Works matching IS 20567189 AND DT 2024 AND VI 10 AND IP 1

Results: 153

Endosomal pH is an evolutionarily conserved driver of phenotypic plasticity in colorectal cancer.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00463-0

By:

Prasad, Hari;
BV, Harshavardhan;
Subbalakshmi, Ayalur Raghu;
Mandal, Susmita;
Jolly, Mohit Kumar;
Visweswariah, Sandhya S.

Publication type:

Article

Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning.

Published in:

2024

By:

Meimetis, Nikolaos;
Pullen, Krista M.;
Zhu, Daniel Y.;
Nilsson, Avlant;
Hoang, Trong Nghia;
Magliacane, Sara;
Lauffenburger, Douglas A.

Publication type:

Correction Notice

Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00475-w

By:

Mateos, Raúl N.;
Winardi, Wira;
Chiba, Kenichi;
Okada, Ai;
Suzuki, Ayako;
Mitsuishi, Yoichiro;
Shiraishi, Yuichi

Publication type:

Article

Microarray integrated spatial transcriptomics (MIST) for affordable and robust digital pathology.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00462-1

By:

Juwayria;
Shrivastava, Priyansh;
Yadav, Kaustar;
Das, Sourabh;
Mittal, Shubham;
Kumar, Sunil;
Jain, Deepali;
Malik, Prabhat Singh;
Gupta, Ishaan

Publication type:

Article

Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00414-9

By:

Jafarinia, Hamidreza;
Khalilimeybodi, Ali;
Barrasa-Fano, Jorge;
Fraley, Stephanie I.;
Rangamani, Padmini;
Carlier, Aurélie

Publication type:

Article

Open problems in synthetic multicellularity.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00477-8

By:

Solé, Ricard;
Conde–Pueyo, Núria;
Pla–Mauri, Jordi;
Garcia–Ojalvo, Jordi;
Montserrat, Nuria;
Levin, Michael

Publication type:

Article

Bridging silicon and carbon worlds with digital twins and on-chip systems in drug discovery.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00476-9

By:

Akbarialiabad, Hossein;
Seyyedi, Mahdiyeh Sadat;
Paydar, Shahram;
Habibzadeh, Adrina;
Haghighi, Alireza;
Kvedar, Joseph C.

Publication type:

Article

A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00472-z

By:

L. Rocha, Heber;
Aguilar, Boris;
Getz, Michael;
Shmulevich, Ilya;
Macklin, Paul

Publication type:

Article

Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphoma.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00474-x

By:

Sarkar, Suryadipto;
Möller, Anna;
Hartebrodt, Anne;
Erdmann, Michael;
Ostalecki, Christian;
Baur, Andreas;
Blumenthal, David B.

Publication type:

Article

Immune digital twins for complex human pathologies: applications, limitations, and challenges.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00450-5

By:

Niarakis, Anna;
Laubenbacher, Reinhard;
An, Gary;
Ilan, Yaron;
Fisher, Jasmin;
Flobak, Åsmund;
Reiche, Kristin;
Rodríguez Martínez, María;
Geris, Liesbet;
Ladeira, Luiz;
Veschini, Lorenzo;
Blinov, Michael L.;
Messina, Francesco;
Fonseca, Luis L.;
Ferreira, Sandra;
Montagud, Arnau;
Noël, Vincent;
Marku, Malvina;
Tsirvouli, Eirini;
Torres, Marcella M.

Publication type:

Article

Mathematical model of the inflammatory response to acute and prolonged lipopolysaccharide exposure in humans.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00473-y

By:

Relouw, Freek J. A.;
Kox, Matthijs;
Taal, H. Rob;
Koch, Birgit C. P.;
Prins, Menno W. J.;
van Riel, Natal A. W.

Publication type:

Article

A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00469-8

By:

Herrera, Joel;
Bensussen, Antonio;
García-Gómez, Mónica L.;
Garay-Arroyo, Adriana;
Álvarez-Buylla, Elena R.

