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1. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Author

Rougny Adrien, Touré Vasundra, Moodie Stuart, Balaur Irina, Czauderna Tobias, Borlinghaus Hanna, Dogrusoz Ugur, Mazein Alexander, Dräger Andreas, Blinov Michael L., Villéger Alice, Haw Robin, Demir Emek, Mi Huaiyu, Sorokin Anatoly, Schreiber Falk, and Luna Augustin

Subjects
biological network, circuit diagram, sbgn, standard, systems biology, visualisation, Biotechnology, TP248.13-248.65
Abstract

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

Published
2019
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2. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Author

Mi Huaiyu, Schreiber Falk, Moodie Stuart, Czauderna Tobias, Demir Emek, Haw Robin, Luna Augustin, Le Novère Nicolas, Sorokin Anatoly, and Villéger Alice

Subjects
Biotechnology, TP248.13-248.65
Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Published
2015
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3. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Author

Sorokin Anatoly, Le Novère Nicolas, Luna Augustin, Czauderna Tobias, Demir Emek, Haw Robin, Mi Huaiyu, Moodie Stuart, Schreiber Falk, and Villéger Alice

Subjects
Biotechnology, TP248.13-248.65
Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Published
2015
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4. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

Author

Moodie Stuart, Le Novère Nicolas, Demir Emek, Mi Huaiyu, and Villéger Alice

Subjects
Biotechnology, TP248.13-248.65
Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Published
2015
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8. Algorithms for effective querying of compound graph-based pathway databases

Author

Demir Emek, Cetintas Ahmet, Dogrusoz Ugur, and Babur Ozgun

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Graph-based pathway ontologies and databases are widely used to represent data about cellular processes. This representation makes it possible to programmatically integrate cellular networks and to investigate them using the well-understood concepts of graph theory in order to predict their structural and dynamic properties. An extension of this graph representation, namely hierarchically structured or compound graphs, in which a member of a biological network may recursively contain a sub-network of a somehow logically similar group of biological objects, provides many additional benefits for analysis of biological pathways, including reduction of complexity by decomposition into distinct components or modules. In this regard, it is essential to effectively query such integrated large compound networks to extract the sub-networks of interest with the help of efficient algorithms and software tools. Results Towards this goal, we developed a querying framework, along with a number of graph-theoretic algorithms from simple neighborhood queries to shortest paths to feedback loops, that is applicable to all sorts of graph-based pathway databases, from PPIs (protein-protein interactions) to metabolic and signaling pathways. The framework is unique in that it can account for compound or nested structures and ubiquitous entities present in the pathway data. In addition, the queries may be related to each other through "AND" and "OR" operators, and can be recursively organized into a tree, in which the result of one query might be a source and/or target for another, to form more complex queries. The algorithms were implemented within the querying component of a new version of the software tool PATIKAweb (Pathway Analysis Tool for Integration and Knowledge Acquisition) and have proven useful for answering a number of biologically significant questions for large graph-based pathway databases. Conclusion The PATIKA Project Web site is http://www.patika.org. PATIKAweb version 2.1 is available at http://web.patika.org.

Published
2009
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9. An expanded universe of cancer targets

