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Results: 1 to 20 of 28

1.

Practical guidelines for the comprehensive analysis of ChIP-seq data.

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J.

PLoS Comput Biol. 2013;9(11):e1003326. doi: 10.1371/journal.pcbi.1003326. Epub 2013 Nov 14.

PMID:
24244136
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii.

Brueggeman AJ, Gangadharaiah DS, Cserhati MF, Casero D, Weeks DP, Ladunga I.

Plant Cell. 2012 May;24(5):1860-75. doi: 10.1105/tpc.111.093435. Epub 2012 May 25. Erratum in: Plant Cell. 2012 Aug;24(8):3483.

PMID:
22634764
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1.

Fang W, Si Y, Douglass S, Casero D, Merchant SS, Pellegrini M, Ladunga I, Liu P, Spalding MH.

Plant Cell. 2012 May;24(5):1876-93. doi: 10.1105/tpc.112.097949. Epub 2012 May 25.

PMID:
22634760
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.

Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Pröschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL.

Genome Biol. 2012 May 25;13(5):R39. doi: 10.1186/gb-2012-13-5-r39.

PMID:
22630137
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses.

Panda D, Das A, Dinh PX, Subramaniam S, Nayak D, Barrows NJ, Pearson JL, Thompson J, Kelly DL, Ladunga I, Pattnaik AK.

Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):19036-41. doi: 10.1073/pnas.1113643108. Epub 2011 Nov 7.

PMID:
22065774
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The sigma-1 receptor enhances brain plasticity and functional recovery after experimental stroke.

Ruscher K, Shamloo M, Rickhag M, Ladunga I, Soriano L, Gisselsson L, Toresson H, Ruslim-Litrus L, Oksenberg D, Urfer R, Johansson BB, Nikolich K, Wieloch T.

Brain. 2011 Mar;134(Pt 3):732-46. doi: 10.1093/brain/awq367. Epub 2011 Jan 28.

PMID:
21278085
[PubMed - indexed for MEDLINE]
Free Article
7.

Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease.

Gonzalez M, Sealls W, Jesch ED, Brosnan MJ, Ladunga I, Ding X, Black PN, DiRusso CC.

Physiol Genomics. 2011 Feb 11;43(3):121-35. doi: 10.1152/physiolgenomics.00209.2010. Epub 2010 Nov 23.

PMID:
21098682
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana.

van Dijk K, Ding Y, Malkaram S, Riethoven JJ, Liu R, Yang J, Laczko P, Chen H, Xia Y, Ladunga I, Avramova Z, Fromm M.

BMC Plant Biol. 2010 Nov 5;10:238. doi: 10.1186/1471-2229-10-238.

PMID:
21050490
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Weakly positioned nucleosomes enhance the transcriptional competency of chromatin.

Belch Y, Yang J, Liu Y, Malkaram SA, Liu R, Riethoven JJ, Ladunga I.

PLoS One. 2010 Sep 24;5(9):e12984. doi: 10.1371/journal.pone.0012984.

PMID:
20886052
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq.

Jiao S, Bailey CP, Zhang S, Ladunga I.

Methods Mol Biol. 2010;674:161-77. doi: 10.1007/978-1-60761-854-6_10.

PMID:
20827591
[PubMed - indexed for MEDLINE]
11.

An overview of the computational analyses and discovery of transcription factor binding sites.

Ladunga I.

Methods Mol Biol. 2010;674:1-22. doi: 10.1007/978-1-60761-854-6_1. Review.

PMID:
20827582
[PubMed - indexed for MEDLINE]
12.

Finding similar nucleotide sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2009 Jun;Chapter 3:Unit 3.3. doi: 10.1002/0471250953.bi0303s26.

PMID:
19496060
[PubMed - indexed for MEDLINE]
13.

Transcriptional profiling of the sperm storage organs of Drosophila melanogaster.

Prokupek AM, Kachman SD, Ladunga I, Harshman LG.

Insect Mol Biol. 2009 Aug;18(4):465-75. doi: 10.1111/j.1365-2583.2009.00887.x. Epub 2009 Apr 24.

PMID:
19453766
[PubMed - indexed for MEDLINE]
14.

Finding homologs in amino acid sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2009 Mar;Chapter 3:Unit 3.4. doi: 10.1002/0471250953.bi0304s25. No abstract available.

PMID:
19274633
[PubMed - indexed for MEDLINE]
15.

Finding homologs to nucleotide sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2002 Aug;Chapter 3:Unit 3.3. doi: 10.1002/0471250953.bi0303s00. Review.

PMID:
18792938
[PubMed - indexed for MEDLINE]
16.

The small ubiquitin-like modifier (SUMO) and SUMO-conjugating system of Chlamydomonas reinhardtii.

Wang Y, Ladunga I, Miller AR, Horken KM, Plucinak T, Weeks DP, Bailey CP.

Genetics. 2008 May;179(1):177-92. doi: 10.1534/genetics.108.089128.

PMID:
18493050
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Finding homologs in amino acid sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 3:Unit 3.4. doi: 10.1002/0471250953.bi0304s00.

PMID:
18428697
[PubMed - indexed for MEDLINE]
18.

The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions.

Saleh A, Alvarez-Venegas R, Yilmaz M, Le O, Hou G, Sadder M, Al-Abdallat A, Xia Y, Lu G, Ladunga I, Avramova Z.

Plant Cell. 2008 Mar;20(3):568-79. doi: 10.1105/tpc.107.056614. Epub 2008 Mar 28.

PMID:
18375658
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature.

Ladunga I.

Nucleic Acids Res. 2007;35(2):433-40. Epub 2006 Dec 14.

PMID:
17169992
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

Thomas PD, Kejariwal A, Campbell MJ, Mi H, Diemer K, Guo N, Ladunga I, Ulitsky-Lazareva B, Muruganujan A, Rabkin S, Vandergriff JA, Doremieux O.

Nucleic Acids Res. 2003 Jan 1;31(1):334-41. Erratum in: Nucleic Acids Res. 2003 Apr 1;31(7):2024.

PMID:
12520017
[PubMed - indexed for MEDLINE]
Free PMC Article

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