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Items: 41

1.

Computational Methods for Analysis of the DNA-Binding Preferences of Cys2His2 Zinc-Finger Proteins.

Doğan B, Najafabadi HS.

Methods Mol Biol. 2018;1867:15-28. doi: 10.1007/978-1-4939-8799-3_2.

PMID:
30155812
2.

Aberration hubs in protein interaction networks highlight actionable targets in cancer.

Karimzadeh M, Jandaghi P, Papadakis AI, Trainor S, Rung J, Gonzàlez-Porta M, Scelo G, Vasudev NS, Brazma A, Huang S, Banks RE, Lathrop M, Najafabadi HS, Riazalhosseini Y.

Oncotarget. 2018 May 18;9(38):25166-25180. doi: 10.18632/oncotarget.25382. eCollection 2018 May 18.

3.

A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes.

Perron G, Jandaghi P, Solanki S, Safisamghabadi M, Storoz C, Karimzadeh M, Papadakis AI, Arseneault M, Scelo G, Banks RE, Tost J, Lathrop M, Tanguay S, Brazma A, Huang S, Brimo F, Najafabadi HS, Riazalhosseini Y.

Cell Rep. 2018 May 8;23(6):1639-1650. doi: 10.1016/j.celrep.2018.04.031.

4.

Inference of RNA decay rate from transcriptional profiling highlights the regulatory programs of Alzheimer's disease.

Alkallas R, Fish L, Goodarzi H, Najafabadi HS.

Nat Commun. 2017 Oct 13;8(1):909. doi: 10.1038/s41467-017-00867-z.

5.

Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding.

Najafabadi HS, Garton M, Weirauch MT, Mnaimneh S, Yang A, Kim PM, Hughes TR.

Genome Biol. 2017 Sep 6;18(1):167. doi: 10.1186/s13059-017-1287-y.

6.

The influence of rAAV2-mediated SOX2 delivery into neonatal and adult human RPE cells; a comparative study.

Ezati R, Etemadzadeh A, Soheili ZS, Samiei S, Ranaei Pirmardan E, Davari M, Najafabadi HS.

J Cell Physiol. 2018 Feb;233(2):1222-1235. doi: 10.1002/jcp.25991. Epub 2017 Jun 22.

PMID:
28480968
7.

The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing.

Kala S, Mehta V, Yip CW, Moshiri H, Najafabadi HS, Ma R, Nikpour N, Zimmer SL, Salavati R.

Mol Biochem Parasitol. 2017 Jan;211:94-103. doi: 10.1016/j.molbiopara.2016.12.003. Epub 2016 Dec 11.

PMID:
27965085
8.

Multiparameter functional diversity of human C2H2 zinc finger proteins.

Schmitges FW, Radovani E, Najafabadi HS, Barazandeh M, Campitelli LF, Yin Y, Jolma A, Zhong G, Guo H, Kanagalingam T, Dai WF, Taipale J, Emili A, Greenblatt JF, Hughes TR.

Genome Res. 2016 Dec;26(12):1742-1752. Epub 2016 Nov 16.

9.

Expression of DRD2 Is Increased in Human Pancreatic Ductal Adenocarcinoma and Inhibitors Slow Tumor Growth in Mice.

Jandaghi P, Najafabadi HS, Bauer AS, Papadakis AI, Fassan M, Hall A, Monast A, von Knebel Doeberitz M, Neoptolemos JP, Costello E, Greenhalf W, Scarpa A, Sipos B, Auld D, Lathrop M, Park M, Büchler MW, Strobel O, Hackert T, Giese NA, Zogopoulos G, Sangwan V, Huang S, Riazalhosseini Y, Hoheisel JD.

Gastroenterology. 2016 Dec;151(6):1218-1231. doi: 10.1053/j.gastro.2016.08.040. Epub 2016 Aug 28.

PMID:
27578530
10.

Motif comparison based on similarity of binding affinity profiles.

Lambert SA, Albu M, Hughes TR, Najafabadi HS.

Bioinformatics. 2016 Nov 15;32(22):3504-3506. Epub 2016 Jul 27.

11.

A Protein Complex Map of Trypanosoma brucei.

