Works matching IS 20567189 AND DT 2025 AND VI 11 AND IP 1

Results: 50

COmmunity and Single Microbe Optimisation System (COSMOS).

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00534-w

By:

Raajaraam, Lavanya;
Raman, Karthik

Publication type:

Article

Genome-scale metabolic modelling identifies reactions mediated by SNP-SNP interactions associated with yeast sporulation.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00503-3

By:

Sasikumar, Srijith;
Kumar, S Pavan;
Bhatt, Nirav Pravinbhai;
Sinha, Himanshu

Publication type:

Article

SEgene identifies links between super enhancers and gene expression across cell types.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00533-x

By:

Shinkai, Norio;
Asada, Ken;
Machino, Hidenori;
Takasawa, Ken;
Takahashi, Satoshi;
Kouno, Nobuji;
Komatsu, Masaaki;
Hamamoto, Ryuji;
Kaneko, Syuzo

Publication type:

Article

Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00518-w

By:

Toscano, Elvira;
Cimmino, Elena;
Boccia, Angelo;
Sepe, Leandra;
Paolella, Giovanni

Publication type:

Article

Assessing the impact of sampling bias on node centralities in synthetic and biological networks.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00526-w

By:

Salehzadeh-Yazdi, Ali;
Hütt, Marc-Thorsten

Publication type:

Article

Computational modeling of cancer cell metabolism along the catabolic-anabolic axes.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00525-x

By:

Villela-Castrejon, Javier;
Levine, Herbert;
Kaipparettu, Benny A.;
Onuchic, José N.;
George, Jason T.;
Jia, Dongya

Publication type:

Article

A Python toolbox for neural circuit parameter inference.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00527-9

By:

Orozco Valero, Alejandro;
Rodríguez-González, Víctor;
Montobbio, Noemi;
Casal, Miguel A.;
Tlaie, Alejandro;
Pelayo, Francisco;
Morillas, Christian;
Poza, Jesús;
Gómez, Carlos;
Martínez-Cañada, Pablo

Publication type:

Article

Patient-specific gene co-expression networks reveal novel subtypes and predictive biomarkers in lung adenocarcinoma.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00522-0

By:

López-Sánchez, Patricio;
Ávila-Moreno, Federico;
Hernández-Lemus, Enrique;
Kuijjer, Marieke L.;
Espinal-Enríquez, Jesús

Publication type:

Article

Effective integration of multi-omics with prior knowledge to identify biomarkers via explainable graph neural networks.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00519-9

By:

Tripathy, Rohit K.;
Frohock, Zachary;
Wang, Hong;
Cary, Gregory A.;
Keegan, Stephen;
Carter, Gregory W.;
Li, Yi

Publication type:

Article

An in silico approach deciphering the commensal dynamics in the cutaneous milieu.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00524-y

By:

Kalankariyan, Sumathi;
Thottapillil, Anjana;
Saxena, Abha;
Srivatsn S, Manoj;
Kadamkode, Vinitha;
Kapoor, Renu;
Mitra, Rupak;
Raut, Janhavi;
Venkatesh, KV

Publication type:

Article

Neural mechanisms balancing accuracy and flexibility in working memory and decision tasks.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00520-2

By:

Yan, Han;
Wang, Jin

Publication type:

Article

The Virtual Parkinsonian patient.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00516-y

By:

Angiolelli, Marianna;
Depannemaecker, Damien;
Agouram, Hasnae;
Régis, Jean;
Carron, Romain;
Woodman, Marmaduke;
Chiodo, Letizia;
Triebkorn, Paul;
Ziaeemehr, Abolfazl;
Hashemi, Meysam;
Eusebio, Alexandre;
Jirsa, Viktor;
Sorrentino, Pierpaolo

Publication type:

Article

Biochemical implementation of acceleration sensing and PIDA control.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00514-0

By:

Alexis, Emmanouil;
Espinel-Ríos, Sebastián;
Kevrekidis, Ioannis G.;
Avalos, José L.

Publication type:

Article

A multidisciplinary approach towards modeling of a virtual human lung.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00517-x

By:

Lam, Timothy;
Quach, Henry T.;
Hall, Lauren;
Abou Chakra, Maria;
Wong, Amy P.

Publication type:

Article

MIRO1 mutation leads to metabolic maladaptation resulting in Parkinson's disease-associated dopaminergic neuron loss.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00509-x

By:

Zagare, Alise;
Sauter, Thomas;
Barmpa, Kyriaki;
Pacheco, Maria;
Krüger, Rejko;
Schwamborn, Jens Christian;
Saraiva, Claudia

Publication type:

Article

Exploring the role of EMT in ovarian cancer progression using a multiscale mathematical model.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00508-y

By:

Oliver, Samuel;
Williams, Michael;
Jolly, Mohit Kumar;
Gonzalez, Deyarina;
Powathil, Gibin

Publication type:

Article

Single cell RNAseq to identify subpopulations of glial progenitors in iPSC-derived oligodendroglial lineage cultures.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00515-z

By:

Blaszczyk, Gabriela J.;
Piscopo, Valerio E. C.;
Goldsmith, Taylor M.;
Chapleau, Alexandra;
Sirois, Julien;
Bernard, Geneviève;
Antel, Jack P.;
Durcan, Thomas M.

