Methods for the analysis of transcriptome dynamics

Daniela F. Rodrigues, Vera M. Costa, Ricardo Silvestre, Maria L. Bastos and Félix Carvalho

Toxicology Research, 2019, 8, 597
DOI: 10.1039/c9tx00088g

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data

Benjamin Alexander-Dann, Lavinia Lorena Pruteanu, Erin Oerton, Nitin Sharma, Ioana Berindan-Neagoe, Dezső Módos and Andreas Bender

Mol. Omics, 2018, 14, 218
DOI: 10.1039/C8MO00042E

From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL

Anika Liu, Panuwat Trairatphisan, Enio Gjerga, Athanasios Didangelos, Jonathan Barratt and Julio Saez-Rodriguez

npj Syst Biol Appl, 2019, 5
DOI: 10.1038/s41540-019-0118-z

Advances in omics for informed pharmaceutical research and development in the era of systems medicine

Jane P. F. Bai, Ioannis N. Melas, Junguk Hur and Ellen Guo

Expert Opinion on Drug Discovery, 2018, 13, 1
DOI: 10.1080/17460441.2018.1394839

Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence

Xi Chen, Jinghua Gu, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan

Sci Rep, 2021, 11
DOI: 10.1038/s41598-020-79603-5

Efficient randomization of biological networks while preserving functional characterization of individual nodes

Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman and Julio Saez-Rodriguez

BMC Bioinformatics, 2016, 17
DOI: 10.1186/s12859-016-1402-1

Characterizing alternative splicing effects on protein interaction networks with LINDA

Enio Gjerga, Isabel S Naarmann-de Vries and Christoph Dieterich

Bioinformatics, 2023, 39, i458
DOI: 10.1093/bioinformatics/btad224

Computational Identification of Potential Multitarget Inhibitors of Nipah Virus by Molecular Docking and Molecular Dynamics

Vinay Randhawa, Shivalika Pathania and Manoj Kumar

Microorganisms, 2022, 10, 1181
DOI: 10.3390/microorganisms10061181

A Biologically-Based Computational Approach to Drug Repurposing for Anthrax Infection

Jane Bai, Theodore Sakellaropoulos and Leonidas Alexopoulos

Toxins, 2017, 9, 99
DOI: 10.3390/toxins9030099

De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet

Sebastian Winkler, Ivana Winkler, Mirjam Figaschewski, Thorsten Tiede, Alfred Nordheim and Oliver Kohlbacher

BMC Bioinformatics, 2022, 23
DOI: 10.1186/s12859-022-04670-6

Transcriptomic Evidence Reveals the Dysfunctional Mechanism of Synaptic Plasticity Control in ASD

Chao Kong, Zhitong Bing, Lei Yang, Zigang Huang, Wenxu Wang and Celso Grebogi

Genes, 2024, 16, 11
DOI: 10.3390/genes16010011

Understanding the Mechanism of Cell Death in Gemcitabine Resistant Pancreatic Ductal Adenocarcinoma: A Systems Biology Approach

Imlimaong Aier and Pritish K. Varadwaj

CG, 2020, 20, 483
DOI: 10.2174/1389202920666191025102726

Tissue‐Specific Analysis of Pharmacological Pathways

Yun Hao, Kayla Quinnies, Ronald Realubit, Charles Karan and Nicholas P. Tatonetti

CPT Pharmacom & Syst Pharma, 2018, 7, 453
DOI: 10.1002/psp4.12305

Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses

Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B. Emdal, Vitor Vieira, Dorte B. Bekker‐Jensen, Jennifer Kranz, Eric.M.J. Bindels, Ana S.H. Costa, Abel Sousa, Pedro Beltrao, Miguel Rocha, Jesper V. Olsen, Christian Frezza, Rafael Kramann and Julio Saez‐Rodriguez

Molecular Systems Biology, 2021, 17
DOI: 10.15252/msb.20209730

Translating New Science Into the Drug Review Process: The US FDA’s Division of Applied Regulatory Science

Rodney Rouse, Naomi Kruhlak, James Weaver, Keith Burkhart, Vikram Patel and David G. Strauss

Ther Innov Regul Sci, 2018, 52, 244
DOI: 10.1177/2168479017720249

In silico models in drug development: where we are

Janet Piñero, Laura I Furlong and Ferran Sanz

Current Opinion in Pharmacology, 2018, 42, 111
DOI: 10.1016/j.coph.2018.08.007

Preclinical side effect prediction through pathway engineering of protein interaction network models

Mohammadali Alidoost and Jennifer L. Wilson

CPT Pharmacom & Syst Pharma, 2024, 13, 1180
DOI: 10.1002/psp4.13150

Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity

Alicia Amadoz, Patricia Sebastian-Leon, Enrique Vidal, Francisco Salavert and Joaquin Dopazo

Sci Rep, 2015, 5
DOI: 10.1038/srep18494

Computed Biological Relations among Five Select Treatment-Related Organ/Tissue Toxicities

Theodore Sakellaropoulos, Timothy J. Herod, Leonidas G Alexopoulos and Jane P.F. Bai

Chem. Res. Toxicol., 2016, 29, 914
DOI: 10.1021/acs.chemrestox.6b00060

Transcription factors: Bridge between cell signaling and gene regulation

Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki and Judith B. Zaugg

Proteomics, 2021, 21
DOI: 10.1002/pmic.202000034

Prediction of synergistic anti-cancer drug combinations based on drug target network and drug induced gene expression profiles

