Liudmila Sergeevna Mainzer

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Research Output

  • 15 Article
  • 2 Conference contribution
  • 1 Review article
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Article
2019

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

Chen, A. H., Ge, W., Metcalf, W., Jakobsson, E., Mainzer, L. S. & Lipka, A. E., May 1 2019, In : Heredity. 122, 5, p. 660-671 12 p.

Research output: Contribution to journalArticle

Managing genomic variant calling workflows with Swift/T

Ahmed, A. E., Heldenbrand, J., Asmann, Y., Fadlelmola, F. M., Katz, D. S., Kendig, K., Kendzior, M. C., Li, T., Ren, Y., Rodriguez, E., Weber, M. R., Wozniak, J. M., Zermeno, J. & Mainzer, L. S., 2019, In : PloS one. 14, 7, e0211608.

Research output: Contribution to journalArticle

Open Access

Recommendations for performance optimizations when using GATK3.8 and GATK4

Heldenbrand, J. R., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S. N., Hudson, M. E., Iyer, R. K., Kalmbach, M. T., Kendig, K. I., Klee, E. W., Mattson, N. R., Wieben, E. D., Wiepert, M., Wildman, D. E. & Mainzer, L. S., Nov 8 2019, In : BMC bioinformatics. 20, 1, 557.

Research output: Contribution to journalArticle

Open Access

SentIeon DNaSeq variant calling workflow demonstrates strong computational performance and accuracy

Kendig, K. I., Baheti, S., Bockol, M. A., Drucker, T. M., Hart, S. N., Heldenbrand, J. R., Hernaez, M., Hudson, M. E., Kalmbach, M. T., Klee, E. W., Mattson, N. R., Ross, C. A., Taschuk, M., Wieben, E. D., Wiepert, M., Wildman, D. & Mainzer, L. S., 2019, In : Frontiers in Genetics. 10, JUL, 736.

Research output: Contribution to journalArticle

Open Access
2018

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

Baichoo, S., Souilmi, Y., Panji, S., Botha, G., Meintjes, A., Hazelhurst, S., Bendou, H., Beste, E. D., Mpangase, P. T., Souiai, O., Alghali, M., Yi, L., O'Connor, B. D., Crusoe, M., Armstrong, D., Aron, S., Joubert, F., Ahmed, A. E., Mbiyavanga, M., Heusden, P. V. & 6 others, Magosi, L. E., Zermeno, J., Mainzer, L. S., Fadlelmola, F. M., Jongeneel, C. V. & Mulder, N., Nov 29 2018, In : BMC bioinformatics. 19, 1, 457.

Research output: Contribution to journalArticle

Identification of missing variants by combining multiple analytic pipelines

Ren, Y., Reddy, J. S., Pottier, C., Sarangi, V., Tian, S., Sinnwell, J. P., McDonnell, S. K., Biernacka, J. M., Carrasquillo, M. M., Ross, O. A., Ertekin-Taner, N., Rademakers, R., Hudson, M., Mainzer, L. S. & Asmann, Y. W., Apr 16 2018, In : BMC bioinformatics. 19, 1, 139.

Research output: Contribution to journalArticle

2017

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

Jongeneel, C. V., Achinike-Oduaran, O., Adebiyi, E., Adebiyi, M., Adeyemi, S., Akanle, B., Aron, S., Ashano, E., Bendou, H., Botha, G., Chimusa, E., Choudhury, A., Donthu, R., Drnevich, J., Falola, O., Fields, C. J., Hazelhurst, S., Hendry, L., Isewon, I., Khetani, R. S. & 20 others, Kumuthini, J., Kimuda, M. P., Magosi, L., Mainzer, L. S., Maslamoney, S., Mbiyavanga, M., Meintjes, A., Mugutso, D., Mpangase, P., Munthali, R., Nembaware, V., Ndhlovu, A., Odia, T., Okafor, A., Oladipo, O., Panji, S., Pillay, V., Rendon, G., Sengupta, D. & Mulder, N., Jun 2017, In : PLoS computational biology. 13, 6, e1005419.

Research output: Contribution to journalArticle

2016

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa

The H3ABioNet Consortium, Feb 2016, In : Genome Research. 26, 2, p. 271-277 7 p.

Research output: Contribution to journalArticle

Simulating next-generation sequencing datasets from empirical mutation and sequencing models

Stephens, Z. D., Hudson, M. E., Mainzer, L. S., Taschuk, M., Weber, M. R. & Iyer, R. K., Nov 2016, In : PloS one. 11, 11, e0167047.

Research output: Contribution to journalArticle

2013

A general framework of persistence strategies for biological systems helps explain domains of life

Yafremava, L. S., Wielgos, M., Thomas, S., Nasir, A., Wang, M., Mittenthal, J. E. & Caetano-Anollés, G., 2013, In : Frontiers in Genetics. 4, FEB, Article 16.

Research output: Contribution to journalArticle

2011

Putative lateral inhibition in sensory processing for directional turns

Yafremava, L. S. & Gillette, R., Jun 1 2011, In : Journal of neurophysiology. 105, 6, p. 2885-2890 6 p.

Research output: Contribution to journalArticle

2008

Origins and evolution of modern biochemistry: Insights from genomes and molecular structure

Caetano-Anolles, G., Sun, F. J., Wang, M., Yafremava, L. S., Harish, A., Kim, H. S., Knudsen, V., Caetano-Anolles, D. & Mittenthal, J. E., May 1 2008, In : Frontiers in Bioscience. 13, 14, p. 5212-5240 29 p.

Research output: Contribution to journalArticle

2007

Orienting and avoidance turning are precisely computed by the predatory sea-slug Pleurobranchaea californica McFarland

Yafremava, L. S., Anthony, C. W., Lane, L., Campbell, J. K. & Gillette, R., Feb 1 2007, In : Journal of Experimental Biology. 210, 4, p. 561-569 9 p.

Research output: Contribution to journalArticle

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

Wang, M., Yafremava, L. S., Caetano-Anollés, D., Mittenthal, J. E. & Caetano-Anollés, G., Nov 1 2007, In : Genome Research. 17, 11, p. 1572-1585 14 p.

Research output: Contribution to journalArticle