Publications

* Corresponding author
† Equal contribution

– – – – – – 2016 – – – – – –

  • 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. Expression of DRD2 is Increased in Human Pancreatic Ductal Adenocarcinoma and Inhibitors Slow Tumor Growth in Mice. Gastroenterology doi:10.1053/j.gastro.2016.08.040. Pubmed
  • Lambert SA, Albu M, Hughes TR *, Najafabadi HS *. Motif comparison based on similarity of binding affinity profiles. Bioinformatics doi:10.1093/bioinformatics/btw489. Pubmed
  • Gazestani VH, Nikpour N, Mehta V, Najafabadi HS, Moshiri H, Jardim A, Salavati R (2016). A Protein Complex Map of Trypanosoma brucei. PLoS Negl Trop Dis 10:e0004533. Pubmed

– – – – – – 2015 – – – – – –

  • Garton M, Najafabadi HS, Schmitges FW, Radovani E, Hughes TR, Kim PM (2015). A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity. Nucleic Acids Res, 43:9147-9157. Pubmed
  • Najafabadi HS, Albu M, Hughes TR (2015). Identification of C2H2-ZF binding preferences from ChIP-seq data using RCADE. Bioinformatics, 31:2879-81. Pubmed
  • 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 (2015). Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. eLife, doi:10.7554/eLife.06967. Pubmed
  • Najafabadi HS †, Mnaimneh S †, Schmitges FW †, Garton M, Lam K, Yang A, Albu M, Weirauch MT, Radovani E, Kim PM, Greenblatt J, Frey BJ, Hughes TR (2015). C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nat Biotechnol, 33:555-562. Pubmed
  • 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 (2015). The human splicing code reveals new insights into the genetic determinants of disease. Science, 347:1254806. Pubmed
  • Razavi R, Najafabadi HS, Abdullah S, Smukler S, Arntfield M, van der Kooy D (2015). Diabetes enhances the proliferation of adult pancreatic multipotent progenitor cells and biases their differentiation to more β-cell production. Diabetes, 64:1311-23. Pubmed

– – – – – – 2014 – – – – – –

  • Weirauch MT, Yang A, Albu M, Cote A, 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 M, Huang E, Mukherjee T, Chen X, Reece-Hoyes JS, Govindarajan S, Shaulsky G, Walhout AJ, Bouget F, Ratsch G, Larrondo LF, Ecker JR, and Hughes TR (2014). Determination and inference of Eukaryotic transcription factor sequence specificity. Cell, 158:1431-1443. Pubmed

– – – – – – 2013 – – – – – –

  • Najafabadi HS †, Lu Z †, MacPherson C, Mehta V, Adoue V, Pastinen T, Salavati R (2013). Global identification of conserved post-transcriptional regulatory programs in trypanosomatids. Nucleic Acids Res 41:8591-8600. Pubmed
  • Ray D †, Kazan H †, Cook K †, Weirauch M †, Najafabadi HS †, Li X, Albu M, Zheng H, Yang A, Na H, Guerrousov S, Irimia M, Matzat L, Dale R, Smith S, Yarosh C, Kelly S, Nabet B, Mecenas D, Li W, Laishram R, Qiao M, Lipshitz H, Piano F, Corbett A, Carstens R, Frey B, Anderson R, Lynch K, Penalva L, Lei E, Blencowe B, Fraser A, Morris Q, Hughes T (2013). A compendium of RNA binding motifs for decoding gene regulation. Nature 499:172–177. Pubmed

– – – – – – 2012 – – – – – –

  • Goodarzi H, Najafabadi HS, Oikonomou P, Greco TM, Fish L, Salavati R, Cristea IM, Tavazoie S (2012). Systematic discovery of structural elements governing stability of mammalian messenger RNAs. Nature 485:264-8. Pubmed

– – – – – – 2011 – – – – – –

  • Moshiri H, Acoca S, Kala S, Najafabadi HS, Hogues H, Purisima E, Salavati R (2011). Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. J Biol Chem 286:14178-89. Pubmed

