List of works by Isidore Rigoutsos

"Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs

scientific article

A generic motif discovery algorithm for sequential data

scientific article

A linguistic model for the rational design of antimicrobial peptides

scientific article published in October 2006

A new computational method for the detection of horizontal gene transfer events

scientific article

A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes

scientific article (publication date: 22 September 2006)

A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

scientific article

Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap

scientific article published on January 2018

Accurate phylogenetic classification of variable-length DNA fragments

scientific article

Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a

scientific article

Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes

scientific article

An extension and novel solution to the (l,d)-motif challenge problem.

scientific article

An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia

scientific article published on 9 May 2017

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs

scientific article

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types

scientific article

Assessment of isomiR Discrimination Using Commercial qPCR Methods.

scientific article published on 24 March 2017

Atypical transcription of microRNA gene fragments

scientific article

BLOSUM62 miscalculations improve search performance

scientific article

Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity.

scientific article

Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes.

scientific article published on January 1999

Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs

scientific article

Consequential considerations when mapping tRNA fragments

scientific article

Correction: Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results

scientific article (publication date: 5 October 2011)

Correction: Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results.

scientific article

Data mining and clinical data repositories: Insights from a 667,000 patient data set.

scientific article

Decoy for microRNAs

scientific article published in Nature

Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins.

scientific article

Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies

scientific article

Dynamic changes in the human methylome during differentiation

scientific article

ERRATUM: Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets

scholarly article published in Scientific Reports

Evaluation of annotation strategies using an entire genome sequence

scientific article

Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results

scientific article (publication date: 2011)

Evolution of distinct EGF domains with specific functions

scientific article

Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme

scientific article published on 12 September 2019

FLASH: a fast look-up algorithm for string homology

scientific article published on January 1, 1993

GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR.

scientific article published on 14 July 2016

Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: “waiting for Godot”

article

Global secondary structure packing angle bias in proteins.

scientific article published in November 2003

High-resolution metagenomics targets specific functional types in complex microbial communities.

scientific article published in September 2008

HuR posttranscriptionally regulates WEE1: implications for the DNA damage response in pancreatic cancer cells

scientific article

HuR's post-transcriptional regulation of Death Receptor 5 in pancreatic cancer cells.

scientific article

In silico pattern-based analysis of the human cytomegalovirus genome

scientific article

In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome.

scientific article

Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells

scientific article

Inhibition of the single downstream target BAG1 activates the latent apoptotic potential of MYC.

scientific article published on 10 October 2011

Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic development

scientific article

Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.

scientific article published on 26 April 2016

Interactive exploration of RNA22 microRNA target predictions

scientific article

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

scientific article

IsomiRs and tRNA-derived fragments are associated with metastasis and patient survival in uveal melanoma

scientific article published on 16 August 2019

Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types

scientific article

MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects

scientific article published on 23 November 2017

MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments.

scientific article published on 13 April 2016

MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data.

scientific article

MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences

scientific article published on 01 January 1998

Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks

scientific article published on 15 January 2004

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

scientific article

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

scientific article (publication date: 22 November 2007)

MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells

scientific article (publication date: September 2014)

MicroRNA 125a and its regulation of the p53 tumor suppressor gene

scientific article published on 8 October 2009

MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1.

scientific article

MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation

scientific article

Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?

scientific article

Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets.

scientific article

Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonists

scientific article published on 01 November 1998

Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer

scientific article published on 31 August 2016

N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration

scientific article

New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites

scientific article published on 07 April 2009

Nuclear and mitochondrial tRNA-lookalikes in the human genome

scientific article published in 2014

OMiR: Identification of associations between OMIM diseases and microRNAs

scientific article published on 23 October 2010

On the expanding roles of tRNA fragments in modulating cell behavior

scientific article published on 05 September 2020

Pattern-based phylogenetic distance estimation and tree reconstruction.

scientific article

Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b

scientific article published on 31 August 2016

Post-transcriptional regulation of BRCA1 through its coding sequence by the miR-15/107 group of miRNAs

scientific article published on 24 July 2015

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer.

scientific article published on 28 March 2018

RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors

scientific article published on 23 July 2021

Race disparities in the contribution of miRNA isoforms and tRNA-derived fragments to triple-negative breast cancer.

scientific article published on 11 December 2017

Reevaluation of human cytomegalovirus coding potential.

scientific article published on 30 October 2003

Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs

scientific article published on 15 May 2015

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner

scientific article published on 13 April 2020

Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families

scientific article published in December 2005

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.

scientific article

Short RNAs: how big is this iceberg?

scientific article

Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

scholarly article

Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

scientific article published on 01 April 2019

Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

scientific article

TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease

scientific article published on 25 May 2019

The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

scientific article

The Evi1, microRNA-143, K-Ras axis in colon cancer.

scientific article published on 26 January 2011

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

scientific article

The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells

scientific article published on 22 June 2017

The complex transcriptional landscape of the anucleate human platelet

scientific article

The emergence of pattern discovery techniques in computational biology.

scientific article

The emerging roles of GPRC5A in diseases

scientific article

The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1.

scientific article

The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.

scientific article published on 14 February 2014

The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells.

scientific article

The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease

scientific article

The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis

scientific article

The web server of IBM's Bioinformatics and Pattern Discovery group

scientific article

The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update

scientific article published on July 2004

Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer

scientific article published on 27 January 2020

Threshold-seq: a tool for determining the threshold in short RNA-seq datasets.

scientific article published on 14 February 2017

Transcriptional organization of the Clostridium acetobutylicum genome.

scientific article published on April 2004

Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis

scientific article published on 12 May 2021

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

scientific article

What's in the mix: phylogenetic classification of metagenome sequence samples

scientific article

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs.

scientific article published on 20 January 2017

miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53.

scientific article

microRNAs in colon cancer: a roadmap for discovery

scientific article published on September 2012

tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities

scientific article published on 17 April 2019

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