List

Publications

PANDA

Gene co-expression analysis for functional classification and gene–disease predictions. S Van Dam and U Vosa and A van der Graaf….

https://academic.oup.com/bib/article-abstract/19/4/575/2888441.

Biomarker development in the precision medicine era: lung cancer as a case study. AJ Vargas and CC Harris.

https://idp.nature.com/authorize/casa?redirect_uri=https://www.nature.com/articles/nrc.2016.56.pdf%3Forigin%3Dppub&casa_token=HLEJOmMbcEYAAAAA:iB71mDAuA_eDTgYqzPI4K-CWrYviZQr-xKCIBCgV1j6LJQm9M3ahV0zRnv0K0iakt1crPVyc6w5G7zgGkA.

Understanding tissue-specific gene regulation. AR Sonawane and J Platig and M Fagny and CY Chen….

https://www.sciencedirect.com/science/article/pii/S2211124717314183.

DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays. A Singh and CP Shannon and B Gautier and F Rohart….

https://academic.oup.com/bioinformatics/article-abstract/35/17/3055/5292387.

A network model for angiogenesis in ovarian cancer. K Glass and J Quackenbush….

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0551-y.

Multi-omics integration—a comparison of unsupervised clustering methodologies. G Tini and L Marchetti and C Priami….

https://academic.oup.com/bib/article-abstract/20/4/1269/4758623.

Context specific and differential gene co-expression networks via Bayesian biclustering. C Gao and IC McDowell and S Zhao and CD Brown….

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004791.

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. T Lao and K Glass and W Qiu and F Polverino….

https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-015-0137-3.

Network medicine in the age of biomedical big data. AR Sonawane and ST Weiss and K Glass and A Sharma.

https://www.frontiersin.org/articles/10.3389/fgene.2019.00294/full.

Sexually-dimorphic targeting of functionally-related genes in COPD. K Glass and J Quackenbush….

https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-014-0118-y.

Estimating sample-specific regulatory networks. ML Kuijjer and MG Tung and GC Yuan and J Quackenbush….

https://www.sciencedirect.com/science/article/pii/S2589004219300872.

DIABLO–an integrative, multi-omics, multivariate method for multi-group classification. A Singh and B Gautier and CP Shannon and M Vacher and F Rohart….

https://www.biorxiv.org/content/10.1101/067611v1.abstract.

Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism. CM Lopes-Ramos and ML Kuijjer and S Ogino and CS Fuchs….

https://cancerres.aacrjournals.org/content/78/19/5538.short.

Network-based approaches to explore complex biological systems towards network medicine. G Fiscon and F Conte and L Farina and P Paci.

https://www.mdpi.com/2073-4425/9/9/437.

BGRMI: A method for inferring gene regulatory networks from time-course gene expression data and its application in breast cancer research. LF Iglesias-Martinez and W Kolch and T Santra.

https://www.nature.com/articles/srep37140.

Sexual dimorphism in gene expression and regulatory networks across human tissues. CY Chen and C Lopes-Ramos and ML Kuijjer and JN Paulson….

https://www.biorxiv.org/content/10.1101/082289v1.abstract.

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. M Padi and J Quackenbush.

https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-015-0228-1.

From systems biology to P4 medicine: applications in respiratory medicine. G Noell and R Faner and A Agustí.

https://err.ersjournals.com/content/27/147/170110.short.

Regulatory network changes between cell lines and their tissues of origin. CM Lopes-Ramos and JN Paulson….

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4111-x?TRILIBIS_EMULATOR_UA=ulvhbdkubeqb.

How difficult is inference of mammalian causal gene regulatory networks?. D Djordjevic and A Yang and A Zadoorian….

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0111661.

A paradigm shift in medicine: A comprehensive review of network-based approaches. F Conte and G Fiscon and V Licursi and D Bizzarri and T D'Antò….

https://www.sciencedirect.com/science/article/pii/S1874939919302500.

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma. W Qiu and F Guo and K Glass and GC Yuan….

https://www.sciencedirect.com/science/article/pii/S0091674917311090?casa_token=Ed_eA56pv-MAAAAA:SswHF85bwFE9PfKO_2uJCy4oj2mlAe12JiT91twr4_HUwSIOSQmSwRLqpiHxP1EPxPBvvJC1XWE.

Molecular networks in Network Medicine: Development and applications. EK Silverman and HHHW Schmidt….

https://onlinelibrary.wiley.com/doi/abs/10.1002/wsbm.1489?casa_token=BjWonCuPIaoAAAAA:sHdgpe64KZoMwAyZ4hhww4Vi7t-3aW7DEZboKzzqQjvMDA71sYyu2UXbsBy4KZmLltke61v7g9k7UKll.

