PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Authors: Olson, Nathan D., Wagner, Justin, McDaniel, Jennifer, Stephens, Sarah H., Westreich, Samuel T., Prasanna, Anish G., Johanson, Elaine, Boja, Emily, Maier, Ezekiel J., Serang, Omar, Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Kyriakidis, Konstantinos, Malousi, Andigoni, Shafin, Kishwar, Pesout, Trevor, Jain, Miten, Paten, Benedict, Chang, Pi-Chuan, Kolesnikov, Alexey, Nattestad, Maria, Baid, Gunjan, Goel, Sidharth, Yang, Howard, Carroll, Andrew, Eveleigh, Robert, Bourgey, Mathieu, Bourque, Guillaume, Li, Gen, Ma, ChouXian, Tang, LinQi, Du, YuanPing, Zhang, ShaoWei, Morata, Jordi, Tonda, Raúl, Parra, Genís, Trotta, Jean-Rémi, Brueffer, Christian, Demirkaya-Budak, Sinem, Kabakci-Zorlu, Duygu, Turgut, Deniz, Kalay, Özem, Budak, Gungor, Narcı, Kübra, Arslan, Elif, Brown, Richard, Johnson, Ivan J., Dolgoborodov, Alexey, Semenyuk, Vladimir, Jain, Amit, Tetikol, H. Serhat, Jain, Varun, Ruehle, Mike, Lajoie, Bryan, Roddey, Cooper, Catreux, Severine, Mehio, Rami, Ahsan, Mian Umair, Liu, Qian, Wang, Kai, Ebrahim Sahraeian, Sayed Mohammad, Fang, Li Tai, Mohiyuddin, Marghoob, Hung, Calvin, Jain, Chirag, Feng, Hanying, Li, Zhipan, Chen, Luoqi, Sedlazeck, Fritz J., Zook, Justin M.

Source: In Cell Genomics 11 May 2022 2(5)

Gene Expression Scoring of Immune Activity Levels for Precision Use of Hydrocortisone in Vasodilatory Shock

Authors: Yao, Lijing, Rey, Diego Ariel, Bulgarelli, Lucas, Kast, Rachel, Osborn, Jeff, Van Ark, Emily, Fang, Li Tai, Lau, Bayo, Lam, Hugo, Teixeira, Leonardo Maestri, Neto, Ary Serpa, Bellomo, Rinaldo, Deliberato, Rodrigo Octávio

Source: Shock. 57(3):384-391

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100155089984.0x000001&indx=1&recIds=ETOCvdc_100155089984.0x000001

Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Cell-Free DNA in Stage I–IV Non–Small Cell Lung Cancer

Authors: Jiang, John, Adams, Hans-Peter, Yao, Lijing, Yaung, Stephanie, Lal, Preeti, Balasubramanyam, Aarthi, Fuhlbrück, Frederike, Tikoo, Nalin, Lovejoy, Alexander F., Froehler, Sebastian, Fang, Li Tai, Achenbach, H. Jost, Floegel, Ralph, Krügel, Rainer, Palma, John F.

Source: In The Journal of Molecular Diagnostics February 2020 22(2):228-235

SomaticSeq: An Ensemble and Machine Learning Method to Detect Somatic Mutations

Authors: Fang, Li Tai

Source: Methods in molecular biology. 2120:47-70

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN623489411&indx=1&recIds=ETOCRN623489411

Methods for the purification and detection of single nucleotide KRAS mutations on extrachromosomal circular DNA in human plasma.

Authors: Bøllehuus Hansen, Lasse, Jakobsen, Sandra Fugl, Zole, Egija, Noer, Julie Boertmann, Fang, Li Tai, Alizadeh, Sefa, Johansen, Julia Sidenius, Mohiyuddin, Marghoob, Regenberg, Birgitte

Source: Cancer Medicine; Sep2023, Vol. 12 Issue 17, p17679-17691, 13p

Subject Terms: EXTRACHROMOSOMAL DNA, CIRCULAR DNA, HUMAN DNA, RAS oncogenes, CELL-free DNA

The end-to-end distance of RNA as a randomly self-paired polymer

Authors: Fang, Li Tai

Source: In Journal of Theoretical Biology 2011 280(1):101-107

Effects of Salt Concentrations and Bending Energy on the Extent of Ejection of Phage Genomes

Authors: Evilevitch, Alex, Fang, Li Tai, Yoffe, Aron M., Castelnovo, Martin, Rau, Donald C., Parsegian, V. Adrian, Gelbart, William M., Knobler, Charles M.

Source: In Biophysical Journal 1 February 2008 94(3):1110-1120

Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies.