Publication type:

Article

Robust parameter estimation and identifiability analysis with hybrid neural ordinary differential equations in computational biology.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00460-3

By:

Giampiccolo, Stefano;
Reali, Federico;
Fochesato, Anna;
Iacca, Giovanni;
Marchetti, Luca

Publication type:

Article

Hybridizing mechanistic modeling and deep learning for personalized survival prediction after immune checkpoint inhibitor immunotherapy.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00415-8

By:

Butner, Joseph D.;
Dogra, Prashant;
Chung, Caroline;
Koay, Eugene J.;
Welsh, James W.;
Hong, David S.;
Cristini, Vittorio;
Wang, Zhihui

Publication type:

Article

Practical parameter identifiability and handling of censored data with Bayesian inference in mathematical tumour models.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00409-6

By:

Porthiyas, Jamie;
Nussey, Daniel;
Beauchemin, Catherine A. A.;
Warren, Donald C.;
Quirouette, Christian;
Wilkie, Kathleen P.

Publication type:

Article

A mathematical framework for comparison of intermittent versus continuous adaptive chemotherapy dosing in cancer.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00461-2

By:

McGehee, Cordelia;
Mori, Yoichiro

Publication type:

Article

A deep learning approach predicting the activity of COVID-19 therapeutics and vaccines against emerging variants.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00471-0

By:

Matson, Robert P.;
Comba, Isin Y.;
Silvert, Eli;
Niesen, Michiel J. M.;
Murugadoss, Karthik;
Patwardhan, Dhruti;
Suratekar, Rohit;
Goel, Elizabeth-Grace;
Poelaert, Brittany J.;
Wan, Kanny K.;
Brimacombe, Kyle R.;
Venkatakrishnan, AJ;
Soundararajan, Venky

Publication type:

Article

Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00457-y

By:

Li, Jiahang;
Weckwerth, Wolfram;
Waldherr, Steffen

Publication type:

Article

Enhancing localized chemotherapy with anti-angiogenesis and nanomedicine synergy for improved tumor penetration in well-vascularized tumors.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00467-w

By:

Souri, Mohammad;
Elahi, Sohail;
Moradi Kashkooli, Farshad;
Kohandel, Mohammad;
Soltani, M.

Publication type:

Article

General relationship of local topologies, global dynamics, and bifurcation in cellular networks.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00470-1

By:

Hu, Qing;
Tang, Ruoyu;
He, Xinyu;
Wang, Ruiqi

Publication type:

Article

Systems-level reconstruction of kinase phosphosignaling networks regulating endothelial barrier integrity using temporal data.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00468-9

By:

Wei, Ling;
Aitchison, John D.;
Kaushansky, Alexis;
Mast, Fred D.

Publication type:

Article

Experimentally-driven mathematical model to understand the effects of matrix deprivation in breast cancer metastasis.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00443-4

By:

Maiti, Sayoni;
Rangarajan, Annapoorni;
Kareenhalli, Venkatesh

Publication type:

Article

Plasmodium vivax antigen candidate prediction improves with the addition of Plasmodium falciparum data.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00465-y

By:

Chou, Renee Ti;
Ouattara, Amed;
Takala-Harrison, Shannon;
Cummings, Michael P.

Publication type:

Article

Automatic construction of Petri net models for computational simulations of molecular interaction network.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00464-z

By:

Lin, Xuefei;
Chang, Xiao;
Zhang, Yizheng;
Gao, Zhanyu;
Chi, Xu

Publication type:

Article

Reliable and easy-to-use calculating tool for the Nail Psoriasis Severity Index using deep learning.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00458-x

By:

Horikawa, Hiroto;
Tanese, Keiji;
Nonaka, Naoki;
Seita, Jun;
Amagai, Masayuki;
Saito, Masataka

Publication type:

Article

Network medicine informed multiomics integration identifies drug targets and repurposable medicines for Amyotrophic Lateral Sclerosis.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00449-y

By:

Yu, Mucen;
Xu, Jielin;
Dutta, Ranjan;
Trapp, Bruce;
Pieper, Andrew A.;
Cheng, Feixiong

Publication type:

Article

Exploring heterogeneous cell population dynamics in different microenvironments by novel analytical strategy based on images.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00459-w

By:

Huang, Yihong;
Zhou, Zidong;
Liu, Tianqi;
Tang, Shengnan;
Xin, Xuegang

Publication type:

Article

Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00455-0

By:

Andersen, Gøran Troseth;
Ianevski, Aleksandr;
Resell, Mathilde;
Pojskic, Naris;
Rabben, Hanne-Line;
Geithus, Synne;
Kodama, Yosuke;
Hiroyuki, Tomita;
Kainov, Denis;
Grønbech, Jon Erik;
Hayakawa, Yoku;
Wang, Timothy C.;
Zhao, Chun-Mei;
Chen, Duan

Publication type:

Article

A practically efficient algorithm for identifying critical control proteins in directed probabilistic biological networks.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00411-y

By:

Tokuhara, Yusuke;
Akutsu, Tatsuya;
Schwartz, Jean-Marc;
Nacher, Jose C.

Publication type:

Article

Transient frequency preference responses in cell signaling systems.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00413-w

By:

Szischik, Candela L.;
Reves Szemere, Juliana;
Balderrama, Rocío;
Sánchez de la Vega, Constanza;
Ventura, Alejandra C.

Publication type:

Article

Multiscale, mechanistic model of Rheumatoid Arthritis to enable decision making in late stage drug development.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00454-1

By:

Bedathuru, Dinesh;
Rengaswamy, Maithreye;
Channavazzala, Madhav;
Ray, Tamara;
Packrisamy, Prakash;
Kumar, Rukmini

Publication type:

Article

An integrative network-based approach to identify driving gene communities in chronic obstructive pulmonary disease.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00425-6

By:

Marino, Roberta;
El Aalamat, Yousef;
Bol, Vanesa;
Caselle, Michele;
Del Giudice, Giuseppe;
Lambert, Christophe;
Medini, Duccio;
Wilkinson, Tom M. A.;
Muzzi, Alessandro

Publication type:

Article

A benchmark of RNA-seq data normalization methods for transcriptome mapping on human genome-scale metabolic networks.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00448-z

By:

Lüleci, Hatice Büşra;
Uzuner, Dilara;
Cesur, Müberra Fatma;
İlgün, Atılay;
Düz, Elif;
Abdik, Ecehan;
Odongo, Regan;
Çakır, Tunahan

Publication type:

Article

Multistability and predominant hybrid phenotypes in a four node mutually repressive network of Th1/Th2/Th17/Treg differentiation.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00433-6

By:

Duddu, Atchuta Srinivas;
Andreas, Elizabeth;
BV, Harshavardhan;
Grover, Kaushal;
Singh, Vivek Raj;
Hari, Kishore;
Jhunjhunwala, Siddharth;
Cummins, Breschine;
Gedeon, Tomas;
Jolly, Mohit Kumar

Publication type:

Article

Emergence of cyclic hypoxia and the impact of PARP inhibitors on tumor progression.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00453-2

By:

Conte, Martina;
Cabeza Fernández, Vanesa;
Oliver, F. Javier;
Alarcón, Tomás;
Soler, Juan

Publication type:

Article

Stochastic Boolean model of normal and aberrant cell cycles in budding yeast.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00452-3

By:

Taoma, Kittisak;
Tyson, John J.;
Laomettachit, Teeraphan;
Kraikivski, Pavel

Publication type:

Article

Computational identification of surface markers for isolating distinct subpopulations from heterogeneous cancer cell populations.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00441-6

By:

Gardner, Andrea L.;
Jost, Tyler A.;
Morgan, Daylin;
Brock, Amy

Publication type:

Article

Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00451-4

By:

Uriu, Koichiro;
Hernandez-Sanchez, Juan P.;
Kojima, Shihoko

Publication type:

Article

Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients' blood.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00447-0

By:

Orcutt-Jahns, Brian;
Lima Junior, Joao Rodrigues;
Lin, Emily;
Rockne, Russell C.;
Matache, Adina;
Branciamore, Sergio;
Hung, Ethan;
Rodin, Andrei S.;
Lee, Peter P.;
Meyer, Aaron S.