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. KE Hill and AD Kelly and ML Kuijjer and W Barry and A Rattani….

https://link.springer.com/article/10.1186/s13045-017-0465-4.

Integrated genomic and network-based analyses of complex diseases and human disease network. O Al-Harazi and S Al Insaif and MA Al-Ajlan and N Kaya….

https://www.sciencedirect.com/science/article/pii/S1673852715002118.

Serotonin receptor 2B signaling with interstitial cell activation and leaflet remodeling in degenerative mitral regurgitation. KH Driesbaugh and E Branchetti and JB Grau….

https://www.sciencedirect.com/science/article/pii/S002228281730370X.

Precision medicine and oncology: an overview of the opportunities presented by next-generation sequencing and big data and the challenges posed to …. M Doherty and T Metcalfe and E Guardino….

https://www.annalsofoncology.org/article/S0923-7534(19)34719-2/abstract.

Strengths and opportunities of network medicine in cardiovascular diseases. G Benincasa and R Marfella and N Della Mura….

https://www.jstage.jst.go.jp/article/circj/84/2/84_CJ-19-0879/_article/-char/ja/.

Identification of the transcription factor relationships associated with androgen deprivation therapy response and metastatic progression in prostate cancer. NV Sharma and KL Pellegrini and V Ouellet and FO Giuste….

https://www.mdpi.com/2072-6694/10/10/379.

Sex differences in gene expression and regulatory networks across 29 human tissues. CM Lopes-Ramos and CY Chen and ML Kuijjer and JN Paulson….

https://www.sciencedirect.com/science/article/pii/S2211124720307762.

Gene regulatory network inference resources: a practical overview. D Mercatelli and L Scalambra and L Triboli and F Ray….

https://www.sciencedirect.com/science/article/pii/S1874939919300410.

Estimating drivers of cell state transitions using gene regulatory network models. D Schlauch and K Glass and CP Hersh and EK Silverman….

https://link.springer.com/article/10.1186/s12918-017-0517-y.

Sufu-and Spop-mediated downregulation of Hedgehog signaling promotes beta cell differentiation through organ-specific niche signals. T Yung and F Poon and M Liang and S Coquenlorge….

https://www.nature.com/articles/s41467-019-12624-5.

Gene regulatory pattern analysis reveals essential role of core transcriptional factors’ activation in triple-negative breast cancer. L Min and C Zhang and L Qu and J Huang and L Jiang and J Liu….

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5400636/.

(Differential) co-expression analysis of gene expression: a survey of best practices. HA Chowdhury and DK Bhattacharyya….

https://ieeexplore.ieee.org/abstract/document/8613814/?casa_token=Nd6TQBG9R14AAAAA:p6sMFti1jkok09MvGjlGt4yEgiBXbkg6RUoXEV5TMvrU7U9RJOhLvycUjoMRmqR94IW61Ph3yA.

Genetics of COPD. EK Silverman.

https://www.annualreviews.org/doi/abs/10.1146/annurev-physiol-021317-121224.

Detecting phenotype-driven transitions in regulatory network structure. M Padi and J Quackenbush.

https://www.nature.com/articles/s41540-018-0052-5.

PyPanda: a Python package for gene regulatory network reconstruction. DGP van IJzendoorn and K Glass and J Quackenbush….

https://academic.oup.com/bioinformatics/article-abstract/32/21/3363/2415289.

Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa. AJ Vargas and J Quackenbush and K Glass.

https://www.sciencedirect.com/science/article/pii/S0888754316300842.

Estimating gene regulatory networks with pandaR. D Schlauch and JN Paulson and A Young and K Glass….

https://academic.oup.com/bioinformatics/article-abstract/33/14/2232/3066290.

Gene regulatory network construction identified NFYA as a diffuse subtype-specific prognostic factor in gastric cancer. B Cao and Y Zhao and Z Zhang and H Li….

https://www.spandidos-publications.com/ijo/53/5/1857.

A multi-view genomic data simulator. M Fratello and A Serra and V Fortino….

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0577-1.

Transcriptomics in toxicogenomics, part III: data modelling for risk assessment. A Serra and M Fratello and L Cattelani and I Liampa and G Melagraki….

https://www.mdpi.com/2079-4991/10/4/708.

Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies. L Shang and JA Smith and X Zhou.

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008734.

