A new method for inferring timetrees from temporally sampled molecular sequences von Miura, Sayaka, Tamura, Koichiro, Tao, Qiqing, Huuki, Louise A., Pond, Sergei L. Kosakovsky, Priest, Jessica, Deng, Jiamin, Kumar, Sudhir

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Computational enhancement of single-cell sequences for inferring tumor evolution von Miura, Sayaka, Huuki, Louise A, Buturla, Tiffany, Vu, Tracy, Gomez, Karen, Kumar, Sudhir

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Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain von Tran, Matthew N., Maynard, Kristen R., Spangler, Abby, Huuki, Louise A., Montgomery, Kelsey D., Sadashivaiah, Vijay, Tippani, Madhavi, Barry, Brianna K., Hancock, Dana B., Hicks, Stephanie C., Kleinman, Joel E., Hyde, Thomas M., Collado-Torres, Leonardo, Jaffe, Andrew E., Martinowich, Keri

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Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics von Tao, Qiqing, Barba-Montoya, Jose, Huuki, Louise A, Durnan, Mary Kathleen, Kumar, Sudhir

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Predicting clone genotypes from tumor bulk sequencing of multiple samples von Miura, Sayaka, Gomez, Karen, Murillo, Oscar, Huuki, Louise A, Vu, Tracy, Buturla, Tiffany, Kumar, Sudhir

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Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets von Maden, Sean K, Kwon, Sang Ho, Huuki-Myers, Louise A, Collado-Torres, Leonardo, Hicks, Stephanie C, Maynard, Kristen R

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Discovering research articles containing evolutionary timetrees by machine learning von Stanojevic, Marija, Andjelkovic, Jovan, Kasprowicz, Adrienne, Huuki, Louise A, Chao, Jennifer, Hedges, S Blair, Kumar, Sudhir, Obradovic, Zoran

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Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue von Huuki-Myers, Louise A, Montgomery, Kelsey D, Kwon, Sang Ho, Page, Stephanie C, Hicks, Stephanie C, Maynard, Kristen R, Collado-Torres, Leonardo

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Somatic evolutionary timings of driver mutations von Gomez, Karen, Miura, Sayaka, Huuki, Louise A, Spell, Brianna S, Townsend, Jeffrey P, Kumar, Sudhir

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Genetics and Brain Transcriptomics of Completed Suicide von Punzi, Giovanna, Ursini, Gianluca, Chen, Qiang, Radulescu, Eugenia, Tao, Ran, Huuki, Louise A, Di Carlo, Pasquale, Collado-Torres, Leonardo, Shin, Joo Heon, Catanesi, Roberto, Jaffe, Andrew E, Hyde, Thomas M, Kleinman, Joel E, Mackay, Trudy F C, Weinberger, Daniel R

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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses von Eagles, Nicholas J., Burke, Emily E., Leonard, Jacob, Barry, Brianna K., Stolz, Joshua M., Huuki, Louise, Phan, BaDoi N., Serrato, Violeta Larios, Gutierrez-Millan, Everardo, Aguilar-Ordonez, Israel, Jaffe, Andrew E., Collado-Torres, Leonardo

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Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses von Eagles, Nicholas J, Burke, Emily E, Leonard, Jacob, Barry, Brianna K, Stolz, Joshua M, Huuki, Louise, Phan, BaDoi N, Serrato, Violeta Larios, Gutiérrez-Millán, Everardo, Aguilar-Ordoéez, Israel, Jaffe, Andrew E, Collado-Torres, Leonardo

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Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and new risk genes von Benjamin, Kynon J. M., Chen, Qiang, Jaffe, Andrew E., Stolz, Joshua M., Collado-Torres, Leonardo, Huuki-Myers, Louise A., Burke, Emily E., Arora, Ria, Feltrin, Arthur S., Barbosa, André Rocha, Radulescu, Eugenia, Pergola, Giulio, Shin, Joo Heon, Ulrich, William S., Deep-Soboslay, Amy, Tao, Ran, Hyde, Thomas M., Kleinman, Joel E., Erwin, Jennifer A., Weinberger, Daniel R., Paquola, Apuã C. M.

