Search Results - "Gene Library"

CBNplot: Bayesian network plots for enrichment analysis by Sato, Noriaki, Tamada, Yoshinori, Yu, Guangchuang, Okuno, Yasushi

“…Abstract Summary When investigating gene expression profiles, determining important directed edges between genes can provide valuable insights in addition to…”
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Scaffold Remodelling of Diazaspirotricycles Enables Synthesis of Diverse sp 3 ‐Rich Compounds With Distinct Phenotypic Effects by Okolo, Ephraim A., Pahl, Axel, Sievers, Sonja, Pask, Christopher M., Nelson, Adam, Marsden, Stephen P.

“…A ‘top down’ scaffold remodelling approach to library synthesis was applied to spirotricyclic ureas prepared by a complexity‐generating oxidative…”
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Enrichr-KG: bridging enrichment analysis across multiple libraries by Evangelista, John Erol, Xie, Zhuorui, Marino, Giacomo B, Nguyen, Nhi, Clarke, Daniel J B, Ma’ayan, Avi

“…Abstract Gene and protein set enrichment analysis is a critical step in the analysis of data collected from omics experiments. Enrichr is a popular gene set…”
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IBS 2.0: an upgraded illustrator for the visualization of biological sequences by Xie, Yubin, Li, Huiqin, Luo, Xiaotong, Li, Hongyu, Gao, Qiuyuan, Zhang, Luowanyue, Teng, Yuyan, Zhao, Qi, Zuo, Zhixiang, Ren, Jian

“…Abstract The visualization of biological sequences with various functional elements is fundamental for the publication of scientific achievements in the field…”
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LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons by Ou, Shujun, Jiang, Ning

“…Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene…”
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Peptide-based drug discovery: Current status and recent advances by Sharma, Komal, Sharma, Krishna K., Sharma, Anku, Jain, Rahul

“…[Display omitted] •A comprehensive compilation and analysis of FDA approved and under clinical trials peptide-based therapeutics.•Clinical trial peptides…”
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A Python library for probabilistic analysis of single-cell omics data by Gayoso, Adam, Lopez, Romain, Xing, Galen, Boyeau, Pierre, Valiollah Pour Amiri, Valeh, Hong, Justin, Wu, Katherine, Jayasuriya, Michael, Mehlman, Edouard, Langevin, Maxime, Liu, Yining, Samaran, Jules, Misrachi, Gabriel, Nazaret, Achille, Clivio, Oscar, Xu, Chenling, Ashuach, Tal, Gabitto, Mariano, Lotfollahi, Mohammad, Svensson, Valentine, da Veiga Beltrame, Eduardo, Kleshchevnikov, Vitalii, Talavera-López, Carlos, Pachter, Lior, Theis, Fabian J., Streets, Aaron, Jordan, Michael I., Regier, Jeffrey, Yosef, Nir

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Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications by Brown, Alex, Brill, Jake, Amini, Ryan, Nurmi, Connor, Li, Yingfu

“…Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are…”
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ChEA3: transcription factor enrichment analysis by orthogonal omics integration by Keenan, Alexandra B, Torre, Denis, Lachmann, Alexander, Leong, Ariel K, Wojciechowicz, Megan L, Utti, Vivian, Jagodnik, Kathleen M, Kropiwnicki, Eryk, Wang, Zichen, Ma’ayan, Avi

“…Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks…”
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Enrichr: a comprehensive gene set enrichment analysis web server 2016 update by Kuleshov, Maxim V., Jones, Matthew R., Rouillard, Andrew D., Fernandez, Nicolas F., Duan, Qiaonan, Wang, Zichen, Koplev, Simon, Jenkins, Sherry L., Jagodnik, Kathleen M., Lachmann, Alexander, McDermott, Michael G., Monteiro, Caroline D., Gundersen, Gregory W., Ma'ayan, Avi

“…Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools…”
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Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition by Greaney, Allison J, Starr, Tyler N, Gilchuk, Pavlo, Zost, Seth J, Binshtein, Elad, Loes, Andrea N, Hilton, Sarah K, Huddleston, John, Eguia, Rachel, Crawford, Katharine H D, Dingens, Adam S, Nargi, Rachel S, Sutton, Rachel E, Suryadevara, Naveenchandra, Rothlauf, Paul W, Liu, Zhuoming, Whelan, Sean P J, Carnahan, Robert H, Crowe, Jr, James E, Bloom, Jesse D

