Ecosyste.ms: Papers

10.3390/metabo9100200

The metaRbolomics Toolbox in Bioconductor and beyond
Cited by: 61
Author(s): Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy A. Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Michael Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski, Michael A. Stravs, Etienne Thévenot, Hendrik Treutler, Ralf Weber, Egon Willighagen, Michael Witting, Steffen Neumann
Software Mentions: 92
Published: about 5 years ago

10.1002/pmic.201400392

Visualization of proteomics data using R and Bioconductor
Cited by: 46
Author(s): Laurent Gatto, Lisa M. Breckels, Thomas Naake, Sebastian Gibb
Software Mentions: 62
Published: over 9 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1093/bib/bbaa390

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
Cited by: 13
Author(s): Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
Software Mentions: 9
Published: almost 4 years ago

10.3389/fgene.2019.01120

Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets
Cited by: 12
Author(s): Pablo Ivan Pereira Ramos, Luis Willian Pacheco Arge, Nicholas Costa Barroso Lima, Kiyoshi F. Fukutani, Artur T. L. Queiroz
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1009263

A multi-objective genetic algorithm to find active modules in multiplex biological networks
Cited by: 7
Author(s): Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaı̈s Baudot
Software Mentions: 6
Published: about 3 years ago

10.1186/1471-2105-12-455

iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database
Cited by: 62
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 6
Published: almost 13 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: over 7 years ago

10.12688/f1000research.5499.1

Visualisation of BioPAX Networks using BioLayout Express3D
Cited by: 16
Author(s): Derek W. Wright, Tim Angus, Anton J. Enright, Tom C. Freeman
Software Mentions: 5
Published: about 10 years ago

10.1093/database/baaa096

The IMEx coronavirus interactome: an evolving map of <i>Coronaviridae</i>–host molecular interactions
Cited by: 31
Author(s): Livia Perfetto, Chiara Pastrello, Noemi del-Toro, Margaret Duesbury, Marta Iannuccelli, Max Kotlyar, Luana Licata, Birgit Meldal, Kalpana Panneerselvam, Simona Panni, Negin Rahimzadeh, Sylvie Ricard‐Blum, Łukasz Salwiński, Anjali Shrivastava, Gianni Cesareni, Matteo Pellegrini, Sandra Orchard, Igor Jurišica, Henning Hermjakob, Pablo Porras
Software Mentions: 5
Published: almost 5 years ago

10.7717/peerj.6660

Music-performance regulates microRNAs in professional musicians
Cited by: 7
Author(s): Preethy Sasidharan Nair, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Irma Järvelä
Software Mentions: 5
Published: over 5 years ago

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: over 6 years ago

10.3390/biomedicines9070751

AKT Signaling Modifies the Balance between Cell Proliferation and Migration in Neural Crest Cells from Patients Affected with Bosma Arhinia and Microphthalmia Syndrome
Cited by: 5
Author(s): Camille Laberthonnière, Elva María Novoa-del-Toro, Raphaël Chevalier, Natacha Broucqsault, Vanitha Venkoba Rao, Jean Philippe Trani, Karine Nguyen, Shifeng Xue, Bruno Reversade, Jérôme D. Robin, Anaı̈s Baudot, Frédérique Magdinier
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-2105-13-294

Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction
Cited by: 25
Author(s): Antonio M. Mora, Ian Donaldson
Software Mentions: 4
Published: about 12 years ago

10.15252/msb.20156351

Fundamentals of protein interaction network mapping
Cited by: 211
Author(s): Jamie Snider, Max Kotlyar, Punit Saraon, Zhong Yao, Igor Jurišica, Igor Štagljar
Software Mentions: 4
Published: almost 9 years ago

10.1186/2041-1480-1-8

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Cited by: 33
Author(s): Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki‐Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Seiichiro Kawashima, Hong‐Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul Jean Pierre Bonnal, Richard Bruskiewich, Jan Christian Bryne, José Marı́a Fernández, Akira Funahashi, Paul M. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Tom Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Łukasz Salwiński, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Tazuko Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
Software Mentions: 4
Published: almost 15 years ago

10.1038/s41598-021-96033-z

Combined genetic and chemical screens indicate protective potential for EGFR inhibition to cardiomyocytes under hypoxia
Cited by: 3
Author(s): Juho Heliste, Anne Jokilammi, Katri Vaparanta, Ilkka Paatero, Klaus Elenius
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.12707.2

CellMap visualizes protein-protein interactions and subcellular localization
Cited by: 4
Author(s): Christian Dallago, Tatyana Goldberg, Miguel A. