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Items: 1 to 50 of 84

1.

MiPepid: MicroPeptide identification tool using machine learning.

Zhu M, Gribskov M.

BMC Bioinformatics. 2019 Nov 8;20(1):559. doi: 10.1186/s12859-019-3033-9.

2.

IRESpy: an XGBoost model for prediction of internal ribosome entry sites.

Wang J, Gribskov M.

BMC Bioinformatics. 2019 Jul 30;20(1):409. doi: 10.1186/s12859-019-2999-7.

3.

Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains.

Yakkala H, Samantarrai D, Gribskov M, Siddavattam D.

PLoS One. 2019 Jun 13;14(6):e0218204. doi: 10.1371/journal.pone.0218204. eCollection 2019.

4.

Three Genes Define a Bacterial-Like Arsenic Tolerance Mechanism in the Arsenic Hyperaccumulating Fern Pteris vittata.

Cai C, Lanman NA, Withers KA, DeLeon AM, Wu Q, Gribskov M, Salt DE, Banks JA.

Curr Biol. 2019 May 20;29(10):1625-1633.e3. doi: 10.1016/j.cub.2019.04.029. Epub 2019 May 9.

PMID:
31080078
5.

Transcriptome analysis identifies metallothionein as biomarkers to predict recurrence in hepatocellular cacinoma.

Wang S, Gribskov M.

Mol Genet Genomic Med. 2019 Jun;7(6):e693. doi: 10.1002/mgg3.693. Epub 2019 May 6.

6.

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
7.

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.

8.

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
9.

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
10.

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.

11.

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.

12.

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
13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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.

26.

A rice kinase-protein interaction map.

Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu F, Bartley LE, Chern M, Bart R, Chen X, Zhu L, Farmerie WG, Gribskov M, Zhu JK, Fromm ME, Ronald PC, Song WY.

Plant Physiol. 2009 Mar;149(3):1478-92. doi: 10.1104/pp.108.128298. Epub 2008 Dec 24.

27.

The emerging world of wikis.

Hu JC, Aramayo R, Bolser D, Conway T, Elsik CG, Gribskov M, Kelder T, Kihara D, Knight TF Jr, Pico AR, Siegele DA, Wanner BL, Welch RD.

Science. 2008 Jun 6;320(5881):1289-90. doi: 10.1126/science.320.5881.1289b. No abstract available.

PMID:
18535227
28.

Spontaneous symmetry breaking in genome evolution.

Ryabov Y, Gribskov M.

Nucleic Acids Res. 2008 May;36(8):2756-63. doi: 10.1093/nar/gkn086. Epub 2008 Mar 26.

29.

Bioinformatics research in the Asia Pacific: a 2007 update.

Ranganathan S, Gribskov M, Tan TW.

BMC Bioinformatics. 2008;9 Suppl 1:S1. doi: 10.1186/1471-2105-9-S1-S1.

30.

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).

Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D.

Science. 2006 Sep 15;313(5793):1596-604.

31.
32.

Wiggle-predicting functionally flexible regions from primary sequence.

Gu J, Gribskov M, Bourne PE.

PLoS Comput Biol. 2006 Jul 14;2(7):e90. Epub 2006 Jun 5.

33.

Protein-protein interactions of tandem affinity purification-tagged protein kinases in rice.

Rohila JS, Chen M, Chen S, Chen J, Cerny R, Dardick C, Canlas P, Xu X, Gribskov M, Kanrar S, Zhu JK, Ronald P, Fromm ME.

Plant J. 2006 Apr;46(1):1-13.

34.

Protein kinase resource: an integrated environment for phosphorylation research.

Niedner RH, Buzko OV, Haste NM, Taylor A, Gribskov M, Taylor SS.

Proteins. 2006 Apr 1;63(1):78-86.

PMID:
16435372
35.
36.

MAASE: an alternative splicing database designed for supporting splicing microarray applications.

Zheng CL, Kwon YS, Li HR, Zhang K, Coutinho-Mansfield G, Yang C, Nair TM, Gribskov M, Fu XD.

RNA. 2005 Dec;11(12):1767-76. Epub 2005 Oct 26.

37.

Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae.

Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF.

Genome Biol. 2005;6(9):R77. Epub 2005 Aug 30.

38.

An open forum for computational biology.

Gribskov M.

PLoS Comput Biol. 2005 Jun;1(1):e5. No abstract available.

39.
40.

Predicting N-terminal myristoylation sites in plant proteins.

Podell S, Gribskov M.

BMC Genomics. 2004 Jun 17;5(1):37.

41.

A database designed to computationally aid an experimental approach to alternative splicing.

Zheng CL, Nair TM, Gribskov M, Kwon YS, Li HR, Fu XD.

Pac Symp Biocomput. 2004:78-88.

42.

Rival penalized competitive learning (RPCL): a topology-determining algorithm for analyzing gene expression data.

Nair TM, Zheng CL, Fink JL, Stuart RO, Gribskov M.

Comput Biol Chem. 2003 Dec;27(6):565-74.

PMID:
14667784
43.
44.

2HAPI: a microarray data analysis system.

Fink JL, Drewes S, Patel H, Welsh JB, Masys DR, Corbeil J, Gribskov M.

Bioinformatics. 2003 Jul 22;19(11):1443-5.

PMID:
12874061
45.

Challenges in data management for functional genomics.

Gribskov M.

OMICS. 2003 Spring;7(1):3-5.

PMID:
12831543
46.

MODULEWRITER: a program for automatic generation of database interfaces.

Zheng CL, Fana F, Udupi PV, Gribskov M.

Comput Biol Chem. 2003 May;27(2):135-9.

PMID:
12821310
47.

The Arabidopsis CDPK-SnRK superfamily of protein kinases.

Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N, Kudla J, Luan S, Nimmo HG, Sussman MR, Thomas M, Walker-Simmons K, Zhu JK, Harmon AC.

Plant Physiol. 2003 Jun;132(2):666-80.

48.

Genomic comparison of P-type ATPase ion pumps in Arabidopsis and rice.

Baxter I, Tchieu J, Sussman MR, Boutry M, Palmgren MG, Gribskov M, Harper JF, Axelsen KB.

Plant Physiol. 2003 Jun;132(2):618-28. Erratum in: Plant Physiol. 2005 Jul;138(3):1807.

49.

Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria.

Kerk D, Bulgrien J, Smith DW, Gribskov M.

Plant Physiol. 2003 Mar;131(3):1209-19.

50.

The PlantsP and PlantsT Functional Genomics Databases.

Tchieu JH, Fana F, Fink JL, Harper J, Nair TM, Niedner RH, Smith DW, Steube K, Tam TM, Veretnik S, Wang D, Gribskov M.

Nucleic Acids Res. 2003 Jan 1;31(1):342-4.

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