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

por Xie, Xiaoman, Kendzior, Matthew C, Ge, Xiyu, Mainzer, Liudmila S, Sinha, Saurabh
Publicado 2021

Health disparities research is enabled by data diversity but requires much tighter integration of collaborative efforts

por Cazier, Jean-Baptiste, Mainzer, Liudmila Sergeevna, Ge, Weihao, Žurauskienė, Justina, Madak-Erdogan, Zeynep
Publicado 2020

An assessment of true and false positive detection rates of stepwise epistatic model selection as a function of sample size and number of markers

por Chen, Angela H., Ge, Weihao, Metcalf, William, Jakobsson, Eric, Mainzer, Liudmila Sergeevna, Lipka, Alexander E.
Publicado 2018

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

por Stephens, Zachary D., Hudson, Matthew E., Mainzer, Liudmila S., Taschuk, Morgan, Weber, Matthew R., Iyer, Ravishankar K.
Publicado 2016

GABAC: an arithmetic coding solution for genomic data

por Voges, Jan, Paridaens, Tom, Müntefering, Fabian, Mainzer, Liudmila S, Bliss, Brian, Yang, Mingyu, Ochoa, Idoia, Fostier, Jan, Ostermann, Jörn, Hernaez, Mikel
Publicado 2020

Managing genomic variant calling workflows with Swift/T

por 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.
Publicado 2019

Identification of missing variants by combining multiple analytic pipelines

por 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.
Publicado 2018

Recommendations for performance optimizations when using GATK3.8 and GATK4

por 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
Publicado 2019

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

por 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.
Publicado 2019

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

por 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.
Publicado 2021

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

por 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.
Publicado 2019

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

por 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.
Publicado 2021

Organizing and running bioinformatics hackathons within Africa: The H3ABioNet cloud computing experience

por Ahmed, Azza E., Mpangase, Phelelani T., Panji, Sumir, Baichoo, Shakuntala, Souilmi, Yassine, Fadlelmola, Faisal M., Alghali, Mustafa, Aron, Shaun, Bendou, Hocine, De Beste, Eugene, Mbiyavanga, Mamana, Souiai, Oussema, Yi, Long, Zermeno, Jennie, Armstrong, Don, O'Connor, Brian D., Mainzer, Liudmila Sergeevna, Crusoe, Michael R., Meintjes, Ayton, Van Heusden, Peter, Botha, Gerrit, Joubert, Fourie, Jongeneel, C. Victor, Hazelhurst, Scott, Mulder, Nicola
Publicado 2019

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

por Baichoo, Shakuntala, Souilmi, Yassine, Panji, Sumir, Botha, Gerrit, Meintjes, Ayton, Hazelhurst, Scott, Bendou, Hocine, Beste, Eugene de, Mpangase, Phelelani T., Souiai, Oussema, Alghali, Mustafa, Yi, Long, O’Connor, Brian D., Crusoe, Michael, Armstrong, Don, Aron, Shaun, Joubert, Fourie, Ahmed, Azza E., Mbiyavanga, Mamana, Heusden, Peter van, Magosi, Lerato E., Zermeno, Jennie, Mainzer, Liudmila Sergeevna, Fadlelmola, Faisal M., Jongeneel, C. Victor, Mulder, Nicola
Publicado 2018

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

por 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, Maslamoney, Suresh, Mbiyavanga, Mamana, Meintjes, Ayton, Mugutso, Danny, Mpangase, Phelelani, Munthali, Richard, Nembaware, Victoria, Ndhlovu, Andrew, Odia, Trust, Okafor, Adaobi, Oladipo, Olaleye, Panji, Sumir, Pillay, Venesa, Rendon, Gloria, Sengupta, Dhriti, Mulder, Nicola
Publicado 2017