Rigoutsos, I.: search on Z-Library

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1

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

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

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 3.04 MB

english, 2018

2

Searching in parallel for similar strings [biological sequences]

Rigoutsos, I., Califano, A.

Journal:

IEEE Computational Science and Engineering

Year:

1994

Language:

english

File:

PDF, 2.40 MB

english, 1994

3

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

Kaoru Azumi, Rosaria Santis, Anthony Tomaso, Isidore Rigoutsos, Fumiko Yoshizaki, Maria Rosaria Pinto, Rita Marino, Kazuhito Shida, Makoto Ikeda, Masami Ikeda, Masafumi Arai, Yasuhito Inoue, Toshio Sh

Journal:

Year:

2003

Language:

english

File:

PDF, 312 KB

english, 2003

4

TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements

Navarro, Fabio CP, Hoops, Jacob, Bellfy, Lauren, Cerveira, Eliza, Zhu, Qihui, Zhang, Chengsheng, Lee, Charles, Gerstein, Mark B., Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 2.12 MB

english, 2019

5

An algorithm for point clustering and grid generation

Berger, M., Rigoutsos, I.

Journal:

IEEE Transactions on Systems Man and Cybernetics

Year:

1991

Language:

english

File:

PDF, 792 KB

english, 1991

6

A Double Deduction System for Quantum Logic Based On Natural Deduction

Yannis Delmas-Rigoutsos

Journal:

Journal of Philosophical Logic

Year:

1997

Language:

english

File:

PDF, 152 KB

english, 1997

7

An Approximation Algorithm for Alignment of Multiple Sequences using Motif Discovery

Laxmi Parida, Aris Floratos, Isidore Rigoutsos

Journal:

Journal of Combinatorial Optimization

Year:

1999

Language:

english

File:

PDF, 850 KB

english, 1999

8

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

Tsirigos, Aristotelis, Rigoutsos, Isidore, Stormo, Gary D.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 390 KB

english, 2009

9

HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data

Berger, Emily, Yorukoglu, Deniz, Peng, Jian, Berger, Bonnie, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 587 KB

english, 2014

10

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

Telonis, Aristeidis G., Magee, Rogan, Loher, Phillipe, Chervoneva, Inna, Londin, Eric, Rigoutsos, Isidore

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.80 MB

english, 2017

11

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

Honda, Shozo, Loher, Phillipe, Morichika, Keisuke, Shigematsu, Megumi, Kawamura, Takuya, Kirino, Yoriko, Rigoutsos, Isidore, Kirino, Yohei

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 4.01 MB

english, 2017

12

DELPHI: A pattern-based method for detecting sequence similarity

Floratos, A., Rigoutsos, I., Parida, L., Gao, Y.

Journal:

IBM Journal of Research and Development

Year:

2001

Language:

english

File:

PDF, 340 KB

english, 2001

13

[IEEE Comput. Soc 1998 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Santa Barbara, CA, USA (23-25 June 1998)] Proceedings. 1998 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (Cat. No.98CB36231) - Well-behaved, tunable 3D-affine invariants

Year:

1998

Language:

english

File:

PDF, 1.15 MB

english, 1998

14

[ACM Press the Thirteenth ACM conference - Washington, D.C., USA (2004.11.08-2004.11.13)] Proceedings of the Thirteenth ACM conference on Information and knowledge management - CIKM '04 - Of parts and relationships

Rigoutsos, Isidore

Year:

2004

Language:

english

File:

PDF, 112 KB

english, 2004

15

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

Huynh, T., Rigoutsos, I.

Journal:

Nucleic Acids Research

Year:

2004

Language:

english

File:

PDF, 553 KB

english, 2004

16

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

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

Journal:

Year:

2016

Language:

english

File:

PDF, 1.19 MB

english, 2016

17

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

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

Journal:

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

18

A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes

Kevin C. Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, Wai-Leong Tam, Andrew M. Thomson, Bing Lim, Isidore Rigoutsos

Journal:

Year:

2006

Language:

english

File:

PDF, 1.16 MB

english, 2006

19

Reevaluation of human cytomegalovirus coding potential

Murphy, E., Rigoutsos, I., Shibuya, T., Shenk, T. E.

Journal:

Proceedings of the National Academy of Sciences

Year:

2003

Language:

english

File:

PDF, 1.22 MB

english, 2003

20

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

Pierson, Emma, Koller, Daphne, Battle, Alexis, Mostafavi, Sara, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 3.55 MB

english, 2015

21

A Double Deduction System for Quantum Logic Based on Natural Deduction

Yannis Delmas-Rigoutsos

Journal:

Journal of Philosophical Logic

Year:

1997

Language:

english

File:

PDF, 812 KB

english, 1997

22

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

Zhou, H, Telonis, A G, Jing, Y, Xia, N L, Biederman, L, Jimbo, M, Blanco, F, Londin, E, Brody, J R, Rigoutsos, I

Journal:

Cell Death and Disease

Year:

2016

Language:

english

File:

PDF, 2.48 MB

english, 2016

23

Comparative molecular moment analysis (CoMMA)

B. David Silverman, Daniel E. Platt, Mike Pitman, Isidore Rigoutsos

Journal:

Perspectives in Drug Discovery and Design

Year:

1998

Language:

english

File:

PDF, 73 KB

english, 1998

24

Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

Sung, Jaeyun, Kim, Pan-Jun, Ma, Shuyi, Funk, Cory C., Magis, Andrew T., Wang, Yuliang, Hood, Leroy, Geman, Donald, Price, Nathan D., Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.78 MB

english, 2013

25

[IEEE Comput. Soc. Press IEEE Conference on Computer Vision and Pattern Recognition - New York, NY, USA (15-17 June 1993)] Proceedings of IEEE Conference on Computer Vision and Pattern Recognition - FLASH: a fast look-up algorithm for string homology

Califano, A., Rigoutsos, I.

