Isidore Rigoutsos

发表

BLOSUM62 miscalculations improve search performance

Mark P. Styczynski, Gregory Stephanopoulos, Kyle L. Jensen, 2008, Nature Biotechnology.

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

Phillipe Loher, Aristeidis G Telonis, Isidore Rigoutsos, 2018, Methods in molecular biology.

IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets

Phillipe Loher, Eric Londin, Venetia Pliatsika, 2021, Bioinform..

Non-α-helical elements modulate polytopic membrane protein architecture

Robert M. Graham, Isidore Rigoutsos, R. Riek, 2001 .

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

Isidore Rigoutsos, I. Rigoutsos, Honglei Zhou, 2014, RNA.

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

Venetia Pliatsika, Isidore Rigoutsos, 2015, Biology Direct.

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

Natalia Ivanova, Ernest Szeto, Héctor García Martín, 2006, Nature Biotechnology.

Coding-Independent Regulation of the Tumor Suppressor PTEN by Competing Endogenous mRNAs

Ferdinando Di Cunto, Judy Lieberman, Ugo Ala, 2011, Cell.

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

Victor Markowitz, Natalia Ivanova, Alice C. McHardy, 2008, Nature Biotechnology.

Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer.

Aristeidis G. Telonis, Isidore Rigoutsos, I. Rigoutsos, 2018, Cancer research.

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

Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos, 2017, Scientific Reports.

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

Yi Jing, Phillipe Loher, Eric Londin, 2015, Nucleic acids research.

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

Aristotelis Tsirigos, Tien Huynh, Daniel Platt, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Global secondary structure packing angle bias in proteins

Giuseppe Zanotti, Concettina Guerra, Isidore Rigoutsos, 2003, Proteins.

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

Rogan Magee, Phillipe Loher, Eric Londin, 2017, Nucleic acids research.

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

Peter Quesenberry, Isidore Rigoutsos, I. Rigoutsos, 2009, FEBS letters.

MicroRNA Target Prediction

Aristotelis Tsirigos, Isidore Rigoutsos, I. Rigoutsos, 2010 .

Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer

Phillipe Loher, Eric Londin, Aristeidis G. Telonis, 2018, Scientific Reports.

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

Isidore Rigoutsos, Gregory N Stephanopoulos, G. Stephanopoulos, 2004, Physiological genomics.

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

Yi Jing, Phillipe Loher, Aristeidis G. Telonis, 2015, Oncotarget.

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

Aristotelis Tsirigos, Isidore Rigoutsos, I. Rigoutsos, 2005, Nucleic acids research.

Transcriptional organization of the Clostridium acetobutylicum genome.

E Terry Papoutsakis, Isidore Rigoutsos, I. Rigoutsos, 2004, Nucleic acids research.

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

Alice C McHardy, Isidore Rigoutsos, I. Rigoutsos, 2007, Current opinion in microbiology.

In Silico Pattern-Based Analysis of the Human Cytomegalovirus Genome

Laxmi Parida, Tien Huynh, Daniel Platt, 2003, Journal of Virology.

Representation and Matching of Small Flexible Molecules in Large Databases of 3D Molecular Information

Isidore Rigoutsos, Andrea Califano, Daniel E. Platt, 1999, Pattern Discovery in Biomolecular Data.

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

Phillipe Loher, Eric Londin, Isidore Rigoutsos, 2015, Proceedings of the National Academy of Sciences.

Comparative molecular moment analysis (CoMMA)

Daniel E. Platt, B. David Silverman, Isidore Rigoutsos, 1998 .

DNA Based Identification

Gustavo Stolovitzky, Norah Rudin, Keith Inman, 1996 .

A linguistic model for the rational design of antimicrobial peptides

Gregory Stephanopoulos, Kyle Jensen, Kyle L. Jensen, 2006, Nature.

The Expression of MicroRNA miR-107 Decreases Early in Alzheimer's Disease and May Accelerate Disease Progression through Regulation of β-Site Amyloid Precursor Protein-Cleaving Enzyme 1

Guiliang Tang, Peter T. Nelson, Isidore Rigoutsos, 2008, The Journal of Neuroscience.

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

Aristeidis G Telonis, Isidore Rigoutsos, I. Rigoutsos, 2015, RNA biology.

Pattern-Based Phylogenetic Distance Estimation and Tree Reconstruction

Mark A. Ragan, Isidore Rigoutsos, Michael Höhl, 2006 .

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

Paul Richardson, David N. Keys, Fumiko Ohta, 2002, Science.

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types

Phillipe Loher, Eric R. Londin, Isidore Rigoutsos, 2014, Scientific Reports.

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

Yi Jing, George A Calin, Chad A Shaw, 2015, Proceedings of the National Academy of Sciences.

OMiR: Identification of associations between OMIM diseases and microRNAs.

Aristotelis Tsirigos, George A Calin, Simona Rossi, 2011, Genomics.

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

Aristotelis Tsirigos, Isidore Rigoutsos, I. Rigoutsos, 2005, Nucleic acids research.

Nuclear and mitochondrial tRNA-lookalikes in the human genome

Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos, 2014, Front. Genet..

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

Phillipe Loher, Isidore Rigoutsos, Takuya Kawamura, 2017, Nucleic acids research.

Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs

Aristotelis Tsirigos, Isidore Rigoutsos, I. Rigoutsos, 2008, Nucleic acids research.

Homotopies: A Panacea or Just Another Method?

Isidore Rigoutsos, 1986 .

Metagenomic analysis of phosphorus removing sludge communities

Natalia Ivanova, Alice C. McHardy, Ernest Szeto, 2008 .

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

Phillipe Loher, Eric R. Londin, Isidore Rigoutsos, 2014, Oncotarget.

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

Phillipe Loher, Megumi Shigematsu, Isidore Rigoutsos, 2015, Proceedings of the National Academy of Sciences.