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Akademický článek

An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients

Autor: Phatnani, Hemali, Kwan, Justin, Sareen, Dhruv, Broach, James R., Simmons, Zachary, Arcila-Londono, Ximena, Lee, Edward B., Van Deerlin, Vivianna M., Shneider, Neil A., Fraenkel, Ernest, Ostrow, Lyle W., Baas, Frank, Zaitlen, Noah, Berry, James D., Malaspina, Andrea, Fratta, Pietro, Cox, Gregory A., Thompson, Leslie M., Finkbeiner, Steve, Dardiotis, Efthimios, Miller, Timothy M., Chandran, Siddharthan, Pal, Suvankar, Hornstein, Eran, MacGowan, Daniel J., Heiman-Patterson, Terry, Hammell, Molly G., Patsopoulos, Nikolaos.A., Butovsky, Oleg, Dubnau, Joshua, Nath, Avindra, Bowser, Robert, Harms, Matt, Poss, Mary, Phillips-Cremins, Jennifer, Crary, John, Atassi, Nazem, Lange, Dale J., Adams, Darius J., Stefanis, Leonidas, Gotkine, Marc, Baloh, Robert H., Babu, Suma, Raj, Towfique, Paganoni, Sabrina, Shalem, Ophir, Smith, Colin, Zhang, Bin, Harris, Brent, Broce, Iris, Drory, Vivian, Ravits, John, McMillan, Corey, Menon, Vilas, Wu, Lani, Altschuler, Steven, Li, Jonathan, Lim, Ryan G., Kaye, Julia A., Dardov, Victoria, Coyne, Alyssa N., Wu, Jie, Milani, Pamela, Cheng, Andrew, Thompson, Terri G., Ornelas, Loren, Frank, Aaron, Adam, Miriam, Banuelos, Maria G., Casale, Malcolm, Cox, Veerle, Escalante-Chong, Renan, Daigle, J. Gavin, Gomez, Emilda, Hayes, Lindsey, Holewenski, Ronald, Lei, Susan, Lenail, Alex, Lima, Leandro, Mandefro, Berhan, Matlock, Andrea, Panther, Lindsay, Patel-Murray, Natasha Leanna, Pham, Jacqueline, Ramamoorthy, Divya, Sachs, Karen, Shelley, Brandon, Stocksdale, Jennifer, Trost, Hannah, Wilhelm, Mark, Venkatraman, Vidya, Wassie, Brook T., Wyman, Stacia, Yang, Stephanie, Van Eyk, Jennifer E., Lloyd, Thomas E., Finkbeiner, Steven, Rothstein, Jeffrey D., Svendsen, Clive N.

Publikováno v: In iScience 19 November 2021 24(11)

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A frame-based representation of genomic sequences for removing errors and rare variant detection in NGS data

Autor: Malhotra, Raunaq, Mukhopadhyay, Manjari, Poss, Mary, Acharya, Raj

We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions, traditiona

Externí odkaz: http://arxiv.org/abs/1604.04803

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Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome

Autor: Schiff, Steven J., Kiwanuka, Julius, Riggio, Gina, Nguyen, Lan, Mu, Kevin, Sproul, Emily, Bazira, Joel, Mwanga, Juliet, Tumusiime, Dickson, Nyesigire, Eunice, Lwanga, Nkangi, Bogale, Kaleb T., Kapur, Vivek, Broach, James, Morton, Sarah, Warf, Benjamin C., Poss, Mary

Neonatal sepsis (NS) is responsible for over a 1 million yearly deaths worldwide. In the developing world NS is often treated without an identified microbial pathogen. Amplicon sequencing of the bacterial 16S rRNA gene can be used to identify organis

Externí odkaz: http://arxiv.org/abs/1602.00600

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Assignment of endogenous retrovirus integration sites using a mixture model

Autor: Hunter, David R., Bao, Le, Poss, Mary

Structural variation occurs in the genomes of individuals because of the different positions occupied by repetitive genome elements like endogenous retroviruses, or ERVs. The presence or absence of ERVs can be determined by identifying the junction w

Externí odkaz: http://arxiv.org/abs/1510.00028

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Maximum Likelihood de novo reconstruction of viral populations using paired end sequencing data

Autor: Malhotra, Raunaq, Wu, Manjari Mukhopadhyay Steven, Rodrigo, Allen, Poss, Mary, Acharya, Raj

We present MLEHaplo, a maximum likelihood de novo assembly algorithm for reconstructing viral haplotypes in a virus population from paired-end next generation sequencing (NGS) data. Using the pairing information of reads in our proposed Viral Path Re

Externí odkaz: http://arxiv.org/abs/1502.04239

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Clustering pipeline for determining consensus sequences in targeted next-generation sequencing

Autor: Malhotra, Raunaq, Elleder, Daniel, Bao, Le, Hunter, David R, Acharya, Raj, Poss, Mary

Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the analyses

Externí odkaz: http://arxiv.org/abs/1410.1608

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