Bayesian shrinkage estimation of high dimensional causal mediation effects in omics studies. Y Song and X Zhou and M Zhang and W Zhao and Y Liu….

https://onlinelibrary.wiley.com/doi/abs/10.1111/biom.13189?casa_token=I3qhqynAirsAAAAA:BZPi5sJLi9U4wua13nEO3NpUwYzSBcLKVN8QNRXpaVbps7Hz520R_SYVmywz-OrAAdBb56hfbFe8eVNR.

LPRP: a gene–gene interaction network construction algorithm and its application in breast cancer data analysis. L Su and X Meng and Q Ma and T Bai and G Liu.

https://link.springer.com/article/10.1007/s12539-016-0185-4.

Construction of transcriptional regulatory network of Alzheimer's disease based on PANDA algorithm. J Ding and W Kong and X Mou and S Wang.

https://idp.springer.com/authorize/casa?redirect_uri=https://link.springer.com/article/10.1007/s12539-018-0297-0&casa_token=2LVwtmj64lgAAAAA:_26dPRGR-LNdYCMCO3rOVdZLFQoSVgwkcoOtVojcHp5cE-BgZBYX-SFMb5Vtk67qy-gUfx_UcrB74oFrkg.

1 Yeast as a Model for Systems Biology Studies on Complex Diseases. JI Castrillo and SG Oliver.

https://link.springer.com/chapter/10.1007/978-3-642-45218-5_1.

High performance computing of gene regulatory networks using a message-passing model. K Glass and J Quackenbush….

https://ieeexplore.ieee.org/abstract/document/7322475/?casa_token=YYuC163eIYsAAAAA:T_DwLfZ2YR1oNzcLLArC1tF0eIl6yZEWV3PQWh1sjR0OoTc7PUUTGf9szYcqZoKNVR9UMPyauA.

Insights into respiratory disease through bioinformatics. B Hurgobin and E de Jong and A Bosco.

https://onlinelibrary.wiley.com/doi/abs/10.1111/resp.13401.

Network control principles for identifying personalized driver genes in cancer. WF Guo and SW Zhang and T Zeng and T Akutsu….

https://academic.oup.com/bib/article-abstract/21/5/1641/5581645.

Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. PT Campbell and CB Ambrosone and R Nishihara….

https://idp.springer.com/authorize/casa?redirect_uri=https://link.springer.com/content/pdf/10.1007/s10552-019-01177-z.pdf&casa_token=CAwHUUfdf10AAAAA:BQ90KIiDnqtnsIQkLRecaNhp094M0qYA8eFo8za_cDNjr4Tahfneh106ftbB42npy708bkaxXG3_H1UCAA.

Prior knowledge driven joint NMF algorithm for ceRNA co-module identification. J Deng and W Kong and S Wang and X Mou….

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231218/.

lionessR: single sample network inference in R. ML Kuijjer and PH Hsieh and J Quackenbush….

https://bmccancer.biomedcentral.com/articles/10.1186/s12885-019-6235-7.

Modeling regulatory networks using machine learning for systems metabolic engineering. MS Kwon and BT Lee and SY Lee and HU Kim.

https://www.sciencedirect.com/science/article/pii/S0958166920300318.

Functional genomics in cancer immunotherapy: computational approaches for biomarker and drug discovery. WL Chin and RM Zemek and WJ Lesterhuis….

https://pubs.rsc.org/en/content/articlehtml/2019/me/c9me00029a.

dyngen: a multi-modal simulator for spearheading new single-cell omics analyses. R Cannoodt and W Saelens and L Deconinck and Y Saeys.

https://www.biorxiv.org/content/10.1101/2020.02.06.936971v1.abstract.

Computational analysis of the mesenchymal signature landscape in gliomas. O Celiku and A Tandle and JY Chung and SM Hewitt….

https://link.springer.com/article/10.1186/s12920-017-0252-7.

Integrative computational epigenomics to build data-driven gene regulation hypotheses. T Chen and S Tyagi.

https://academic.oup.com/gigascience/article-abstract/9/6/giaa064/5858063.

Phenotype-driven transitions in regulatory network structure. M Padi and J Quackenbush.

https://www.biorxiv.org/content/10.1101/142281v1.abstract.

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. AT Young and X Carette and M Helmel and H Steen and RN Husson….

https://www.biorxiv.org/content/10.1101/584177v1.abstract.

Transcriptional landscape of cell lines and their tissues of origin. CM Lopes-Ramos and JN Paulson and CY Chen and ML Kuijjer….

https://www.biorxiv.org/content/10.1101/082065v1.abstract.

Big Data and Network Medicine in COPD. EK Silverman.

https://link.springer.com/chapter/10.1007/978-3-662-47178-4_22.