Author

Hahn, William C, Bader, Joel S, Braun, Theodore P, Califano, Andrea, Clemons, Paul A, Druker, Brian J, Ewald, Andrew J, Fu, Haian, Jagu, Subhashini, Kemp, Christopher J, Kim, William, Kuo, Calvin J, McManus, Michael T, B. Mills, Gordon, Mo, Xiulei, Sahni, Nidhi, Schreiber, Stuart L, Talamas, Jessica A, Tamayo, Pablo, Tyner, Jeffrey W, Wagner, Bridget K, Weiss, William A, Gerhard, Daniela S, Dancik, Vlado, Gill, Shubhroz, Hua, Bruce, Sharifnia, Tanaz, Viswanathan, Vasanthi, Zou, Yilong, Dela Cruz, Filemon, Kung, Andrew, Stockwell, Brent, Boehm, Jesse, Dempster, Josh, Manguso, Robert, Vazquez, Francisca, Cooper, Lee AD, Du, Yuhong, Ivanov, Andrey, Lonial, Sagar, Moreno, Carlos S, Niu, Qiankun, Owonikoko, Taofeek, Ramalingam, Suresh, Reyna, Matthew, Zhou, Wei, Grandori, Carla, Shmulevich, Ilya, Swisher, Elizabeth, Cai, Jitong, Chan, Issac S, Dunworth, Matthew, Ge, Yuchen, Georgess, Dan, Grasset, Eloïse M, Henriet, Elodie, Knútsdóttir, Hildur, Lerner, Michael G, Padmanaban, Veena, Perrone, Matthew C, Suhail, Yasir, Tsehay, Yohannes, Warrier, Manisha, Morrow, Quin, Nechiporuk, Tamilla, Long, Nicola, Saultz, Jennifer, Kaempf, Andy, Minnier, Jessica, Tognon, Cristina E, Kurtz, Stephen E, Agarwal, Anupriya, Brown, Jordana, Watanabe-Smith, Kevin, Vu, Tania Q, Jacob, Thomas, Yan, Yunqi, Robinson, Bridget, Lind, Evan F, Kosaka, Yoko, Demir, Emek, Estabrook, Joseph, Grzadkowski, Michael, Nikolova, Olga, Chen, Ken, Deneen, Ben, Liang, Han, Bassik, Michael C, Bhattacharya, Asmita, Brennan, Kevin, Curtis, Christina, Gevaert, Olivier, Ji, Hanlee P, Karlsson, Kasper AJ, Karagyozova, Kremena, Lo, Yuan-Hung, Liu, Katherine, Nakano, Michitaka, Sathe, Anuja, and Smith, Amber R

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Cancer, Biotechnology, Genetics, Orphan Drug, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Animals, Clinical Trials as Topic, Disease Models, Animal, Drug Delivery Systems, Genomics, Humans, Neoplasms, Tumor Escape, Tumor Microenvironment, Cancer Target Discovery and Development Network, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.

Published
2021

11. SBML Level 3: an extensible format for the exchange and reuse of biological models

Author

Keating, Sarah M, Waltemath, Dagmar, König, Matthias, Zhang, Fengkai, Dräger, Andreas, Chaouiya, Claudine, Bergmann, Frank T, Finney, Andrew, Gillespie, Colin S, Helikar, Tomáš, Hoops, Stefan, Malik‐Sheriff, Rahuman S, Moodie, Stuart L, Moraru, Ion I, Myers, Chris J, Naldi, Aurélien, Olivier, Brett G, Sahle, Sven, Schaff, James C, Smith, Lucian P, Swat, Maciej J, Thieffry, Denis, Watanabe, Leandro, Wilkinson, Darren J, Blinov, Michael L, Begley, Kimberly, Faeder, James R, Gómez, Harold F, Hamm, Thomas M, Inagaki, Yuichiro, Liebermeister, Wolfram, Lister, Allyson L, Lucio, Daniel, Mjolsness, Eric, Proctor, Carole J, Raman, Karthik, Rodriguez, Nicolas, Shaffer, Clifford A, Shapiro, Bruce E, Stelling, Joerg, Swainston, Neil, Tanimura, Naoki, Wagner, John, Meier‐Schellersheim, Martin, Sauro, Herbert M, Palsson, Bernhard, Bolouri, Hamid, Kitano, Hiroaki, Funahashi, Akira, Hermjakob, Henning, Doyle, John C, Hucka, Michael, Adams, Richard R, Allen, Nicholas A, Angermann, Bastian R, Antoniotti, Marco, Bader, Gary D, Červený, Jan, Courtot, Mélanie, Cox, Chris D, Pezze, Piero Dalle, Demir, Emek, Denney, William S, Dharuri, Harish, Dorier, Julien, Drasdo, Dirk, Ebrahim, Ali, Eichner, Johannes, Elf, Johan, Endler, Lukas, Evelo, Chris T, Flamm, Christoph, Fleming, Ronan MT, Fröhlich, Martina, Glont, Mihai, Gonçalves, Emanuel, Golebiewski, Martin, Grabski, Hovakim, Gutteridge, Alex, Hachmeister, Damon, Harris, Leonard A, Heavner, Benjamin D, Henkel, Ron, Hlavacek, William S, Hu, Bin, Hyduke, Daniel R, de Jong, Hidde, Juty, Nick, Karp, Peter D, Karr, Jonathan R, Kell, Douglas B, Keller, Roland, Kiselev, Ilya, Klamt, Steffen, Klipp, Edda, Knüpfer, Christian, Kolpakov, Fedor, Krause, Falko, Kutmon, Martina, and Laibe, Camille

Subjects
Bioengineering, Networking and Information Technology R&D (NITRD), Animals, Humans, Logistic Models, Models, Biological, Software, Systems Biology, computational modeling, file format, interoperability, reproducibility, systems biology, SBML Level 3 Community members, Biochemistry and Cell Biology, Other Biological Sciences, Bioinformatics
Abstract

Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.

Published
2020

12. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution.

Author

Rozenblatt-Rosen, Orit, Regev, Aviv, Oberdoerffer, Philipp, Nawy, Tal, Hupalowska, Anna, Rood, Jennifer E, Ashenberg, Orr, Cerami, Ethan, Coffey, Robert J, Demir, Emek, Ding, Li, Esplin, Edward D, Ford, James M, Goecks, Jeremy, Ghosh, Sharmistha, Gray, Joe W, Guinney, Justin, Hanlon, Sean E, Hughes, Shannon K, Hwang, E Shelley, Iacobuzio-Donahue, Christine A, Jané-Valbuena, Judit, Johnson, Bruce E, Lau, Ken S, Lively, Tracy, Mazzilli, Sarah A, Pe'er, Dana, Santagata, Sandro, Shalek, Alex K, Schapiro, Denis, Snyder, Michael P, Sorger, Peter K, Spira, Avrum E, Srivastava, Sudhir, Tan, Kai, West, Robert B, Williams, Elizabeth H, and Human Tumor Atlas Network

Subjects
Human Tumor Atlas Network, Humans, Neoplasms, Cell Transformation, Neoplastic, Genomics, Atlases as Topic, Single-Cell Analysis, Tumor Microenvironment, Precision Medicine, AI, Cancer Moonshot, Human Tumor Atlas, cancer transitions, data integration, data visualization, metastasis, pre-cancer, resistance, single-cell genomics, spatial genomics, spatial imaging, tumor, Human Genome, Clinical Research, Genetics, Cancer, Bioengineering, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.

Published
2020

13. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer

Author

Johnson, Brett E., Creason, Allison L., Stommel, Jayne M., Keck, Jamie M., Parmar, Swapnil, Betts, Courtney B., Blucher, Aurora, Boniface, Christopher, Bucher, Elmar, Burlingame, Erik, Camp, Todd, Chin, Koei, Eng, Jennifer, Estabrook, Joseph, Feiler, Heidi S., Heskett, Michael B., Hu, Zhi, Kolodzie, Annette, Kong, Ben L., Labrie, Marilyne, Lee, Jinho, Leyshock, Patrick, Mitri, Souraya, Patterson, Janice, Riesterer, Jessica L., Sivagnanam, Shamilene, Somers, Julia, Sudar, Damir, Thibault, Guillaume, Weeder, Benjamin R., Zheng, Christina, Nan, Xiaolin, Thompson, Reid F., Heiser, Laura M., Spellman, Paul T., Thomas, George, Demir, Emek, Chang, Young Hwan, Coussens, Lisa M., Guimaraes, Alexander R., Corless, Christopher, Goecks, Jeremy, Bergan, Raymond, Mitri, Zahi, Mills, Gordon B., and Gray, Joe W.

Published
2022
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15. 2D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2

Author

Unal, Mehmet Altay, Bayrakdar, Fatma, Fusco, Laura, Besbinar, Omur, Shuck, Christopher E., Yalcin, Süleyman, Erken, Mine Turktas, Ozkul, Aykut, Gurcan, Cansu, Panatli, Oguzhan, Summak, Gokce Yagmur, Gokce, Cemile, Orecchioni, Marco, Gazzi, Arianna, Vitale, Flavia, Somers, Julia, Demir, Emek, Yildiz, Serap Suzuk, Nazir, Hasan, Grivel, Jean-Charles, Bedognetti, Davide, Crisanti, Andrea, Akcali, Kamil Can, Gogotsi, Yury, Delogu, Lucia Gemma, and Yilmazer, Açelya

