Ki Kang
Software Mentions: 1
Published: almost 10 years ago

10.1186/2047-2501-1-6

Bio and health informatics meets cloud : BioVLab as an example
Cited by: 12
Author(s): Han‐Jung Chae, Il Bong Jung, Hyungro Lee, Suresh Marru, Seong–Whan Lee, Sun Kim
Software Mentions: 1
Published: almost 12 years ago

10.1186/1472-6947-13-42

Deployment of assistive living technology in a nursing home environment: methods and lessons learned
Cited by: 96
Author(s): Hamdi Aloulou, Mounir Mokhtari, Thibaut Tiberghien, Jit Biswas, Clifton Phua, Jinhong Kenneth Lin, Philip Yap
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-13-200

Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds
Cited by: 45
Author(s): Sebastian Schönherr, Lukas Forer, Hansi Weißensteiner, Florian Kronenberg, Günther Specht, Anita Kloss‐Brandstätter
Software Mentions: 1
Published: over 12 years ago

10.1155/2014/528410

Development and Application of a ZigBee-Based Building Energy Monitoring and Control System
Cited by: 11
Author(s): Changhai Peng, Kun Qian
Software Mentions: 1
Published: almost 11 years ago

10.3390/s100807236

Wireless Sensor Network Deployment for Monitoring Wildlife Passages
Cited by: 89
Author(s): Antonio-Javier García-Sánchez, Felipe García‐Sánchez, Fernando Losilla, Paweł Kułakowski, Joan García-Haro, Alejandro Rodrı́guez, José Vicente López‐Bao, Francisço Palomares
Software Mentions: 1
Published: over 14 years ago

10.3390/s100605443

Modeling of Current Consumption in 802.15.4/ZigBee Sensor Motes
Cited by: 111
Author(s): E. Casilari, José Manuel Cano-García, Gonzalo Campos-Garrido
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-017-1723-8

SparkBLAST: scalable BLAST processing using in-memory operations
Cited by: 25
Author(s): Marcelo Rodrigo de Castro, Catherine dos Santos Tostes, Alberto M. R. Dávila, Hermes Senger, Fabrício Silva
Software Mentions: 1
Published: over 7 years ago

10.3390/s91210309

Field Measurements and Guidelines for the Application of Wireless Sensor Networks to the Environment and Security
Cited by: 15
Author(s): Víctor P. Gil Jiménez, Ana García Armada
Software Mentions: 1
Published: almost 15 years ago

10.3390/s110101192

Developing a New Wireless Sensor Network Platform and Its Application in Precision Agriculture
Cited by: 43
Author(s): Raúl Aquino-Santos, Apolinar González, Arthur Edwards-Block, Raúl Alejandro Virgen-Ortiz
Software Mentions: 1
Published: almost 14 years ago

10.3390/s90705664

A Survey of Geosensor Networks: Advances in Dynamic Environmental Monitoring
Cited by: 104
Author(s): Silvia Nittel
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2105-11-S12-S4

Galaxy CloudMan: delivering cloud compute clusters
Cited by: 157
Author(s): Enis Afgan, Dannon Baker, Nathan Coraor, Brad Chapman, Anton Nekrutenko, James Taylor
Software Mentions: 1
Published: almost 14 years ago

10.3390/ijms18020412

Big Data Analytics for Genomic Medicine
Cited by: 116
Author(s): Karen Y. He, Dongliang Ge, Max M. He
Software Mentions: 1
Published: almost 8 years ago

10.3390/s91008007

Collaborative Distributed Scheduling Approaches for Wireless Sensor Network
Cited by: 4
Author(s): Jianjun Niu, Zhidong Deng
Software Mentions: 1
Published: about 15 years ago

10.3390/s90503240

Development of a Sensor Node for Precision Horticulture
Cited by: 34
Author(s): Juan Antonio López, F. Soto, Pedro Sánchez, Andrés Iborra, Juan Suardíaz Muro, J. A. Vera
Software Mentions: 1
Published: over 15 years ago

10.1186/s12859-018-2498-2

BiSpark: a Spark-based highly scalable aligner for bisulfite sequencing data
Cited by: 4
Author(s): S. S. E. Soe, Yoonjae Park, Han‐Jung Chae
Software Mentions: 1
Published: almost 6 years ago

10.3390/s131216384

Wireless Sensor Networks for Ambient Assisted Living
Cited by: 27
Author(s): Raúl Aquino-Santos, Diego Martínez-Castro, Arthur Edwards-Block, Andrés Felipe Murillo-Piedrahita
Software Mentions: 1
Published: almost 11 years ago

10.1155/2016/3617572

Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine
Cited by: 29
Author(s): Tonia C. Carter, Max M. He
Software Mentions: 1
Published: almost 9 years ago

10.3390/s150819560

Secure and Authenticated Data Communication in Wireless Sensor Networks
Cited by: 12
Author(s): Omar Alfandi, Arne Bochem, Ansgar Kellner, Christian Göge, Dieter Hogrefe
Software Mentions: 1
Published: over 9 years ago

10.3390/s18082434

Smart Portable Devices Suitable for Cultural Heritage: A Review
Cited by: 12
Author(s): Federica Valentini, Andrea Calcaterra, Simonetta Antonaroli, Maurizio Talamo
Software Mentions: 1
Published: over 6 years ago

10.3390/s19051219

Efficient Recognition of Informative Measurement in the RF-Based Device-Free Localization
Cited by: 3
Author(s): Jiaju Tan, Xuemei Guo, Xin Zhao, Guoli Wang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0108490

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets
Cited by: 11
Author(s): Seyhan Yazar, George E C Gooden, David A. Mackey, Alex W. Hewitt
Software Mentions: 1
Published: about 10 years ago

10.3390/s19163544

Robust Evolutionary-Game-Based Routing for Wireless Multimedia Sensor Networks
Cited by: 14
Author(s): Arafat Habib, Sangman Moh
Software Mentions: 1
Published: over 5 years ago

10.3390/s19235126

Exploring the Laplace Prior in Radio Tomographic Imaging with Sparse Bayesian Learning towards the Robustness to Multipath Fading
Cited by: 5
Author(s): Guoli Wang, Xuemei Guo
Software Mentions: 1
Published: almost 5 years ago

10.3389/fgene.2012.00280

Now and Next-Generation Sequencing Techniques: Future of Sequence Analysis Using Cloud Computing
Cited by: 14
Author(s): Radhe Shyam Thakur, Rajib Bandopadhyay, Bratati Chaudhary, Sourav Chatterjee
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0129277

Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes
Cited by: 13
Author(s): Suyash Shringarpure, Andrew Carroll, Francisco Vega, Carlos D. Bustamante
Software Mentions: 1
Published: over 9 years ago

10.1186/gb-2009-10-11-r134

Searching for SNPs with cloud computing
Cited by: 437
Author(s): Ben Langmead, Michael C. Schatz, Jimmy Lin, Mihai Pop, Steven L. Salzberg
Software Mentions: 1
Published: almost 16 years ago