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List of works by Hamed S. Najafabadi

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

scientific article published on 01 May 2018

A Protein Complex Map of Trypanosoma brucei

scientific article

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

scientific article

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

scientific article published on 17 September 2015

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

scientific article

Age-related variations in gene expression patterns of renal cell carcinoma

scientific article published on 23 November 2018

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

scientific article published on 5 October 2007

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

scientific article published on 2 August 2005

Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

scientific article published on 07 August 2020

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

scientific article published on 18 February 2015

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

scientific article published on 01 January 2018

Correspondence regarding Bharanidharan et al., "Correlations between nucleotide frequencies and amino acid composition in 115 bacterial species"

scientific article published on 01 December 2004

Designing a neural network for the constraint optimization of the fitness functions devised based on the load minimization of the genetic code

scientific article published on 01 August 2005

Designing multiple degenerate primers via consecutive pairwise alignments

scientific article

Determination and inference of eukaryotic transcription factor sequence specificity

scientific article

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

scientific article published on 12 November 2014

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

scientific article

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

scientific article published on 28 August 2016

Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus.

scientific article

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

scientific article published on 4 August 2009

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids

scientific article published on 22 July 2013

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

scientific article

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

scientific article

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

scientific article published on 13 October 2017

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

scientific article

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

scientific article published in April 2008

Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities.

scientific article published on 23 April 2015

Model-based analysis of sample index hopping reveals its widespread artifacts in multiplexed single-cell RNA-sequencing

scientific article published on 01 June 2020

Motif comparison based on similarity of binding affinity profiles.

scientific article published on 27 July 2016

Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma

scientific article published on 22 June 2020

Multiparameter functional diversity of human C2H2 zinc finger proteins.

scientific article published on 16 November 2016

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

scientific article

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

scientific article published on 6 September 2017

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

scientific article published on 01 August 2005

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

scientific article published in June 2005

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

scientific article published in Nature Communications

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

scientific article published on 18 December 2014

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

scientific article published on 6 May 2009

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

scientific article published on 06 March 2010

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

scientific article published on 23 May 2008

Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy

scientific article published on 08 July 2020

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

scientific article published on 19 December 2006

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

scientific article published on 10 December 2016

Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding

scientific article published in 2022

Transcriptional reprogramming of skeletal muscle stem cells by the niche environment

scientific article published in 2023

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