GFF Utilities: GffRead and GffCompare

by Pertea, Geo, Pertea, Mihaela
Published in F1000Res (2020)

Detection of lineage-specific evolutionary changes among primate species

by Pertea, Mihaela, Pertea, Geo M, Salzberg, Steven L
Published 2011

The TIGR Gene Indices: reconstruction and representation of expressed gene sequences

by Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Published 2000

Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus

by Wang, Minghua, Guerrero, Felix D, Pertea, Geo, Nene, Vishvanath M
Published 2007

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown

by Pertea, Mihaela, Kim, Daehwan, Pertea, Geo, Leek, Jeffrey T., Salzberg, Steven L.
Published in Nat Protoc (2016)

An optimized protocol for analysis of EST sequences

by Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L., Quackenbush, John
Published 2000

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

by Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L
Published 2013

Ballgown bridges the gap between transcriptome assembly and expression analysis

by Frazee, Alyssa C, Pertea, Geo, Jaffe, Andrew E, Langmead, Ben, Salzberg, Steven L, Leek, Jeffrey T
Published in Nat Biotechnol (2015)

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

by Kovaka, Sam, Zimin, Aleksey V., Pertea, Geo M., Razaghi, Roham, Salzberg, Steven L., Pertea, Mihaela
Published in Genome Biol (2019)

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

by Pertea, Mihaela, Pertea, Geo M, Antonescu, Corina M, Chang, Tsung-Cheng, Mendell, Joshua T, Salzberg, Steven L
Published in Nat Biotechnol (2015)

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

by Quackenbush, John, Cho, Jennifer, Lee, Daniel, Liang, Feng, Holt, Ingeborg, Karamycheva, Svetlana, Parvizi, Babak, Pertea, Geo, Sultana, Razvan, White, Joseph
Published 2001

RESOURCERER: a database for annotating and linking microarray resources within and across species

by Tsai, Jennifer, Sultana, Razvan, Lee, Yudan, Pertea, Geo, Karamycheva, Svetlana, Antonescu, Valentin, Cho, Jennifer, Parvizi, Babak, Cheung, Foo, Quackenbush, John
Published 2001

CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise

by Pertea, Mihaela, Shumate, Alaina, Pertea, Geo, Varabyou, Ales, Breitwieser, Florian P., Chang, Yu-Chi, Madugundu, Anil K., Pandey, Akhilesh, Salzberg, Steven L.
Published in Genome Biol (2018)

Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

by Trapnell, Cole, Williams, Brian A., Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J., Salzberg, Steven L., Wold, Barbara J., Pachter, Lior
Published 2010

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

by Trapnell, Cole, Roberts, Adam, Goff, Loyal, Pertea, Geo, Kim, Daehwan, Kelley, David R, Pimentel, Harold, Salzberg, Steven L, Rinn, John L, Pachter, Lior
Published 2012

Applying Rapid Whole-Genome Sequencing To Predict Phenotypic Antimicrobial Susceptibility Testing Results among Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates

by Tamma, Pranita D., Fan, Yunfan, Bergman, Yehudit, Pertea, Geo, Kazmi, Abida Q., Lewis, Shawna, Carroll, Karen C., Schatz, Michael C., Timp, Winston, Simner, Patricia J.
Published in Antimicrob Agents Chemother (2018)

Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)

by Lee, Yuandan, Sultana, Razvan, Pertea, Geo, Cho, Jennifer, Karamycheva, Svetlana, Tsai, Jennifer, Parvizi, Babak, Cheung, Foo, Antonescu, Valentin, White, Joseph, Holt, Ingeborg, Liang, Feng, Quackenbush, John
Published 2002

Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

by Read, Andrew C., Moscou, Matthew J., Zimin, Aleksey V., Pertea, Geo, Meyer, Rachel S., Purugganan, Michael D., Leach, Jan E., Triplett, Lindsay R., Salzberg, Steven L., Bogdanove, Adam J.
Published in PLoS Genet (2020)

First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans)

by Luo, Ruibang, Zimin, Aleksey, Workman, Rachael, Fan, Yunfan, Pertea, Geo, Grossman, Nina, Wear, Maggie P., Jia, Bei, Miller, Heather, Casadevall, Arturo, Timp, Winston, Zhang, Sean X., Salzberg, Steven L.
Published in G3 (Bethesda) (2017)

The TIGR Maize Database

by Chan, Agnes P., Pertea, Geo, Cheung, Foo, Lee, Dan, Zheng, Li, Whitelaw, Cathy, Pontaroli, Ana C., SanMiguel, Phillip, Yuan, Yinan, Bennetzen, Jeffrey, Barbazuk, William Brad, Quackenbush, John, Rabinowicz, Pablo D.
Published 2006