Volume 4; Issue 1

npj Systems Biology and Applications

Volume 4; Issue 1

1

VEGFR1 promotes cell migration and proliferation through PLCγ and PI3K pathways

Weddell, Jared C., Chen, Si, Imoukhuede, P. I.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.74 MB

english, 2018

2

PECAplus: statistical analysis of time-dependent regulatory changes in dynamic single-omics and dual-omics experiments

Teo, Guoshou, Bin Zhang, Yun, Vogel, Christine, Choi, Hyungwon

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.22 MB

english, 2018

3

Regeneration in distantly related species: common strategies and pathways

Fumagalli, Maria Rita, Zapperi, Stefano, La Porta, Caterina A. M.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.66 MB

english, 2018

4

Mapping the operational landscape of microRNAs in synthetic gene circuits

Quarton, Tyler, Ehrhardt, Kristina, Lee, James, Kannan, Srijaa, Li, Yi, Ma, Lan, Bleris, Leonidas

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.13 MB

english, 2018

5

Handling variability and incompleteness of biological data by flexible nets: a case study for Wilson disease

Júlvez, Jorge, Dikicioglu, Duygu, Oliver, Stephen G.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.23 MB

english, 2018

6

Regulatory feedback response mechanisms to phosphate starvation in rice

Ajmera, Ishan, Shi, Jing, Giri, Jitender, Wu, Ping, Stekel, Dov J., Lu, Chungui, Hodgman, T. Charlie

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.64 MB

english, 2018

7

A diseasome cluster-based drug repurposing of soluble guanylate cyclase activators from smooth muscle relaxation to direct neuroprotection

Langhauser, Friederike, Casas, Ana I., Dao, Vu-Thao-Vi, Guney, Emre, Menche, Jörg, Geuss, Eva, Kleikers, Pamela W. M., López, Manuela G., Barabási, Albert-L., Kleinschnitz, Christoph, Schmidt, Harald

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 4.62 MB

english, 2018

8

Classification of gene signatures for their information value and functional redundancy

Cantini, Laura, Calzone, Laurence, Martignetti, Loredana, Rydenfelt, Mattias, Blüthgen, Nils, Barillot, Emmanuel, Zinovyev, Andrei

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.27 MB

english, 2018

9

A roadmap towards personalized immunology

Delhalle, Sylvie, Bode, Sebastian F. N., Balling, Rudi, Ollert, Markus, He, Feng Q.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.30 MB

english, 2018

10

Population-based mechanistic modeling allows for quantitative predictions of drug responses across cell types

Gong, Jingqi Q. X., Sobie, Eric A.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.10 MB

english, 2018

11

A personalized, multiomics approach identifies genes involved in cardiac hypertrophy and heart failure

Santolini, Marc, Romay, Milagros C., Yukhtman, Clara L., Rau, Christoph D., Ren, Shuxun, Saucerman, Jeffrey J., Wang, Jessica J., Weiss, James N., Wang, Yibin, Lusis, Aldons J., Karma, Alain

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.24 MB

english, 2018

12

Integration of genome-scale metabolic networks into whole-body PBPK models shows phenotype-specific cases of drug-induced metabolic perturbation

Cordes, Henrik, Thiel, Christoph, Baier, Vanessa, Blank, Lars M., Kuepfer, Lars

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.17 MB

english, 2018

13

Large-scale computational drug repositioning to find treatments for rare diseases

Govindaraj, Rajiv Gandhi, Naderi, Misagh, Singha, Manali, Lemoine, Jeffrey, Brylinski, Michal

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.20 MB

english, 2018

14

Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects

Ohashi, Kaoru, Fujii, Masashi, Uda, Shinsuke, Kubota, Hiroyuki, Komada, Hisako, Sakaguchi, Kazuhiko, Ogawa, Wataru, Kuroda, Shinya

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.51 MB

english, 2018

15

Detecting phenotype-driven transitions in regulatory network structure

Padi, Megha, Quackenbush, John

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.83 MB

english, 2018

16

Stochastic system identification without an a priori chosen kinetic model—exploring feasible cell regulation with piecewise linear functions

Hoffmann, Martin, Galle, Jörg

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.32 MB

english, 2018

17

A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data

Costello, Zak, Martin, Hector Garcia

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.55 MB

english, 2018

18

Pathway crosstalk enables cells to interpret TGF-β duration

Zhang, Jingyu, Tian, Xiao-Jun, Chen, Yi-Jiun, Wang, Weikang, Watkins, Simon, Xing, Jianhua

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.79 MB

english, 2018

19

A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis

Vafaee, Fatemeh, Diakos, Connie, Kirschner, Michaela B., Reid, Glen, Michael, Michael Z., Horvath, Lisa G., Alinejad-Rokny, Hamid, Cheng, Zhangkai Jason, Kuncic, Zdenka, Clarke, Stephen

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.23 MB

english, 2018

20

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms

Mazein, Alexander, Ostaszewski, Marek, Kuperstein, Inna, Watterson, Steven, Le Novère, Nicolas, Lefaudeux, Diane, De Meulder, Bertrand, Pellet, Johann, Balaur, Irina, Saqi, Mansoor, Nogueira, Maria Ma

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 4.52 MB

english, 2018

21

Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds

Oppelt, Angela, Kaschek, Daniel, Huppelschoten, Suzanna, Sison-Young, Rowena, Zhang, Fang, Buck-Wiese, Marie, Herrmann, Franziska, Malkusch, Sebastian, Krüger, Carmen L., Meub, Mara, Merkt, Benjamin,

