An open resource for accurately benchmarking small variant and reference calls
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
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Journal Article
Best practices for benchmarking germline small-variant calls in human genomes
Krusche, Peter, Trigg, Len, Boutros, Paul C., Mason, Christopher E., De La Vega, Francisco M., Moore, Benjamin L., Gonzalez-Porta, Mar, Eberle, Michael A., Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A., Salit, Marc, Zook, Justin M.
Published in Nature biotechnology (01.05.2019)
Published in Nature biotechnology (01.05.2019)
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Journal Article
A robust benchmark for detection of germline large deletions and insertions
Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc
Published in Nature biotechnology (01.11.2020)
Published in Nature biotechnology (01.11.2020)
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Journal Article
Assembly and annotation of an Ashkenazi human reference genome
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
Published in Genome Biology (02.06.2020)
Published in Genome Biology (02.06.2020)
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Journal Article
Measurements of translation initiation from all 64 codons in E. coli
Hecht, Ariel, Glasgow, Jeff, Jaschke, Paul R, Bawazer, Lukmaan A, Munson, Matthew S, Cochran, Jennifer R, Endy, Drew, Salit, Marc
Published in Nucleic acids research (20.04.2017)
Published in Nucleic acids research (20.04.2017)
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Journal Article
Synthetic spike-in standards for RNA-seq experiments
Jiang, Lichun, Schlesinger, Felix, Davis, Carrie A, Zhang, Yu, Li, Renhua, Salit, Marc, Gingeras, Thomas R, Oliver, Brian
Published in Genome research (01.09.2011)
Published in Genome research (01.09.2011)
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Journal Article
Multiplexed precision genome editing with trackable genomic barcodes in yeast
Roy, Kevin R, Smith, Justin D, Vonesch, Sibylle C, Lin, Gen, Tu, Chelsea Szu, Lederer, Alex R, Chu, Angela, Suresh, Sundari, Nguyen, Michelle, Horecka, Joe, Tripathi, Ashutosh, Burnett, Wallace T, Morgan, Maddison A, Schulz, Julia, Orsley, Kevin M, Wei, Wu, Aiyar, Raeka S, Davis, Ronald W, Bankaitis, Vytas A, Haber, James E, Salit, Marc L, St.Onge, Robert P, Steinmetz, Lars M
Published in Nature biotechnology (01.07.2018)
Published in Nature biotechnology (01.07.2018)
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Journal Article
The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing
MacKay, Matthew J., Hooker, Anna C., Afshinnekoo, Ebrahim, Salit, Marc, Kelly, Jason, Feldstein, Jonathan V., Haft, Nick, Schenkel, Doug, Nambi, Subhalaxmi, Cai, Yizhi, Zhang, Feng, Church, George, Dai, Junbiao, Wang, Cliff L., Levy, Shawn, Huber, Jeff, Ji, Hanlee P., Kriegel, Alison, Wyllie, Anne L., Mason, Christopher E.
Published in Nature biotechnology (01.09.2020)
Published in Nature biotechnology (01.09.2020)
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Journal Article
Genome-wide reconstruction of complex structural variants using read clouds
Spies, Noah, Weng, Ziming, Bishara, Alex, McDaniel, Jennifer, Catoe, David, Zook, Justin M, Salit, Marc, West, Robert B, Batzoglou, Serafim, Sidow, Arend
Published in Nature methods (01.09.2017)
Published in Nature methods (01.09.2017)
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Journal Article
The determination of stem cell fate by 3D scaffold structures through the control of cell shape
Kumar, Girish, Tison, Christopher K, Chatterjee, Kaushik, Pine, P. Scott, McDaniel, Jennifer H, Salit, Marc L, Young, Marian F, Simon, Carl G
Published in Biomaterials (01.12.2011)
Published in Biomaterials (01.12.2011)
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Journal Article
Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2
Huggett, Jim F, Benes, Vladimir, Bustin, Stephen A, Garson, Jeremy A, Harris, Karthyn, Kammel, Martin, Kubista, Mikael, McHugh, Timothy D, Moran-Gilad, Jacob, Nolan, Tania, Pfaffl, Michael W, Salit, Marc, Shipley, Greg, Vallone, Peter M, Vandesompele, Jo, Wittwer, Carl, Zeichhardt, Heinz
Published in Clinical chemistry (Baltimore, Md.) (01.11.2020)
Published in Clinical chemistry (Baltimore, Md.) (01.11.2020)
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Journal Article
One in seven pathogenic variants can be challenging to detect by NGS: an analysis of 450,000 patients with implications for clinical sensitivity and genetic test implementation
Lincoln, Stephen E., Hambuch, Tina, Zook, Justin M., Bristow, Sara L., Hatchell, Kathryn, Truty, Rebecca, Kennemer, Michael, Shirts, Brian H., Fellowes, Andrew, Chowdhury, Shimul, Klee, Eric W., Mahamdallie, Shazia, Cleveland, Megan H., Vallone, Peter M., Ding, Yan, Seal, Sheila, DeSilva, Wasanthi, Tomson, Farol L., Huang, Catherine, Garlick, Russell K., Rahman, Nazneen, Salit, Marc, Kingsmore, Stephen F., Ferber, Matthew J., Aradhya, Swaroop, Nussbaum, Robert L.
Published in Genetics in medicine (01.09.2021)
Published in Genetics in medicine (01.09.2021)
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Journal Article
svviz: a read viewer for validating structural variants
Spies, Noah, Zook, Justin M, Salit, Marc, Sidow, Arend
Published in Bioinformatics (Oxford, England) (15.12.2015)
Published in Bioinformatics (Oxford, England) (15.12.2015)
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Journal Article
Best practices for evaluating single nucleotide variant calling methods for microbial genomics
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
Published in Frontiers in genetics (07.07.2015)
Published in Frontiers in genetics (07.07.2015)
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Journal Article
svclassify: a method to establish benchmark structural variant calls
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
Published in BMC genomics (16.01.2016)
Published in BMC genomics (16.01.2016)
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Journal Article
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Chin, Chen-Shan, Wagner, Justin, Zeng, Qiandong, Garrison, Erik, Garg, Shilpa, Fungtammasan, Arkarachai, Rautiainen, Mikko, Aganezov, Sergey, Kirsche, Melanie, Zarate, Samantha, Schatz, Michael C., Xiao, Chunlin, Rowell, William J., Markello, Charles, Farek, Jesse, Sedlazeck, Fritz J., Bansal, Vikas, Yoo, Byunggil, Miller, Neil, Zhou, Xin, Carroll, Andrew, Barrio, Alvaro Martinez, Salit, Marc, Marschall, Tobias, Dilthey, Alexander T., Zook, Justin M.
Published in Nature communications (22.09.2020)
Published in Nature communications (22.09.2020)
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