for_dryad

Additional file 10: of Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Amanda Grusz (3460853)
Carl Rothfels (3251628)
Eric Schuettpelz (3194496)

August 2016

Orthogroup data file. Zipped folder containing fasta-formatted reads identified by ProteinOrtho, use...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project

Itoh, T.
Tanaka, T.
Barrero, R. A.
Yamasaki, C.
Fujii, Y.
Hilton, P. B.
Antonio, B. A.
Aono, H.
Apweiler, R.
Bruskiewich, R.
Bureau, T.
Burr, F.
De Oliveira, A. C.
Fuks, G.
Habara, T.
Haberer, G.
Han, B.
Harada, E.
Hiraki, A. T.
Hirochika, H.
Hoen, D.
Hokari, H.
Hosokawa, S.
Hsing, Y. I.
Ikawa, H.
Ikeo, K.
Imanishi, T.
Ito, Y.
Jaiswal, P.
Kanno, M.
Kawahara, Y.
Kawamura, T.
Kawashima, H.
Khurana, J. P.
Kikuchi, S.
Komatsu, S.
Koyanagi, K. O.
Kubooka, H.
Lieberherr, D.
Lin, Y. C.
Lonsdale, D.
Matsumoto, T.
Matsuya, A.
McCombie, W. R.
Messing, J.
Miyao, A.
Mulder, N.
Nagamura, Y.
Nam, J.
Namiki, N.
Numa, H.
Nurimoto, S.
O'Donovan, C.
Ohyanagi, H.
Okido, T.
Oota, S.
Osato, N.
Palmer, L. E.
Quetier, F.
Raghuvanshi, S.
Saichi, N.
Sakai, H.
Sakai, Y.
Sakata, K.
Sakurai, T.
Sato, F.
Sato, Y.
Schoof, H.
Seki, M.
Shibata, M.
Shimizu, Y.
Shinozaki, K.
Shinso, Y.
Singh, N. K.
Smith-White, B.
Takeda, J. I.
Tanino, M.
Tatusova, T.
Thongjuea, S.
Todokoro, F.
Tsugane, M.
Tyagi, A. K.
Vanavichit, A.
Wang, A.
Wing, R. A.
Yamaguchi, K.
Yamamoto, M.
Yamamoto, N.
Yu, Y.
Zhang, H.
Zhao, Q.
Higo, K.
Burr, B.
Gojobori, T.
Sasaki, T.

January 2007

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar...

Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes

Gong, W
Shen, YP
Ma, LG
Pan, Y
Du, YL
Wang, DH
Yang, JY
Hu, LD
Liu, XF
Dong, CX
Ma, L
Chen, YH
Yang, XY
Gao, Y
Zhu, DM
Tan, XL
Mu, JY
Zhang, DB
Liu, YL
Dinesh-Kumar, SP
Li, Y
Wang, XP
Gu, HY
Qu, LJ
Bai, SN
Lu, YT
Li, JY
Zhao, JD
Zuo, JR
Huang, H
Deng, XW
Zhu, YX

January 2004

Here, we report our effort in generating an ORFeome collection for the Arabidopsis transcription fac...

for_dryad

Polly Y. Hsu (3251619)
Lorenzo Calviello (3251622)
Hsin-Yen L. Wu (3251631)
Fay-Wei Li (199955)
Uwe Ohler (20245)
Carl Rothfels (3251628)
Philip Benfey (188536)

October 2016

Using ribosome profiling, we identified novel translated ORFs in annotated ncRNAs and pseudogenes i...

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, Polly Yingshan
Calviello, Lorenzo
Wu, Hsin-Yen Larry
Li, Fay-Wei
Rothfels, Carl J
Ohler, Uwe
Benfey, Philip N

November 2016

Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Be...

Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, Polly Y.
Calviello, Lorenzo
Wu, Hsin-Yen Larry
Li, Fay-Wei
Rothfels, Carl J.
Ohler, Uwe
Benfey, Philip N.

Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Be...

Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

Lewinski, Martin
Hallmann, Armin
Staiger, Dorothee

January 2016

Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA...