Year:

1993

Language:

english

File:

PDF, 755 KB

english, 1993

26

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

Londin, Eric, Loher, Phillipe, Rigoutsos, Isidore

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 528 KB

english, 2015

27

Nuclear and mitochondrial tRNA-lookalikes in the human genome

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

Journal:

Frontiers in Genetics

Year:

2014

Language:

english

File:

PDF, 3.22 MB

english, 2014

28

[ACM Press the second annual international conference - New York, New York, United States (1998.03.22-1998.03.25)] Proceedings of the second annual international conference on Computational molecular biology - RECOMB '98 - Motif discovery without alignment or enumeration (extended abstract)

Rigoutsos, Isidore, Floratos, Aris

Year:

1998

Language:

english

File:

PDF, 726 KB

english, 1998

29

Assessment of isomiR Discrimination Using Commercial qPCR Methods

Magee, Rogan, Telonis, Aristeidis G., Cherlin, Tess, Rigoutsos, Isidore, Londin, Eric

Journal:

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

30

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

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

Journal:

Year:

2009

File:

PDF, 92 KB

2009

31

[IEEE Comput. Soc. Press IEEE Conference on Computer Vision and Pattern Recognition - New York, NY, USA (15-17 June 1993)] Proceedings of IEEE Conference on Computer Vision and Pattern Recognition - Distributed Bayesian object recognition

Rigoutsos, I., Hummel, R.

Year:

1993

Language:

english

File:

PDF, 783 KB

english, 1993

32

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

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, Isid

Journal:

Cancer Biology & Therapy

Year:

2012

Language:

english

File:

PDF, 1.28 MB

english, 2012

33

IsomiRs and tRNA ‐derived Fragments are Associated with Metastasis and Patient Survival in Uveal Melanoma

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

Journal:

Pigment Cell & Melanoma Research

Year:

2019

File:

PDF, 535 KB

2019

34

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

Read, David F., Cook, Kate, Lu, Yang Y., Le Roch, Karine G., Noble, William Stafford, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 2.82 MB

2019

35

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

Yvonne Tay, Lev Kats, Leonardo Salmena, Dror Weiss, Shen Mynn Tan, Ugo Ala, Florian Karreth, Laura Poliseno, Paolo Provero, Ferdinando Di Cunto, Judy Lieberman, Isidore Rigoutsos, Pier Paolo Pandolfi

Journal:

Year:

2011

Language:

english

File:

PDF, 2.03 MB

english, 2011

36

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

Blanco, F F, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L, Meisner-Kober, N, Londin, E, Rigoutsos, I, Sawicki, J A, Risbud, M V, Witkiewicz, A K, McCue, P A, Jiang, W, Rui, H, Yeo, C J,

Journal:

Year:

2015

Language:

english

File:

PDF, 3.06 MB

english, 2015

37

Dictionary-driven protein annotation

Journal:

Nucleic Acids Research

Year:

2002

Language:

english

File:

PDF, 674 KB

english, 2002

38

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

Haiminen, Niina, Kuhn, David N., Parida, Laxmi, Rigoutsos, Isidore, Rzhetsky, Andrey

Journal:

Year:

2011

Language:

english

File:

PDF, 528 KB

english, 2011

39

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

Quann, Kevin, Jing, Yi, Rigoutsos, Isidore

Journal:

Frontiers in Genetics

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

40

On the expanding roles of tRNA fragments in modulating cell behavior

Magee, Rogan, Rigoutsos, Isidore

Journal:

Nucleic Acids Research

Year:

2020

File:

PDF, 1.95 MB

2020

41

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

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 306 KB

english, 1999

42

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

Jiri Novotny, Isidore Rigoutsos, David Coleman, Thomas Shenk

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 365 KB

english, 2001

43

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm [published erratum appears in Bioinformatics 1998;14(2):229]

Rigoutsos, I., Floratos, A.

Journal:

Year:

1998

Language:

english

File:

PDF, 940 KB

english, 1998

44

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

Xia, Rui, Vattathil, Selina, Scheet, Paul, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 2.57 MB

english, 2014

45

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

Honda, Shozo, Loher, Phillipe, Shigematsu, Megumi, Palazzo, Juan P., Suzuki, Ryusuke, Imoto, Issei, Rigoutsos, Isidore, Kirino, Yohei

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

46

[ACM Press Tutorial notes of the sixth ACM SIGKDD international conference - Boston, Massachusetts, United States (2000.08.20-2000.08.23)] Tutorial notes of the sixth ACM SIGKDD international conference on Knowledge discovery and data mining - KDD '00 - Knowledge discovery in biological domains (tutorial AM-3)

Floratos, A., Jurisica, I., Rigoutsos, I.

Year:

2000

Language:

english

File:

PDF, 7.39 MB

english, 2000

47

Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability

Kirino, Yohei, Kim, Namwoo, de Planell-Saguer, Mariàngels, Khandros, Eugene, Chiorean, Stephanie, Klein, Peter S., Rigoutsos, Isidore, Jongens, Thomas A., Mourelatos, Zissimos

Journal:

Nature Cell Biology

Year:

2009

Language:

english

File:

PDF, 1.89 MB

english, 2009

48

microRNAs in colon cancer: A roadmap for discovery

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

Journal:

Year:

2012

Language:

english

File:

PDF, 239 KB

english, 2012

49

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

Pliatsika, Venetia, Rigoutsos, Isidore

Journal:

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

50

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

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

Journal:

Year:

2019

Language:

english

File:

PDF, 2.65 MB

english, 2019

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