Gazestani VH, Nikpour N, Mehta V, Najafabadi HS, Moshiri H, Jardim A, Salavati R.

PLoS Negl Trop Dis. 2016 Mar 18;10(3):e0004533. doi: 10.1371/journal.pntd.0004533. eCollection 2016 Mar.

12.

Behavior of a Spontaneously Arising Human Retinal Pigment Epithelial Cell Line Cultivated on Thin Alginate Film.

Najafabadi HS, Soheili ZS, Ganji SM.

J Ophthalmic Vis Res. 2015 Jul-Sep;10(3):286-94. doi: 10.4103/2008-322X.170357.

13.

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity.

Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM.

Nucleic Acids Res. 2015 Oct 30;43(19):9147-57. doi: 10.1093/nar/gkv919. Epub 2015 Sep 17.

14.

Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE.

Najafabadi HS, Albu M, Hughes TR.

Bioinformatics. 2015 Sep 1;31(17):2879-81. doi: 10.1093/bioinformatics/btv284. Epub 2015 May 6.

15.

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.

Narasimhan K, Lambert SA, Yang AW, Riddell J, Mnaimneh S, Zheng H, Albu M, Najafabadi HS, Reece-Hoyes JS, Fuxman Bass JI, Walhout AJ, Weirauch MT, Hughes TR.

Elife. 2015 Apr 23;4. doi: 10.7554/eLife.06967.

16.

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Najafabadi HS, Mnaimneh S, Schmitges FW, Garton M, Lam KN, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR.

Nat Biotechnol. 2015 May;33(5):555-62. doi: 10.1038/nbt.3128. Epub 2015 Feb 18.

PMID:
25690854
17.

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ.

Science. 2015 Jan 9;347(6218):1254806. doi: 10.1126/science.1254806. Epub 2014 Dec 18.

18.

Diabetes enhances the proliferation of adult pancreatic multipotent progenitor cells and biases their differentiation to more β-cell production.

Razavi R, Najafabadi HS, Abdullah S, Smukler S, Arntfield M, van der Kooy D.

Diabetes. 2015 Apr;64(4):1311-23. doi: 10.2337/db14-0070. Epub 2014 Nov 12.

19.

Determination and inference of eukaryotic transcription factor sequence specificity.

Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, Najafabadi HS, Lambert SA, Mann I, Cook K, Zheng H, Goity A, van Bakel H, Lozano JC, Galli M, Lewsey MG, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJM, Bouget FY, Ratsch G, Larrondo LF, Ecker JR, Hughes TR.

Cell. 2014 Sep 11;158(6):1431-1443. doi: 10.1016/j.cell.2014.08.009.

20.

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids.

Najafabadi HS, Lu Z, MacPherson C, Mehta V, Adoue V, Pastinen T, Salavati R.

Nucleic Acids Res. 2013 Oct;41(18):8591-600. doi: 10.1093/nar/gkt647. Epub 2013 Jul 22.

21.

A compendium of RNA-binding motifs for decoding gene regulation.

Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A, Na H, Irimia M, Matzat LH, Dale RK, Smith SA, Yarosh CA, Kelly SM, Nabet B, Mecenas D, Li W, Laishram RS, Qiao M, Lipshitz HD, Piano F, Corbett AH, Carstens RP, Frey BJ, Anderson RA, Lynch KW, Penalva LO, Lei EP, Fraser AG, Blencowe BJ, Morris QD, Hughes TR.

Nature. 2013 Jul 11;499(7457):172-7. doi: 10.1038/nature12311.

22.

Insights into the insect salivary gland proteome: diet-associated changes in caterpillar labial salivary proteins.

Afshar K, Dube FF, Najafabadi HS, Bonneil E, Thibault P, Salavati R, Bede JC.

J Insect Physiol. 2013 Mar;59(3):351-66. doi: 10.1016/j.jinsphys.2013.01.002. Epub 2013 Jan 23.

PMID:
23353727
23.

Systematic discovery of structural elements governing stability of mammalian messenger RNAs.

Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S.

Nature. 2012 Apr 8;485(7397):264-8. doi: 10.1038/nature11013.

24.

Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei.

