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Computational pipelines

GeneTEFlow: A Nextflow-based pipeline for analysing gene and transposable elements expression from RNA-Seq data

Xiaochuan Liu, Jadwiga R. Bienkowska, Wenyan Zhong

published 31 Aug 2020

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Compressive Big Data Analytics: An ensemble meta-algorithm for high-dimensional multisource datasets

Simeone Marino, Yi Zhao, Nina Zhou, Yiwang Zhou, Arthur W. Toga, Lu Zhao, Yingsi Jian, Yichen Yang, Yehu Chen, Qiucheng Wu, Jessica Wild, Brandon Cummings, Ivo D. Dinov

published 28 Aug 2020

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Automated data extraction from historical city directories: The rise and fall of mid-century gas stations in Providence, RI

Samuel Bell, Thomas Marlow, Kai Wombacher, Anina Hitt, Neev Parikh, Andras Zsom, Scott Frickel

published 19 Aug 2020

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FeAture Explorer (FAE): A tool for developing and comparing radiomics models

Yang Song, Jing Zhang, Yu-dong Zhang, Ying Hou, Xu Yan, Yida Wang, Minxiong Zhou, Ye-feng Yao, Guang Yang

published 17 Aug 2020

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A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry

Joshua J. Medina, James M. Maley, Siddharth Sannapareddy, Noah N. Medina, Cyril M. Gilman, John E. McCormack

published 13 Aug 2020

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A high-throughput imaging and quantification pipeline for the EVOS imaging platform

Stefan Donovan Klimaj, Yamhilette Licon Munoz, Katelyn Del Toro, William Curtis Hines

published 05 Aug 2020

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Automatic three-dimensional reconstruction of fascicles in peripheral nerves from histological images

Daniel Tovbis, Anne Agur, Jeremy P. M. Mogk, José Zariffa

published 14 May 2020

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Comparison of quality control methods for automated diffusion tensor imaging analysis pipelines

Seyyed M. H. Haddad, Christopher J. M. Scott, Miracle Ozzoude, Melissa F. Holmes, Stephen R. Arnott, Nuwan D. Nanayakkara, Joel Ramirez, Sandra E. Black, Dar Dowlatshahi, Stephen C. Strother, Richard H. Swartz, Sean Symons, Manuel Montero-Odasso, ONDRI Investigators , Robert Bartha

published 20 Dec 2019

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SparkGA2: Production-quality memory-efficient Apache Spark based genome analysis framework

Hamid Mushtaq, Nauman Ahmed, Zaid Al-Ars

published 05 Dec 2019

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A feature selection strategy for gene expression time series experiments with hidden Markov models

Roberto A. Cárdenas-Ovando, Edith A. Fernández-Figueroa, Héctor A. Rueda-Zárate, Julieta Noguez, Claudia Rangel-Escareño

published 10 Oct 2019

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gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Juhana I. Kammonen, Olli-Pekka Smolander, Lars Paulin, Pedro A. B. Pereira, Pia Laine, Patrik Koskinen, Jukka Jernvall, Petri Auvinen

published 09 Sep 2019

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Cardiovascular disease risk prediction using automated machine learning: A prospective study of 423,604 UK Biobank participants

Ahmed M. Alaa, Thomas Bolton, Emanuele Di Angelantonio, James H. F. Rudd, Mihaela van der Schaar

published 15 May 2019

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From invisibility to readability: Recovering the ink of Herculaneum

Clifford Seth Parker, Stephen Parsons, Jack Bandy, Christy Chapman, Frederik Coppens, William Brent Seales

published 08 May 2019

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