Underwood J - Search Results

1

Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.

Gordon SP, Tseng E, Salamov A, Zhang J, Meng X, Zhao Z, Kang D, Underwood J, Grigoriev IV, Figueroa M, Schilling JS, Chen F, Wang Z. Gordon SP, et al. Among authors: underwood j. PLoS One. 2015 Jul 15;10(7):e0132628. doi: 10.1371/journal.pone.0132628. eCollection 2015. PLoS One. 2015. PMID: 26177194 Free PMC article.

2

Long-read sequencing of chicken transcripts and identification of new transcript isoforms.

Thomas S, Underwood JG, Tseng E, Holloway AK; Bench To Basinet CvDC Informatics Subcommittee. Thomas S, et al. PLoS One. 2014 Apr 15;9(4):e94650. doi: 10.1371/journal.pone.0094650. eCollection 2014. PLoS One. 2014. PMID: 24736250 Free PMC article.

3

Transcriptional fates of human-specific segmental duplications in brain.

Dougherty ML, Underwood JG, Nelson BJ, Tseng E, Munson KM, Penn O, Nowakowski TJ, Pollen AA, Eichler EE. Dougherty ML, et al. Among authors: underwood jg. Genome Res. 2018 Oct;28(10):1566-1576. doi: 10.1101/gr.237610.118. Epub 2018 Sep 18. Genome Res. 2018. PMID: 30228200 Free PMC article.

4

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.

Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF. Weirather JL, et al. Among authors: underwood jg. Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3. Nucleic Acids Res. 2015. PMID: 26040699 Free PMC article.

5

Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos).

Tseng E, Underwood JG, Evans Hutzenbiler BD, Trojahn S, Kingham B, Shevchenko O, Bernberg E, Vierra M, Robbins CT, Jansen HT, Kelley JL. Tseng E, et al. G3 (Bethesda). 2022 Mar 4;12(3):jkab422. doi: 10.1093/g3journal/jkab422. G3 (Bethesda). 2022. PMID: 35100340 Free PMC article.

6

ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.

Sheynkman GM, Tuttle KS, Laval F, Tseng E, Underwood JG, Yu L, Dong D, Smith ML, Sebra R, Willems L, Hao T, Calderwood MA, Hill DE, Vidal M. Sheynkman GM, et al. Nat Commun. 2020 May 11;11(1):2326. doi: 10.1038/s41467-020-16174-z. Nat Commun. 2020. PMID: 32393825 Free PMC article.

7

Improving PacBio long read accuracy by short read alignment.

Au KF, Underwood JG, Lee L, Wong WH. Au KF, et al. PLoS One. 2012;7(10):e46679. doi: 10.1371/journal.pone.0046679. Epub 2012 Oct 4. PLoS One. 2012. PMID: 23056399 Free PMC article.

8

Gene isoform specificity through enhancer-associated antisense transcription.

Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. Onodera CS, et al. PLoS One. 2012;7(8):e43511. doi: 10.1371/journal.pone.0043511. Epub 2012 Aug 24. PLoS One. 2012. PMID: 22937057 Free PMC article.

9

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Fiddes IT, et al. Among authors: underwood jg. Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8. Genome Res. 2018. PMID: 29884752 Free PMC article.

10

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW. Brannan KW, et al. Among authors: underwood jg. Nat Methods. 2021 May;18(5):507-519. doi: 10.1038/s41592-021-01128-0. Epub 2021 May 7. Nat Methods. 2021. PMID: 33963355 Free PMC article.

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