Translation and evolutionary evidence indicates that unannotated ORF YFR035W-A is likely a conserved gene.

Aaron Wacholder (8460039)
Anne-Ruxandra Carvunis (149561)

December 2023

(A) ribo-seq reads on unannotated ORF YFR035W-A (top) and annotated ORF YFR035C (bottom). The bounds...

Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana

van der Horst, Sjors
Snel, Berend
Hanson, Johannes
Smeekens, Sjef
Sub Molecular Plant Physiology
Sub Bioinformatics
Theoretical Biology and Bioinformatics
Molecular Plant Physiology

January 2019

Eukaryotic mRNAs contain a 5' leader preceding the main open reading frame (mORF) and, depending on ...

Phylogenomics of plant genomes : A methodology for genome-wide searches for orthologs in plants.

Conte, Matthieu
Gaillard, Sylvain
Droc, Gaëtan
Perin, Christophe

January 2008

Background: Gene ortholog identification is now a major objective for mining the increasing amount o...

FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing

Fabio Fassetti
Claudia Giallombardo
Ofelia Leone
Luigi Palopoli
Simona E. Rombo
Adolfo Saiardi

April 2019

Abstract Background RNA editing is an important mechanism for gene expression in plants organelles. ...

Analysis of the Arabidopsis Cytosolic Ribosome Proteome Provides Detailed Insights into Its Components and Their Post-translational Modification

Carroll, Adam
Heazlewood, Joshua
Ito, Jun
Millar, AH

December 2015

Finding gene-specific peptides by mass spectrometry analysis to pinpoint gene loci responsible for p...

Improved sequence-based orthologs identification using genomic context information and their impact on pathway analysis in plants

Tulpan, Dan
Lger, Serge
Cuperlovic-Culf, Miroslava
Pan, Youlian

January 2013

With the advent of sequencing techniques, a deluge of plant genome projects have emerged, all prompt...

The emerging world of small ORFs

Hellens, Roger
Brown, Christopher
Chisnall, Matthew
Waterhouse, Peter
Macknight, Richard

January 2016

Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found ...

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.

Song, Dandan
Yang, Yang
Yu, Bin
Zheng, Binglian
Deng, Zhidong
Lu, Bao-Liang
Chen, Xuemei
Jiang, Tao

January 2009

BackgroundNon-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules t...

Additional file 10: of Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Amanda Grusz (3460853)
Carl Rothfels (3251628)
Eric Schuettpelz (3194496)

August 2016

Orthogroup data file. Zipped folder containing fasta-formatted reads identified by ProteinOrtho, use...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project

Itoh, T.
Tanaka, T.
Barrero, R. A.
Yamasaki, C.
Fujii, Y.
Hilton, P. B.
Antonio, B. A.
Aono, H.
Apweiler, R.
Bruskiewich, R.
Bureau, T.
Burr, F.
De Oliveira, A. C.
Fuks, G.
Habara, T.
Haberer, G.
Han, B.
Harada, E.
Hiraki, A. T.
Hirochika, H.
Hoen, D.
Hokari, H.
Hosokawa, S.
Hsing, Y. I.
Ikawa, H.
Ikeo, K.
Imanishi, T.
Ito, Y.
Jaiswal, P.
Kanno, M.
Kawahara, Y.
Kawamura, T.
Kawashima, H.
Khurana, J. P.
Kikuchi, S.
Komatsu, S.
Koyanagi, K. O.
Kubooka, H.
Lieberherr, D.
Lin, Y. C.
Lonsdale, D.
Matsumoto, T.
Matsuya, A.
McCombie, W. R.
Messing, J.
Miyao, A.
Mulder, N.
Nagamura, Y.
Nam, J.
Namiki, N.
Numa, H.
Nurimoto, S.
O'Donovan, C.
Ohyanagi, H.
Okido, T.
Oota, S.
Osato, N.
Palmer, L. E.
Quetier, F.
Raghuvanshi, S.
Saichi, N.
Sakai, H.
Sakai, Y.
Sakata, K.
Sakurai, T.
Sato, F.
Sato, Y.
Schoof, H.
Seki, M.
Shibata, M.
Shimizu, Y.
Shinozaki, K.
Shinso, Y.
Singh, N. K.
Smith-White, B.
Takeda, J. I.
Tanino, M.
Tatusova, T.
Thongjuea, S.
Todokoro, F.
Tsugane, M.
Tyagi, A. K.
Vanavichit, A.
Wang, A.
Wing, R. A.
Yamaguchi, K.
Yamamoto, M.
Yamamoto, N.
Yu, Y.
Zhang, H.
Zhao, Q.
Higo, K.
Burr, B.
Gojobori, T.
Sasaki, T.

January 2007

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar...

Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes

Gong, W
Shen, YP
Ma, LG
Pan, Y
Du, YL
Wang, DH
Yang, JY
Hu, LD
Liu, XF
Dong, CX
Ma, L
Chen, YH
Yang, XY
Gao, Y
Zhu, DM
Tan, XL
Mu, JY
Zhang, DB
Liu, YL
Dinesh-Kumar, SP
Li, Y
Wang, XP
Gu, HY
Qu, LJ
Bai, SN
Lu, YT
Li, JY
Zhao, JD
Zuo, JR
Huang, H
Deng, XW
Zhu, YX

January 2004

Here, we report our effort in generating an ORFeome collection for the Arabidopsis transcription fac...

for_dryad

Polly Y. Hsu (3251619)
Lorenzo Calviello (3251622)
Hsin-Yen L. Wu (3251631)
Fay-Wei Li (199955)
Uwe Ohler (20245)
Carl Rothfels (3251628)
Philip Benfey (188536)

October 2016

Using ribosome profiling, we identified novel translated ORFs in annotated ncRNAs and pseudogenes i...

Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, Polly Yingshan
Calviello, Lorenzo
Wu, Hsin-Yen Larry
Li, Fay-Wei
Rothfels, Carl J
Ohler, Uwe
Benfey, Philip N

November 2016

Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Be...

Data from: Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis

Hsu, Polly Y.
Calviello, Lorenzo
Wu, Hsin-Yen Larry
Li, Fay-Wei
Rothfels, Carl J.
Ohler, Uwe
Benfey, Philip N.

Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Be...

Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues

Lewinski, Martin
Hallmann, Armin
Staiger, Dorothee

January 2016

Lewinski M, Hallmann A, Staiger D. Genome-wide identification and phylogenetic analysis of plant RNA...

Translation and evolutionary evidence indicates that unannotated ORF YFR035W-A is likely a conserved gene.

Aaron Wacholder (8460039)
Anne-Ruxandra Carvunis (149561)

December 2023

(A) ribo-seq reads on unannotated ORF YFR035W-A (top) and annotated ORF YFR035C (bottom). The bounds...

Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs in Arabidopsis thaliana

van der Horst, Sjors
Snel, Berend
Hanson, Johannes
Smeekens, Sjef
Sub Molecular Plant Physiology
Sub Bioinformatics
Theoretical Biology and Bioinformatics
Molecular Plant Physiology

January 2019

Eukaryotic mRNAs contain a 5' leader preceding the main open reading frame (mORF) and, depending on ...

Phylogenomics of plant genomes : A methodology for genome-wide searches for orthologs in plants.

Conte, Matthieu
Gaillard, Sylvain
Droc, Gaëtan
Perin, Christophe

January 2008

Background: Gene ortholog identification is now a major objective for mining the increasing amount o...

FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing

Fabio Fassetti
Claudia Giallombardo
Ofelia Leone
Luigi Palopoli
Simona E. Rombo
Adolfo Saiardi

April 2019

Abstract Background RNA editing is an important mechanism for gene expression in plants organelles. ...

Analysis of the Arabidopsis Cytosolic Ribosome Proteome Provides Detailed Insights into Its Components and Their Post-translational Modification

Carroll, Adam
Heazlewood, Joshua
Ito, Jun
Millar, AH

December 2015

Finding gene-specific peptides by mass spectrometry analysis to pinpoint gene loci responsible for p...