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.81 MB

english, 2018

22

Mapping biological process relationships and disease perturbations within a pathway network

Stoney, Ruth, Robertson, David L, Nenadic, Goran, Schwartz, Jean-Marc

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.81 MB

english, 2018

23

Transcriptional timing and noise of yeast cell cycle regulators—a single cell and single molecule approach

Amoussouvi, Aouefa, Teufel, Lotte, Reis, Matthias, Seeger, Martin, Schlichting, Julia Katharina, Schreiber, Gabriele, Herrmann, Andreas, Klipp, Edda

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.57 MB

english, 2018

24

Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes

Sharma, Amitabh, Halu, Arda, Decano, Julius L., Padi, Megha, Liu, Yang-Yu, Prasad, Rashmi B., Fadista, Joao, Santolini, Marc, Menche, Jörg, Weiss, Scott T., Vidal, Marc, Silverman, Edwin K., Aikawa, M

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.24 MB

english, 2018

25

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer

Ebhardt, H. Alexander, Root, Alex, Liu, Yansheng, Gauthier, Nicholas Paul, Sander, Chris, Aebersold, Ruedi

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.47 MB

english, 2018

26

A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer

Wilson, Stephen, Filipp, Fabian Volker

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.46 MB

english, 2018

27

Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

Maldonado, Elaina M., Fisher, Ciarán P., Mazzatti, Dawn J., Barber, Amy L., Tindall, Marcus J., Plant, Nicholas J., Kierzek, Andrzej M., Moore, J. Bernadette

Journal:

npj Systems Biology and Applications

Year:

2018

File:

PDF, 1.56 MB

2018

28

From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease

Bauer, Eugen, Thiele, Ines

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.17 MB

english, 2018

29

Using quantitative systems pharmacology to evaluate the drug efficacy of COX-2 and 5-LOX inhibitors in therapeutic situations

Thiel, Christoph, Smit, Ines, Baier, Vanessa, Cordes, Henrik, Fabry, Brigida, Blank, Lars Mathias, Kuepfer, Lars

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.11 MB

english, 2018

30

Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators

Cholley, Pierre-Etienne, Moehlin, Julien, Rohmer, Alexia, Zilliox, Vincent, Nicaise, Samuel, Gronemeyer, Hinrich, Mendoza-Parra, Marco Antonio

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.04 MB

english, 2018

31

Flux-dependent graphs for metabolic networks

Beguerisse-Díaz, Mariano, Bosque, Gabriel, Oyarzún, Diego, Picó, Jesús, Barahona, Mauricio

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 3.21 MB

english, 2018

32

Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease

Maldonado, Elaina M., Fisher, Ciarán P., Mazzatti, Dawn J., Barber, Amy L., Tindall, Marcus J., Plant, Nicholas J., Kierzek, Andrzej M., Moore, J. Bernadette

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.56 MB

english, 2018

33

A landscape view on the interplay between EMT and cancer metastasis

Li, Chunhe, Balazsi, Gabor

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.55 MB

english, 2018

34

Redefining environmental exposure for disease etiology

Rappaport, Stephen M.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 554 KB

english, 2018

35

Prevalence and patterns of higher-order drug interactions in Escherichia coli

Tekin, Elif, White, Cynthia, Kang, Tina Manzhu, Singh, Nina, Cruz-Loya, Mauricio, Damoiseaux, Robert, Savage, Van M., Yeh, Pamela J.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.70 MB

english, 2018

36

Dynamic modeling of transcriptional gene regulatory network uncovers distinct pathways during the onset of Arabidopsis leaf senescence

Mishra, Bharat, Sun, Yali, Howton, TC, Kumar, Nilesh, Mukhtar, M. Shahid

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.43 MB

english, 2018

37

The interaction of transcription factors controls the spatial layout of plant aerial stem cell niches

Gruel, Jérémy, Deichmann, Julia, Landrein, Benoit, Hitchcock, Thomas, Jönsson, Henrik

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 6.53 MB

english, 2018

38

Context-dependent prediction of protein complexes by SiComPre

Rizzetto, Simone, Moyseos, Petros, Baldacci, Bianca, Priami, Corrado, Csikász-Nagy, Attila

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

39

Systemic network analysis identifies XIAP and IκBα as potential drug targets in TRAIL resistant BRAF mutated melanoma

Del Mistro, Greta, Lucarelli, Philippe, Müller, Ines, De Landtsheer, Sébastien, Zinoveva, Anna, Hutt, Meike, Siegemund, Martin, Kontermann, Roland E., Beissert, Stefan, Sauter, Thomas, Kulms, Dagmar

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

40

Role of noise and parametric variation in the dynamics of gene regulatory circuits

Kohar, Vivek, Lu, Mingyang

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 2.73 MB

english, 2018

41

Expression-based analyses indicate a central role for hypoxia in driving tumor plasticity through microenvironment remodeling and chromosomal instability

Jing, Anqi, Vizeacoumar, Frederick S., Parameswaran, Sreejit, Haave, Bjorn, Cunningham, Chelsea E., Wu, Yuliang, Arnold, Roland, Bonham, Keith, Freywald, Andrew, Han, Jie, Vizeacoumar, Franco J.

Journal:

npj Systems Biology and Applications

Year:

2018

Language:

english

File:

PDF, 5.23 MB

english, 2018

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