Xiangyi Li, Yingjie Xu, Hui Cui, Tao Huang, Disong Wang, Baofeng Lian, Wei Li, Guangrong Qin, Lanming Chen and Lu Xie

Artificial Intelligence in Medicine, 2017, 83, 35
DOI: 10.1016/j.artmed.2017.05.008

The active kinome: The modern view of how active protein kinase networks fit in biological research

Khaled Alganem, Abdul-Rizaq Hamoud, Justin F. Creeden, Nicholas D. Henkel, Ali S. Imami, Alex W. Joyce, William G Ryan V, Jacob B. Rethman, Rammohan Shukla, Sinead M. O'Donovan, Jarek Meller and Robert McCullumsmith

Current Opinion in Pharmacology, 2022, 62, 117
DOI: 10.1016/j.coph.2021.11.007

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks

Luca Csabai, Dávid Fazekas, Tamás Kadlecsik, Máté Szalay-Bekő, Balázs Bohár, Matthew Madgwick, Dezső Módos, Márton Ölbei, Lejla Gul, Padhmanand Sudhakar, János Kubisch, Oyebode James Oyeyemi, Orsolya Liska, Eszter Ari, Bernadette Hotzi, Viktor A Billes, Eszter Molnár, László Földvári-Nagy, Kitti Csályi, Amanda Demeter, Nóra Pápai, Mihály Koltai, Máté Varga, Katalin Lenti, Illés J Farkas, Dénes Türei, Péter Csermely, Tibor Vellai and Tamás Korcsmáros

Nucleic Acids Research, 2022, 50, D701
DOI: 10.1093/nar/gkab909

Quality by design (QbD) approach of pharmacogenomics in drug designing and formulation development for optimization of drug delivery systems

Sumeet Gupta and Vikas Jhawat

Journal of Controlled Release, 2017, 245, 15
DOI: 10.1016/j.jconrel.2016.11.018

Learning feedback molecular network models using integer linear programming

Mustafa Ozen, Effat S Emamian and Ali Abdi

Phys. Biol., 2022, 19, 066004
DOI: 10.1088/1478-3975/ac920d

Identifying potential entry inhibitors for emerging Nipah virus by molecular docking and chemical-protein interaction network

Shivalika Pathania, Vinay Randhawa and Manoj Kumar

Journal of Biomolecular Structure and Dynamics, 2020, 38, 5108
DOI: 10.1080/07391102.2019.1696705

Translational Systems Pharmacology‐Based Predictive Assessment of Drug‐Induced Cardiomyopathy

Dimitris E. Messinis, Ioannis N. Melas, Junguk Hur, Navya Varshney, Leonidas G. Alexopoulos and Jane P.F. Bai

CPT Pharmacom & Syst Pharma, 2018, 7, 166
DOI: 10.1002/psp4.12272

Inhibiting the alarmin‐driven hematopoiesis‐stromal cell crosstalk in primary myelofibrosis ameliorates bone marrow fibrosis

Hélène F. E. Gleitz, Stijn N. R. Fuchs, Inge A. M. Snoeren, Charlotte Boys, James Nagai, Hector Tejeda‐Mora, Vanessa Klöker, Jessica E. Pritchard, Iris J. Bakker, Marta Gargallo Garasa, Eric Bindels, Julio Saez‐Rodriguez, Thomas Vogl, Rafael Kramann, Aurélien Dugourd, Ivan G. Costa and Rebekka K. Schneider

HemaSphere, 2025, 9
DOI: 10.1002/hem3.70179

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development

Jennifer L. Wilson, Rebecca Racz, Tianyun Liu, Oluseyi Adeniyi, Jielin Sun, Anuradha Ramamoorthy, Michael Pacanowski, Russ Altman and Avner Schlessinger

PLoS Comput Biol, 2018, 14, e1006614
DOI: 10.1371/journal.pcbi.1006614

Biomarkers: Delivering on the expectation of molecularly driven, quantitative health

Jennifer L Wilson and Russ B Altman

Exp Biol Med (Maywood), 2018, 243, 313
DOI: 10.1177/1535370217744775

Benchmarking network algorithms for contextualizing genes of interest

Abby Hill, Scott Gleim, Florian Kiefer, Frederic Sigoillot, Joseph Loureiro, Jeremy Jenkins, Melody K. Morris and Luonan Chen

PLoS Comput Biol, 2019, 15, e1007403
DOI: 10.1371/journal.pcbi.1007403

Blood handling and leukocyte isolation methods impact the global transcriptome of immune cells

Brittany A. Goods, Jacqueline M. Vahey, Arthur F. Steinschneider, Michael H. Askenase, Lauren Sansing and J. Christopher Love

BMC Immunol, 2018, 19
DOI: 10.1186/s12865-018-0268-6

Pharmacodynamics and Systems Pharmacology Approaches to Repurposing Drugs in the Wake of Global Health Burden

Jane P.F. Bai

Journal of Pharmaceutical Sciences, 2016, 105, 3007
DOI: 10.1016/j.xphs.2016.07.004

Contextualization of causal regulatory networks from toxicogenomics data applied to drug-induced liver injury

Panuwat Trairatphisan, Terezinha Maria de Souza, Jos Kleinjans, Danyel Jennen and Julio Saez-Rodriguez

Toxicology Letters, 2021, 350, 40
DOI: 10.1016/j.toxlet.2021.06.020