Genomes and Genes
Affiliation: Thomas Jefferson University
Location: Philadelphia, USA
non-coding RNA, process regulation, genomics, genetics, protein annotation, gene discovery, metagenomics
- Huynh T, Rigoutsos I. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update. Nucleic Acids Res. 2004;32:W10-5 pubmed..The tools and code bundles continue to be accessible from http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/. ..
- Murphy E, Rigoutsos I, Shibuya T, Shenk T. Reevaluation of human cytomegalovirus coding potential. Proc Natl Acad Sci U S A. 2003;100:13585-90 pubmed..Support for several of the predictions of our in silico analysis was obtained by sequencing several domains within a clinical isolate of human cytomegalovirus. ..
- Azumi K, De Santis R, De Tomaso A, Rigoutsos I, Yoshizaki F, Pinto M, et al. Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: "waiting for Godot". Immunogenetics. 2003;55:570-81 pubmed..However, there are key V regions, the essential feature of an immunoglobulin superfamily VC1-like core, and possible proto-MHC regions scattered throughout the genome waiting for Godot. ..
- Huynh T, Rigoutsos I, Parida L, Platt D, Shibuya T. The web server of IBM's Bioinformatics and Pattern Discovery group. Nucleic Acids Res. 2003;31:3645-50 pubmed..The tools and code bundles can be accessed beginning at http://cbcsrv.watson.ibm.com/Tspd.html whereas the genomics annotations are available at http://cbcsrv.watson.ibm.com/Annotations/. ..
- ..Studies of additional organisms support the new pathway's presence across animals. ..
- Rigoutsos I, Novotny J, Huynh T, Chin Bow S, Parida L, Platt D, et al. In silico pattern-based analysis of the human cytomegalovirus genome. J Virol. 2003;77:4326-44 pubmed..All of the results of the present study can be found and interactively explored online (http://cbcsrv.watson.ibm.com/virus/). ..
- Hohl M, Rigoutsos I, Ragan M. Pattern-based phylogenetic distance estimation and tree reconstruction. Evol Bioinform Online. 2007;2:359-75 pubmed..The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances. ..
- Rigoutsos I, Huynh T, Floratos A, Parida L, Platt D. Dictionary-driven protein annotation. Nucleic Acids Res. 2002;30:3901-16 pubmed..Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/. ..
- McHardy A, Martin H, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007;4:63-72 pubmed..The method requires no more than 100 kb of training sequence for the creation of accurate models of sample-specific populations and can assign fragments >or=1 kb with high specificity...
- Parida -, Floratos -, Rigoutsos -. MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences. Genome Inform Ser Workshop Genome Inform. 1998;9:112-119 pubmed..The usefulness of the alignment number is corroborated by the users who view this as a natural constraint while dealing with a large number of sequences. ..
- Gao J, Zhang Y, Tang X, Tucker L, Tarwater P, Quesenberry P, et al. The Evi1, microRNA-143, K-Ras axis in colon cancer. FEBS Lett. 2011;585:693-9 pubmed publisher..We find an indirect relationship between miRNA-143 and Evi1 expression. A complex molecular axis linking Evi1, miRNA-143 is operational in human colon cancer. ..
- Rigoutsos I. New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res. 2009;69:3245-8 pubmed publisher..Recent work has shown that miRNAs can target extensively the amino acid coding region of animal mRNAs and can do so at locations that are not necessarily conserved across organisms. ..
- Mullins I, Siadaty M, Lyman J, Scully K, Garrett C, Miller W, et al. Data mining and clinical data repositories: Insights from a 667,000 patient data set. Comput Biol Med. 2006;36:1351-77 pubmed..The initial results from this study suggest that these approaches have the potential to expand research capabilities through identification of potentially novel clinical disease associations. ..
- Zhang Y, Gao J, Tang X, Tucker L, Quesenberry P, Rigoutsos I, et al. MicroRNA 125a and its regulation of the p53 tumor suppressor gene. FEBS Lett. 2009;583:3725-30 pubmed publisher..The basis of this activity is the high degree of sequence homology between the seed sequence of miR-125a and the 3'-UTR of p53. Our findings add miRNA-125a to the growing list of miRNA with oncogenic targets. ..
- Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson T, Stege J, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450:560-5 pubmed..Our results underscore how complex even a 1-microl environment can be. ..
