Authors: Smith, Lucian P.^{j_jib-2024-0008_aff_001}, Bergmann, Frank T.^{j_jib-2024-0008_aff_002}, Garny, Alan^{j_jib-2024-0008_aff_003}, Helikar, Tomáš^{j_jib-2024-0008_aff_004}, Karr, Jonathan^{j_jib-2024-0008_aff_005}, Nickerson, David^{j_jib-2024-0008_aff_003}, Sauro, Herbert^{j_jib-2024-0008_aff_001}, Waltemath, Dagmar^{j_jib-2024-0008_aff_006}, König, Matthias^{j_jib-2024-0008_aff_007}

Superior Title: Journal of Integrative Bioinformatics.

Availability: https://www.degruyter.com/document/doi/10.1515/jib-2024-0008/html

Authors: McMahon-Cole, Hana, Johnson, Alicia, Aghamiri, Sara Sadat, Helikar, Tomáš, Crawford, Lindsey B.^{Aff1, Aff2, Aff3, IDs4058802300201w_cor5}

Superior Title: Current Clinical Microbiology Reports. 10(3):141-151

Authors: Musilová, Jana, Vafek, Zdeněk, Punyia, Bhanwar, Zimmer, Ralf, Helikar, Tomáš, Sedlář, Karel

Subject Terms: Python package, gene interactions, mutual information, transcription factor, binding motifs, databases

Time: December 2024

File Description: text; 783-790; application/pdf

Relation: Computational and Structural Biotechnology Journal; https://www.sciencedirect.com/science/article/pii/S2001037024000138?via%3Dihub; Computational and Structural Biotechnology Journal. 2024, vol. 23, issue December 2024, p. 783-790.; 187210; http://hdl.handle.net/11012/245285; orcid:0000-0001-6910-6047; orcid:0000-0002-8269-4020; AHB-1545-2022; K-1120-2014; 56309904900

Availability: https://doi.org/10.1016/j.csbj.2024.01.013
http://hdl.handle.net/11012/245285

Authors: Laubenbacher, Reinhard^{Aff1, IDs41540024003455_cor1}, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L., Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E.^{Aff14, Aff15}, Ziemssen, Tjalf

Superior Title: npj Systems Biology and Applications. 10(1)

Authors: Dauer, Joseph^Aff20, Dauer, Jenny^Aff20, Lucas, Lyrica^Aff20, Helikar, Tomáš^Aff20, Long, Tammy^Aff21

Contributors: Ergazaki, Marida, Series Editor^Aff1, Kampourakis, Kostas, Series Editor^Aff2, Grace, Marcus, Editorial Board Member^Aff3, Knippels, Marie Christine, Editorial Board Member^Aff4, Zabel, Jörg, Editorial Board Member^Aff5, Korfiatis, Constantinos, Editorial Board Member^Aff6, Jimenez Aleixandre, Maria Pilar, Editorial Board Member^Aff7, Yarden, Anat, Editorial Board Member^Aff8, Hammann, Marcus, Editorial Board Member^Aff9, Harms, Ute, Editorial Board Member^Aff10, Reiss, Michael, Editorial Board Member^Aff11, Gericke, Niklas, Editorial Board Member^Aff12, El-Hani, Charbel Nino, Editorial Board Member^Aff13, Dawson, Vaille, Editorial Board Member^Aff14, Nehm, Ross, Editorial Board Member^Aff15, McComas, William, Editorial Board Member^Aff16, Passmore, Cynthia, Editorial Board Member^Aff17, Ben Zvi Assaraf, Orit, editor^Aff18, Knippels, Marie-Christine P. J., editor^Aff19

Superior Title: Fostering Understanding of Complex Systems in Biology Education : Pedagogies, Guidelines and Insights from Classroom-based Research. :63-82

Authors: Yook, Jin-Seon, You, Mikyoung, Kim, Jiyoung, Toney, Ashley M., Fan, Rong, Puniya, Bhanwar Lal, Helikar, Tomáš, Vaulont, Sophie, Deschemin, Jean-Christoph, Okla, Meshail, Xie, Liwei, Ghosh, Manik C., Rouault, Tracey A., Lee, Jaekwon, Chung, Soonkyu

Superior Title: Proceedings of the National Academy of Sciences of the United States of America, 2021 Oct 01. 118(40), 1-11.