Understanding the Molecular Mechanisms of Asthma through Transcriptomics.. HW Park and ST Weiss.

https://synapse.koreamed.org/upload/SynapseData/PDFData/0166AAIR/aair-12-399.pdf.

Transcriptomics and Network Medicine. J Quackenbush and K Glass.

https://books.google.com/books?hl=en&lr=&id=UQOHDwAAQBAJ&oi=fnd&pg=PA177&ots=UUf3vV-cNx&sig=M01uOmeczZr7rrvxMbZGsT0TFMc.

ANANSE: An enhancer network-based computational approach for predicting key transcription factors in cell fate determination. Q Xu and G Georgiou and GJC Veenstra and H Zhou….

https://www.biorxiv.org/content/10.1101/2020.06.05.135798v1.abstract.

Immune network dysregulation precedes clinical diagnosis of asthma. C Yi-Shin and T Benjamin and C Schott….

https://search.proquest.com/openview/80337824a4e7f19faa75c858f8eefe8f/1?pq-origsite=gscholar&cbl=2041939.

Constructing Gene Regulatory Networks using Epigenetic Data. AR Sonawane and DL DeMeo and J Quackenbush and K Glass.

https://www.biorxiv.org/content/10.1101/2020.10.19.345827v1.abstract.

Data-driven Gene Regulatory Network Inference based on Classification Algorithms. S Peignier and P Schmitt and F Calevro.

https://ieeexplore.ieee.org/abstract/document/8995194/?casa_token=JRsA2ylOJIUAAAAA:EZ9yzGPZiGvKGgb4mv1GppBi6Ec9hCubaxHQC563oCSpoPvf0Rp8_S_8pbrietMan4yEEkktNQ.

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks. M Fagny and ML Kuijjer and M Stam and J Joets and O Turc….

https://www.frontiersin.org/articles/10.3389/fgene.2020.606285/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Genetics&id=606285.

Single-cell analysis of human trophoblast stem cell specification reveals activation of fetal cytotrophoblast expression programs including coronavirus associated host …. E Tietze and AR Barbosa and V Euclydes and HJ Cho and YK Lee….

https://www.biorxiv.org/content/10.1101/2020.08.29.273425v1.abstract.

Characterisation of Human TDRD12 and LKAAEAR1 as Potential Oncogenic Cancer Testis Antigen Genes with Clinical Potential. MO Alsulami.

https://search.proquest.com/openview/4f8a72163cdcf6fb02c646bdc47f01fa/1?pq-origsite=gscholar&cbl=51922&diss=y.

Methods for Estimating Hidden Structure and Network Transitions in Genomics. D Schlauch.

https://dash.harvard.edu/handle/1/40046439.

Next-Generation Roadmap for Patient-Centered Genomics. N Smedemark-Margulies.

https://dash.harvard.edu/handle/1/33789915.

Unbiased, network theoretic approaches to identify novel therapeutic targets in cardiovascular comorbidities. BK Ágg.

http://old.semmelweis.hu/wp-content/phd/phd_live/vedes/export/aggbencekaroly.d.pdf.

The axis of progression of disease. AM Tartakoff and D Wu.

https://journals.sagepub.com/doi/abs/10.4137/CIN.S17683.

Blood biomarker panels of the late phase asthmatic response. A Singh.

https://open.library.ubc.ca/collections/24/24/items/1.0307528.

The Influence of Granularity on Bioinformatics: Theoretical Foundations and Practical Applications. S West.

https://search.proquest.com/openview/65bf52176573ce4fc8a6253f562eb784/1?pq-origsite=gscholar&cbl=44156.

Data will Drive the Healthcare Revolution. J Quackenbush.

https://ieeexplore.ieee.org/abstract/document/9059311/?casa_token=Eg55D71Dw34AAAAA:WKcpiaxp7fDoBiQ8kanVWcT8yC9DRVv8NQPy74PwbeifrIpkGTZ05L9LVkHCwJfaH4HIRq1MZQ.

PUMA: PANDA Using MicroRNA Associations. ML Kuijjer and M Fagny and A Marin and J Quackenbush….

https://academic.oup.com/bioinformatics/article-abstract/36/18/4765/5858977.

Immune network dysregulation precedes clinical diagnosis of asthma. YS Chang and B Turturice and C Schott and P Finn and D Perkins.

https://www.nature.com/articles/s41598-020-69494-x.

Toward an understanding of the relation between gene regulation and 3D genome organization. H Tian and Y Yang and S Liu and H Quan and YQ Gao.

https://link.springer.com/article/10.1007/s40484-020-0221-6.

