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Voges, Jan [Author]; Paridaens, Tom [Author]; Müntefering, Fabian [Author]; Mainzer, Liudmila S. [Author]; Bliss, Brian [Author]; Yang, Mingyu [Author]; Ochoa, Idoia [Author]; Fostier, Jan [Author]; Ostermann, Jörn [Author]; Hernaez, Mikel [Author]

GABAC : An arithmetic coding solution for genomic data - [published Version]

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Oxford : Oxford Univ. Press, 2020

Published in: Bioinformatics 36 (2020), Nr. 7
Voges, Jan [Author]; Paridaens, Tom [Author]; Müntefering, Fabian [Author]; Mainzer, Liudmila S. [Author]; Bliss, Brian [Author]; Yang, Mingyu [Author]; Ochoa, Idoia [Author]; Fostier, Jan [Author]; Ostermann, Jörn [Author]; Hernaez, Mikel [Author]

GABAC : An arithmetic coding solution for genomic data

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Hannover: Gottfried Wilhelm Leibniz Universität Hannover, 2020 ; Hannover: Technische Informationsbibliothek (TIB), 2020

Published in: Bioinformatics ; 36 (2020), Nr. 7, S. 2275-2277
Xie, Xiaoman; Kendzior, Matthew C; Ge, Xiyu; Mainzer, Liudmila S; Sinha, Saurabh

VarSAn: associating pathways with a set of genomic variants using network analysis

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Oxford University Press (OUP), 2021

Published in: Nucleic Acids Research, 49 (2021) 15, Seite 8471-8487
Stephens, Zachary D.; Hudson, Matthew E.; Mainzer, Liudmila S.; Taschuk, Morgan; Weber, Matthew R.; Iyer, Ravishankar K.

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

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Public Library of Science (PLoS), 2016

Published in: PLOS ONE, 11 (2016) 11, Seite e0167047
Voges, Jan; Paridaens, Tom; Müntefering, Fabian; Mainzer, Liudmila S; Bliss, Brian; Yang, Mingyu; Ochoa, Idoia; Fostier, Jan; Ostermann, Jörn; Hernaez, Mikel

GABAC: an arithmetic coding solution for genomic data

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Oxford University Press (OUP), 2020

Published in: Bioinformatics, 36 (2020) 7, Seite 2275-2277
Ahmed, Azza E.; Heldenbrand, Jacob; Asmann, Yan; Fadlelmola, Faisal M.; Katz, Daniel S.; Kendig, Katherine; Kendzior, Matthew C.; Li, Tiffany; Ren, Yingxue; Rodriguez, Elliott; Weber, Matthew R.; Wozniak, Justin M.; Zermeno, Jennie; Mainzer, Liudmila S.

Managing genomic variant calling workflows with Swift/T

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Public Library of Science (PLoS), 2019

Published in: PLOS ONE, 14 (2019) 7, Seite e0211608
Ren, Yingxue; Reddy, Joseph S.; Pottier, Cyril; Sarangi, Vivekananda; Tian, Shulan; Sinnwell, Jason P.; McDonnell, Shannon K.; Biernacka, Joanna M.; Carrasquillo, Minerva M.; Ross, Owen A.; Ertekin-Taner, Nilüfer; Rademakers, Rosa; Hudson, Matthew; Mainzer, Liudmila Sergeevna; Asmann, Yan W.

Identification of missing variants by combining multiple analytic pipelines

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Springer Science and Business Media LLC, 2018

Published in: BMC Bioinformatics, 19 (2018) 1
Ahmed, Azza E.; Allen, Joshua M.; Bhat, Tajesvi; Burra, Prakruthi; Fliege, Christina E.; Hart, Steven N.; Heldenbrand, Jacob R.; Hudson, Matthew E.; Istanto, Dave Deandre; Kalmbach, Michael T.; Kapraun, Gregory D.; Kendig, Katherine I.; Kendzior, Matthew Charles; Klee, Eric W.; Mattson, Nate; Ross, Christian A.; Sharif, Sami M.; Venkatakrishnan, Ramshankar; Fadlelmola, Faisal M.; Mainzer, Liudmila S.

Design considerations for workflow management systems use in production genomics research and the clinic

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Springer Science and Business Media LLC, 2021

Published in: Scientific Reports, 11 (2021) 1
Wickland, Daniel P.; Ren, Yingxue; Sinnwell, Jason P.; Reddy, Joseph S.; Pottier, Cyril; Sarangi, Vivekananda; Carrasquillo, Minerva M.; Ross, Owen A.; Younkin, Steven G.; Ertekin-Taner, Nilüfer; Rademakers, Rosa; Hudson, Matthew E.; Mainzer, Liudmila Sergeevna; Biernacka, Joanna M.; Asmann, Yan W.

Impact of variant-level batch effects on identification of genetic risk factors in large sequencing studies

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Public Library of Science (PLoS), 2021

Published in: PLOS ONE, 16 (2021) 4, Seite e0249305
Heldenbrand, Jacob R.; Baheti, Saurabh; Bockol, Matthew A.; Drucker, Travis M.; Hart, Steven N.; Hudson, Matthew E.; Iyer, Ravishankar K.; Kalmbach, Michael T.; Kendig, Katherine I.; Klee, Eric W.; Mattson, Nathan R.; Wieben, Eric D.; Wiepert, Mathieu; Wildman, Derek E.; Mainzer, Liudmila S.

Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4

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Springer Science and Business Media LLC, 2019

Published in: BMC Bioinformatics, 20 (2019) 1
Heldenbrand, Jacob R; Baheti, Saurabh; Bockol, Matthew A; Drucker, Travis M; Hart, Steven N; Hudson, Matthew E; Iyer, Ravishankar K; Kalmbach, Michael T; Kendig, Katherine I; Klee, Eric W; Mattson, Nathan R; Wieben, Eric D; Wiepert, Mathieu; Wildman, Derek E; Mainzer, Liudmila S

Recommendations for performance optimizations when using GATK3.8 and GATK4

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Springer Science and Business Media LLC, 2019

Published in: BMC Bioinformatics, 20 (2019) 1
Kendig, Katherine I.; Baheti, Saurabh; Bockol, Matthew A.; Drucker, Travis M.; Hart, Steven N.; Heldenbrand, Jacob R.; Hernaez, Mikel; Hudson, Matthew E.; Kalmbach, Michael T.; Klee, Eric W.; Mattson, Nathan R.; Ross, Christian A.; Taschuk, Morgan; Wieben, Eric D.; Wiepert, Mathieu; Wildman, Derek E.; Mainzer, Liudmila S.

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

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Frontiers Media SA, 2019

Published in: Frontiers in Genetics, 10 (2019)
Jongeneel, C. Victor; Achinike-Oduaran, Ovokeraye; Adebiyi, Ezekiel; Adebiyi, Marion; Adeyemi, Seun; Akanle, Bola; Aron, Shaun; Ashano, Efejiro; Bendou, Hocine; Botha, Gerrit; Chimusa, Emile; Choudhury, Ananyo; Donthu, Ravikiran; Drnevich, Jenny; Falola, Oluwadamila; Fields, Christopher J.; Hazelhurst, Scott; Hendry, Liesl; Isewon, Itunuoluwa; Khetani, Radhika S.; Kumuthini, Judit; Kimuda, Magambo Phillip; Magosi, Lerato; Mainzer, Liudmila Sergeevna; [...]

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network

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Public Library of Science (PLoS), 2017

Published in: PLOS Computational Biology, 13 (2017) 6, Seite e1005419

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