Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 25

1.

Prioritizing bona fide bacterial small RNAs with machine learning classifiers.

Eppenhof EJJ, Peña-Castillo L.

PeerJ. 2019 Jan 24;7:e6304. doi: 10.7717/peerj.6304. eCollection 2019.

2.

Genetic variation associated with healthy traits and environmental conditions in Vaccinium vitis-idaea.

Alam Z, Roncal J, Peña-Castillo L.

BMC Genomics. 2018 Jan 2;19(1):4. doi: 10.1186/s12864-017-4396-9.

3.

GeNET: a web application to explore and share Gene Co-expression Network Analysis data.

Desai AP, Razeghin M, Meruvia-Pastor O, Peña-Castillo L.

PeerJ. 2017 Aug 14;5:e3678. doi: 10.7717/peerj.3678. eCollection 2017.

4.

CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo.

Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL.

Sci Rep. 2017 Aug 17;7(1):8642. doi: 10.1038/s41598-017-08094-8.

5.

Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA.

Grüll MP, Peña-Castillo L, Mulligan ME, Lang AS.

RNA Biol. 2017 Jul 3;14(7):914-925. doi: 10.1080/15476286.2017.1306175. Epub 2017 Mar 15.

6.

REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data.

Patra P, Izawa T, Pena-Castillo L.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1270-1283. doi: 10.1109/TCBB.2015.2453948. Epub 2015 Jul 8.

PMID:
27019499
7.

OMARC: An online multimedia application for training health care providers in the assessment of respiratory conditions.

Meruvia-Pastor O, Patra P, Andres K, Twomey C, Peña-Castillo L.

Int J Med Inform. 2016 May;89:15-24. doi: 10.1016/j.ijmedinf.2016.02.007. Epub 2016 Feb 21.

PMID:
26980355
8.

Proteomics analysis of global regulatory cascades involved in clavulanic acid production and morphological development in Streptomyces clavuligerus.

Ferguson NL, Peña-Castillo L, Moore MA, Bignell DR, Tahlan K.

J Ind Microbiol Biotechnol. 2016 Apr;43(4):537-55. doi: 10.1007/s10295-016-1733-y. Epub 2016 Jan 20.

PMID:
26790415
9.

DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT.

Peña-Castillo L, Grüell M, Mulligan ME, Lang AS.

Pac Symp Biocomput. 2016;21:456-67.

10.

Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast.

Peña-Castillo L, Badis G.

Methods Mol Biol. 2016;1361:203-25. doi: 10.1007/978-1-4939-3079-1_12.

PMID:
26483024
11.

Private rare deletions in SEC16A and MAMDC4 may represent novel pathogenic variants in familial axial spondyloarthritis.

O'Rielly DD, Uddin M, Codner D, Hayley M, Zhou J, Pena-Castillo L, Mostafa AA, Hasan SM, Liu W, Haroon N, Inman R, Rahman P.

Ann Rheum Dis. 2016 Apr;75(4):772-9. doi: 10.1136/annrheumdis-2014-206484. Epub 2015 May 8.

12.

Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides.

Peña-Castillo L, Mercer RG, Gurinovich A, Callister SJ, Wright AT, Westbye AB, Beatty JT, Lang AS.

BMC Genomics. 2014 Aug 28;15:730. doi: 10.1186/1471-2164-15-730.

13.

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays.

Stead MB, Marshburn S, Mohanty BK, Mitra J, Pena Castillo L, Ray D, van Bakel H, Hughes TR, Kushner SR.

Nucleic Acids Res. 2011 Apr;39(8):3188-203. doi: 10.1093/nar/gkq1242. Epub 2010 Dec 11.

14.

Two-color cell array screen reveals interdependent roles for histone chaperones and a chromatin boundary regulator in histone gene repression.

Fillingham J, Kainth P, Lambert JP, van Bakel H, Tsui K, Peña-Castillo L, Nislow C, Figeys D, Hughes TR, Greenblatt J, Andrews BJ.

Mol Cell. 2009 Aug 14;35(3):340-51. doi: 10.1016/j.molcel.2009.06.023.

15.

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Ray D, Kazan H, Chan ET, Peña Castillo L, Chaudhry S, Talukder S, Blencowe BJ, Morris Q, Hughes TR.

Nat Biotechnol. 2009 Jul;27(7):667-70. doi: 10.1038/nbt.1550. Epub 2009 Jun 28.

PMID:
19561594
16.

Comprehensive genetic analysis of transcription factor pathways using a dual reporter gene system in budding yeast.

Kainth P, Sassi HE, Peña-Castillo L, Chua G, Hughes TR, Andrews B.

Methods. 2009 Jul;48(3):258-64. doi: 10.1016/j.ymeth.2009.02.015. Epub 2009 Mar 6.

PMID:
19269327
17.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.

18.

Predicting the binding preference of transcription factors to individual DNA k-mers.

Alleyne TM, Peña-Castillo L, Badis G, Talukder S, Berger MF, Gehrke AR, Philippakis AA, Bulyk ML, Morris QD, Hughes TR.

Bioinformatics. 2009 Apr 15;25(8):1012-8. doi: 10.1093/bioinformatics/btn645. Epub 2008 Dec 16.

19.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, Lin GN, Berriz GF, Gibbons FD, Lanckriet G, Qiu J, Grant C, Barutcuoglu Z, Hill DP, Warde-Farley D, Grouios C, Ray D, Blake JA, Deng M, Jordan MI, Noble WS, Morris Q, Klein-Seetharaman J, Bar-Joseph Z, Chen T, Sun F, Troyanskaya OG, Marcotte EM, Xu D, Hughes TR, Roth FP.

Genome Biol. 2008;9 Suppl 1:S2. doi: 10.1186/gb-2008-9-s1-s2. Epub 2008 Jun 27.

20.

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Berger MF, Badis G, Gehrke AR, Talukder S, Philippakis AA, Peña-Castillo L, Alleyne TM, Mnaimneh S, Botvinnik OB, Chan ET, Khalid F, Zhang W, Newburger D, Jaeger SA, Morris QD, Bulyk ML, Hughes TR.

Cell. 2008 Jun 27;133(7):1266-76. doi: 10.1016/j.cell.2008.05.024.

21.

Plasmodium falciparum shows transcriptional versatility within the human host.

Lovegrove FE, Peña-Castillo L, Liles WC, Hughes TR, Kain KC.

Trends Parasitol. 2008 Jul;24(7):288-91. doi: 10.1016/j.pt.2008.04.004. Epub 2008 Jun 5.

PMID:
18538633
22.

Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model.

Lovegrove FE, Gharib SA, Peña-Castillo L, Patel SN, Ruzinski JT, Hughes TR, Liles WC, Kain KC.

PLoS Pathog. 2008 May 16;4(5):e1000068. doi: 10.1371/journal.ppat.1000068.

23.

Why are there still over 1000 uncharacterized yeast genes?

Peña-Castillo L, Hughes TR.

Genetics. 2007 May;176(1):7-14. Epub 2007 Apr 15. Review.

24.
25.

A survey of essential gene function in the yeast cell division cycle.

Yu L, Peña Castillo L, Mnaimneh S, Hughes TR, Brown GW.

Mol Biol Cell. 2006 Nov;17(11):4736-47. Epub 2006 Aug 30.

Supplemental Content

Loading ...
Support Center