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1

Benzalkonium chlorides: Uses, regulatory status, and microbial resistance

Merchel Piovesan Pereira, Beatriz, Tagkopoulos, Ilias

Journal:

Applied and Environmental Microbiology

Year:

2019

Language:

english

File:

PDF, 1.21 MB

english, 2019

2

Promoter Element Arising from the Fusion of Standard BioBrick Parts

Yao, Andrew I., Fenton, Timothy A., Owsley, Keegan, Seitzer, Phillip, Larsen, David J., Sit, Holly, Lau, Jennifer, Nair, Arjun, Tantiongloc, Justin, Tagkopoulos, Ilias, Facciotti, Marc T.

Journal:

ACS Synthetic Biology

Year:

2013

Language:

english

File:

PDF, 460 KB

english, 2013

3

Predictive Behavior Within Microbial Genetic Networks

Tagkopoulos, I., Liu, Y.-C., Tavazoie, S.

Journal:

Year:

2008

Language:

english

File:

PDF, 617 KB

english, 2008

4

From vital signs to clinical outcomes for patients with sepsis: a machine learning basis for a clinical decision support system

Gultepe, Eren, Green, Jeffrey P, Nguyen, Hien, Adams, Jason, Albertson, Timothy, Tagkopoulos, Ilias

Journal:

Journal of the American Medical Informatics Association

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

5

Data integration and predictive modeling methods for multi-omics datasets

Kim, Minseung, Tagkopoulos, Ilias

Journal:

Molecular Omics

Year:

2018

Language:

english

File:

PDF, 2.74 MB

english, 2018

6

Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming

Huynh, Linh, Kececioglu, John, Köppe, Matthias, Tagkopoulos, Ilias, Thattai, Mukund

Journal:

Year:

2012

Language:

english

File:

PDF, 474 KB

english, 2012

7

Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose

Chin, Elizabeth L., Simmons, Gabriel, Bouzid, Yasmine Y., Kan, Annie, Burnett, Dustin J., Tagkopoulos, Ilias, Lemay, Danielle G.

Journal:

Year:

2019

Language:

english

File:

PDF, 1.65 MB

english, 2019

8

Nutrient Estimation from 24-Hour Food Recalls Using Machine Learning and Database Mapping: A Case Study with Lactose

Chin, Elizabeth L., Simmons, Gabriel, Bouzid, Yasmine Y., Kan, Annie, Burnett, Dustin J., Tagkopoulos, Ilias, Lemay, Danielle G.

Journal:

Year:

2019

File:

PDF, 1.65 MB

2019

9

A synthetic biology approach to self-regulatory recombinant protein production inEscherichia coli

Dragosits, Martin, Nicklas, Daniel, Tagkopoulos, Ilias

Journal:

Journal of Biological Engineering

Year:

2012

Language:

english

File:

PDF, 546 KB

english, 2012

10

Horizontal gene transfer dynamics and distribution of fitness effects during microbialin silicoevolution

Mozhayskiy, Vadim, Tagkopoulos, Ilias

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.49 MB

english, 2012

11

Guided evolution ofin silicomicrobial populations in complex environments accelerates evolutionary rates through a step-wise adaptation

Mozhayskiy, Vadim, Tagkopoulos, Ilias

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 726 KB

english, 2012

12

[IEEE 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2012.02.23-2012.02.25)] 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - A Bayesian network for early diagnosis of sepsis patients: a basis for a clinical decision support system

Gultepe, Eren, Hien Nguyen,, Albertson, Timothy, Tagkopoulos, Ilias

Year:

2012

Language:

english

File:

PDF, 313 KB

english, 2012

13

Transcriptional Network Analysis Identifies BACH1 as a Master Regulator of Breast Cancer Bone Metastasis

Liang, Y., Wu, H., Lei, R., Chong, R. A., Wei, Y., Lu, X., Tagkopoulos, I., Kung, S.-Y., Yang, Q., Hu, G., Kang, Y.

