GFF Utilities: GffRead and GffCompare

von Pertea, Geo, Pertea, Mihaela
Veröffentlicht in F1000Res (2020)

Detection of lineage-specific evolutionary changes among primate species

von Pertea, Mihaela, Pertea, Geo M, Salzberg, Steven L
Veröffentlicht 2011

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

von Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Veröffentlicht 2000

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

von Wang, Minghua, Guerrero, Felix D, Pertea, Geo, Nene, Vishvanath M
Veröffentlicht 2007

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

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

An optimized protocol for analysis of EST sequences

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

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

von Kim, Daehwan, Pertea, Geo, Trapnell, Cole, Pimentel, Harold, Kelley, Ryan, Salzberg, Steven L
Veröffentlicht 2013

Ballgown bridges the gap between transcriptome assembly and expression analysis

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

von 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.
Veröffentlicht in Antimicrob Agents Chemother (2018)

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

von 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
Veröffentlicht 2002

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

von 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.
Veröffentlicht in PLoS Genet (2020)

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

von 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.
Veröffentlicht in G3 (Bethesda) (2017)

The TIGR Maize Database

von 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.
Veröffentlicht 2006