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ArticlesPeer ReviewedFull Text
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy
Author / Creator:Jiménez-Sánchez, Alejandro ; Cybulska, Paulina ; Mager, Katherine LaVigne ; Koplev, Simon ; Cast, Oliver ; Couturier, Dominique-Laurent ; Memon, Danish ; Selenica, Pier ; Nikolovski, Ines ; Mazaheri, Yousef ; Bykov, Yonina ; Geyer, Felipe C. ; Macintyre, Geoff ; Gavarró, Lena Morrill ; Drews, Ruben M. ; Gill, Michael B. ; Papanastasiou, Anastasios D. ; Sosa, Ramon E. ; Soslow, Robert A. ; Walther, Tyler ; Shen, Ronglai ; Chi, Dennis S. ; Park, Kay J. ; Hollmann, Travis ; Reis-Filho, Jorge S. ; Markowetz, Florian ; Beltrao, Pedro ; Vargas, Hebert Alberto ; Zamarin, Dmitriy ; Brenton, James D. ; Snyder, Alexandra ; Weigelt, Britta ; Sala, Evis ; Miller, Martin L.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2020-06, Vol.52 (6), p.582-593
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ArticlesPeer ReviewedFull Text
ROC curves are a suitable and flexible tool for the analysis of gene expression profiles
Author / Creator:Parodi, S. ; Muselli, M. ; Fontana, V. ; Bonassi, S.
Publisher:Basel, Switzerland: Karger
Journal title:Cytogenetic and genome research, 2003-01, Vol.101 (1), p.90-91
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ArticlesPeer ReviewedFull Text
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Author / Creator:Luecken, Malte D. ; Sikkema, Lisa ; Waghray, Avinash ; Heimberg, Graham ; Kobayashi, Yoshihiko ; Vaishnav, Eeshit Dhaval ; Subramanian, Ayshwarya ; Smillie, Christopher ; Jagadeesh, Karthik A. ; Duong, Elizabeth Thu ; Torlai Triglia, Elena ; Ansari, Meshal ; Cai, Peiwen ; Lin, Brian ; Chen, Sijia ; Shu, Jian ; Haber, Adam L. ; Chung, Hattie ; Montoro, Daniel T. ; Adams, Taylor ; Aliee, Hananeh ; Andrusivova, Zaneta ; Angelidis, Ilias ; Ashenberg, Orr ; Bassler, Kevin ; Bécavin, Christophe ; Benhar, Inbal ; Bergenstråhle, Joseph ; Bergenstråhle, Ludvig ; Braun, Emelie ; Bui, Linh T. ; Chaffin, Mark ; Chichelnitskiy, Evgeny ; Chiou, Joshua ; Conlon, Thomas M. ; Cuoco, Michael S. ; Cuomo, Anna S. E. ; Deprez, Marie ; Duclos, Grant ; Fischer, David S. ; Ghazanfar, Shila ; Gillich, Astrid ; Giotti, Bruno ; Gould, Joshua ; Guo, Minzhe ; Gutierrez, Austin J. ; Habermann, Arun C. ; Harvey, Tyler ; He, Peng ; Hou, Xiaomeng ; Hu, Yan ; Jaiswal, Alok ; Ji, Lu ; Jiang, Peiyong ; Kapellos, Theodoros S. ; Kuo, Christin S. ; Leney-Greene, Michael A. ; Lim, Kyungtae ; Litviňuková, Monika ; Ludwig, Leif S. ; Lukassen, Soeren ; Luo, Wendy ; Maatz, Henrike ; Madissoon, Elo ; Mamanova, Lira ; Manakongtreecheep, Kasidet ; Leroy, Sylvie ; Mayr, Christoph H. ; McAdams, Alexi M. ; Nabhan, Ahmad N. ; Nyquist, Sarah K. ; Penland, Lolita ; Poirion, Olivier B. ; Poli, Sergio ; Qi, CanCan ; Queen, Rachel ; Reichart, Daniel ; Rosas, Ivan ; Schupp, Jonas C. ; Shea, Conor V. ; Shi, Xingyi ; Sinha, Rahul ; Slowikowski, Kamil ; Smith, Neal P. ; Sountoulidis, Alex ; Strunz, Maximilian ; Sullivan, Travis B. ; Sun, Dawei ; Talavera-López, Carlos ; Tan, Peng ; Tantivit, Jessica ; Travaglini, Kyle J. ; Tucker, Nathan R. ; Vernon, Katherine A. ; Wadsworth, Marc H. ; Waldman, Julia ; Wang, Xiuting ; Yan, Wenjun ; Zhao, William ; Ziegler, Carly G. K.
Publisher:New York: Nature Publishing Group US
Journal title:Nature medicine, 2021-03, Vol.27 (3), p.546-559
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ArticlesPeer ReviewedFull Text
Salmon provides fast and bias-aware quantification of transcript expression
Author / Creator:Patro, Rob ; Duggal, Geet ; Love, Michael I ; Irizarry, Rafael A ; Kingsford, Carl
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2017-04, Vol.14 (4), p.417-419
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ArticlesPeer ReviewedFull Text
Census and evaluation of p53 target genes
Author / Creator:Fischer, M
Publisher:London: Nature Publishing Group UK
Journal title:Oncogene, 2017-07, Vol.36 (28), p.3943-3956
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ArticlesPeer ReviewedFull Text
A review of methods and databases for metagenomic classification and assembly
Author / Creator:Breitwieser, Florian P ; Lu, Jennifer ; Salzberg, Steven L
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1125-1136
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ArticlesPeer ReviewedFull Text
Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing
Author / Creator:Deshmukh, Abhijeet P. ; Vasaikar, Suhas V. ; Tomczak, Katarzyna ; Tripathi, Shubham ; den Hollander, Petra ; Arslan, Emre ; Chakraborty, Priyanka ; Soundararajan, Rama ; Jolly, Mohit Kumar ; Rai, Kunal ; Levine, Herbert ; Mani, Sendurai A.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2021-05, Vol.118 (19), p.1-10
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ArticlesPeer ReviewedFull Text
Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
Author / Creator:Finucane, Hilary K. ; Reshef, Yakir A. ; Anttila, Verneri ; Slowikowski, Kamil ; Gusev, Alexander ; Byrnes, Andrea ; Gazal, Steven ; Loh, Po-Ru ; Lareau, Caleb ; Shoresh, Noam ; Genovese, Giulio ; Saunders, Arpiar ; Macosko, Evan ; Pollack, Samuela ; Perry, John R. B. ; Buenrostro, Jason D. ; Bernstein, Bradley E. ; Raychaudhuri, Soumya ; McCarroll, Steven ; Neale, Benjamin M. ; Price, Alkes L.
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2018-04, Vol.50 (4), p.621-629
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ArticlesPeer ReviewedFull Text
Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions
Author / Creator:Urbut, Sarah M. ; Wang, Gao ; Carbonetto, Peter ; Stephens, Matthew
Publisher:New York: Nature Publishing Group US
Journal title:Nature genetics, 2019-01, Vol.51 (1), p.187-195
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ArticlesPeer ReviewedFull Text
Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data
