Publications by authors named "Geo Pertea"

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Transcriptomic Analysis of the Human Habenula in Schizophrenia.
Ege A Yalcinbas, Bukola Ajanaku, Erik D Nelson, Renee Garcia-Flores, Nicholas J Eagles, Geo Pertea

Am J Psychiatry· November 2025

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: Novel Genes in the locus.
Svitlana V Bach, Giovanna Punzi, Nuri E Smith, Sreya Mukherjee, Joo Heon Shin, Geo Pertea

medRxiv· July 2025

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StringTie3 Improves Total RNA-seq Assembly by Resolving Nascent and Mature Transcripts.
Ida Shinder, Geo Pertea, Richard Hu, Zoe Rudnick, Mihaela Pertea

bioRxiv· May 2025

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Molecular impact of nicotine and smoking exposure on the developing and adult mouse brain.
Daianna Gonzalez-Padilla, Nicholas J Eagles, Marisol Cano, Geo Pertea, Andrew E Jaffe

bioRxiv· November 2024

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Transcriptomic analysis of the human habenula in schizophrenia.
Ege A Yalcinbas, Bukola Ajanaku, Erik D Nelson, Renee Garcia-Flores, Nicholas J Eagles, Geo Pertea

bioRxiv· July 2024

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Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry.
Kynon J M Benjamin, Qiang Chen, Nicholas J Eagles, Louise A Huuki-Myers, Leonardo Collado-Torres, Geo Pertea

Nat Neurosci· June 2024

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Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus.
Kynon J M Benjamin, Ria Arora, Arthur S Feltrin, Geo Pertea, Hunter H Giles

Nat Commun· May 2024

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Systems biology dissection of PTSD and MDD across brain regions, cell types, and blood.
Nikolaos P Daskalakis, Artemis Iatrou, Chris Chatzinakos, Aarti Jajoo, Clara Snijders, Geo Pertea

Science· May 2024

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Genetic and environmental contributions to ancestry differences in gene expression in the human brain.
Kynon J M Benjamin, Qiang Chen, Nicholas J Eagles, Louise A Huuki-Myers, Leonardo Collado-Torres, Geo Pertea

bioRxiv· October 2023

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Improved transcriptome assembly using a hybrid of long and short reads with StringTie.
Alaina Shumate, Brandon Wong, Geo Pertea, Mihaela Pertea

PLoS Comput Biol· June 2022

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TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets.
Ales Varabyou, Geo Pertea, Christopher Pockrandt, Mihaela Pertea

Bioinformatics· October 2021

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GFF Utilities: GffRead and GffCompare.
Geo Pertea, Mihaela Pertea

F1000Res· September 2020

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Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing.
Andrew C Read, Matthew J Moscou, Aleksey V Zimin, Geo Pertea, Rachel S Meyer

PLoS Genet· January 2020

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Transcriptome assembly from long-read RNA-seq alignments with StringTie2.
Sam Kovaka, Aleksey V Zimin, Geo M Pertea, Roham Razaghi, Steven L Salzberg, Mihaela Pertea

Genome Biol· December 2019

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Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates.
Pranita D Tamma, Yunfan Fan, Yehudit Bergman, Geo Pertea, Abida Q Kazmi

Antimicrob Agents Chemother· January 2019

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CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise.
Mihaela Pertea, Alaina Shumate, Geo Pertea, Ales Varabyou, Florian P Breitwieser

Genome Biol· November 2018

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First Draft Genome Sequence of the Pathogenic Fungus (Formerly ).
Ruibang Luo, Aleksey Zimin, Rachael Workman, Yunfan Fan, Geo Pertea

G3 (Bethesda)· November 2017

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Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
Ming-Cheng Luo, Yong Q Gu, Daniela Puiu, Hao Wang, Sven O Twardziok, Geo Pertea

Nature· November 2017

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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae.
David B Neale, Patrick E McGuire, Nicholas C Wheeler, Kristian A Stevens, Marc W Crepeau, Geo M Pertea

G3 (Bethesda)· September 2017

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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.
Mihaela Pertea, Daehwan Kim, Geo M Pertea, Jeffrey T Leek, Steven L Salzberg

Nat Protoc· September 2016

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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell

Nat Biotechnol· March 2015

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Ballgown bridges the gap between transcriptome assembly and expression analysis.
Alyssa C Frazee, Geo Pertea, Andrew E Jaffe, Ben Langmead, Steven L Salzberg

Nat Biotechnol· March 2015

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley

Genome Biol· April 2013

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Cole Trapnell, Adam Roberts, Loyal Goff, Geo Pertea, Daehwan Kim

Nat Protoc· March 2012

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