Estimating Sample-Specific Regulatory Networks. M Tung.

https://dash.harvard.edu/handle/1/40621380.

Epigenetic and Transcriptional Regulation of the Reproductive Hypothalamus. CF Aylwin and A Lomniczi.

https://link.springer.com/chapter/10.1007/978-3-030-40002-6_8.

Gene Regulatory Network Inference as Relaxed Graph Matching. D Weighill and MB Guebila and C Lopes-Ramos and K Glass….

https://www.biorxiv.org/content/10.1101/2020.06.23.167999v2.abstract.

Di Wu. 2014.“. AM Tartakoff.

https://core.ac.uk/download/pdf/28952235.pdf.

Inference of genetic networks from time-series and static gene expression data: combining a random-forest-based inference method with feature selection …. S Kimura and R Fukutomi and M Tokuhisa and M Okada.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7770182/.

Gene Regulatory Network Construction of Ovarian Cancer Based on Passing Attributes between Network for Data Assimilation. YZE Isaac and K Moorthy and L Machap….

https://ieeexplore.ieee.org/abstract/document/9243432/.

Understanding the Genetic Nature of Multiple Sclerosis Using Next-Generation Sequencing Genomic Analysis Methods. FM Almsned.

https://search.proquest.com/openview/24f3d51eb6f38f98d548f7bdd024929a/1?pq-origsite=gscholar&cbl=18750&diss=y.

Development and exploitation of GeneFriends: An online database for gene and transcript co-expression analysis. S Van Dam.

https://livrepository.liverpool.ac.uk/3006075/.

Bioinformatics Advancements for Detecting Epidemic Disease Using Machine Learning Approaches. B Baruah and MP Dutta.

https://link.springer.com/chapter/10.1007/978-981-15-7031-5_100.

Generating ensembles of gene regulatory networks to assess robustness of disease modules. JT Lim and C Chen and AD Grant and M Padi.

https://www.biorxiv.org/content/10.1101/2020.07.12.198747v1.abstract.

The influence of the inclusion of biological knowledge in statistical methods to integrate multi-omics data. G Tini.

http://eprints-phd.biblio.unitn.it/2981/.

Inferring Genetic Regulatory Networks Using Cost-based Abduction and Its Relation to Bayesian Inference. EAT Andrews.

https://tspace.library.utoronto.ca/handle/1807/65634.

WGCNA: Weighted Gene Co-Expression Network Analysis. J Ferlic and S Tracy.

https://scholar.harvard.edu/files/stracy/files/finalproject_multivariate.pdf.

Investigating transcriptome-wide sex dimorphism by multi-level analysis of single-cell RNA sequencing data in ten mouse cell types. T Lu and JC Mar.

https://link.springer.com/article/10.1186/s13293-020-00335-2.

Modeling Transcriptional Regulation Using Gene Regulatory Networks Based on Multi-Omics Data Sources. N Patel and W Bush.

https://www.researchsquare.com/article/rs-112300/latest.pdf.

Unravelling vascular tumors: combining molecular and computational biology. DGP IJzendoorn.

https://openaccess.leidenuniv.nl/bitstream/handle/1887/82754/01.pdf?sequence=6.

Towards Reliable Gene Regulatory Network Inference. D Morgan.

https://www.diva-portal.org/smash/record.jsf?pid=diva2:1279914.

Improving GRN re-construction by mining hidden regulatory signals. M Shi and W Shen and Y Chong and HQ Wang.

https://digital-library.theiet.org/content/journals/10.1049/iet-syb.2017.0013.

Predicting genotype-specific gene regulatory networks. DA Weighill and MB Guebila and K Glass and J Quackenbush….

https://www.biorxiv.org/content/10.1101/2021.01.18.427134v1.abstract.

Supplementary Material: Gene Regulatory Network Inference as Relaxed Graph Matching. D Weighill and MB Guebila and C Lopes-Ramos and K Glass….

https://www.biorxiv.org/content/biorxiv/early/2020/06/24/2020.06.23.167999.1/DC1/embed/media-1.pdf?download=true.

LIONESS

Personalized characterization of diseases using sample-specific networks. X Liu and Y Wang and H Ji and K Aihara and L Chen.

https://academic.oup.com/nar/article-abstract/44/22/e164/2691334.

Cardiomyocyte gene programs encoding morphological and functional signatures in cardiac hypertrophy and failure. S Nomura and M Satoh and T Fujita and T Higo and T Sumida….

https://www.nature.com/articles/s41467-018-06639-7.

Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism. CM Lopes-Ramos and ML Kuijjer and S Ogino and CS Fuchs….

https://cancerres.aacrjournals.org/content/78/19/5538.short.