Access URL: https://www.jstor.org/stable/27075988

Authors: Niarakis, Anna, Ostaszewski, Marek, Mazein, Alexander, Kuperstein, Inna, Kutmon, Martina, Gillespie, Marc E., Funahashi, Akira, Acencio, Marcio Luis, Hemedan, Ahmed, Aichem, Michael, Klein, Karsten, Czauderna, Tobias, Burtscher, Felicia, Yamada, Takahiro G., Hiki, Yusuke, Hiroi, Noriko F., Hu, Finterly, Pham, Nhung, Ehrhart, Friederike, Willighagen, Egon L., Valdeolivas, Alberto, Dugourd, Aurelien, Messina, Francesco, Esteban-Medina, Marina, Peña-Chilet, María, Rian, Kinza, Soliman, Sylvain, Aghamiri, Sara Sadat, Lal Puniya, Bhanwar, Naldi, Aurelien, Helikar, Tomas, Singh, Vidisha, Fariñas Fernández, Marco, Bermudez, Viviam, Tsirvouli, Eirini, Montagud, Arnau, Noël, Vincent, Ponce de León, Miguel, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M., Bachman, John A., Luna, Augustin, Piñero, Janet, Furlong, Laura I., Balaur, Irina BalaurIrina, Rougny, Adrien, Jarosz, Yohan, Overall, Rupert W., Phair, Robert, Perfetto, Livia, Matthews, Lisa, Balaya Rex, Devasahayam Arokia, Orlic-Milacic, Marija, Monraz Gómez, Luis Cristóbal, De Meulder, Bertrand, Ravel, Jean Marie, Jassal, Bijay, Satagopam, Venkata, Wu, Guanming, Golebiewski, Martin, Gawron, Piotr, Calzone, Laurence, Beckmann, Jacques S., Evelo, Chris T., D’Eustachio, Peter, Schreiber, Falk, Sáez-Rodríguez, Julio, Dopazo, Joaquín, Kuiper, Martin, Valencia, Alfonso, Wolkenhauer, Olaf, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard, COVID- Disease Map Community the COVID-19 Disease Map Community

Contributors: Sanofi, Instituto de Salud Carlos III, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), German Research Foundation, Ministero della Salute, European Commission, Generalitat de Catalunya, National Institutes of Health (US), Klaus Tschira Foundation, National Library of Medicine (US)

Subject Terms: SARS-CoV-2, Systems biology, Disease maps, Mechanistic models, Dynamic models, Systems medicine, Large-scale community effort

File Description: application/pdf

Relation: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117979RB-I00/ES/MEDICINA INTERCEPTIVA, DESCUBRIMIENTO DE DIANAS Y REUTILIZACION DE FARMACOS MEDIANTE MODELOS MECANISTICOS Y APRENDIZAJE SUPERVISADO/; info:eu-repo/grantAgreement/EC/H2020/101046203; info:eu-repo/grantAgreement/EC/H2020/777365; info:eu-repo/grantAgreement/EC/H2020/964537; info:eu-repo/grantAgreement/EC/H2020/825070; info:eu-repo/grantAgreement/EC/H2020/951773; info:eu-repo/grantAgreement/EC/H2020/825843; Publisher's version; https://doi.org/10.3389/fimmu.2023.1282859; Sí; Frontiers in Immunology 14: 1282859 (2023); http://hdl.handle.net/10261/353584

Availability: https://doi.org/10.3389/fimmu.2023.1282859
http://hdl.handle.net/10261/353584

Authors: Laubenbacher, Reinhard, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L., Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E., Ziemssen, Tjalf

