Genomes in a bottle: creating standard reference materials for genomic variation - why, what and how?

por Zook, Justin M, Salit, Marc
Publicado 2011

Challenging a bioinformatic tool’s ability to detect microbial contaminants using in silico whole genome sequencing data

por Olson, Nathan D., Zook, Justin M., Morrow, Jayne B., Lin, Nancy J.
Publicado 2017

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

por Zook, Justin M., Samarov, Daniel, McDaniel, Jennifer, Sen, Shurjo K., Salit, Marc
Publicado 2012

An analytical framework for optimizing variant discovery from personal genomes

por Highnam, Gareth, Wang, Jason J., Kusler, Dean, Zook, Justin, Vijayan, Vinaya, Leibovich, Nir, Mittelman, David
Publicado 2015

PEPR: pipelines for evaluating prokaryotic references

por Olson, Nathan D., Zook, Justin M., Samarov, Daniel V., Jackson, Scott A., Salit, Marc L.
Publicado 2016

Tools for annotation and comparison of structural variation

por Sedlazeck, Fritz J., Dhroso, Andi, Bodian, Dale L., Paschall, Justin, Hermes, Farrah, Zook, Justin M.
Publicado 2017

Development and Characterization of Reference Materials for Genetic Testing: Focus on Public Partnerships

por Kalman, Lisa V., Datta, Vivekananda, Williams, Mickey, Zook, Justin M., Salit, Marc L., Han, Jin-Yeong
Publicado 2016

Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

por Chin, Chen-Shan, Behera, Sairam, Khalak, Asif, Sedlazeck, Fritz J., Sudmant, Peter H., Wagner, Justin, Zook, Justin M.
Publicado 2023

Medical implications of technical accuracy in genome sequencing

por Goldfeder, Rachel L., Priest, James R., Zook, Justin M., Grove, Megan E., Waggott, Daryl, Wheeler, Matthew T., Salit, Marc, Ashley, Euan A.
Publicado 2016

Genome-wide reconstruction of complex structural variants using read clouds

por Spies, Noah, Weng, Ziming, Bishara, Alex, McDaniel, Jennifer, Catoe, David, Zook, Justin M., Salit, Marc, West, Robert B., Batzoglou, Serafim, Sidow, Arend
Publicado 2017

svclassify: a method to establish benchmark structural variant calls

por Parikh, Hemang, Mohiyuddin, Marghoob, Lam, Hugo Y. K., Iyer, Hariharan, Chen, Desu, Pratt, Mark, Bartha, Gabor, Spies, Noah, Losert, Wolfgang, Zook, Justin M., Salit, Marc
Publicado 2016

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing–Detected Variants with an Orthogonal Method in Clinical Genetic Testing

por Lincoln, Stephen E., Truty, Rebecca, Lin, Chiao-Feng, Zook, Justin M., Paul, Joshua, Ramey, Vincent H., Salit, Marc, Rehm, Heidi L., Nussbaum, Robert L., Lebo, Matthew S.
Publicado 2019

Assembly and annotation of an Ashkenazi human reference genome

por Shumate, Alaina, Zimin, Aleksey V., Sherman, Rachel M., Puiu, Daniela, Wagner, Justin M., Olson, Nathan D., Pertea, Mihaela, Salit, Marc L., Zook, Justin M., Salzberg, Steven L.
Publicado 2020

Best practices for evaluating single nucleotide variant calling methods for microbial genomics

por Olson, Nathan D., Lund, Steven P., Colman, Rebecca E., Foster, Jeffrey T., Sahl, Jason W., Schupp, James M., Keim, Paul, Morrow, Jayne B., Salit, Marc L., Zook, Justin M.
Publicado 2015

High-coverage, long-read sequencing of Han Chinese trio reference samples

por Wang, Ying-Chih, Olson, Nathan D., Deikus, Gintaras, Shah, Hardik, Wenger, Aaron M., Trow, Jonathan, Xiao, Chunlin, Sherry, Stephen, Salit, Marc L., Zook, Justin M., Smith, Melissa, Sebra, Robert
Publicado 2019

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons

por Olson, Nathan D., Lund, Steven P., Zook, Justin M., Rojas-Cornejo, Fabiola, Beck, Brian, Foy, Carole, Huggett, Jim, Whale, Alexandra S., Sui, Zhiwei, Baoutina, Anna, Dobeson, Michael, Partis, Lina, Morrow, Jayne B.
Publicado 2015

FixItFelix: improving genomic analysis by fixing reference errors

por Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F., Farek, Jesse, Soto, Daniela C., Parker, Stephen C. J., Smith, Albert V., Dennis, Megan Y., Zook, Justin M., Sedlazeck, Fritz J.
Publicado 2023

An open resource for accurately benchmarking small variant and reference calls

por Zook, Justin M., McDaniel, Jennifer, Olson, Nathan D., Wagner, Justin, Parikh, Hemang, Heaton, Haynes, Irvine, Sean A., Trigg, Len, Truty, Rebecca, McLean, Cory Y., De La Vega, Francisco M., Xiao, Chunlin, Sherry, Stephen, Salit, Marc
Publicado 2019

Chromosome-scale, haplotype-resolved assembly of human genomes

por Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., Li, Heng
Publicado 2020

Achieving high-sensitivity for clinical applications using augmented exome sequencing

por Patwardhan, Anil, Harris, Jason, Leng, Nan, Bartha, Gabor, Church, Deanna M., Luo, Shujun, Haudenschild, Christian, Pratt, Mark, Zook, Justin, Salit, Marc, Tirch, Jeanie, Morra, Massimo, Chervitz, Stephen, Li, Ming, Clark, Michael, Garcia, Sarah, Chandratillake, Gemma, Kirk, Scott, Ashley, Euan, Snyder, Michael, Altman, Russ, Bustamante, Carlos, Butte, Atul J., West, John, Chen, Richard
Publicado 2015