Works by Rigoutsos, Isidore

Results: 73

Re-Analyses of Samples From Amyotrophic Lateral Sclerosis Patients and Controls Identify Many Novel Small RNAs With Diagnostic And Prognostic Potential.

Published in:

Molecular Neurobiology, 2025, v. 62, n. 7, p. 8135, doi. 10.1007/s12035-025-04747-2

By:

Loher, Phillipe;
Londin, Eric;
Ilieva, Hristelina;
Pasinelli, Piera;
Rigoutsos, Isidore

Publication type:

Article

Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types.

Published in:

Scientific Reports, 2014, p. 1, doi. 10.1038/srep05947

By:

Clark, Peter M.;
Loher, Phillipe;
Quann, Kevin;
Brody, Jonathan;
Londin, Eric R.;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Pigment Cell & Melanoma Research, 2020, v. 33, n. 1, p. 52, doi. 10.1111/pcmr.12810

By:

Londin, Eric;
Magee, Rogan;
Shields, Carol L.;
Lally, Sara E.;
Sato, Takami;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nature Biotechnology, 2006, v. 24, n. 10, p. 1263, doi. 10.1038/nbt1247

By:

Martín, Héctor García;
Ivanova, Natalia;
Kunin, Victor;
Warnecke, Falk;
Barry, Kerrie W.;
McHardy, Alice C.;
Yeates, Christine;
He, Shaomei;
Salamov, Asaf A.;
Szeto, Ernest;
Dalin, Eileen;
Putnam, Nik H.;
Shapiro, Harris J.;
Pangilinan, Jasmyn L.;
Rigoutsos, Isidore;
Kyrpides, Nikos C.;
Blackall, Linda Louise;
McMahon, Katherine D.;
Hugenholtz, Philip

Publication type:

Article

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

Published in:

2009

By:

Tay, Yvonne;
Zhang, Jinqiu;
Thomson, Andrew M.;
Lim, Bing;
Rigoutsos, Isidore

Publication type:

Correction Notice

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

Published in:

Nature, 2008, v. 455, n. 7216, p. 1124, doi. 10.1038/nature07299

By:

Tay, Yvonne;
Jinqiu Zhang;
Thomson, Andrew M.;
Bing Lim;
Rigoutsos, Isidore

Publication type:

Article

A linguistic model for the rational design of antimicrobial peptides.

Published in:

Nature, 2006, v. 443, n. 7113, p. 867, doi. 10.1038/nature05233

By:

Loose, Christopher;
Jensen, Kyle;
Rigoutsos, Isidore;
Stephanopoulos, Gregory

Publication type:

Article

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

Published in:

Bioinformatics, 2021, v. 37, n. 13, p. 1828, doi. 10.1093/bioinformatics/btab016

By:

Loher, Phillipe;
Karathanasis, Nestoras;
Londin, Eric;
Bray, Paul F.;
Pliatsika, Venetia;
Telonis, Aristeidis G.;
Rigoutsos, Isidore

Publication type:

Article

The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease.

Published in:

Non-Coding RNA, 2023, v. 9, n. 6, p. 69, doi. 10.3390/ncrna9060069

By:

Akins, Robert Brian;
Ostberg, Kayleigh;
Cherlin, Tess;
Tsiouplis, Nikolas J.;
Loher, Phillipe;
Rigoutsos, Isidore

Publication type:

Article

Atypical transcription of microRNA gene fragments.

Published in:

Nucleic Acids Research, 2010, v. 38, n. 9, p. 2775, doi. 10.1093/nar/gkp1242

By:

Song Gao, Jin;
Zhang, Yingjie;
Li, Ming;
Tucker, Lynne D.;
Machan, Jason T.;
Quesenberry, Peter;
Rigoutsos, Isidore;
Ramratnam, Bharat

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2008, v. 36, n. 10, p. 3484, doi. 10.1093/nar/gkn155

By:

Tsirigos, Aristotelis;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. 12, p. 3699, doi. 10.1093/nar/gki660

By:

Tsirigos, Aristotelis;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2005, v. 33, n. 3, p. 922, doi. 10.1093/nar/gki187

By:

Tsirigos, Aristotelis;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w10, doi. 10.1093/nar/gkh367

By:

Huynh, Tien;
Rigoutsos, Isidore

Publication type:

Article

Transcriptional organization of the Clostridium acetobutylicum genome.