Journal:

Journal of Biological Chemistry

Year:

2012

Language:

english

File:

PDF, 3.03 MB

english, 2012

14

SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design

Huynh, Linh, Tsoukalas, Athanasios, Köppe, Matthias, Tagkopoulos, Ilias

Journal:

ACS Synthetic Biology

Year:

2013

Language:

english

File:

PDF, 2.32 MB

english, 2013

15

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

Dragosits, M., Mozhayskiy, V., Quinones-Soto, S., Park, J., Tagkopoulos, I.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 2.16 MB

english, 2014

16

A flood-based information flow analysis and network minimization method for gene regulatory networks

Andreas Pavlogiannis, Vadim Mozhayskiy, Ilias Tagkopoulos

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 899 KB

english, 2013

17

Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation

Huynh, Linh, Tagkopoulos, Ilias

Journal:

ACS Synthetic Biology

Year:

2014

Language:

english

File:

PDF, 1.18 MB

english, 2014

18

[IEEE 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) - Stanford, CA, USA (2005.08.11-2005.08.11)] 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05) - Multi-metric and multi-substructure biclustering analysis for gene expression data

Kung, S.Y., Man-Wai Mak,, Tagkopoulos, I.

Year:

2005

Language:

english

File:

PDF, 320 KB

english, 2005

19

Correction to Promoter Element Arising from the Fusion of Standard BioBrick Parts

Yao, Andrew I., Fenton, Timothy A., Owsley, Keegan, Seitzer, Phillip, Larsen, David J., Sit, Holly, Lau, Jennifer, Nair, Arjun, Tantiongloc, Justin, Tagkopoulos, Ilias, Facciotti, Marc T.

Journal:

ACS Synthetic Biology

Year:

2013

File:

PDF, 99 KB

2013

20

[IEEE Fifth IEEE International Symposium on Signal Processing and Information Technology, 2005. - Athens, Greece (Dec. 18 - 21, 2005)] Proceedings of the Fifth IEEE International Symposium on Signal Processing and Information Technology, 2005. - Gene classification and regulatory prediction based on transcriptional modeling

Tagkopoulos, I., Serpanos, D.

Year:

2005

Language:

english

File:

PDF, 1.25 MB

english, 2005

21

[IEEE 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Las Vegas, NV, USA (2012.02.23-2012.02.25)] 2012 IEEE 2nd International Conference on Computational Advances in Bio and medical Sciences (ICCABS) - A robust, library-based, optimization-driven method for automatic gene circuit design

Linh Hunyh,, Tagkopoulos, Ilias

Year:

2012

Language:

english

File:

PDF, 356 KB

english, 2012

22

[IEEE 2011 IEEE Symposium on Biological Data Visualization (BioVis) - Providence, RI, USA (2011.10.23-2011.10.24)] 2011 IEEE Symposium on Biological Data Visualization (BioVis). - EVEVis: A multi-scale visualization system for dense evolutionary data

Miller, Robert, Mozhayskiy, Vadim, Tagkopoulos, Llias, Ma, Kwan-Liu

Year:

2011

Language:

english

File:

PDF, 2.38 MB

english, 2011

23

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

Carrera, J., Estrela, R., Luo, J., Rai, N., Tsoukalas, A., Tagkopoulos, I.

Journal:

Molecular Systems Biology

Year:

2014

Language:

english

File:

PDF, 2.62 MB

english, 2014

24

[IEEE 2012 16th Panhellenic Conference on Informatics (PCI) - Piraeus, Greece (2012.10.5-2012.10.7)] 2012 16th Panhellenic Conference on Informatics - A Methodology for Evaluating PSI E-infrastructures Based on Multiple Value Models

Alexopoulos, C., Loukis, E., Charalabidis, Y., Tagkopoulos, I.

Year:

2012

Language:

english

File:

PDF, 165 KB

english, 2012

25

[IEEE 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - La Jolla, CA, USA (2005.11.15-2005.11.15)] 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - A Transcriptional Approach to Gene Clustering

Tagkopoulos, I.

Year:

2005

Language:

english

File:

PDF, 1.40 MB

english, 2005

26

[IEEE Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05) - Minneapolis, MN, USA (19-21 Oct. 2005)] Fifth IEEE Symposium on Bioinformatics and Bioengineering (BIBE'05) - Multi-Class Biclustering and Classification Based on Modeling of Gene Regulatory Networks

Tagkopoulos, I., Slavov, N., Kung, S.Y.

Year:

2005

Language:

english

File:

PDF, 438 KB

english, 2005

27

SYMMETRIC AND ASYMMETRIC MULTI-MODALITY BICLUSTERING ANALYSIS FOR MICROARRAY DATA MATRIX

KUNG, SUN-YUAN, MAK, MAN-WAI, TAGKOPOULOS, ILIAS

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2006

Language:

english

File:

PDF, 1.02 MB

english, 2006

28

Microbial factories under control

Tagkopoulos, Ilias

Journal:

Year:

2013

Language:

english

File:

PDF, 664 KB

english, 2013

29

A systems biology analysis of brain microvascular endothelial cell lipotoxicity

Aung, Hnin H, Tsoukalas, Athanasios, Rutledge, John C, Tagkopoulos, Ilias

Journal:

BMC Systems Biology

Year:

2014

Language:

english

File:

PDF, 3.40 MB

english, 2014

30

RiboTALE: A modular, inducible system for accurate gene expression control

Rai, Navneet, Ferreiro, Aura, Neckelmann, Alexander, Soon, Amy, Yao, Andrew, Siegel, Justin, Facciotti, Marc T., Tagkopoulos, Ilias

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

31

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

Kim, Minseung, Zorraquino, Violeta, Tagkopoulos, Ilias, Troyanskaya, Olga G.

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 4.25 MB

english, 2015

32

[ACM Press the 2011 TeraGrid Conference - Salt Lake City, Utah (2011.07.18-2011.07.21)] Proceedings of the 2011 TeraGrid Conference on Extreme Digital Discovery - TG '11 - A scalable multi-scale framework for parallel simulation and visualization of microbial evolution

Mozhayskiy, Vadim, Miller, Bob, Ma, Kwan-Liu, Tagkopoulos, Ilias

Year:

2011

Language:

english

File:

PDF, 449 KB

english, 2011

33

Fast and Accurate Circuit Design Automation through Hierarchical Model Switching

Huynh, Linh, Tagkopoulos, Ilias

Journal:

ACS Synthetic Biology

Year:

2015

Language:

english

File:

PDF, 1.41 MB

english, 2015

34

A data-driven, machine learning framework for optimal pest management in cotton

Meisner, Matthew H., Rosenheim, Jay A., Tagkopoulos, Ilias, Peters, D. P. C.

Journal:

Year:

2016

Language:

english

File:

PDF, 452 KB

english, 2016

35

A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design

Huynh, Linh, Tagkopoulos, Ilias

Journal:

ACS Synthetic Biology

Year:

2016

Language:

english

File:

PDF, 1.25 MB

english, 2016

36

Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli

Kim, Minseung, Rai, Navneet, Zorraquino, Violeta, Tagkopoulos, Ilias

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 784 KB

english, 2016

37

The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli

Zorraquino, Violeta, Kim, Minseung, Rai, Navneet, Tagkopoulos, Ilias

Journal:

Molecular Biology and Evolution

Year:

2016

Language:

english

File:

PDF, 1.10 MB

english, 2016

38

Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata

Bjornson, Marta, Balcke, Gerd Ulrich, Xiao, Yanmei, de Souza, Amancio, Wang, Jin-Zheng, Zhabinskaya, Dina, Tagkopoulos, Ilias, Tissier, Alain, Dehesh, Katayoon

Journal:

The Plant Journal

Year:

2017

Language:

english

File:

PDF, 862 KB

english, 2017

39

Elucidating Substrate Promiscuity within the FabI Enzyme Family.