Publication type:

Article

Predicting gene expression changes from chromatin structure modification.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00510-4

By:

Senapati, Swayamshree;
Irshad, Inayat Ullah;
Sharma, Ajeet K.;
Kumar, Hemant

Publication type:

Article

Quantitative cancer-immunity cycle modeling for predicting disease progression in advanced metastatic colorectal cancer.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00513-1

By:

Li, Chenghang;
Wei, Yongchang;
Lei, Jinzhi

Publication type:

Article

Understanding therapeutic tolerance through a mathematical model of drug-induced resistance.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00511-3

By:

Gevertz, Jana L.;
Greene, James M.;
Prosperi, Samantha;
Comandante-Lou, Natacha;
Sontag, Eduardo D.

Publication type:

Article

Exploring cell-to-cell variability and functional insights through differentially variable gene analysis.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00507-z

By:

Gatlin, Victoria;
Gupta, Shreyan;
Romero, Selim;
Chapkin, Robert S.;
Cai, James J.

Publication type:

Article

Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00505-1

By:

Adler, Stephan O.;
Kitashova, Anastasia;
Bulović, Ana;
Nägele, Thomas;
Klipp, Edda

Publication type:

Article

Plant cold acclimation and its impact on sensitivity of carbohydrate metabolism.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00505-1

By:

Adler, Stephan O.;
Kitashova, Anastasia;
Bulović, Ana;
Nägele, Thomas;
Klipp, Edda

Publication type:

Article

A molecular systems architecture of neuromuscular junction in amyotrophic lateral sclerosis.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00501-5

By:

Ayyadurai, V. A. Shiva;
Deonikar, Prabhakar;
Kamm, Roger D.

Publication type:

Article

A single-cell network approach to decode metabolic regulation in gynecologic and breast cancers.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00506-0

By:

Srivastava, Akansha;
Vinod, P. K.

Publication type:

Article

Enhancing yeast cell tracking with a time-symmetric deep learning approach.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00466-x

By:

Szabó, Gergely;
Bonaiuti, Paolo;
Ciliberto, Andrea;
Horváth, András

Publication type:

Article

An integrative phenotype-structured partial differential equation model for the population dynamics of epithelial-mesenchymal transition.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00502-4

By:

Guilberteau, Jules;
Jain, Paras;
Jolly, Mohit Kumar;
Pouchol, Camille;
Pouradier Duteil, Nastassia

Publication type:

Article

Gene regulatory network inference during cell fate decisions by perturbation strategies.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00504-2

By:

Hu, Qing;
Lu, Xiaoqi;
Xue, Zhuozhen;
Wang, Ruiqi

Publication type:

Article

Gene regulatory network inference during cell fate decisions by perturbation strategies.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00504-2

By:

Hu, Qing;
Lu, Xiaoqi;
Xue, Zhuozhen;
Wang, Ruiqi

Publication type:

Article

Loss formulations for assumption-free neural inference of SDE coefficient functions.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00500-6

By:

Vaisband, Marc;
von Bornhaupt, Valentin;
Schmid, Nina;
Abulizi, Izdar;
Hasenauer, Jan

Publication type:

Article

Integrative systems biology framework discovers common gene regulatory signatures in mechanistically distinct inflammatory skin diseases.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00498-x

By:

Mishra, Bharat;
Gou, Yifei;
Tan, Zhengzhi;
Wang, Yiqing;
Hu, Getian;
Athar, Mohammad;
Mukhtar, M. Shahid

Publication type:

Article

Mathematical modeling of multicellular tumor spheroids quantifies inter-patient and intra-tumor heterogeneity.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00492-3

By:

Malik, Adam A.;
Nguyen, Kyle C.;
Nardini, John T.;
Krona, Cecilia C.;
Flores, Kevin B.;
Nelander, Sven

Publication type:

Article

Deep learning for detecting and early predicting chronic obstructive pulmonary disease from spirogram time series.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00489-y

By:

Mei, Shuhao;
Li, Xin;
Zhou, Yuxi;
Xu, Jiahao;
Zhang, Yong;
Wan, Yuxuan;
Cao, Shan;
Zhao, Qinghao;
Geng, Shijia;
Xie, Junqing;
Chen, Shengyong;
Hong, Shenda

Publication type:

Article

Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00487-6

By:

Pullen, Krista M.;
Finethy, Ryan;
Ko, Seung-Hyun B.;
Reames, Charlotte J.;
Sassetti, Christopher M.;
Lauffenburger, Douglas A.