– – – – – – 2010 – – – – – –

  • Najafabadi HS, Salavati R (2010). Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. PLoS Negl Trop Dis 4:e810.  Pubmed
  • Salavati R, Najafabadi HS (2010). Sequence-based functional annotation: what if most of the genes are unique to a genome? Trends Parasitol 26:225-229.  Pubmed

– – – – – – 2009 – – – – – –

  • Najafabadi HS †, Goodarzi H †, Salavati R (2009). Universal function-specificity of codon usage. Nucleic Acids Res 37:7014-23.  Pubmed
  • Mao Y †, Najafabadi HS †, Salavati R (2009). Genome-wide computational identification of functional RNA elements in Trypanosoma brucei. BMC Genomics 10:355.  Pubmed
  • Azizi H, Hassani K, Taslimi Y, Najafabadi HS, Papadopoulou B, Rafati S (2009). Searching for virulence factors in the non-pathogenic parasite to humans Leishmania tarentolae. Parasitology 136:723-35.  Pubmed

– – – – – – 2008 – – – – – –

  • Najafabadi HS, Salavati R (2008). Sequence-based prediction of protein-protein interactions by means of codon usage. Genome Biol 9:R87.  Pubmed
  • Najafabadi HS, Torabi N, Chamankhah M (2008). Designing multiple degenerate primers via consecutive pairwise alignments. BMC Bioinformatics 9:55.  Pubmed
  • Najafabadi HS, Saberi A, Torabi N, Chamankhah M (2008). MAD-DPD: designing highly degenerate primers with maximum amplification specificity. Biotechniques 44:519-526.  Pubmed

– – – – – – 2007 – – – – – –

  • Goodarzi H, Torabi N, Najafabadi HS, Archetti M (2007). Amino Acid and Codon Usage Profiles: Adaptive Changes in the Frequency of Amino Acids and Codons. Gene 407:30-41.  Pubmed
  • Goodarzi H, Katanforoush A, Torabi N, Najafabadi HS (2007). Solvent accessibility, residue charge and residue volume, the three ingredients of a robust amino acid substitution matrix. J Theor Biol 245:715-725.  Pubmed

– – – – – – 2006 – – – – – –

  • Najafabadi HS *, Lehmann J, Omidi M (2006). Error minimization explains the codon usage of highly expressed genes in Escherichia coli. Gene 387:150-155.  Pubmed
  • Torabi N, Goodarzi H, Najafabadi HS (2006). The case for an error minimizing set of coding amino acids. J Theor Biol 244:737-744.  Pubmed
  • Najafabadi HS *, Goodarzi H, Torabi N (2006). Applying a neural network to predict the thermodynamic parameters for an expanded nearest neighbor model. J Theor Biol 238:657-665.  Pubmed

– – – – – – 2005 – – – – – –

  • Goodarzi H, Najafabadi HS, Torabi N (2005). On the coevolution of genes and genetic code. Gene 362:133-140.  Pubmed
  • Najafabadi HS *, Goodarzi H, Torabi N (2005). Optimality of codon usage in Escherichia coli due to load minimization. J Theor Biol 237:203-209.  Pubmed
  • Goodarzi H, Najafabadi HS, Torabi N (2005). The impact of including tRNA content on the optimality of the genetic code. Bull Math Biol 67:1355-1368.  Pubmed
  • Goodarzi H, Najafabadi HS, Torabi N (2005). On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol 235:318-325.  Pubmed
  • Goodarzi H, Najafabadi HS, Torabi N (2005). Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code. Biosystems 81:91-100.  Pubmed

– – – – – – 2004 – – – – – –

  • Najafabadi HS *, Goodarzi H (2004). Correspondence regarding Bharanidharan et al., “Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species”. Biochem Biophys Res Commun 325:1-2.  Pubmed
  • Marashi SA, Najafabadi HS (2004). How reliable re-adjustment is: correspondence regarding A. Fuglsang, ‘‘The ‘effective number of codons’ revisited’’. Biochem Biophys Res Commun 324:1-2.  Pubmed
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