Improved sequence-based orthologs identification using genomic context information and their impact on pathway analysis in plants

Tulpan, Dan
Lger, Serge
Cuperlovic-Culf, Miroslava
Pan, Youlian

January 2013

With the advent of sequencing techniques, a deluge of plant genome projects have emerged, all prompt...

The emerging world of small ORFs

Hellens, Roger
Brown, Christopher
Chisnall, Matthew
Waterhouse, Peter
Macknight, Richard

January 2016

Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found ...

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana.

Song, Dandan
Yang, Yang
Yu, Bin
Zheng, Binglian
Deng, Zhidong
Lu, Bao-Liang
Chen, Xuemei
Jiang, Tao

January 2009

BackgroundNon-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules t...

Additional file 10: of Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Amanda Grusz (3460853)
Carl Rothfels (3251628)
Eric Schuettpelz (3194496)

August 2016

Orthogroup data file. Zipped folder containing fasta-formatted reads identified by ProteinOrtho, use...

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana: The Rice Annotation Project

Itoh, T.
Tanaka, T.
Barrero, R. A.
Yamasaki, C.
Fujii, Y.
Hilton, P. B.
Antonio, B. A.
Aono, H.
Apweiler, R.
Bruskiewich, R.
Bureau, T.
Burr, F.
De Oliveira, A. C.
Fuks, G.
Habara, T.
Haberer, G.
Han, B.
Harada, E.
Hiraki, A. T.
Hirochika, H.
Hoen, D.
Hokari, H.
Hosokawa, S.
Hsing, Y. I.
Ikawa, H.
Ikeo, K.
Imanishi, T.
Ito, Y.
Jaiswal, P.
Kanno, M.
Kawahara, Y.
Kawamura, T.
Kawashima, H.
Khurana, J. P.
Kikuchi, S.
Komatsu, S.
Koyanagi, K. O.
Kubooka, H.
Lieberherr, D.
Lin, Y. C.
Lonsdale, D.
Matsumoto, T.
Matsuya, A.
McCombie, W. R.
Messing, J.
Miyao, A.
Mulder, N.
Nagamura, Y.
Nam, J.
Namiki, N.
Numa, H.
Nurimoto, S.
O'Donovan, C.
Ohyanagi, H.
Okido, T.
Oota, S.
Osato, N.
Palmer, L. E.
Quetier, F.
Raghuvanshi, S.
Saichi, N.
Sakai, H.
Sakai, Y.
Sakata, K.
Sakurai, T.
Sato, F.
Sato, Y.
Schoof, H.
Seki, M.
Shibata, M.
Shimizu, Y.
Shinozaki, K.
Shinso, Y.
Singh, N. K.
Smith-White, B.
Takeda, J. I.
Tanino, M.
Tatusova, T.
Thongjuea, S.
Todokoro, F.
Tsugane, M.
Tyagi, A. K.
Vanavichit, A.
Wang, A.
Wing, R. A.
Yamaguchi, K.
Yamamoto, M.
Yamamoto, N.
Yu, Y.
Zhang, H.
Zhao, Q.
Higo, K.
Burr, B.
Gojobori, T.
Sasaki, T.

January 2007

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar...

Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes

Gong, W
Shen, YP
Ma, LG
Pan, Y
Du, YL
Wang, DH
Yang, JY
Hu, LD
Liu, XF
Dong, CX
Ma, L
Chen, YH
Yang, XY
Gao, Y
Zhu, DM
Tan, XL
Mu, JY
Zhang, DB
Liu, YL
Dinesh-Kumar, SP
Li, Y
Wang, XP
Gu, HY
Qu, LJ
Bai, SN
Lu, YT
Li, JY
Zhao, JD
Zuo, JR
Huang, H
Deng, XW
Zhu, YX

January 2004

Here, we report our effort in generating an ORFeome collection for the Arabidopsis transcription fac...

Abstract

Extracted data

for_dryad

Abstract

Extracted data

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