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Items: 32

1.

Installing, Maintaining, and Using a Local Copy of BLAST for Compute Cluster or Workstation Use.

Ladunga I.

Curr Protoc Bioinformatics. 2018 Sep;63(1):e54. doi: 10.1002/cpbi.54. Epub 2018 Aug 31.

PMID:
30168910
2.

Finding Homologs in Amino Acid Sequences Using Network BLAST Searches.

Ladunga I.

Curr Protoc Bioinformatics. 2017 Sep 13;59:3.4.1-3.4.24. doi: 10.1002/cpbi.34.

PMID:
28902395
3.

Finding Similar Nucleotide Sequences Using Network BLAST Searches.

Ladunga I.

Curr Protoc Bioinformatics. 2017 Jun 27;58:3.3.1-3.3.25. doi: 10.1002/cpbi.29.

PMID:
28654728
4.

Pluralistic and stochastic gene regulation: examples, models and consistent theory.

Salas EN, Shu J, Cserhati MF, Weeks DP, Ladunga I.

Nucleic Acids Res. 2016 Jun 2;44(10):4595-609. doi: 10.1093/nar/gkw042. Epub 2016 Jan 28.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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
15.

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
16.

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
17.

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
18.

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
19.

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
20.

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.

21.

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
22.

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. Erratum in: Plant Cell. 2016 Jan;28(1):265.

23.
24.

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.

26.

Large-scale predictions of secretory proteins from mammalian genomic and EST sequences.

Ladunga I.

Curr Opin Biotechnol. 2000 Feb;11(1):13-8. Review.

PMID:
10679337
27.
28.
29.

Heterogeneity of genomes: measures and values.

Karlin S, Ladunga I, Blaisdell BE.

Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12837-41.

30.

Comparisons of eukaryotic genomic sequences.

Karlin S, Ladunga I.

Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12832-6.

32.

Improving signal peptide prediction accuracy by simulated neural network.

Ladunga I, Czakó F, Csabai I, Geszti T.

Comput Appl Biosci. 1991 Oct;7(4):485-7.

PMID:
1747780

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