False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5′ UTR annotations

Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency

(2022) Ivaylo P. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

VELCRO-IP RNA-seq reveals ribosome expansion segment function in translation genome-wide

(2021) Kathrin Leppek et al.   Cell Reports

Knockdown of the Ribosomal Protein eL38 in HEK293 Cells Changes the Translational Efficiency of Specific Genes

(2021) Alexander V. Gopanenko et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional and structural basis of extreme conservation in vertebrate 5′ untranslated regions

(2021) Gun Woo Byeon et al.   NATURE GENETICS

Mechanisms of Binding Specificity among bHLH Transcription Factors

(2021) Xabier de Martin et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structured elements drive extensive circular RNA translation

(2021) Chun-Kan Chen et al.   MOLECULAR CELL

Estimating the power of sequence covariation for detecting conserved RNA structure

(2020) Elena Rivas et al.   BIOINFORMATICS

Corruption of the Pearson correlation coefficient by measurement error and its estimation, bias, and correction under different error models

(2020) Edoardo Saccenti et al.   Scientific Reports

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia

(2020) Özgen Deniz et al.   Nature Communications

Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling

(2020) Mattia Furlan et al.   GENOME RESEARCH

Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen

(2020) Hao Zhang et al.   eLife

Gene- and Species-Specific Hox mRNA Translation by Ribosome Expansion Segments

(2020) Kathrin Leppek et al.   MOLECULAR CELL

S-adenosyl-l-homocysteine hydrolase links methionine metabolism to the circadian clock and chromatin remodeling

(2020) Carolina Magdalen Greco et al.   Science Advances

Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions

(2019) Joshua R. Beytebiere et al.   GENES & DEVELOPMENT

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

(2019) Imad Abugessaisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Functional Landscape of PCGF Proteins Reveals Both RING1A/B-Dependent-and RING1A/B-Independent-Specific Activities

(2019) Andrea Scelfo et al.   MOLECULAR CELL

Bhlhe40 mediates tissue-specific control of macrophage proliferation in homeostasis and type 2 immunity

(2019) Nicholas N. Jarjour et al.   NATURE IMMUNOLOGY

The Organizing Principles of Eukaryotic Ribosome Recruitment

(2019) Jerry Pelletier et al.   Annual Review of Biochemistry

MYC-Driven Small-Cell Lung Cancer is Metabolically Distinct and Vulnerable to Arginine Depletion

(2019) Milind D. Chalishazar et al.   CLINICAL CANCER RESEARCH

An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation

(2019) Alessandra Tesi et al.   EMBO REPORTS

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function

(2018) Verena M. Link et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Bhlhe40 is an essential repressor of IL-10 duringMycobacterium tuberculosisinfection

(2018) Jeremy P. Huynh et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Integrative analysis of RNA polymerase II and transcriptional dynamics upon MYC activation

(2017) Stefano de Pretis et al.   GENOME RESEARCH

­­­Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia­­

(2017) Trinna L. Cuellar et al.   JOURNAL OF CELL BIOLOGY

Identification of MYC-Dependent Transcriptional Programs in Oncogene-Addicted Liver Tumors

(2016) T. R. Kress et al.   CANCER RESEARCH

A researcher’s guide to the galaxy of IRESs

(2016) Ilya M. Terenin et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

TFEB and TFE3 are novel components of the integrated stress response

(2016) J. A. Martina et al.   EMBO JOURNAL

Cofactors of LIM Domains Associate with Estrogen Receptor α to Regulate the Expression of Noncoding RNA H19 and Corneal Epithelial Progenitor Cell Function

(2016) Rachel Herndon Klein et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner

(2016) Yi-Ying Chiou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Systematic discovery of cap-independent translation sequences in human and viral genomes

(2016) Shira Weingarten-Gabbay et al.   SCIENCE

Tunable protein synthesis by transcript isoforms in human cells

(2016) Stephen N Floor et al.   eLife

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice

(2016) Xing Tang et al.   Scientific Data

Redeployment of Myc and E2f1–3 drives Rb-deficient cell cycles

(2015) Huayang Liu et al.   NATURE CELL BIOLOGY

SHIELD: an integrative gene expression database for inner ear research

(2015) Jun Shen et al.   Database-The Journal of Biological Databases and Curation

C-MYC Transcriptionally Amplifies SOX2 Target Genes to Regulate Self-Renewal in Multipotent Otic Progenitor Cells

(2015) Kelvin Y. Kwan et al.   Stem Cell Reports

RNA polymerase II pausing during development

(2014) B. Gaertner et al.   DEVELOPMENT

RNA regulons in Hox 5′ UTRs confer ribosome specificity to gene regulation

(2014) Shifeng Xue et al.   NATURE

Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis

(2014) Arianna Sabò et al.   NATURE

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

(2014) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Comparison of the transcriptional landscapes between human and mouse tissues

(2014) Shin Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

(2014) Jingyi Jessica Li et al.   PeerJ

HAL: a hierarchical format for storing and analyzing multiple genome alignments

(2013) Glenn Hickey et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3

(2013) Joerg Betschinger et al.   CELL

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

The Current Status of Vertebrate Cellular mRNA IRESs

(2013) R. J. Jackson   Cold Spring Harbor Perspectives in Biology

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Cryptic transcripts from a ubiquitous plasmid origin of replication confound tests for cis-regulatory function

(2012) Nathan A. Lemp et al.   NUCLEIC ACIDS RESEARCH

So you want to know if your message has an IRES?

(2012) Sunnie R. Thompson   Wiley Interdisciplinary Reviews-RNA

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Ribosome-Mediated Specificity in Hox mRNA Translation and Vertebrate Tissue Patterning

(2011) Nadya Kondrashov et al.   CELL

The Vienna RNA Websuite

(2008) A. R. Gruber et al.   NUCLEIC ACIDS RESEARCH

Splicing mediates the activity of four putative cellular internal ribosome entry sites

(2008) B. T. Baranick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA