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1

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

Boue, S., Talikka, M., Westra, J. W., Hayes, W., Di Fabio, A., Park, J., Schlage, W. K., Sewer, A., Fields, B., Ansari, S., Martin, F., Veljkovic, E., Kenney, R., Peitsch, M. C., Hoeng, J.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.28 MB

english, 2015

2

Tobacco Heating System 2.2 has a limited impact on DNA methylation of candidate enhancers in mouse lung compared with cigarette smoke

Choukrallah, Mohamed-Amin, Sierro, Nicolas, Martin, Florian, Baumer, Karine, Thomas, Jerome, Ouadi, Sonia, Hoeng, Julia, Peitsch, Manuel C., Ivanov, Nikolai V.

Journal:

Food and Chemical Toxicology

Year:

2019

Language:

english

File:

PDF, 2.17 MB

english, 2019

3

A meta-analysis of microRNAs expressed in human aerodigestive epithelial cultures and their role as potential biomarkers of exposure response to nicotine-containing products

Sewer, Alain, Zanetti, Filippo, Iskandar, Anita R., Guedj, Emmanuel, Dulize, Remi, Peric, Dariusz, Bornand, David, Mathis, Carole, Martin, Florian, Ivanov, Nikolai V., Peitsch, Manuel C., Hoeng, Julia

Journal:

Toxicology Reports

Year:

2020

File:

PDF, 9.52 MB

2020

4

[Methods in Pharmacology and Toxicology] Computational Systems Toxicology ||

Hoeng, Julia, Peitsch, Manuel C.

Year:

2015

Language:

english

File:

PDF, 19.22 MB

english, 2015

5

Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL)

Fluck, Juliane, Madan, Sumit, Ansari, Sam, Kodamullil, Alpha T., Karki, Reagon, Rastegar-Mojarad, Majid, Catlett, Natalie L., Hayes, William, Szostak, Justyna, Hoeng, Julia, Peitsch, Manuel

Journal:

Year:

2016

Language:

english

File:

PDF, 698 KB

english, 2016

6

Verification of systems biology research in the age of collaborative competition

Meyer, Pablo, Alexopoulos, Leonidas G, Bonk, Thomas, Califano, Andrea, Cho, Carolyn R, de la Fuente, Alberto, de Graaf, David, Hartemink, Alexander J, Hoeng, Julia, Ivanov, Nikolai V, Koeppl, Heinz, L

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 492 KB

english, 2011

7

Use of nanocellulose in printed electronics: A review

Hoeng, Fanny, Denneulin, Aurore, Bras, Julien

Journal:

Year:

2016

Language:

english

File:

PDF, 1.65 MB

english, 2016

8

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

Madan, Sumit, Hodapp, Sven, Senger, Philipp, Ansari, Sam, Szostak, Justyna, Hoeng, Julia, Peitsch, Manuel, Fluck, Juliane

Journal:

Year:

2016

Language:

english

File:

PDF, 943 KB

english, 2016

9

Physiological and biological characterization of smokers with and without COPD

Chaudhary, Nveed, Luettich, Karsta, Peck, Michael J., Pierri, Elena, Felber-Medlin, Loyse, Vuillaume, Gregory, Leroy, Patrice, Hoeng, Julia, Peitsch, Manuel C.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.10 MB

english, 2018

10

Antiparasitic properties of leaf extracts derived from selected Nicotiana species and Nicotiana tabacum varieties

Schorderet Weber, Sandra, Kaminski, Kacper P., Perret, Jean-Luc, Leroy, Patrice, Mazurov, Anatoly, Peitsch, Manuel C., Ivanov, Nikolai V., Hoeng, Julia

Journal:

Food and Chemical Toxicology

Year:

2019

Language:

english

File:

PDF, 1.26 MB

english, 2019

11

The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track

Madan, Sumit, Szostak, Justyna, Komandur Elayavilli, Ravikumar, Tsai, Richard Tzong-Han, Ali, Mehdi, Qian, Longhua, Rastegar-Mojarad, Majid, Hoeng, Julia, Fluck, Juliane

Journal:

Year:

2019

Language:

english

File:

PDF, 2.07 MB

english, 2019

12

Bridging inhaled aerosol dosimetry to physiologically based pharmacokinetic modeling for toxicological assessment: nicotine delivery systems and beyond

Kolli, A. R., Kuczaj, A. K., Martin, F., Hayes, A. W., Peitsch, M. C., Hoeng, J.

Journal:

Critical Reviews in Toxicology

Year:

2020

Language:

english

File:

PDF, 2.75 MB

english, 2020

13

Analysis of chemical deposits on tooth enamel exposed to total particulate matter from cigarette smoke and tobacco heating system 2.2 aerosol by novel GCâMS deconvolution procedures

Haiduc, Adrian, Zanetti, Filippo, Zhao, Xiaoyi, Schlage, Walter K., Scherer, Max, Pluym, Nikola, Schlenger, Patrick, Ivanov, Nikolai V., Majeed, Shoaib, Hoeng, Julia, Peitsch, Manuel C., Ren, Yanfang,

Journal:

Journal of Chromatography B

Year:

2020

File:

PDF, 3.02 MB

2020

14

A network-based approach to quantifying the impact of biologically active substances

Julia Hoeng, Renée Deehan, Dexter Pratt, Florian Martin, Alain Sewer, Ty M. Thomson, David A. Drubin, Christina A. Waters, David de Graaf, Manuel C. Peitsch

Journal:

Drug Discovery Today

Year:

2012

Language:

english

File:

PDF, 978 KB

english, 2012

15

Smoker bronchial epithelium: A multi-dimensional in vivo/in vitro comparison

Carole Mathis, Carine Poussin, Dirk Weisensee, Stephan Gebel, Vincenzo Belcastro, Yang Xiang, Alain Sewer, Arnd Hengstermann, Sam Ansari, Sandra Wagner, Julia Hoeng, Manuel Peitsch

Journal:

Toxicology Letters

Year:

2012

Language:

english

File:

PDF, 86 KB

english, 2012

16

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

Florian Martin, Ty M Thomson, Alain Sewer, David A Drubin, Carole Mathis, Dirk Weisensee, Dexter Pratt, Julia Hoeng, Manuel C Peitsch

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 571 KB

english, 2012

17

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

Tarca, A. L., Lauria, M., Unger, M., Bilal, E., Boue, S., Kumar Dey, K., Hoeng, J., Koeppl, H., Martin, F., Meyer, P., Nandy, P., Norel, R., Peitsch, M., Rice, J. J., Romero, R., Stolovitzky, G., Tali

Journal:

Year:

2013

Language:

english

File:

PDF, 495 KB

english, 2013

18

Systems Toxicology: From Basic Research to Risk Assessment

Sturla, Shana J., Boobis, Alan R., FitzGerald, Rex E., Hoeng, Julia, Kavlock, Robert J., Schirmer, Kristin, Whelan, Maurice, Wilks, Martin F., Peitsch, Manuel C.

Journal:

Chemical Research in Toxicology

Year:

2014

Language:

english

File:

PDF, 4.17 MB

english, 2014

19

Case study: the role of mechanistic network models in systems toxicology

Hoeng, Julia, Talikka, Marja, Martin, Florian, Sewer, Alain, Yang, Xiang, Iskandar, Anita, Schlage, Walter K., Peitsch, Manuel C.

Journal:

Drug Discovery Today

Year:

2014

Language:

english

File:

PDF, 3.50 MB

english, 2014

20

A 28-day rat inhalation study with an integrated molecular toxicology endpoint demonstrates reduced exposure effects for a prototypic modified risk tobacco product compared with conventional cigarettes

Kogel, Ulrike, Schlage, Walter K., Martin, Florian, Xiang, Yang, Ansari, Sam, Leroy, Patrice, Vanscheeuwijck, Patrick, Gebel, Stephan, Buettner, Ansgar, Wyss, Christoph, Esposito, Marco, Hoeng, Julia,

Journal:

Food and Chemical Toxicology

Year:

2014

Language:

english

File:

PDF, 2.73 MB

english, 2014

21

Corrigendum to “Identification of New Human Cadherin Genes Using a Combination of Protein Motif Search and Gene Finding Methods” [J. Mol. Biol. 337 (2004) 307–317]

Hoeng, Julia C., Ivanov, Nikolai V., Hodor, Paul, Xia, Menghang, Wei, Nan, Blevins, Richard, Gerhold, David, Borodovsky, Mark, Liu, Yuan

Journal:

Journal of Molecular Biology

Year:

2014

Language:

english

File:

PDF, 169 KB

english, 2014

22

Systems biology approach reveals a dose-dependent recovery of primary human airway epithelium culture after exposure to cigarette smoke

Mathis, Carole, Gebel, Stephan, Poussin, Carine, Hengstermann, Arnd, Weisensee, Dirk, Sewer, Alain, Belcastro, Vincenzo, Ansari, Sam, Wagner, Sandra, Hoeng, Julia, Peitsch, Manuel C.

Journal:

Toxicology Letters

Year:

2013

Language:

english

File:

PDF, 72 KB

english, 2013

23

In vitro systems toxicology approach to investigate the effects of repeated cigarette smoke exposure on respiratory tract tissue cultures

Kostadinova, R., Mathis, C., Wagner, S., Frentzel, S., Talamo, F., Ivanov, N., Xiang, Y., Sewer, A., Martin, F., Constant, S., Peitsch, M., Hoeng, J.

Journal:

Toxicology Letters

Year:

2013

Language:

english

File:

PDF, 83 KB

english, 2013

24

Mechanism of an indirect effect of aqueous cigarette smoke extract on the adhesion of monocytic cells to endothelial cells in an in vitro assay revealed by transcriptomics analysis

Poussin, Carine, Gallitz, Inka, Schlage, Walter K., Steffen, Yvonne, Stolle, Katrin, Lebrun, Stefan, Hoeng, Julia, Peitsch, Manual C., Lietz, Michael

Journal:

Toxicology in Vitro

Year:

2014

Language:

english

File:

PDF, 2.85 MB

english, 2014

25

Systems-toxicology approach to evaluate the biological impact of a subset of harmful/potentially harmful constituents of tobacco smoke

Gonzalez-Suarez, Ignacio, Mathis, Carole, Guedj, Emmanuel, Walker, Paul, Ellis, Samantha, Woodhouse, Heather, Dulize, Remi, Wagner, Sandra, Martin, Florian, Ivanov, Nikolai, Hoeng, Julia, Peitsch, Man

Journal:

Toxicology Letters

Year:

2013

Language:

english

File:

PDF, 73 KB

english, 2013

26

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models

Florian Martin,Alain Sewer,Marja Talikka,Yang Xiang,Julia Hoeng…

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 2.27 MB

english, 2014

27

The Response of Human Nasal and Bronchial Organotypic Tissue Cultures to Repeated Whole Cigarette Smoke Exposure

Talikka, M., Kostadinova, R., Xiang, Y., Mathis, C., Sewer, A., Majeed, S., Kuehn, D., Frentzel, S., Merg, C., Geertz, M., Martin, F., Ivanov, N. V., Peitsch, M. C., Hoeng, J.

Journal:

International Journal of Toxicology

Year:

2014

Language:

english

File:

PDF, 1.50 MB

english, 2014

28

Reduced impact of a prototypic modified risk tobacco product compared with conventional cigarette smoke on exposed human and rat primary normal bronchial epithelial cells

Mathis, Carole, Messinis, Dimitris E., Kogel, Ulrike, Poussin, Carine, Frentzel, Stefan, Guedj, Emmanuel, Merg, Celine, Ivanov, Nikolai, Peitsch, Manuel C., Hoeng, Julia

Journal:

Toxicology Letters

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

29

Aqueous cigarette smoke extract promotes the adhesion of monocytic cells to human coronary artery endothelial cells in direct and indirect-dependent ways

Poussin, Carine, Laurent, Alexandra, Hoeng, Julia, Peitsch, Manuel C., De Leon, Hector

Journal:

Toxicology Letters

Year:

2014

Language:

english

File:

PDF, 67 KB

english, 2014

30

Genomic impact of cigarette smoke, with application to three smoking-related diseases

Talikka, M., Sierro, N., Ivanov, N. V., Chaudhary, N., Peck, M. J., Hoeng, J., Coggins, C. R. E., Peitsch, M. C.

Journal:

Critical Reviews in Toxicology

Year:

2012

Language:

english

File:

PDF, 767 KB

english, 2012

31

Proteomics for systems toxicology

Titz, Bjoern, Elamin, Ashraf, Martin, Florian, Schneider, Thomas, Dijon, Sophie, Ivanov, Nikolai V., Hoeng, Julia, Peitsch, Manuel C.

Journal:

Computational and Structural Biotechnology Journal

Year:

2014

Language:

english

File:

PDF, 1.48 MB

english, 2014

32

sbv IMPROVER Diagnostic Signature Challenge

Hoeng, Julia, Stolovitzky, Gustavo, Peitsch, Manuel C

Journal:

Systems Biomedicine

Year:

2013

Language:

english

File:

PDF, 171 KB

english, 2013

33

sbv IMPROVER Diagnostic Signature Challenge

Rhrissorrakrai, Kahn, Rice, J Jeremy, Boue, Stephanie, Talikka, Marja, Bilal, Erhan, Martin, Florian, Meyer, Pablo, Norel, Raquel, Xiang, Yang, Stolovitzky, Gustavo, Hoeng, Julia, Peitsch, Manuel C

Journal:

Systems Biomedicine

Year:

2013

Language:

english

File:

PDF, 1.15 MB

english, 2013

34

Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge

Rhrissorrakrai, K., Belcastro, V., Bilal, E., Norel, R., Poussin, C., Mathis, C., Dulize, R. H. J., Ivanov, N. V., Alexopoulos, L., Jeremy Rice, J., Peitsch, M. C., Stolovitzky, G., Meyer, P., Hoeng,

Journal:

Year:

2015

Language:

english

File:

PDF, 966 KB

english, 2015

35

Where are we at regarding species translation? A review of the sbv IMPROVER challenge

Hoeng, J., Peitsch, M. C., Meyer, P., Jurisica, I.

Journal:

Year:

2015

Language:

english

File:

PDF, 63 KB

english, 2015

36

A crowd-sourcing approach for the construction of species-specific cell signaling networks

Bilal, E., Sakellaropoulos, T., Participants, C., Melas, I. N., Messinis, D. E., Belcastro, V., Rhrissorrakrai, K., Meyer, P., Norel, R., Iskandar, A., Blaese, E., Rice, J. J., Peitsch, M. C., Hoeng,

Journal:

Year:

2015

Language:

english

File:

PDF, 711 KB

english, 2015

37

Characterization of the Vitrocell® 24/48in vitroaerosol exposure system using mainstream cigarette smoke

Majeed, Shoaib, Frentzel, Stefan, Wagner, Sandra, Kuehn, Diana, Leroy, Patrice, Guy, Philippe A, Knorr, Arno, Hoeng, Julia, Peitsch, Manuel C

Journal:

Chemistry Central Journal

Year:

2014

Language:

english

File:

PDF, 1.64 MB

english, 2014

38

High-Resolution Crystal Structure and In Vivo Function of a Kinesin-2 Homologue in Giardia intestinalis

Hoeng, J. C., Dawson, S. C., House, S. A., Sagolla, M. S., Pham, J. K., Mancuso, J. J., Lowe, J., Cande, W. Z.

Journal:

Molecular Biology of the Cell

Year:

2008

Language:

english

File:

PDF, 1.17 MB

english, 2008

39

Systems Toxicology: The Future of Risk Assessment

Sauer, J. M., Hartung, T., Leist, M., Knudsen, T. B., Hoeng, J., Hayes, A. W.

Journal:

International Journal of Toxicology

Year:

2015

Language:

english

File:

PDF, 90 KB

english, 2015

40

An ATP Gate Controls Tubulin Binding by the Tethered Head of Kinesin-1

Alonso, M. C., Drummond, D. R., Kain, S., Hoeng, J., Amos, L., Cross, R. A.

Journal:

Year:

2007

Language:

english

File:

PDF, 346 KB

english, 2007

41

Industrial methodology for process verification in research (IMPROVER): toward systems biology verification

Meyer, P., Hoeng, J., Rice, J. J., Norel, R., Sprengel, J., Stolle, K., Bonk, T., Corthesy, S., Royyuru, A., Peitsch, M. C., Stolovitzky, G.