- Tay Y, Peter S, Rigoutsos I, Barahona P, Ahmed S, Droge P. Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic development. Stem Cell Rev. 2009;5:328-33 pubmed publisher..We briefly discuss this result in the context of other known functions for miR-196b during vertebrate development. ..
- Wouters M, Rigoutsos I, Chu C, Feng L, Sparrow D, Dunwoodie S. Evolution of distinct EGF domains with specific functions. Protein Sci. 2005;14:1091-103 pubmed
- Styczynski M, Jensen K, Rigoutsos I, Stephanopoulos G. An extension and novel solution to the (l,d)-motif challenge problem. Genome Inform. 2004;15:63-71 pubmed..We demonstrate the performance of the algorithm on publicly available datasets and show that the algorithm deterministically enumerates the optimal motifs. ..
- Platt D, Guerra C, Zanotti G, Rigoutsos I. Global secondary structure packing angle bias in proteins. Proteins. 2003;53:252-61 pubmed..Selection for interactive segment triplets shows results consistent with prior studies. ..
- Shibuya T, Rigoutsos I. Dictionary-driven prokaryotic gene finding. Nucleic Acids Res. 2002;30:2710-25 pubmed..Examples of previously unreported genes are also shown and discussed in detail. ..
- Rossi S, Tsirigos A, Amoroso A, Mascellani N, Rigoutsos I, Calin G, et al. OMiR: Identification of associations between OMIM diseases and microRNAs. Genomics. 2011;97:71-6 pubmed publisher..Our findings indicate that inclusion of miRNAs among the candidate genes to be considered could assist geneticists in their hunt for disease genes, particularly in the case of rare diseases. ..
- Riek R, Rigoutsos I, Novotny J, Graham R. Non-alpha-helical elements modulate polytopic membrane protein architecture. J Mol Biol. 2001;306:349-62 pubmed..Deconvolution of these non-canonical features into their composite elements is essential for understanding the pleiotropy of polytopic protein structure and function, and must be considered in developing valid macromolecular models. ..
- Rigoutsos I, Floratos A, Parida L, Gao Y, Platt D. The emergence of pattern discovery techniques in computational biology. Metab Eng. 2000;2:159-77 pubmed..In this presentation, and after defining the problem in its generality, we review some of the algorithms that have appeared in the literature and describe several applications of pattern discovery to problems from computational biology. ..
- Rigoutsos I, Gao Y, Floratos A, Parida L. Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes. Proc Int Conf Intell Syst Mol Biol. 1999;:223-33 pubmed
- Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics. 1998;14:55-67 pubmed..Finally, experimental analysis indicates that the algorithm is output sensitive, i.e. its running time is quasi-linear to the size of the generated output. ..
- Loose C, Jensen K, Rigoutsos I, Stephanopoulos G. A linguistic model for the rational design of antimicrobial peptides. Nature. 2006;443:867-9 pubmed..We used this set of grammars to create new, unnatural AmP sequences. Our peptides conform to the formal syntax of natural antimicrobial peptides but populate a previously unexplored region of protein sequence space. ..
- Song Gao J, Zhang Y, Li M, Tucker L, Machan J, Quesenberry P, et al. Atypical transcription of microRNA gene fragments. Nucleic Acids Res. 2010;38:2775-87 pubmed publisher..Taken together, our findings suggest the existence of a previously unrecognized atypical transcription program for miRNA precursor sequences. ..
- Kalyuzhnaya M, Lapidus A, Ivanova N, Copeland A, McHardy A, Szeto E, et al. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol. 2008;26:1029-34 pubmed publisher..This high-resolution, targeted metagenomics approach may be applicable to a wide variety of ecosystems...
- Tsirigos A, Rigoutsos I. Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs. Nucleic Acids Res. 2008;36:3484-93 pubmed publisher..We highlight the ramifications of this observation with a concrete example that involves the microsatellite instability gene MLH1. ..
- Novotny J, Rigoutsos I, Coleman D, Shenk T. In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome. J Mol Biol. 2001;310:1151-66 pubmed
- Califano A, Rigoutsos I. FLASH: a fast look-up algorithm for string homology. Proc Int Conf Intell Syst Mol Biol. 1993;1:56-64 pubmed..It contains the full Swiss-Prot database rel 25 (10 MR) and the genome of E. Coli (2 MR). The system is currently being expanded to include the complete Genbank database.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Miranda K, Huynh T, Tay Y, Ang Y, Tam W, Thomson A, et al. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell. 2006;126:1203-17 pubmed..We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands. ..
- Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc Natl Acad Sci U S A. 2006;103:6605-10 pubmed..These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome. ..
- Rigoutsos I, Riek P, Graham R, Novotny J. Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. Nucleic Acids Res. 2003;31:4625-31 pubmed..The method described here has been implemented and is available on the World Wide Web at http://cbcsrv.watson.ibm.com/Ttkw.html. ..
- Darzentas N, Rigoutsos I, Ouzounis C. Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families. Proteins. 2005;61:926-37 pubmed..Our analysis suggests that pattern discovery methods can be substantially more sensitive in detecting remote protein relationships while at the same time guaranteeing high specificity. ..
- Wong M, Raab R, Rigoutsos I, Stephanopoulos G, Kelleher J. Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Physiol Genomics. 2004;16:247-55 pubmed..In conclusion, this model may be useful as a prototype physiological regulatory network where gene expression profiles are analyzed in concert with changes in cell function. ..
- Holland L, Albalat R, Azumi K, Benito Gutiérrez E, Blow M, Bronner Fraser M, et al. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008;18:1100-11 pubmed publisher..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...
- Silverman B, Pitman M, Platt D, Rigoutsos I. Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonists. J Comput Aided Mol Des. 1998;12:525-32 pubmed..The proximity of the dopamine D4 antagonist clozapine to the molecules of this series is also examined in the moment space. ..
- Dehal P, Satou Y, Campbell R, Chapman J, Degnan B, De Tomaso A, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002;298:2157-67 pubmed..The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi...
- Iliopoulos I, Tsoka S, Andrade M, Enright A, Carroll M, Poullet P, et al. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 2003;19:717-26 pubmed..The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences. ..
- Paredes C, Rigoutsos I, Papoutsakis E. Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res. 2004;32:1973-81 pubmed..Based on the set of known C.acetobutylicum TUs, the presented TU map offers an 88% prediction accuracy. ..
- Jensen K, Styczynski M, Rigoutsos I, Stephanopoulos G. A generic motif discovery algorithm for sequential data. Bioinformatics. 2006;22:21-8 pubmed..Gemoda is freely available at http://web.mit.edu/bamel/gemoda ..
- Garcia Martin H, Ivanova N, Kunin V, Warnecke F, Barry K, McHardy A, et al. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol. 2006;24:1263-9 pubmed..The present study provides a much needed blueprint for a systems-level understanding of EBPR and illustrates that metagenomics enables detailed, often novel, insights into even well-studied biological systems. ..
- Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy A, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods. 2007;4:495-500 pubmed..The simulated data sets are available online to facilitate standardized benchmarking of tools for metagenomic analysis. ..
- McHardy A, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol. 2007;10:499-503 pubmed..This step is essential for the reconstruction of the metabolic capabilities of individual organisms or phylogenetic clades of a community, and the study of their interactions. ..
- Loher P, Telonis A, Rigoutsos I. Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol Biol. 2018;1680:237-255 pubmed publisher..We discuss the various complicating factors and their ramifications, and how to use and run MINTmap, a tool that addresses these considerations...
- Bray P, McKenzie S, Edelstein L, Nagalla S, Delgrosso K, Ertel A, et al. The complex transcriptional landscape of the anucleate human platelet. BMC Genomics. 2013;14:1 pubmed publisher..The data are available through a local mirror of the UCSC genome browser and can be accessed at: http://cm.jefferson.edu/platelets_2012/. ..
- Telonis A, Rigoutsos I. Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. Cancer Res. 2018;78:1140-1154 pubmed publisher..i>Cancer Res; 78(5); 1140-54. Â©2017 AACR. ..
- Londin E, Loher P, Telonis A, Quann K, Clark P, Jing Y, et al. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc Natl Acad Sci U S A. 2015;112:E1106-15 pubmed publisher..Our findings suggest that the repertoire of human miRNAs is far more extensive than currently represented by public repositories and that there is a significant number of lineage- and/or tissue-specific miRNAs that are uncharacterized. ..