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Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry von Benjamin, Kynon J. M., Chen, Qiang, Eagles, Nicholas J., Huuki-Myers, Louise A., Collado-Torres, Leonardo, Stolz, Joshua M., Pertea, Geo, Shin, Joo Heon, Paquola, Apuã C. M., Hyde, Thomas M., Kleinman, Joel E., Jaffe, Andrew E., Han, Shizhong, Weinberger, Daniel R.

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A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex von Huuki-Myers, Louise A, Spangler, Abby, Eagles, Nicholas J, Montgomery, Kelsey D, Kwon, Sang Ho, Guo, Boyi, Grant-Peters, Melissa, Divecha, Heena R, Tippani, Madhavi, Sriworarat, Chaichontat, Nguyen, Annie B, Ravichandran, Prashanthi, Tran, Matthew N, Seyedian, Arta, Hyde, Thomas M, Kleinman, Joel E, Battle, Alexis, Page, Stephanie C, Ryten, Mina, Hicks, Stephanie C, Martinowich, Keri, Collado-Torres, Leonardo, Maynard, Kristen R

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escheR: unified multi-dimensional visualizations with Gestalt principles von Guo, Boyi, Huuki-Myers, Louise A, Grant-Peters, Melissa, Collado-Torres, Leonardo, Hicks, Stephanie C

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RNA Sequencing of the Limbic System in Major Depressive Disorder von Goes, Fernando, Zandi, Peter, Torres, Leonardo Collado, Weinberger, Daniel, Kleinman, Joel, Huuki, Louise, Hyde, Thomas

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SINGLE-NUCLEUS RNA-SEQUENCING OF THE SUBGENUAL ANTERIOR CINGULATE CORTEX IN MAJOR DEPRESSIVE DISORDER von Goes, Fernando, Braun, Patricia, Collardo-Torres, Leo, Huuki, Louise, Kleinman, Joel, Tao, Ran, Shin, Joo Heon, Hyde, Thomas

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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses (vol 22, 224, 2021) von Eagles, Nicholas J., Burke, Emily E., Leonard, Jacob, Barry, Brianna K., Stolz, Joshua M., Huuki, Louise, Phan, BaDoi N., Serrato, Violeta Larios, Gutierrez-Millan, Everardo, Aguilar-Ordonez, Israel, Jaffe, Andrew E., Collado-Torres, Leonardo

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Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood von Daskalakis, Nikolaos P, Iatrou, Artemis, Chatzinakos, Chris, Jajoo, Aarti, Snijders, Clara, Wylie, Dennis, DiPietro, Christopher P, Tsatsani, Ioulia, Chen, Chia-Yen, Pernia, Cameron D, Soliva-Estruch, Marina, Arasappan, Dhivya, Bharadwaj, Rahul A, Collado-Torres, Leonardo, Wuchty, Stefan, Alvarez, Victor E, Dammer, Eric B, Deep-Soboslay, Amy, Duong, Duc M, Eagles, Nick, Huber, Bertrand R, Huuki, Louise, Holstein, Vincent L, Logue, Mark W, Lugenbühl, Justina F, Maihofer, Adam X, Miller, Mark W, Nievergelt, Caroline M, Pertea, Geo, Ross, Deanna, Sendi, Mohammad S E, Sun, Benjamin B, Tao, Ran, Tooke, James, Wolf, Erika J, Zeier, Zane, Berretta, Sabina, Champagne, Frances A, Hyde, Thomas, Seyfried, Nicholas T, Shin, Joo Heon, Weinberger, Daniel R, Nemeroff, Charles B, Kleinman, Joel E, Ressler, Kerry J

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