EndNote: Feature-based classification of networks. I Barnett and N Malik and ML Kuijjer and PJ Mucha….

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6980283/.

A novel network control model for identifying personalized driver genes in cancer. WF Guo and SW Zhang and T Zeng and Y Li and J Gao….

https://journals.plos.org/ploscompbiol/article?rev=1&id=10.1371/journal.pcbi.1007520.

Microbiome-transcriptome interactions related to severity of respiratory syncytial virus infection. AR Sonawane and L Tian and CY Chu and X Qiu and L Wang….

https://www.nature.com/articles/s41598-019-50217-w.

Sex differences in gene expression and regulatory networks across 29 human tissues. CM Lopes-Ramos and CY Chen and ML Kuijjer and JN Paulson….

https://www.sciencedirect.com/science/article/pii/S2211124720307762.

Personalized regression enables sample-specific pan-cancer analysis. BJ Lengerich and B Aragam and EP Xing.

https://academic.oup.com/bioinformatics/article-abstract/34/13/i178/5045771.

MODA: MOdule Differential Analysis for weighted gene co-expression network. D Li and JB Brown and L Orsini and Z Pan and G Hu and S He.

https://arxiv.org/abs/1605.04739.

PyPanda: a Python package for gene regulatory network reconstruction. DGP van IJzendoorn and K Glass and J Quackenbush….

https://academic.oup.com/bioinformatics/article-abstract/32/21/3363/2415289.

Estimating gene regulatory networks with pandaR. D Schlauch and JN Paulson and A Young and K Glass….

https://academic.oup.com/bioinformatics/article-abstract/33/14/2232/3066290.

Network science in clinical trials: A patient-centered approach. VSK Manem and R Salgado and P Aftimos and C Sotiriou….

https://www.sciencedirect.com/science/article/pii/S1044579X17302365?casa_token=S27YljkWrp0AAAAA:it46HH_GEDJ-A5vlt1UOt496xEbHKBxsbnD9wPU1CIOEaQYyQ-q4K6eBhopRFL_TmY3ac8LopIY.

An omnidirectional visualization model of personalized gene regulatory networks. C Chen and L Jiang and G Fu and M Wang and Y Wang….

https://www.nature.com/articles/s41540-019-0116-1.

Network control principles for identifying personalized driver genes in cancer. WF Guo and SW Zhang and T Zeng and T Akutsu….

https://academic.oup.com/bib/article-abstract/21/5/1641/5581645.

System-Based Differential Gene Network Analysis for Characterizing a Sample-Specific Subnetwork. Y Tanaka and Y Tamada and M Ikeguchi and F Yamashita….

https://www.mdpi.com/2218-273X/10/2/306.

lionessR: single sample network inference in R. ML Kuijjer and PH Hsieh and J Quackenbush….

https://bmccancer.biomedcentral.com/articles/10.1186/s12885-019-6235-7.

Modeling regulatory networks using machine learning for systems metabolic engineering. MS Kwon and BT Lee and SY Lee and HU Kim.

https://www.sciencedirect.com/science/article/pii/S0958166920300318.

Centralization within sub-experiments enhances the biological relevance of gene co-expression networks: a plant mitochondrial case study. SR Law and TG Kellgren and R Björk and P Ryden….

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dyngen: a multi-modal simulator for spearheading new single-cell omics analyses. R Cannoodt and W Saelens and L Deconinck and Y Saeys.

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Disease characterization using a partial correlation-based sample-specific network. Y Huang and X Chang and Y Zhang and L Chen….

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Applications of weighted association networks applied to compositional data in biology. JL Espinoza and N Shah and S Singh….

https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15091.

Computational Identification of Gene Networks as a Biomarker of Neuroblastoma Risk. L Sun and L Jiang and CN Grant and HG Wang and C Gragnoli and Z Liu….

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Evaluation of Single Sample Network Inference Methods for Metabolomics-Based Systems Medicine. S Jahagirdar and E Saccenti.

https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00696.

Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. WF Guo and SW Zhang and YH Feng and J Liang….

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Data will Drive the Healthcare Revolution. J Quackenbush.

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Gene targeting in disease networks. D Weighill and MB Guebila and K Glass and J Platig….

https://arxiv.org/abs/2101.03985.

PUMA: PANDA Using MicroRNA Associations. ML Kuijjer and M Fagny and A Marin and J Quackenbush….

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Sample-Specific Models for Precision Medicine. B Lengerich.

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Active modules identification in multilayer intracellular networks. D Li.