Published in:

Nucleic Acids Research, 2004, v. 32, n. 6, p. 1973, doi. 10.1093/nar/gkh509

By:

Paredes, Carlos J.;
Rigoutsos, Isidore;
Papoutsakis, E. Terry

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2003, v. 31, n. 15, p. 4625, doi. 10.1093/nar/gkg639

By:

Rigoutsos, Isidore;
Riek, Peter;
Graham, Robert M.;
Novotny, Jiri

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2003, v. 31, n. 13, p. 3645, doi. 10.1093/nar/gkg621

By:

Huynh, Tien;
Rigoutsos, Isidore;
Parida, Laxmi;
Platt, Daniel;
Shibuya, Tetsuo

Publication type:

Article

Dictionary‐driven protein annotation.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 17, p. 3901, doi. 10.1093/nar/gkf464

By:

Rigoutsos, Isidore;
Huynh, Tien;
Floratos, Aris;
Parida, Laxmi;
Platt, Daniel

Publication type:

Article

Dictionary-driven prokaryotic gene finding.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 12, p. 2710, doi. 10.1093/nar/gkf338

By:

Shibuya, Tetsuo;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24681-w

By:

Shigematsu, Megumi;
Kawamura, Takuya;
Morichika, Keisuke;
Izumi, Natsuko;
Kiuchi, Takashi;
Honda, Shozo;
Pliatsika, Venetia;
Matsubara, Ryuma;
Rigoutsos, Isidore;
Katsuma, Susumu;
Tomari, Yukihide;
Kirino, Yohei

Publication type:

Article

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

Published in:

Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1224-0

By:

Rigoutsos, Isidore;
Sang Kil Lee;
Su Youn Nam;
Anfossi, Simone;
Pasculli, Barbara;
Pichler, Martin;
Yi Jing;
Rodriguez-Aguayo, Cristian;
Telonis, Aristeidis G.;
Rossi, Simona;
Ivan, Cristina;
Ivkovic, Tina Catela;
Fabris, Linda;
Clark, Peter M.;
Hui Ling;
Shimizu, Masayoshi;
Redis, Roxana S.;
Shah, Maitri Y.;
Xinna Zhang;
Yoshinaga Okugawa

Publication type:

Article

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

Published in:

RNA Biology, 2019, v. 16, n. 12, p. 1817, doi. 10.1080/15476286.2019.1664885

By:

Pawar, Kamlesh;
Shigematsu, Megumi;
Loher, Phillipe;
Honda, Shozo;
Rigoutsos, Isidore;
Kirino, Yohei

Publication type:

Article

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

Published in:

Proteins, 2005, v. 61, n. 4, p. 926, doi. 10.1002/prot.20608

By:

Darzentas, Nikos;
Rigoutsos, Isidore;
Ouzounis, Christos A.

Publication type:

Article

Global secondary structure packing angle bias in proteins.

Published in:

Proteins, 2003, v. 53, n. 2, p. 252, doi. 10.1002/prot.10448

By:

Daniel E. Platt;
Concettina Guerra;
Giuseppe Zanotti;
Isidore Rigoutsos

Publication type:

Article

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

Published in:

Proteins, 1999, v. 37, n. 2, p. 264, doi. 10.1002/(SICI)1097-0134(19991101)37:2<264::AID-PROT11>3.0.CO;2-C

By:

Rigoutsos, Isidore;
Floratos, Aris;
Ouzounis, Christos;
Gao, Yuan;
Parida, Laxmi

Publication type:

Article

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

Published in:

Journal of Neuroscience, 2008, v. 28, n. 5, p. 1213, doi. 10.1523/JNEUROSCI.5065-07.2008

By:

Wang-Xia Wang;
Rajeev, Bernard W.;
Stromberg, Arnold J.;
Na Ren;
Guiliang Tang;
Qingwei Huang;
Rigoutsos, Isidore;
Nelson, Peter T.

Publication type:

Article

A generic motif discovery algorithm for sequential data.

Published in:

Bioinformatics, 2006, v. 22, n. 1, p. 21, doi. 10.1093/bioinformatics/bti745

By:

Kyle L. Jensen;
Mark P. Styczynski;
Isidore Rigoutsos;
Gregory N. Stephanopoulos

Publication type:

Article

Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm.