Authors: Talsania, Keyur, Shen, Tsai-wei, Chen, Xiongfong, Jaeger, Erich, Li, Zhipan, Chen, Zhong, Chen, Wanqiu, Tran, Bao, Kusko, Rebecca, Wang, Limin, Pang, Andy Wing Chun, Yang, Zhaowei, Choudhari, Sulbha, Colgan, Michael, Fang, Li Tai, Carroll, Andrew, Shetty, Jyoti, Kriga, Yuliya, German, Oksana, Smirnova, Tatyana

Source: Genome Biology; 12/13/2022, Vol. 23 Issue 1, p1-33, 33p

Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples.

Authors: Xiao, Chunlin, Chen, Zhong, Chen, Wanqiu, Padilla, Cory, Colgan, Michael, Wu, Wenjun, Fang, Li-Tai, Liu, Tiantian, Yang, Yibin, Schneider, Valerie, Wang, Charles, Xiao, Wenming

Source: Genome Biology; 11/9/2022, Vol. 23 Issue 1, p1-34, 34p

The physics of DNA, RNA, and RNA-like polymers

Authors: Fang, Li Tai, 1981

Access URL: http://hdl.handle.net/2027/uc1.l0100551076

Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample.

Authors: Sahraeian, Sayed Mohammad Ebrahim, Fang, Li Tai, Karagiannis, Konstantinos, Moos, Malcolm, Smith, Sean, Santana-Quintero, Luis, Xiao, Chunlin, Colgan, Michael, Hong, Huixiao, Mohiyuddin, Marghoob, Xiao, Wenming

Source: Genome Biology; 1/7/2022, Vol. 23 Issue 1, p1-20, 20p

Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.

Authors: Zhao, Yongmei, Fang, Li Tai, Shen, Tsai-wei, Choudhari, Sulbha, Talsania, Keyur, Chen, Xiongfong, Shetty, Jyoti, Kriga, Yuliya, Tran, Bao, Zhu, Bin, Chen, Zhong, Chen, Wanqiu, Wang, Charles, Jaeger, Erich, Meerzaman, Daoud, Lu, Charles, Idler, Kenneth, Ren, Luyao, Zheng, Yuanting, Shi, Leming

Source: Scientific Data; 11/9/2021, Vol. 8 Issue 1, p1-14, 14p

Subject Terms: WHOLE genome sequencing, GENETIC mutation, SOMATIC mutation, EARLY detection of cancer, INDIVIDUALIZED medicine, GENOMES

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Authors: Fang, Li Tai¹ (AUTHOR), Zhu, Bin² (AUTHOR), Zhao, Yongmei³ (AUTHOR), Chen, Wanqiu⁴ (AUTHOR), Yang, Zhaowei^4,5 (AUTHOR), Kerrigan, Liz⁶ (AUTHOR), Langenbach, Kurt⁶ (AUTHOR), de Mars, Maryellen⁶ (AUTHOR), Lu, Charles⁷ (AUTHOR), Idler, Kenneth⁷ (AUTHOR), Jacob, Howard⁷ (AUTHOR), Zheng, Yuanting⁸ (AUTHOR), Ren, Luyao⁸ (AUTHOR), Yu, Ying⁸ (AUTHOR), Jaeger, Erich⁹ (AUTHOR), Schroth, Gary P.⁹ (AUTHOR), Abaan, Ogan D.⁹ (AUTHOR), Talsania, Keyur³ (AUTHOR), Lack, Justin³ (AUTHOR), Shen, Tsai-Wei³ (AUTHOR)

Source: Nature Biotechnology. Sep2021, Vol. 39 Issue 9, p1151-1160. 10p.

Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.

Authors: Xiao, Wenming, Ren, Luyao, Chen, Zhong, Fang, Li Tai, Zhao, Yongmei, Lack, Justin, Guan, Meijian, Zhu, Bin, Jaeger, Erich, Kerrigan, Liz, Blomquist, Thomas M., Hung, Tiffany, Sultan, Marc, Idler, Kenneth, Lu, Charles, Scherer, Andreas, Kusko, Rebecca, Moos, Malcolm, Xiao, Chunlin, Sherry, Stephen T.

Source: Nature Biotechnology; Sep2021, Vol. 39 Issue 9, p1141-1150, 10p

The size of RNA as an ideal branched polymer.

Authors: Fang, Li Tai¹, Gelbart, William M.², Ben-Shaul, Avinoam¹

Source: Journal of Chemical Physics. 10/21/2011, Vol. 135 Issue 15, p155105. 5p. 1 Diagram, 2 Graphs.

Subject Terms: *RNA, *POLYMERS, *MONOMERS, *ROOT-mean-squares, *NUCLEOTIDE sequence, *VIRUSES, *MOLECULAR structure

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