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Gene Regulatory Network Construction of Ovarian Cancer Based on Passing Attributes between Network for Data Assimilation. YZE Isaac and K Moorthy and L Machap….

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Pushing the Limits of Heterogeneous Models with Personalized Regression. B Lengerich and B Aragam and EP Xing.

http://www.cs.cmu.edu/~blengeri/downloads/posters/personalization_workshop_poster.pdf.

lionessR: single-sample network reconstruction in R. ML Kuijjer and J Quackenbush and K Glass.

https://www.biorxiv.org/content/10.1101/582098v1.abstract.

CONDOR

Quantized neural networks: Training neural networks with low precision weights and activations. I Hubara and M Courbariaux and D Soudry and R El-Yaniv….

https://www.jmlr.org/papers/volume18/16-456/16-456.pdf.

Exploring regulation in tissues with eQTL networks. M Fagny and JN Paulson and ML Kuijjer….

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Network medicine in the age of biomedical big data. AR Sonawane and ST Weiss and K Glass and A Sharma.

https://www.frontiersin.org/articles/10.3389/fgene.2019.00294/full.

Transcription-driven genome organization: a model for chromosome structure and the regulation of gene expression tested through simulations. PR Cook and D Marenduzzo.

https://academic.oup.com/nar/article-abstract/46/19/9895/5099447.

Bipartite graphs in systems biology and medicine: a survey of methods and applications. GA Pavlopoulos and PI Kontou and A Pavlopoulou….

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A paradigm shift in medicine: A comprehensive review of network-based approaches. F Conte and G Fiscon and V Licursi and D Bizzarri and T D'Antò….

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The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry). M Buti and M Moretto and E Barghini and F Mascagni….

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Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. JD Morrow and MH Cho and J Platig and X Zhou and DL DeMeo….

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Significance-based community detection in weighted networks. J Palowitch and S Bhamidi and AB Nobel.

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The continuous configuration model: A null for community detection on weighted networks. J Palowitch and AB Nobel and S Bhamidi.

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Detecting phenotype-driven transitions in regulatory network structure. M Padi and J Quackenbush.

https://www.nature.com/articles/s41540-018-0052-5.

Network science in clinical trials: A patient-centered approach. VSK Manem and R Salgado and P Aftimos and C Sotiriou….

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A guide to conquer the biological network era using graph theory. M Koutrouli and E Karatzas and D Paez-Espino….

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A network-based approach to eQTL interpretation and SNP functional characterization. M Fagny and JN Paulson and ML Kuijjer and AR Sonawane….

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Nongenic cancer-risk SNPs affect oncogenes, tumour-suppressor genes, and immune function. M Fagny and J Platig and ML Kuijjer and X Lin….

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Proceedings of the fourth international molecular pathological epidemiology (MPE) meeting. PT Campbell and CB Ambrosone and R Nishihara….

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Complex network approach for the structural optimization of global crude oil trade system. G Dong and T Qing and R Du and C Wang and R Li and M Wang….

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Phenotype-driven transitions in regulatory network structure. M Padi and J Quackenbush.

https://www.biorxiv.org/content/10.1101/142281v1.abstract.

Spectral clustering in regression-based biological networks. SM Gaynor and X Lin and J Quackenbush.

https://www.biorxiv.org/content/10.1101/651950v1.abstract.

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis. AT Young and X Carette and M Helmel and H Steen and RN Husson….

https://www.biorxiv.org/content/10.1101/584177v1.abstract.

Connectivity of variants in eQTL networks dictates reproducibility and functionality. SM Gaynor and M Fagny and X Lin and J Platig and J Quackenbush.

https://www.biorxiv.org/content/10.1101/515551v1.abstract.

CrosstalkNet: A visualization tool for differential co-expression networks and communities. V Manem and GA Adam and T Gruosso and M Gigoux and N Bertos….

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Peripheral blood microbial signatures in COPD. JD Morrow and PJ Castaldi and RP Chase and JH Yun and S Lee….

https://www.biorxiv.org/content/10.1101/2020.05.31.126367v1.abstract.

Understanding the adaptation of polygenic traits: the importance of gene regulatory networks. M Fagny and F Austerlitz.

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Computational Investigation of Endothelial Heterogeneity During Homeostasis and Inflammation. A Jambusaria.

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An Integrative Systems Bioinformatics Approach of the Environmental, Genetic and Molecular Factors Regulating Sleep. M Jan.

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Bipartite Network Community Detection: Algorithms and Applications. PGP Cabrera.

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Bipartite Network Community Detection: Algorithms and Applications. PG Pesántez Cabrera.

https://research.wsulibs.wsu.edu/xmlui/handle/2376/16377.

