False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors

od Saha, Ashis, Battle, Alexis
Wydane w F1000Res (2019)

Where are the disease-associated eQTLs?

od Umans, Benjamin D., Battle, Alexis, Gilad, Yoav
Wydane w Trends Genet (2020)

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

od Pierson, Emma, Koller, Daphne, Battle, Alexis, Mostafavi, Sara
Wydane w PLoS Comput Biol (2015)

Automated identification of pathways from quantitative genetic interaction data

od Battle, Alexis, Jonikas, Martin C, Walter, Peter, Weissman, Jonathan S, Koller, Daphne
Wydane 2010

Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration

od Parsana, Princy, Amend, Sarah R., Hernandez, James, Pienta, Kenneth J., Battle, Alexis
Wydane w BMC Cancer (2017)

High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing

od Cho, Hyunghoon, Davis, Joe, Li, Xin, Smith, Kevin S., Battle, Alexis, Montgomery, Stephen B.
Wydane 2014

Addressing confounding artifacts in reconstruction of gene co-expression networks

od Parsana, Princy, Ruberman, Claire, Jaffe, Andrew E., Schatz, Michael C., Battle, Alexis, Leek, Jeffrey T.
Wydane w Genome Biol (2019)

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

od Mostafavi, Sara, Battle, Alexis, Zhu, Xiaowei, Urban, Alexander E., Levinson, Douglas, Montgomery, Stephen B., Koller, Daphne
Wydane 2013

Genetic variation in MHC proteins is associated with T cell receptor expression biases

od Sharon, Eilon, Sibener, Leah V., Battle, Alexis, Fraser, Hunter B., Garcia, K. Christopher, Pritchard, Jonathan K.
Wydane w Nat Genet (2016)

Impact of Regulatory Variation from RNA to Protein

od Battle, Alexis, Khan, Zia, Wang, Sidney H., Mitrano, Amy, Ford, Michael J., Pritchard, Jonathan K., Gilad, Yoav
Wydane w Science (2014)

A Linear and Non-Linear Mendelian Randomization Analysis of the Association Between Diastolic Blood Pressure and Cardiovascular Events: The J Curve Revisited

od Arvanitis, Marios, Qi, Guanghao, Bhatt, Deepak L., Post, Wendy S., Chatterjee, Nilanjan, Battle, Alexis, McEvoy, John W.
Wydane w Circulation (2020)

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants

od Davis, Joe R., Fresard, Laure, Knowles, David A., Pala, Mauro, Bustamante, Carlos D., Battle, Alexis, Montgomery, Stephen B.
Wydane w Am J Hum Genet (2016)

GBAT: a gene-based association test for robust detection of trans-gene regulation

od Liu, Xuanyao, Mefford, Joel A., Dahl, Andrew, He, Yuan, Subramaniam, Meena, Battle, Alexis, Price, Alkes L., Zaitlen, Noah
Wydane w Genome Biol (2020)

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

od Saha, Ashis, Kim, Yungil, Gewirtz, Ariel D.H., Jo, Brian, Gao, Chuan, McDowell, Ian C., Engelhardt, Barbara E., Battle, Alexis
Wydane w Genome Res (2017)

Transcriptome Analysis Reveals Differential Splicing Events in IPF Lung Tissue

od Nance, Tracy, Smith, Kevin S., Anaya, Vanessa, Richardson, Rhea, Ho, Lawrence, Pala, Mauro, Mostafavi, Sara, Battle, Alexis, Feghali-Bostwick, Carol, Rosen, Glenn, Montgomery, Stephen B.
Wydane 2014

Transcriptome Sequencing of a Large Human Family Identifies the Impact of Rare Noncoding Variants

od Li, Xin, Battle, Alexis, Karczewski, Konrad J., Zappala, Zach, Knowles, David A., Smith, Kevin S., Kukurba, Kim R., Wu, Eric, Simon, Noah, Montgomery, Stephen B.
Wydane 2014

Imputed gene associations identify replicable trans‐acting genes enriched in transcription pathways and complex traits

od Wheeler, Heather E., Ploch, Sally, Barbeira, Alvaro N., Bonazzola, Rodrigo, Andaleon, Angela, Fotuhi Siahpirani, Alireza, Saha, Ashis, Battle, Alexis, Roy, Sushmita, Im, Hae Kyung
Wydane w Genet Epidemiol (2019)

EIF3G is associated with narcolepsy across ethnicities

od Holm, Anja, Lin, Ling, Faraco, Juliette, Mostafavi, Sara, Battle, Alexis, Zhu, Xiaowei, Levinson, Douglas F, Han, Fang, Gammeltoft, Steen, Jennum, Poul, Mignot, Emmanuel, Kornum, Birgitte R
Wydane w Eur J Hum Genet (2015)

Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure

od Arvanitis, Marios, Tampakakis, Emmanouil, Zhang, Yanxiao, Wang, Wei, Auton, Adam, Dutta, Diptavo, Glavaris, Stephanie, Keramati, Ali, Chatterjee, Nilanjan, Chi, Neil C., Ren, Bing, Post, Wendy S., Battle, Alexis
Wydane w Nat Commun (2020)

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression

od He, Yuan, Chhetri, Surya B., Arvanitis, Marios, Srinivasan, Kaushik, Aguet, François, Ardlie, Kristin G., Barbeira, Alvaro N., Bonazzola, Rodrigo, Im, Hae Kyung, Brown, Christopher D., Battle, Alexis
Wydane w Genome Biol (2020)