Subject Terms: Other Quantitative Biology q-bio.OT, FOS Biological sciences

Relation: https://dx.doi.org/10.1038/s41540-024-00345-5

Availability: https://doi.org/10.48550/arxiv.2310.1837410.1038/s41540-024-00345-5
https://arxiv.org/abs/2310.18374

Authors: Song, Changsoo, Helikar, Resa, Smith, Wendy M., Helikar, Tomáš

Superior Title: CBE Life Sci Educ

Subject Terms: General Essays and Articles

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10424226/; http://www.ncbi.nlm.nih.gov/pubmed/37279087; http://dx.doi.org/10.1187/cbe.22-11-0239

Availability: https://doi.org/10.1187/cbe.22-11-0239
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10424226/
http://www.ncbi.nlm.nih.gov/pubmed/37279087

Authors: Shakyawar, Sushil K, Mishra, Nitish K, Vellichirammal, Neetha N, Cary, Lynnette, Helikar, Tomáš, Powers, Robert, Oberley-Deegan, Rebecca E, Berkowitz, David B, Bayles, Kenneth W, Singh, Vijay K, Guda, Chittibabu

Superior Title: Radiat Res

Subject Terms: Article

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10279411/; http://www.ncbi.nlm.nih.gov/pubmed/36368026; http://dx.doi.org/10.1667/RADE-21-00187.1

Availability: https://doi.org/10.1667/RADE-21-00187.1
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10279411/
http://www.ncbi.nlm.nih.gov/pubmed/36368026

Authors: Aghamiri, Sara Sadat, Puniya, Bhanwar Lal, Amin, Rada, Helikar, Tomáš

Superior Title: Front Immunol

Subject Terms: Immunology

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10040975/; http://www.ncbi.nlm.nih.gov/pubmed/36993954; http://dx.doi.org/10.3389/fimmu.2023.1112985

Availability: https://doi.org/10.3389/fimmu.2023.1112985
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10040975/
http://www.ncbi.nlm.nih.gov/pubmed/36993954

Authors: Zhang, Tongli^{Aff1, IDs1092802209805z_cor1}, Androulakis, Ioannis P., Bonate, Peter, Cheng, Limei, Helikar, Tomáš, Parikh, Jaimit, Rackauckas, Christopher^{Aff7, Aff8}, Subramanian, Kalyanasundaram, Cho, Carolyn R.^{Aff10, IDs1092802209805z_cor9}

Superior Title: Journal of Pharmacokinetics and Pharmacodynamics. 49(1):5-18

Authors: Aghamiri, Sara Sadat, Amin, Rada^{Aff1, IDs10928021097909_cor2}, Helikar, Tomáš^{Aff1, IDs10928021097909_cor3}

Superior Title: Journal of Pharmacokinetics and Pharmacodynamics. 49(1):19-37

Authors: Laubenbacher, Reinhard, Adler, Fred, An, Gary, Castiglione, Filippo, Eubank, Stephen, Fonseca, Luis L, Glazier, James, Helikar, Tomas, Jett-Tilton, Marti, Kirschner, Denise, Macklin, Paul, Mehrad, Borna, Moore, Beth, Pasour, Virginia, Shmulevich, Ilya, Smith, Amber, Voigt, Isabel, Yankeelov, Thomas E, Ziemssen, Tjalf

Superior Title: Articles, Abstracts, and Reports

Subject Terms: washington, isb, machine learning, Artificial Intelligence and Robotics

Relation: https://digitalcommons.providence.org/publications/8627; https://pubmed.ncbi.nlm.nih.gov/38515550

Availability: https://digitalcommons.providence.org/publications/8627
https://pubmed.ncbi.nlm.nih.gov/38515550

Authors: Niarakis, Anna, Waltemath, Dagmar, Glazier, James, Schreiber, Falk, Keating, Sarah, Nickerson, David, Chaouiya, Claudine, Siegel, Anne, Noël, Vincent, Hermjakob, Henning, Helikar, Tomáš, Soliman, Sylvain, Calzone, Laurence