VarSAn: Associating pathways with a set of genomic variants using network analysis. X Xie and M Kendzior and X Ge and LS Mainzer and S Sinha.

https://www.biorxiv.org/content/10.1101/2020.12.22.424077v1.abstract.

Testing-Based Community Detection Methods for Complex Networks. J Palowitch.

https://cdr.lib.unc.edu/concern/dissertations/rv042v45w.

Finding Stable Groups of Cross-Correlated Features in Multi-View data. M Dewaskar and J Palowitch and M He and MI Love….

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Generating ensembles of gene regulatory networks to assess robustness of disease modules. JT Lim and C Chen and AD Grant and M Padi.

https://www.biorxiv.org/content/10.1101/2020.07.12.198747v1.abstract.

Towards Reliable Gene Regulatory Network Inference. D Morgan.

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Eigenvector-based identification of bipartite subgraphs. D Paul and D Stevanović.

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ALPACA

Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development. T Pearson and JG Caporaso and M Yellowhair….

https://onlinelibrary.wiley.com/doi/abs/10.1002/cam4.1965.

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer. DD Bhuva and J Cursons and GK Smyth….

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1851-8.

Insights into respiratory disease through bioinformatics. B Hurgobin and E de Jong and A Bosco.

https://onlinelibrary.wiley.com/doi/abs/10.1111/resp.13401.

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks. M Fagny and ML Kuijjer and M Stam and J Joets and O Turc….

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Generating ensembles of gene regulatory networks to assess robustness of disease modules. JT Lim and C Chen and AD Grant and M Padi.

https://www.biorxiv.org/content/10.1101/2020.07.12.198747v1.abstract.

Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. A Savino and P Provero and V Poli.

https://www.mdpi.com/1422-0067/21/24/9461.

Genome-Wide Sex and Gender Differences in Cancer. CM Lopes-Ramos and J Quackenbush….

https://www.frontiersin.org/articles/10.3389/fonc.2020.597788/full.

Towards Reliable Gene Regulatory Network Inference. D Morgan.

https://www.diva-portal.org/smash/record.jsf?pid=diva2:1279914.

Predicting genotype-specific gene regulatory networks. DA Weighill and MB Guebila and K Glass and J Quackenbush….

https://www.biorxiv.org/content/10.1101/2021.01.18.427134v1.abstract.

MONSTER

Estimating sample-specific regulatory networks. ML Kuijjer and MG Tung and GC Yuan and J Quackenbush….

https://www.sciencedirect.com/science/article/pii/S2589004219300872.

Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. M Daya and N Rafaels and TM Brunetti and S Chavan….

https://www.nature.com/articles/s41467-019-08469-7.

A paradigm shift in medicine: A comprehensive review of network-based approaches. F Conte and G Fiscon and V Licursi and D Bizzarri and T D'Antò….

https://www.sciencedirect.com/science/article/pii/S1874939919302500.

Predicting growth rate from gene expression. TP Wytock and AE Motter.

https://www.pnas.org/content/116/2/367.short.

Gene networks with transcriptional bursting recapitulate rare transient coordinated high expression states in cancer. L Schuh and M Saint-Antoine and EM Sanford and BL Emert….

https://www.sciencedirect.com/science/article/pii/S2405471220301101.

Insights into respiratory disease through bioinformatics. B Hurgobin and E de Jong and A Bosco.

https://onlinelibrary.wiley.com/doi/abs/10.1111/resp.13401.

Genetic modulation of neurocognitive development in cancer patients throughout the lifespan: a systematic review. C Sleurs and A Madoe and L Lagae and S Jacobs and S Deprez….

https://idp.springer.com/authorize/casa?redirect_uri=https://link.springer.com/article/10.1007/s11065-019-09399-3&casa_token=0B7m0jy4ywEAAAAA:Q-PLYFa8nXE7nI2Lt9gHmSCW4tyN5DFTdyMKVIbGIsRXgDBWPw1x7mVfGOmElizpjgYVKVyR8zOIIHMpzA.

Novel Roles for the Terminal RNA Uridylyltransferases ZCCHC6 and ZCCHC11 in Development and Disease. DS Pearson.

https://dash.harvard.edu/handle/1/41127147.

Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer. K Jo and B Santos-Buitrago and M Kim and S Rhee and C Talcott….

https://www.sciencedirect.com/science/article/pii/S104620232030044X.

Towards Reliable Gene Regulatory Network Inference. D Morgan.

https://www.diva-portal.org/smash/record.jsf?pid=diva2:1279914.