Journal:

Year:

2012

Language:

english

File:

PDF, 407 KB

english, 2012

42

On Crowd-verification of Biological Networks

Hoeng, Julia, Ansari, Sam, Kleiman, Robin, Binder, Jean, Hayes, William, Iskandar, Anita, Rhrissorrakrai, Kahn, Norel, Raquel, O'Neel, Bruce, Peitsch, Manuel, Poussin, Carine, Talikka, Marja, Schlage,

Journal:

Bioinformatics and Biology Insights

Year:

2013

Language:

english

File:

PDF, 4.99 MB

english, 2013

43

Discovery of Emphysema Relevant Molecular Networks from an A/J Mouse Inhalation Study Using Reverse Engineering and Forward Simulation (REFS™)

Xiang,, Kogel, Ulrike, Gebel, Stephan, Peck, Michael, Peitsch, Manuel, Akmaev, Viatcheslav, Hoeng, Julia

Journal:

Gene Regulation and Systems Biology

Year:

2014

Language:

english

File:

PDF, 1.68 MB

english, 2014

44

Systems Approaches Evaluating the Perturbation of Xenobiotic Metabolism in Response to Cigarette Smoke Exposure in Nasal and Bronchial Tissues

Iskandar, Anita R., Martin, Florian, Talikka, Marja, Schlage, Walter K., Kostadinova, Radina, Mathis, Carole, Hoeng, Julia, Peitsch, Manuel C.

Journal:

BioMed Research International

Year:

2013

Language:

english

File:

PDF, 5.75 MB

english, 2013

45

Systematic Verification of Upstream Regulators of a Computable Cellular Proliferation Network Model on Non-Diseased Lung Cells Using a Dedicated Dataset

Belcastro,, Poussin, Carine, Gebel, Stephan, Mathis, Carole, Lichtner, Rosemarie, Wagner, Sandra, Quadt-Humme, Sibille, Schlage, Walter, Hoeng, Julia, Peitsch, Manuel

Journal:

Bioinformatics and Biology Insights

Year:

2013

Language:

english

File:

PDF, 1.30 MB

english, 2013

46

Systems approaches to computational modeling of the oral microbiome

Dimitrov, Dimiter V., Hoeng, Julia

Journal:

Frontiers in Physiology

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

47

Charge density modification of carboxylated cellulose nanocrystals for stable silver nanoparticles suspension preparation

Hoeng, Fanny, Denneulin, Aurore, Neuman, Charles, Bras, Julien

Journal:

Journal of Nanoparticle Research

Year:

2015

Language:

english

File:

PDF, 1.07 MB

english, 2015

48

Human bronchial epithelial cells exposed in vitro to cigarette smoke at the air-liquid interface resemble bronchial epithelium from human smokers

Mathis, C., Poussin, C., Weisensee, D., Gebel, S., Hengstermann, A., Sewer, A., Belcastro, V., Xiang, Y., Ansari, S., Wagner, S., Hoeng, J., Peitsch, M. C.

Journal:

AJP Lung Cellular and Molecular Physiology

Year:

2013

Language:

english

File:

PDF, 1.44 MB

english, 2013

49

A prototypic modified risk tobacco product exhibits reduced effects on chemotaxis and transendothelial migration of monocytes compared with a reference cigarette

van der Toorn, Marco, Frentzel, Stefan, Goedertier, Didier, Peitsch, Manuel, Hoeng, Julia, De Leon, Hector

Journal:

Food and Chemical Toxicology

Year:

2015

Language:

english

File:

PDF, 2.50 MB

english, 2015

50

Impact Assessment of Cigarette Smoke Exposure on Organotypic Bronchial Epithelial Tissue Cultures: A Comparison of Mono-Culture and Coculture Model Containing Fibroblasts

Iskandar, Anita R., Xiang, Yang, Frentzel, Stefan, Talikka, Marja, Leroy, Patrice, Kuehn, Diana, Guedj, Emmanuel, Martin, Florian, Mathis, Carole, Ivanov, Nikolai V., Peitsch, Manuel C., Hoeng, Julia

Journal:

Toxicological Sciences

Year:

2015

Language:

english

File:

PDF, 1.52 MB

english, 2015

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