Published
2021
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16. Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro

Author

Unal, Mehmet Altay, Bitirim, Ceylan Verda, Summak, Gokce Yagmur, Bereketoglu, Sidar, Zeytin, Inci Cevher, Besbinar, Omur, Gurcan, Cansu, Aydos, Dunya, Goksoy, Ezgi, Kocakaya, Ebru, Eran, Zeynep, Murat, Merve, Demir, Nil, Ozer, Zeynep Busra Aksoy, Somers, Julia, Demir, Emek, Nazir, Hasan, Ozkan, Sibel Aysil, Ozkul, Aykut, Azap, Alpay, Yilmazer, Acelya, and Akcali, Kamil Can

Subjects
Ribavirin -- Dosage and administration, Proteases -- Physiological aspects, Angiotensin converting enzyme -- Physiological aspects, Biological sciences
Abstract

Ribavirin is a guanosine analog with broad-spectrum antiviral activity against RNA viruses. Based on this, we aimed to show the anti-SARS-CoV-2 activity of this drug molecule via in vitro, in silico, and molecular techniques. Ribavirin showed antiviral activity in Vero E6 cells following SARS-CoV-2 infection, whereas the drug itself did not show any toxic effect over the concentration range tested. In silico analysis suggested that ribavirin has a broad-spectrum impact on SARS-CoV-2, acting at different viral proteins. According to the detailed molecular techniques, ribavirin was shown to decrease the expression of TMPRSS2 at both mRNA and protein levels 48 h after treatment. The suppressive effect of ribavirin in ACE2 protein expression was shown to be dependent on cell types. Finally, proteolytic activity assays showed that ribavirin also showed an inhibitory effect on the TMPRSS2 enzyme. Based on these results, we hypothesized that ribavirin may inhibit the expression of TMPRSS2 by modulating the formation of inhibitory G-quadruplex structures at the TMPRSS2 promoter. As a conclusion, ribavirin is a potential antiviral drug for the treatment against SARS-CoV-2, and it interferes with the effects of TMPRSS2 and ACE2 expression. Key words: COVID-19, in silico, in vitro, pathway analysis, drug. La ribavirine est un analogue de la guanosine avec une activite antivirale de large spectre contre les virus a ARN. Sur cette base, nous avons tente de montrer l'activite anti-SARS-CoV-2 de cette molecule pharmacologique a l'aide de techniques in vitro, in silico et moleculaires. La ribavirine a presente une activite antivirale contre les cellules Vero E6 a la suite d'une infection par le SARS-CoV-2 tandis que le medicament lui-meme n'avait aucun effet toxique dans la plage de concentrations evaluee. L'etude in silico a laisse entrevoir que la ribavirine a un effet a large spectre sur le SARS-CoV- 2, avec une action sur differentes proteines virales. A l'aide des techniques moleculaires detaillees, nous avons montre que la ribavirine entraine une diminution de l'expression de TMPRSS2 en taux d'ARNm comme de proteines 48 h apres son administration. Nous avons observe que l'effet suppresseur de la ribavirine sur l'expression d'ACE2 en proteines etait dependant du type de cellules. Enfin, les epreuves sur l'activite proteolytique ont montre que la ribavirine presentait aussi un effet inhibiteur sur l'enzyme TMPRSS2. De ces resultats, nous avons tire l'hypothese selon laquelle la ribavirine pourrait permettre d'inhiber l'expression de TMPRSS2 par l'intermediaire d'une modulation de la formation de structures inhibitrices G-quadruplex au niveau du promoteur de TMPRSS2. En conclusion, la ribavirine est un medicament antiviral eventuel pour le traitement contre le SARS-CoV-2, et elle interfere avec l'expression de TMPRSS2 et d'ACE2. Mots-cles: COVID-19, in silico, in vitro, etude de voie de signalisation, medicament., Introduction The coronavirus 2019 (COVID-19) pandemic represents the strongest global public health threat since the influenza outbreak in 1918 and has rapidly resulted in significant health and economic burdens worldwide [...]