Contributors: Laboratoire de recherche européen pour la polyarthrite rhumatoïde (GenHotel), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay, Computational systems biology and optimization (Lifeware), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), University of Medicine Greifswald, Indiana University Bloomington, Indiana University System, University of Konstanz, Monash University Melbourne, University College of London London (UCL), University of Auckland Auckland, Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Dynamics, Logics and Inference for biological Systems and Sequences (Dyliss), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT), Centre de Bioinformatique (CBIO), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), European Bioinformatics Institute Hinxton (EMBL-EBI), EMBL Heidelberg, University of Nebraska–Lincoln, University of Nebraska System, ANR-17-CE40-0036,SYMBIONT,Méthodes symboliques pour les réseaux biologiques(2017)

Superior Title: ISSN: 1467-5463.

Subject Terms: computational modelling, model annotations, reproducibility, systems biology, community standards, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]

Relation: hal-03690604; https://inria.hal.science/hal-03690604; https://inria.hal.science/hal-03690604/document; https://inria.hal.science/hal-03690604/file/Addressing%2520barriers%2520in%2520comprehensiveness%252C%2520accessibility%252C%2520reusability%252C%2520interoperability%2520and%2520reproducibility%2520of%2520computational%2520.pdf

Availability: https://doi.org/10.1093/bib/bbac212
https://inria.hal.science/hal-03690604
https://inria.hal.science/hal-03690604/document
https://inria.hal.science/hal-03690604/file/Addressing%2520barriers%2520in%2520comprehensiveness%252C%2520accessibility%252C%2520reusability%252C%2520interoperability%2520and%2520reproducibility%2520of%2520computational%2520.pdf

Authors: Niarakis, Anna, Thakar, Juilee, Barberis, Matteo, Rodríguez Martínez, María, Helikar, Tomáš, Birtwistle, Marc, Chaouiya, Claudine, Calzone, Laurence, Dräger, Andreas

Superior Title: Bioinformatics

Subject Terms: Message from ISCB

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9620821/; http://dx.doi.org/10.1093/bioinformatics/btac609

Availability: https://doi.org/10.1093/bioinformatics/btac609
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9620821/

Authors: Fan, Rong, Thomas, Shalom, You, Mikyoung, Li, Zhuoheng, Bessell, Brandt, Puniya, Bhanwar Lal, Helikar, Tomáš, Liu, Zhenhua, Chung, Soonkyu

Superior Title: Curr Dev Nutr

Subject Terms: Maternal, Perinatal and Pediatric Nutrition

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9194029/; http://dx.doi.org/10.1093/cdn/nzac061.024

Availability: https://doi.org/10.1093/cdn/nzac061.024
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9194029/

Authors: Yue, Yinshi, Puniya, Bhanwar Lal, Helikar, Tomáš, Girardo, Benjamin, Hinrichs, Steven H., Larson, Marilynn A.

Superior Title: Front Microbiol

Subject Terms: Microbiology

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9251427/; http://www.ncbi.nlm.nih.gov/pubmed/35794913; http://dx.doi.org/10.3389/fmicb.2022.890856

Availability: https://doi.org/10.3389/fmicb.2022.890856
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9251427/
http://www.ncbi.nlm.nih.gov/pubmed/35794913

Authors: Grove, Ryan A., Madhavan, Deepak, Boone, Cory H.T., Braga, Camila Pereira, Papackova, Zuzana, Kyllo, Hannah, Samson, Kaeli, Simeone, Kristina, Simeone, Timothy, Helikar, Tomas, Hanson, Corrine K., Adamec, Jiri

Superior Title: In Journal of Proteomics 15 July 2020 223

Authors: Puniya, Bhanwar Lal, Amin, Rada, Lichter, Bailee, Moore, Robert, Ciurej, Alex, Bennett, Sydney J., Shah, Ab Rauf, Barberis, Matteo^{Aff2, Aff3, Aff4}, Helikar, Tomáš^Aff1

Superior Title: npj Systems Biology and Applications. 7(1)