Freund, Gabriel S., O'Brien, Terrence e, Vinson, Logan, Carlin, Dylan Alexander, Yao, Andrew, Mak, Wai Shun, Tagkopoulos, Ilias, Facciotti, Marc T, Tantillo, Dean J, Siegel, Justin B.

Journal:

ACS Chemical Biology

Year:

2017

Language:

english

File:

PDF, 1.71 MB

english, 2017

40

Predictive Behavior within Microbial Genetic Networks

Tagkopoulos, I., Liu, Y.-C., Tavazoie, S.

Journal:

Year:

2009

File:

PDF, 99 KB

2009

41

Predicting the evolution of Escherichia coli by a data-driven approach

Wang, Xiaokang, Zorraquino, Violeta, Kim, Minseung, Tsoukalas, Athanasios, Tagkopoulos, Ilias

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 1.15 MB

english, 2018

42

Genetic Neural Networks: An artificial neural network architecture for capturing gene expression relationships

Eetemadi, Ameen, Tagkopoulos, Ilias, Berger, Bonnie

Journal:

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

43

Population collapse and adaptive rescue during long‐term chemostat fermentation

Rai, Navneet, Huynh, Linh, Kim, Minseung, Tagkopoulos, Ilias

Journal:

Biotechnology and Bioengineering

Year:

2018

Language:

english

File:

PDF, 1.15 MB

english, 2018

44

Predicting early risk of chronic kidney disease in cats using routine clinical laboratory tests and machine learning

Bradley, Richard, Tagkopoulos, Ilias, Kim, Minseung, Kokkinos, Yiannis, Panagiotakos, Theodoros, Kennedy, James, De Meyer, Geert, Watson, Phillip, Elliott, Jonathan

Journal:

Journal of Veterinary Internal Medicine

Year:

2019

Language:

english

File:

PDF, 1.81 MB

english, 2019

45

Predicting early risk of chronic kidney disease in cats using routine clinical laboratory tests and machine learning

Bradley, Richard, Tagkopoulos, Ilias, Kim, Minseung, Kokkinos, Yiannis, Panagiotakos, Theodoros, Kennedy, James, De Meyer, Geert, Watson, Phillip, Elliott, Jonathan

Journal:

Journal of Veterinary Internal Medicine

Year:

2019

File:

PDF, 1.81 MB

2019

46

A systems analysis of E. coli short and long-term transcriptomic response to biocides

Merchel Piovesan Pereira, Beatriz, Wang, Xiaokang, Tagkopoulos, Ilias

Journal:

Applied and Environmental Microbiology

Year:

2020

File:

PDF, 1.74 MB

2020

47

Discovery, Design, and Structural Characterization of Alkane Producing Enzymes across the Ferritin-like Superfamily

Mak, Wai Shun, Wang, Xiaokang, Arenas, Rigoberto, cui, youtian, Bertolani, Steve J., Deng, Wen Qiao, Tagkopoulos, Ilias, Wilson, David K., Siegel, Justin B.

Journal:

Year:

2020

File:

PDF, 1.92 MB

2020

48

Identification of Differential, Health-Related Compounds in Chardonnay Marc through Network-Based Meta-Analysis

Simmons, Gabriel, Lee, Fanny, Kim, Minseung, Holt, Roberta, Tagkopoulos, Ilias

Journal:

Current Developments in Nutrition

Year:

2020

File:

PDF, 84 KB

2020

49

Accelerated knowledge discovery from omics data by optimal experimental design

Wang, Xiaokang, Rai, Navneet, Merchel Piovesan Pereira, Beatriz, Eetemadi, Ameen, Tagkopoulos, Ilias

Journal:

Nature Communications

Year:

2020

File:

PDF, 1.87 MB

2020

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