Published
2021
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17. Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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19. COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

Author

Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff-Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2021
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21. Longitudinal and multimodal auditing of tumor adaptation to CDK4/6 inhibitors in HR+ metastatic breast cancers

Author

Creason, Allison L., primary, Egger, Jay, additional, Watson, Cameron, additional, Sivagnanam, Shamilene, additional, Chin, Koei, additional, MacPherson, Kevin, additional, Lin, Jia-Ren, additional, Chen, Yu-An, additional, Johnson, Brett E., additional, Feiler, Heidi S., additional, Galipeau, Danielle, additional, Navin, Nicholas E., additional, Demir, Emek, additional, Chang, Young Hwan, additional, Corless, Christopher L., additional, Mitri, Zahi I., additional, Thomas, George, additional, Sorger, Peter K., additional, Adey, Andrew C., additional, Coussens, Lisa M., additional, Gray, Joe W., additional, Mills, Gordon B., additional, and Goecks, Jeremy, additional

Published
2023
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22. Multiplex imaging of localized prostate tumors reveals changes in mast cell type composition and spatial organization of AR-positive cells in the tumor microenvironment

Author

Eksi, Sebnem Ece, primary, Ak, Cigdem, additional, Sayar, Zeynep, additional, Thibault, Guillaume, additional, Burlingame, Erik, additional, Eng, Jenny, additional, Chitsazan, Alex, additional, Adey, Andrew, additional, Boniface, Christopher, additional, Spellman, Paul T, additional, Thomas, George V, additional, Kopp, Ryan, additional, Demir, Emek, additional, Chang, Young Hwan, additional, and Stavrinides, Vasilis, additional

Published
2023
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23. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Author

Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2020
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24. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Author

Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, and Schneider, Reinhard

Published
2020
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26. Supplementary Table 5 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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27. Supplementary Table 4 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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28. Supplementary Table 9 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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29. Supplementary Table 2 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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30. Supplementary Fig. 11 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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31. Supplementary Table 7 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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32. Supplementary Table 11 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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33. Supplementary Fig. 3 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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34. Supplementary Fig. 6 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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35. Data from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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36. Supplementary Fig. 5 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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37. Supplementary Table 6 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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38. Supplementary Fig. 7 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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39. Supplementary Table 8 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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40. Supplementary Fig. 4 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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41. Supplementary Materials and Methods from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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42. Supplementary Table 3 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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43. Supplementary Fig. 2 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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44. Supplementary Fig. 9 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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45. Supplementary Fig. 8 from Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., primary, Coleman, Daniel J., primary, VanCampen, Jake, primary, Kong, Garth, primary, Macaraeg, Jommel, primary, Estabrook, Joseph, primary, Demir, Emek, primary, Long, Nicola, primary, Bottomly, Daniel, primary, McWeeney, Shannon K., primary, Tyner, Jeffrey W., primary, Druker, Brian J., primary, Maxson, Julia E., primary, and Braun, Theodore P., primary

Published
2023
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47. Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia

Author

Yashar, William M., primary, Curtiss, Brittany M., additional, Coleman, Daniel J., additional, VanCampen, Jake, additional, Kong, Garth, additional, Macaraeg, Jommel, additional, Estabrook, Joseph, additional, Demir, Emek, additional, Long, Nicola, additional, Bottomly, Daniel, additional, McWeeney, Shannon K., additional, Tyner, Jeffrey W., additional, Druker, Brian J., additional, Maxson, Julia E., additional, and Braun, Theodore P., additional

Published
2023
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49. Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors

Author

Braun, Theodore P., primary, Estabrook, Joseph, additional, Schonrock, Zachary, additional, Curtiss, Brittany M., additional, Darmusey, Lucie, additional, Macaraeg, Jommel, additional, Enright, Trevor, additional, Coblentz, Cody, additional, Callahan, Rowan, additional, Yashar, William, additional, Taherinasab, Akram, additional, Mohammed, Hisham, additional, Coleman, Daniel J., additional, Druker, Brian J., additional, Demir, Emek, additional, Lusardi, Theresa A., additional, and Maxson, Julia E., additional

Published
2022
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50. A Compound Graph Layout Algorithm for Biological Pathways

Author

Dogrusoz, Ugur, Giral, Erhan, Cetintas, Ahmet, Civril, Ali, Demir, Emek, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Pach, János, editor

Published
2005
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