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Items: 1 to 20 of 79

1.

Effect of high-fat diet on secreted milk transcriptome in midlactation mice.

Chen Y, Wang J, Yang S, Utturkar S, Crodian J, Cummings S, Thimmapuram J, San Miguel P, Kuang S, Gribskov M, Plaut K, Casey T.

Physiol Genomics. 2017 Dec 1;49(12):747-762. doi: 10.1152/physiolgenomics.00080.2017. Epub 2017 Nov 1.

PMID:
29093195
2.

DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates.

Peng H, Yang Y, Zhe S, Wang J, Gribskov M, Qi Y.

Bioinformatics. 2017 Oct 1;33(19):3018-3027. doi: 10.1093/bioinformatics/btx357.

PMID:
28595376
3.

AptRank: an adaptive PageRank model for protein function prediction on   bi-relational graphs.

Jiang B, Kloster K, Gleich DF, Gribskov M.

Bioinformatics. 2017 Jun 15;33(12):1829-1836. doi: 10.1093/bioinformatics/btx029.

PMID:
28200073
4.

Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis.

Wang S, Gribskov M.

Bioinformatics. 2017 Feb 1;33(3):327-333. doi: 10.1093/bioinformatics/btw625.

PMID:
28172640
5.

Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera).

Andino GK, Gribskov M, Anderson DL, Evans JD, Hunt GJ.

BMC Genomics. 2016 Nov 16;17(1):926.

6.

Accurate Classification of RNA Structures Using Topological Fingerprints.

Huang J, Li K, Gribskov M.

PLoS One. 2016 Oct 18;11(10):e0164726. doi: 10.1371/journal.pone.0164726. eCollection 2016.

7.

CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data.

Wang S, Gribskov M, Hazbun TR, Pascuzzi PE.

Bioinformatics. 2016 Aug 1;32(15):2399-401. doi: 10.1093/bioinformatics/btw162. Epub 2016 Mar 25.

PMID:
27153600
8.

A Search for Parent-of-Origin Effects on Honey Bee Gene Expression.

Kocher SD, Tsuruda JM, Gibson JD, Emore CM, Arechavaleta-Velasco ME, Queller DC, Strassmann JE, Grozinger CM, Gribskov MR, San Miguel P, Westerman R, Hunt GJ.

G3 (Bethesda). 2015 Jun 5;5(8):1657-62. doi: 10.1534/g3.115.017814.

9.

Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss.

McKinney GJ, Hale MC, Goetz G, Gribskov M, Thrower FP, Nichols KM.

Mol Ecol. 2015 Apr;24(8):1792-809. doi: 10.1111/mec.13143. Epub 2015 Apr 2.

PMID:
25735875
10.

Assessment of subnetwork detection methods for breast cancer.

Jiang B, Gribskov M.

Cancer Inform. 2014 Dec 2;13(Suppl 6):15-23. doi: 10.4137/CIN.S17641. eCollection 2014.

11.

GenoBase: comprehensive resource database of Escherichia coli K-12.

Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H.

Nucleic Acids Res. 2015 Jan;43(Database issue):D606-17. doi: 10.1093/nar/gku1164. Epub 2014 Nov 15.

12.

Making models match measurements: model optimization for morphogen patterning networks.

Hengenius JB, Gribskov M, Rundell AE, Umulis DM.

Semin Cell Dev Biol. 2014 Nov;35:109-23. doi: 10.1016/j.semcdb.2014.06.017. Epub 2014 Jul 9. Review.

13.

Identifying complete RNA structural ensembles including pseudoknots.

Gupta A, Rahman R, Li K, Gribskov M.

RNA Biol. 2012 Feb;9(2):187-99. doi: 10.4161/rna.18386. Epub 2012 Feb 1.

PMID:
22418849
14.

Analysis of gap gene regulation in a 3D organism-scale model of the Drosophila melanogaster embryo.

Hengenius JB, Gribskov M, Rundell AE, Fowlkes CC, Umulis DM.

PLoS One. 2011;6(11):e26797. doi: 10.1371/journal.pone.0026797. Epub 2011 Nov 16.

15.

A physical interaction network of dengue virus and human proteins.

Khadka S, Vangeloff AD, Zhang C, Siddavatam P, Heaton NS, Wang L, Sengupta R, Sahasrabudhe S, Randall G, Gribskov M, Kuhn RJ, Perera R, LaCount DJ.

Mol Cell Proteomics. 2011 Dec;10(12):M111.012187. doi: 10.1074/mcp.M111.012187. Epub 2011 Sep 12.

16.

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.

17.

The role of RNA sequence and structure in RNA--protein interactions.

Gupta A, Gribskov M.

J Mol Biol. 2011 Jun 17;409(4):574-87. doi: 10.1016/j.jmb.2011.04.007. Epub 2011 Apr 15.

PMID:
21514302
18.

Calcium-dependent protein kinases from Arabidopsis show substrate specificity differences in an analysis of 103 substrates.

Curran A, Chang IF, Chang CL, Garg S, Miguel RM, Barron YD, Li Y, Romanowsky S, Cushman JC, Gribskov M, Harmon AC, Harper JF.

Front Plant Sci. 2011 Aug 30;2:36. doi: 10.3389/fpls.2011.00036. eCollection 2011.

19.

The genome of Nectria haematococca: contribution of supernumerary chromosomes to gene expansion.

Coleman JJ, Rounsley SD, Rodriguez-Carres M, Kuo A, Wasmann CC, Grimwood J, Schmutz J, Taga M, White GJ, Zhou S, Schwartz DC, Freitag M, Ma LJ, Danchin EG, Henrissat B, Coutinho PM, Nelson DR, Straney D, Napoli CA, Barker BM, Gribskov M, Rep M, Kroken S, Molnár I, Rensing C, Kennell JC, Zamora J, Farman ML, Selker EU, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev IV, Geiser DM, Covert SF, Temporini E, Vanetten HD.

PLoS Genet. 2009 Aug;5(8):e1000618. doi: 10.1371/journal.pgen.1000618. Epub 2009 Aug 28.

20.

Protein-protein interactions of tandem affinity purified protein kinases from rice.

Rohila JS, Chen M, Chen S, Chen J, Cerny RL, Dardick C, Canlas P, Fujii H, Gribskov M, Kanrar S, Knoflicek L, Stevenson B, Xie M, Xu X, Zheng X, Zhu JK, Ronald P, Fromm ME.

PLoS One. 2009 Aug 19;4(8):e6685. doi: 10.1371/journal.pone.0006685.

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