“…Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing…”
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Towards complete and error-free genome assemblies of all vertebrate species by McCarthy, Shane A., Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Chaisson, Mark, Gedman, Gregory L., Cantin, Lindsey J., Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C., Grutzner, Frank, Balakrishnan, Christopher N., Burt, Dave, George, Julia M., Biegler, Matthew T., Iorns, David, Digby, Andrew, Robertson, Bruce, Edwards, Taylor, Meyer, Axel, Kautt, Andreas F., Franchini, Paolo, Detrich, H. William, Naylor, Gavin J. P., Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T., Pesout, Trevor, Misuraca, Ann, Kingan, Sarah B., Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Lee, Joyce, Selvaraj, Siddarth, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Dagnew, Robel E., Guan, Dengfeng, London, Sarah E., Clayton, David F., Mello, Claudio V., Friedrich, Samantha R., Lovell, Peter V., Osipova, Ekaterina, Al-Ajli, Farooq O., Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S., Makova, Kateryna D., Medvedev, Paul, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Walenz, Brian P., Kwak, Woori, Clawson, Hiram, Diekhans, Mark, Paten, Benedict, Gilbert, M. Thomas P., Zhang, Guojie, Venkatesh, Byrappa, Murphy, Robert W., Koepfli, Klaus-Peter, Shapiro, Beth, Di Palma, Federica, Marques-Bonet, Tomas, Teeling, Emma C., Warnow, Tandy, Graves, Jennifer Marshall, Ryder, Oliver A., Haussler, David, Howe, Kerstin, Myers, Eugene W., Durbin, Richard, Phillippy, Adam M.

“…High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation…”
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Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform by Kircher, Martin, Sawyer, Susanna, Meyer, Matthias

“…Due to the increasing throughput of current DNA sequencing instruments, sample multiplexing is necessary for making economical use of available sequencing…”
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DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work by Weigand, Hannah, Beermann, Arne J., Čiampor, Fedor, Costa, Filipe O., Csabai, Zoltán, Duarte, Sofia, Geiger, Matthias F., Grabowski, Michał, Rimet, Frédéric, Rulik, Björn, Strand, Malin, Szucsich, Nikolaus, Weigand, Alexander M., Willassen, Endre, Wyler, Sofia A., Bouchez, Agnès, Borja, Angel, Čiamporová-Zaťovičová, Zuzana, Ferreira, Sónia, Dijkstra, Klaas-Douwe B., Eisendle, Ursula, Freyhof, Jörg, Gadawski, Piotr, Graf, Wolfram, Haegerbaeumer, Arne, van der Hoorn, Berry B., Japoshvili, Bella, Keresztes, Lujza, Keskin, Emre, Leese, Florian, Macher, Jan N., Mamos, Tomasz, Paz, Guy, Pešić, Vladimir, Pfannkuchen, Daniela Maric, Pfannkuchen, Martin Andreas, Price, Benjamin W., Rinkevich, Buki, Teixeira, Marcos A.L., Várbíró, Gábor, Ekrem, Torbjørn

“…Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known…”
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Small-molecule discovery through DNA-encoded libraries by Peterson, Alexander A, Liu, David R

“…The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly…”
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Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs by Rohland, Nadin, Mallick, Swapan, Mah, Matthew, Maier, Robert, Patterson, Nick, Reich, David

“…The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with…”
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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data by Czech, Lucas, Barbera, Pierre, Stamatakis, Alexandros

“…Abstract Summary We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses…”
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High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities by Hart, Traver, Chandrashekhar, Megha, Aregger, Michael, Steinhart, Zachary, Brown, Kevin R, MacLeod, Graham, Mis, Monika, Zimmermann, Michal, Fradet-Turcotte, Amelie, Sun, Song, Mero, Patricia, Dirks, Peter, Sidhu, Sachdev, Roth, Frederick P, Rissland, Olivia S, Durocher, Daniel, Angers, Stephane, Moffat, Jason

“…The ability to perturb genes in human cells is crucial for elucidating gene function and holds great potential for finding therapeutic targets for diseases…”
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Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning by Arbab, Mandana, Shen, Max W, Mok, Beverly, Wilson, Christopher, Matuszek, Żaneta, Cassa, Christopher A, Liu, David R

“…Although base editors are widely used to install targeted point mutations, the factors that determine base editing outcomes are not well understood. We…”
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High-throughput illumina strand-specific RNA sequencing library preparation by Zhong, Silin, Joung, Je-Gun, Zheng, Yi, Chen, Yun-ru, Liu, Bao, Shao, Ying, Xiang, Jenny Z, Fei, Zhangjun, Giovannoni, James J

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