Published in:

Bioinformatics, 1998, v. 14, n. 1, p. 55, doi. 10.1093/bioinformatics/14.1.55

By:

Rigoutsos, Isidore;
Floratos, Aris

Publication type:

Article

Reproducibility efforts as a teaching tool: A pilot study.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 11, p. 1, doi. 10.1371/journal.pcbi.1010615

By:

Karathanasis, Nestoras;
Hwang, Daniel;
Heng, Vibol;
Abhimannyu, Rimal;
Slogoff-Sevilla, Phillip;
Buchel, Gina;
Frisbie, Victoria;
Li, Peiyao;
Kryoneriti, Dafni;
Rigoutsos, Isidore

Publication type:

Article

Using medicare claims to estimate risk-adjusted performance of Pennsylvania trauma centers.

Published in:

PLoS Digital Health, 2023, v. 1, n. 6, p. 1, doi. 10.1371/journal.pdig.0000263

By:

Zebrowski, Alexis M.;
Loher, Phillipe;
Buckler, David G.;
Rigoutsos, Isidore;
Carr, Brendan G.;
Wiebe, Douglas J.

Publication type:

Article

HuR's post-transcriptional regulation of death receptor 5 in pancreatic cancer cells.

Published in:

Cancer Biology & Therapy, 2012, v. 13, n. 10, p. 946, doi. 10.4161/cbt.20952

By:

Pineda, Danielle M.;
Rittenhouse, David W.;
Valley, Christopher C.;
Cozzitorto, Joseph A.;
Burkhart, Richard A.;
Leiby, Benjamin;
Winter, Jordan M.;
Weber, Matthew C.;
Londin, Eric R.;
Rigoutsos, Isidore;
Yeo, Charles J.;
Gorospe, Myriam;
Witkiewicz, Agnieska K.;
Sachs, Jonathan N.;
Brody, Jonathan R.

Publication type:

Article

Evolution of distinct EGF domains with specific functions.

Published in:

Protein Science: A Publication of the Protein Society, 2005, v. 14, n. 4, p. 1091, doi. 10.1110/ps.041207005

By:

Wouters, Merridee A.;
Rigoutsos, Isidore;
Chu, Carmen K.;
Feng, Lina L.;
Sparrow, Duncan B.;
Dunwoodie, Sally L.

Publication type:

Article

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.

Published in:

Bioinformatics, 2020, v. 36, n. 3, p. 698, doi. 10.1093/bioinformatics/btz675

By:

Desvignes, Thomas;
Loher, Phillipe;
Eilbeck, Karen;
Ma, Jeffery;
Urgese, Gianvito;
Fromm, Bastian;
Sydes, Jason;
Aparicio-Puerta, Ernesto;
Barrera, Victor;
Espín, Roderic;
Thibord, Florian;
Ros, Xavier Bofill-De;
Londin, Eric;
Telonis, Aristeidis G;
Ficarra, Elisa;
Friedländer, Marc R;
Postlethwait, John H;
Rigoutsos, Isidore;
Hackenberg, Michael;
Vlachos, Ioannis S

Publication type:

Article

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

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 2034, doi. 10.1093/bioinformatics/btx073

By:

Magee, Rogan;
Loher, Phillipe;
Londin, Eric;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Bioinformatics, 2016, v. 32, n. 16, p. 2481, doi. 10.1093/bioinformatics/btw194

By:

Pliatsika, Venetia;
Loher, Phillipe;
Telonis, Aristeidis G.;
Rigoutsos, Isidore

Publication type:

Article

Interactive exploration of RNA22 microRNA target predictions.

Published in:

Bioinformatics, 2012, v. 28, n. 24, p. 3322, doi. 10.1093/bioinformatics/bts615

By:

Loher, Phillipe;
Rigoutsos, Isidore

Publication type:

Article

microRNAs in colon cancer: A roadmap for discovery

Published in:

FEBS Letters, 2012, v. 586, n. 19, p. 3000, doi. 10.1016/j.febslet.2012.07.048

By:

Rossi, Simona;
Di Narzo, Antonio Fabio;
Mestdagh, Pieter;
Jacobs, Bart;
Bosman, Fredrik T.;
Gustavsson, Bengt;
Majoie, Bernard;
Roth, Arnaud;
Vandesompele, Jo;
Rigoutsos, Isidore;
Delorenzi, Mauro;
Tejpar, Sabine

Publication type:

Article

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

Published in:

FEBS Letters, 2011, v. 585, n. 4, p. 693, doi. 10.1016/j.febslet.2011.01.033

By:

