GFF Utilities: GffRead and GffCompare

Autor Pertea, Geo, Pertea, Mihaela
Vydáno v F1000Res (2020)

Detection of lineage-specific evolutionary changes among primate species

Autor Pertea, Mihaela, Pertea, Geo M, Salzberg, Steven L
Vydáno 2011

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

Autor Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Vydáno 2000

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

Autor Wang, Minghua, Guerrero, Felix D, Pertea, Geo, Nene, Vishvanath M
Vydáno 2007

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

Autor Pertea, Mihaela, Kim, Daehwan, Pertea, Geo, Leek, Jeffrey T., Salzberg, Steven L.
Vydáno v Nat Protoc (2016)

An optimized protocol for analysis of EST sequences

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

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

Autor Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L
Vydáno 2013

Ballgown bridges the gap between transcriptome assembly and expression analysis

Autor Frazee, Alyssa C, Pertea, Geo, Jaffe, Andrew E, Langmead, Ben, Salzberg, Steven L, Leek, Jeffrey T
Vydáno v Nat Biotechnol (2015)

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

Autor Kovaka, Sam, Zimin, Aleksey V., Pertea, Geo M., Razaghi, Roham, Salzberg, Steven L., Pertea, Mihaela
Vydáno v Genome Biol (2019)

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

Autor Pertea, Mihaela, Pertea, Geo M, Antonescu, Corina M, Chang, Tsung-Cheng, Mendell, Joshua T, Salzberg, Steven L
Vydáno v Nat Biotechnol (2015)

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

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

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

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

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

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

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

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

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

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

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

Autor 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.
Vydáno v Antimicrob Agents Chemother (2018)

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

Autor 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
Vydáno 2002

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

Autor 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.
Vydáno v PLoS Genet (2020)

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

Autor 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.
Vydáno v G3 (Bethesda) (2017)

The TIGR Maize Database

Autor 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.
Vydáno 2006