Publication type:

Article

Overall biomass yield on multiple nutrient sources.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00497-y

By:

Golan, Ohad;
Gampp, Olivia;
Eckert, Lina;
Sauer, Uwe

Publication type:

Article

Modeling critical dosing strategies for stromal-induced resistance to cancer therapy.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00495-0

By:

Kraut, Anna K.;
Garvey, Colleen M.;
Strelez, Carly;
Mumenthaler, Shannon M.;
Foo, Jasmine

Publication type:

Article

Leveraging public AI tools to explore systems biology resources in mathematical modeling.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00496-z

By:

Kannan, Meera;
Bridgewater, Gabrielle;
Zhang, Ming;
Blinov, Michael L.

Publication type:

Article

Network analyses of brain tumor multiomic data reveal pharmacological opportunities to alter cell state transitions.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00493-2

By:

Bumbaca, Brandon;
Huggins, Jonah R.;
Birtwistle, Marc R.;
Gallo, James M.

Publication type:

Article

Nucleus pulposus cell network modelling in the intervertebral disc.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00479-6

By:

Tseranidou, Sofia;
Segarra-Queralt, Maria;
Chemorion, Francis Kiptengwer;
Le Maitre, Christine Lyn;
Piñero, Janet;
Noailly, Jérôme

Publication type:

Article

Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00494-1

By:

Tavakoli, Niki;
Fong, Emma J.;
Coleman, Abigail;
Huang, Yu-Kai;
Bigger, Mathias;
Doche, Michael E.;
Kim, Seungil;
Lenz, Heinz-Josef;
Graham, Nicholas A.;
Macklin, Paul;
Finley, Stacey D.;
Mumenthaler, Shannon M.

Publication type:

Article

Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00482-x

By:

Arshad, Sanya;
Cameron, Benjamin;
Joglekar, Alok V.

Publication type:

Article

Classification of NSCLC subtypes using lung microbiome from resected tissue based on machine learning methods.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00491-4

By:

Kashyap, Pragya;
Raj, Kalbhavi Vadhi;
Sharma, Jyoti;
Dutt, Naveen;
Yadav, Pankaj

Publication type:

Article

Simulation of clinical trials of oral treprostinil in pulmonary arterial hypertension using a virtual population.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00481-y

By:

Stine, Andrew E.;
Parmar, Jignesh;
Smith, Amy K.;
Cummins, Zachary;
Pillalamarri, Narasimha Rao;
Bender, R. Joseph

Publication type:

Article

Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00480-z

By:

Banerjee, Deepanwita;
Menasalvas, Javier;
Chen, Yan;
Gin, Jennifer W.;
Baidoo, Edward E. K.;
Petzold, Christopher J.;
Eng, Thomas;
Mukhopadhyay, Aindrila

Publication type:

Article

Dysregulated autoantibodies targeting AGTR1 are associated with the accumulation of COVID-19 symptoms.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00488-z

By:

Fonseca, Dennyson Leandro M.;
Jäpel, Maj;
Gyamfi, Michael Adu;
Filgueiras, Igor Salerno;
Baiochi, Gabriela Crispim;
Ostrinski, Yuri;
Halpert, Gilad;
Lavi, Yael Bublil;
Vojdani, Elroy;
Silva-Sousa, Thayna;
Usuda, Júlia Nakanishi;
e Silva, Juan Carlo Santos;
Freire, Paula P.;
Nóbile, Adriel Leal;
Adri, Anny Silva;
Barcelos, Pedro Marçal;
Corrêa, Yohan Lucas Gonçalves;
do Vale, Fernando Yuri Nery;
Lopes, Letícia Oliveira;
Schmidt, Solveig Lea

Publication type:

Article

Deterministic patterns in single-cell transcriptomic data.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-025-00490-5

By:

Cao, Zhixing;
Wang, Yiling;
Grima, Ramon

Publication type:

Article

Network-based transfer of pan-cancer immunotherapy responses to guide breast cancer prognosis.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00486-7

By:

Ding, Xiaobao;
Zhang, Lin;
Fan, Ming;
Li, Lihua

Publication type:

Article

Biopsy location and tumor-associated macrophages in predicting malignant glioma recurrence using an in-silico model.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00478-7

By:

Shojaee, Pejman;
Weinholtz, Edwin;
Schaadt, Nadine S.;
Feuerhake, Friedrich;
Hatzikirou, Haralampos

Publication type:

Article

A joint analysis of single cell transcriptomics and proteomics using transformer.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00484-9

By:

Chen, Yuanyuan;
Fan, Xiaodan;
Shi, Chaowen;
Shi, Zhiyan;
Wang, Chaojie

Publication type:

Article

Operating principles of interconnected feedback loops driving cell fate transitions.

Published in:

NPJ Systems Biology & Applications, 2025, v. 11, n. 1, p. 1, doi. 10.1038/s41540-024-00483-w

By:

Rashid, Mubasher;
Hegade, Abhiram

Publication type:

Article