Gao, Jin-Song;
Zhang, Yingjie;
Tang, Xiaoli;
Tucker, Lynne D.;
Tarwater, Patrick M.;
Quesenberry, Peter J.;
Rigoutsos, Isidore;
Ramratnam, Bharat

Publication type:

Article

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

Published in:

FEBS Letters, 2009, v. 583, n. 22, p. 3725, doi. 10.1016/j.febslet.2009.10.002

By:

Zhang, Yingjie;
Gao, Jin-Song;
Tang, Xiaoli;
Tucker, Lynne D.;
Quesenberry, Peter;
Rigoutsos, Isidore;
Ramratnam, Bharat

Publication type:

Article

The complex transcriptional landscape of the anucleate human platelet.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-1

By:

Bray, Paul F.;
McKenzie, Steven E.;
Edelstein, Leonard C.;
Nagalla, Srikanth;
Delgrosso, Kathleen;
Ertel, Adam;
Kupper, Joan;
Yi Jing;
Londin, Eric;
Loher, Phillipe;
Huang-Wen Chen;
Fortina, Paolo;
Rigoutsos, Isidore

Publication type:

Article

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content.

Published in:

BMC Biology, 2021, v. 19, n. 1, p. 1, doi. 10.1186/s12915-020-00928-8

By:

Telonis, Aristeidis G.;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

BMC Biology, 2020, v. 18, n. 1, p. 1, doi. 10.1186/s12915-020-0763-0

By:

Cherlin, Tess;
Magee, Rogan;
Jing, Yi;
Pliatsika, Venetia;
Loher, Phillipe;
Rigoutsos, Isidore

Publication type:

Article

Consequential considerations when mapping tRNA fragments.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-0921-0

By:

Telonis, Aristeidis G.;
Loher, Phillipe;
Yohei Kirino;
Rigoutsos, Isidore

Publication type:

Article

Inhibition of the Single Downstream Target BAG1 Activates the Latent Apoptotic Potential of MYC.

Published in:

Molecular & Cellular Biology, 2011, v. 31, n. 24, p. 5037, doi. 10.1128/MCB.06297-11

By:

Xiao-Yong Zhang;
Pfeiffer, Harla K.;
Mellert, Hestia S.;
Stanek, Timothy J.;
Sussman, Robyn T.;
Kumari, Alpana;
Duonan Yu;
Rigoutsos, Isidore;
Thomas-Tikhonenko, Andrei;
Seidel, Hans E.;
Chodosh, Lewis A.;
Packham, Graham;
Baserga, Renato;
McMahon, Steven B.

Publication type:

Article

Alu and B1 Repeats Have Been Selectively Retained in the Upstream and Intronic Regions of Genes of Specific Functional Classes.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 12, p. 1, doi. 10.1371/journal.pcbi.1000610

By:

Tsirigos, Aristotelis;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Frontiers in Genetics, 2015, p. 1, doi. 10.3389/fgene.2015.00242

By:

Quann, Kevin;
Yi Jing;
Rigoutsos, Isidore

Publication type:

Article

Nuclear and mitochondrial tRNA-lookalikes in the human genome.

Published in:

Frontiers in Genetics, 2014, v. 5, p. 1, doi. 10.3389/fgene.2014.00344

By:

Telonis, Aristeidis G.;
Loher, Phillipe;
Kirino, Yohei;
Rigoutsos, Isidore

Publication type:

Article

CorrAdjust unveils biologically relevant transcriptomic correlations by efficiently eliminating hidden confounders Open Access.

Published in:

Nucleic Acids Research, 2025, v. 53, n. 10, p. 1, doi. 10.1093/nar/gkaf444

By:

Nersisyan, Stepan;
Loher, Phillipe;
Rigoutsos, Isidore

Publication type:

Article

On the expanding roles of tRNA fragments in modulating cell behavior.

Published in:

Nucleic Acids Research, 2020, v. 48, n. 17, p. 9433, doi. 10.1093/nar/gkaa657

By:

Magee, Rogan;
Rigoutsos, Isidore

Publication type:

Article

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

Published in:

Nucleic Acids Research, 2018, v. 46, n. D1, p. D152, doi. 10.1093/nar/gkx1075

By:

Pliatsika, Venetia;
Loher, Phillipe;
Magee, Rogan;
Telonis, Aristeidis G;
Londin, Eric;
Shigematsu, Megumi;
Kirino, Yohei;
Rigoutsos, Isidore

Publication type:

Article