Moshiri H, Acoca S, Kala S, Najafabadi HS, Hogues H, Purisima E, Salavati R.

J Biol Chem. 2011 Apr 22;286(16):14178-89. doi: 10.1074/jbc.M110.199646. Epub 2011 Mar 4.

25.

Sequence-based functional annotation: what if most of the genes are unique to a genome?

Salavati R, Najafabadi HS.

Trends Parasitol. 2010 May;26(5):225-9. doi: 10.1016/j.pt.2010.02.001. Epub 2010 Mar 6. Review.

PMID:
20211583
26.

Universal function-specificity of codon usage.

Najafabadi HS, Goodarzi H, Salavati R.

Nucleic Acids Res. 2009 Nov;37(21):7014-23. doi: 10.1093/nar/gkp792.

27.

Genome-wide computational identification of functional RNA elements in Trypanosoma brucei.

Mao Y, Najafabadi HS, Salavati R.

BMC Genomics. 2009 Aug 4;10:355. doi: 10.1186/1471-2164-10-355.

28.

Searching for virulence factors in the non-pathogenic parasite to humans Leishmania tarentolae.

Azizi H, Hassani K, Taslimi Y, Najafabadi HS, Papadopoulou B, Rafati S.

Parasitology. 2009 Jun;136(7):723-35. doi: 10.1017/S0031182009005873. Epub 2009 May 6.

PMID:
19416551
29.

Sequence-based prediction of protein-protein interactions by means of codon usage.

Najafabadi HS, Salavati R.

Genome Biol. 2008;9(5):R87. doi: 10.1186/gb-2008-9-5-r87. Epub 2008 May 23.

30.

MAD-DPD: designing highly degenerate primers with maximum amplification specificity.

Najafabadi HS, Saberi A, Torabi N, Chamankhah M.

Biotechniques. 2008 Apr;44(4):519-20, 522, 524-6. doi: 10.2144/000112694.

31.

Designing multiple degenerate primers via consecutive pairwise alignments.

Najafabadi HS, Torabi N, Chamankhah M.

BMC Bioinformatics. 2008 Jan 27;9:55. doi: 10.1186/1471-2105-9-55.

32.

Amino acid and codon usage profiles: adaptive changes in the frequency of amino acids and codons.

Goodarzi H, Torabi N, Najafabadi HS, Archetti M.

Gene. 2008 Jan 15;407(1-2):30-41. Epub 2007 Oct 5.

PMID:
17977670
33.

Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix.

Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS.

J Theor Biol. 2007 Apr 21;245(4):715-25. Epub 2006 Dec 19.

PMID:
17240399
34.

Error minimization explains the codon usage of highly expressed genes in Escherichia coli.

Najafabadi HS, Lehmann J, Omidi M.

Gene. 2007 Jan 31;387(1-2):150-5. Epub 2006 Sep 26.

PMID:
17097242
35.

Applying a neural network to predict the thermodynamic parameters for an expanded nearest-neighbor model.

Najafabadi HS, Goodarzi H, Torabi N, Banihosseini SS.

J Theor Biol. 2006 Feb 7;238(3):657-65. Epub 2005 Aug 2.

PMID:
16061260
36.

The impact of including tRNA content on the optimality of the genetic code.

Goodarzi H, Najafabadi HS, Nejad HA, Torabi N.

Bull Math Biol. 2005 Nov;67(6):1355-68.

PMID:
16005951
37.
38.

Optimality of codon usage in Escherichia coli due to load minimization.

Najafabadi HS, Goodarzi H, Torabi N.

J Theor Biol. 2005 Nov 21;237(2):203-9. Epub 2005 Jun 1.

PMID:
15932760
39.

On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices.

Goodarzi H, Najafabadi HS, Hassani K, Nejad HA, Torabi N.

J Theor Biol. 2005 Aug 7;235(3):318-25.

PMID:
15882694
40.
41.

How reliable re-adjustment is: correspondence regarding A. Fuglsang, "The 'effective number of codons' revisited".

Marashi SA, Najafabadi HS.

Biochem Biophys Res Commun. 2004 Nov 5;324(1):1-2.

PMID:
15464973

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