Publication type:

Article

Systems immunology approaches to study T cells in health and disease.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00446-1

By:

Yang, Aaron;
Poholek, Amanda C.

Publication type:

Article

YAP/TAZ drives Notch and angiogenesis mechanoregulation in silico.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00444-3

By:

Passier, Margot;
Bentley, Katie;
Loerakker, Sandra;
Ristori, Tommaso

Publication type:

Article

Peptide hemolytic activity analysis using visual data mining of similarity-based complex networks.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00429-2

By:

Castillo-Mendieta, Kevin;
Agüero-Chapin, Guillermin;
Marquez, Edgar A.;
Perez-Castillo, Yunierkis;
Barigye, Stephen J.;
Vispo, Nelson Santiago;
García-Jacas, Cesar R.;
Marrero-Ponce, Yovani

Publication type:

Article

Network modeling links kidney developmental programs and the cancer type-specificity of VHL mutations.

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NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00445-2

By:

Dong, Xiaobao;
Zhang, Donglei;
Zhang, Xian;
Liu, Yun;
Liu, Yuanyuan

Publication type:

Article

A web portal for exploring kinase-substrate interactions.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00442-5

By:

Sekar, John A. P.;
Li, Yan Chak;
Schlessinger, Avner;
Pandey, Gaurav

Publication type:

Article

Calibrating tumor growth and invasion parameters with spectral spatial analysis of cancer biopsy tissues.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00439-0

By:

Pasetto, Stefano;
Montejo, Michael;
Zahid, Mohammad U.;
Rosa, Marilin;
Gatenby, Robert;
Schlicke, Pirmin;
Diaz, Roberto;
Enderling, Heiko

Publication type:

Article

Neutral evolution of rare cancer mutations in the computer and the clinic.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00436-3

By:

Beckman, Robert A.

Publication type:

Article

Inertial effect of cell state velocity on the quiescence-proliferation fate decision.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00428-3

By:

Venkatachalapathy, Harish;
Brzakala, Cole;
Batchelor, Eric;
Azarin, Samira M.;
Sarkar, Casim A.

Publication type:

Article

Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00440-7

By:

Khanijou, Jasmeet Kaur;
Hee, Yan Ting;
Scipion, Clement P. M.;
Chen, Xixian;
Selvarajoo, Kumar

Publication type:

Article

Spatial interactions modulate tumor growth and immune infiltration.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00438-1

By:

Marzban, Sadegh;
Srivastava, Sonal;
Kartika, Sharon;
Bravo, Rafael;
Safriel, Rachel;
Zarski, Aidan;
Anderson, Alexander R. A.;
Chung, Christine H.;
Amelio, Antonio L.;
West, Jeffrey

Publication type:

Article

Time and dose selective glucose metabolism for glucose homeostasis and energy conversion in the liver.

Published in:

NPJ Systems Biology & Applications, 2024, v. 10, n. 1, p. 1, doi. 10.1038/s41540-024-00437-2

By:

Pan, Yifei;
Hatano, Atsushi;
Ohno, Satoshi;
Morita, Keigo;
Kokaji, Toshiya;
Bai, Yunfan;
Sugimoto, Hikaru;
Egami, Riku;
Terakawa, Akira;
Li, Dongzi;
Uematsu, Saori;
Maehara, Hideki;
Fujita, Suguru;
Inoue, Hiroshi;
Inaba, Yuka;
Nagano, Atsushi J.;
Hirayama, Akiyoshi;
Soga, Tomoyoshi;
Kuroda, Shinya

Publication type:

Article