Author / Creator:Ching, Travers ; Zhu, Xun ; Garmire, Lana X.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2018-04, Vol.14 (4), p.e1006076-e1006076
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ArticlesPeer ReviewedFull Text
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions
Author / Creator:Evans, Ciaran ; Hardin, Johanna ; Stoebel, Daniel M
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2018-09, Vol.19 (5), p.776-792
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ArticlesPeer ReviewedFull Text
Microarray is an efficient tool for circRNA profiling
Author / Creator:Li, Shasha ; Teng, Shuaishuai ; Xu, Junquan ; Su, Guannan ; Zhang, Yu ; Zhao, Jianqing ; Zhang, Suwei ; Wang, Haiyan ; Qin, Wenyan ; Lu, Zhi John ; Guo, Yong ; Zhu, Qianyong ; Wang, Dong
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1420-1433
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ArticlesPeer ReviewedFull Text
Comparison of co-expression measures: mutual information, correlation, and model based indices
Author / Creator:Song, Lin ; Langfelder, Peter ; Horvath, Steve
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2012-12, Vol.13 (1), p.328-328, Article 328
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ArticlesPeer ReviewedFull Text
Computational methods for transcriptome annotation and quantification using RNA-seq
Author / Creator:Garber, Manuel ; Grabherr, Manfred G ; Guttman, Mitchell ; Trapnell, Cole
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2011-06, Vol.8 (6), p.469-477
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ArticlesPeer ReviewedFull Text
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses
Author / Creator:Stegle, Oliver ; Parts, Leopold ; Piipari, Matias ; Winn, John ; Durbin, Richard
Publisher:London: Nature Publishing Group UK
Journal title:Nature protocols, 2012-03, Vol.7 (3), p.500-507
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ArticlesPeer ReviewedFull Text
Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data
Author / Creator:Yip, Shun H ; Sham, Pak Chung ; Wang, Junwen
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1583-1589
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ArticlesPeer ReviewedFull Text
DNA methylation profiling in the clinic: applications and challenges
Author / Creator:Heyn, Holger ; Esteller, Manel
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2012-10, Vol.13 (10), p.679-692
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Quantifying the impact of public omics data
Author / Creator:Perez-Riverol, Yasset ; Zorin, Andrey ; Dass, Gaurhari ; Vu, Manh-Tu ; Xu, Pan ; Glont, Mihai ; Vizcaíno, Juan Antonio ; Jarnuczak, Andrew F. ; Petryszak, Robert ; Ping, Peipei ; Hermjakob, Henning
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-08, Vol.10 (1), p.3512-10, Article 3512
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Computational challenges and opportunities in spatially resolved transcriptomic data analysis
Author / Creator:Atta, Lyla ; Fan, Jean
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2021-09, Vol.12 (1), p.5283-5283, Article 5283
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Reuse of public genome-wide gene expression data
Author / Creator:Rung, Johan ; Brazma, Alvis
Publisher:London: Nature Publishing Group UK
Journal title:Nature reviews. Genetics, 2013-02, Vol.14 (2), p.89-99
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Showing 1 to 20 of 490 results

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Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

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ROC curves are a suitable and flexible tool for the analysis of gene expression profiles

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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

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Salmon provides fast and bias-aware quantification of transcript expression

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Census and evaluation of p53 target genes

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A review of methods and databases for metagenomic classification and assembly

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Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing

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Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

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Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions

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Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data

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Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions

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Microarray is an efficient tool for circRNA profiling

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Comparison of co-expression measures: mutual information, correlation, and model based indices

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Computational methods for transcriptome annotation and quantification using RNA-seq

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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

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Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

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DNA methylation profiling in the clinic: applications and challenges

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Quantifying the impact of public omics data

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Computational challenges and opportunities in spatially resolved transcriptomic data analysis

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Reuse of public genome-wide gene expression data

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