Rigoutsos, Isidore: 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

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

3

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

4

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

5

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

6

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

7

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

8

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

9

[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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

17

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

18

[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

19

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

20

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

21

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

22

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

23

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

24

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

25

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

26

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

27

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

28

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

29

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

30

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

31

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

32

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

33

“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

34

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

35

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

Telonis, Aristeidis G, Kirino, Yohei, Rigoutsos, Isidore

Journal:

Year:

2015

Language:

english

File:

PDF, 221 KB

english, 2015

36

119. HIV-1 Proviral DNA Excision and Deactivation Using a CRISPR/Cas9 “Nickase” Targeted to the 5’ and 3’ LTR

Scott, Tristan, Saayman, Sheena, Lazar, Daniel, Arbuthnot, Patrick, Rigoutsos, Isidor, Morris, Kevin, Kashanchi, Fatah, Weinberg, Marco

Journal:

Molecular Therapy

Year:

2015

Language:

english

File:

PDF, 310 KB

english, 2015

37

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

Zhou, Honglei, Rigoutsos, Isidore

Journal:

Year:

2014

Language:

english

File:

PDF, 806 KB

english, 2014

38

Leveraging functional annotations in genetic risk prediction for human complex diseases

Hu, Yiming, Lu, Qiongshi, Powles, Ryan, Yao, Xinwei, Yang, Can, Fang, Fang, Xu, Xinran, Zhao, Hongyu, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 2.22 MB

english, 2017

39

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

Telonis, Aristeidis G, Rigoutsos, Isidore

Journal:

Cancer Research

Year:

2017

Language:

english

File:

PDF, 1.23 MB

english, 2017

40

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

Nikos Darzentas, Isidore Rigoutsos, Christos A. Ouzounis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 1.01 MB

english, 2005

41

BLOSUM62 miscalculations improve search performance

Styczynski, Mark P, Jensen, Kyle L, Rigoutsos, Isidore, Stephanopoulos, Gregory

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 182 KB

english, 2008

42

OMiR: Identification of associations between OMIM diseases and microRNAs

Simona Rossi, Aristotelis Tsirigos, Antonio Amoroso, Nicoletta Mascellani, Isidore Rigoutsos, George A. Calin, Stefano Volinia

Journal:

Year:

2011

Language:

english

File:

PDF, 301 KB

english, 2011

43

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

Simon, Lukas M., Chen, Edward S., Edelstein, Leonard C., Kong, Xianguo, Bhatlekar, Seema, Rigoutsos, Isidore, Bray, Paul F., Shaw, Chad A.

Journal:

The American Journal of Human Genetics

Year:

2016

Language:

english

File:

PDF, 1.64 MB

english, 2016

44

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

Xia, Zhen, Clark, Peter, Huynh, Tien, Loher, Phillipe, Zhao, Yue, Chen, Huang-Wen, Ren, Pengyu, Rigoutsos, Isidore, Zhou, Ruhong

Journal:

Scientific Reports

Year:

2012

Language:

english

File:

PDF, 139 KB

english, 2012

45

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

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

Journal:

Cancer Research

Year:

2019

Language:

english

File:

PDF, 1.63 MB

english, 2019

46

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

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

Journal:

Year:

2009

Language:

english

File:

PDF, 1.07 MB

english, 2009

47

Biomolecular Events in Cancer Revealed by Attractor Metagenes

Cheng, Wei-Yi, Yang, Tai-Hsien Ou, Anastassiou, Dimitris, Rigoutsos, Isidore

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 804 KB

english, 2013

48

Report on BIOKDD04

Zaki, Mohammed J., Morishita, Shinichi, Rigoutsos, Isidore

Journal:

ACM SIGKDD Explorations Newsletter

Year:

2004

Language:

english

File:

PDF, 85 KB

english, 2004

49

Gene-expression forum: Decoy for microRNAs

Rigoutsos, Isidore, Furnari, Frank

Journal:

Year:

2010

Language:

english

File:

PDF, 195 KB

english, 2010

50

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

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

Journal:

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

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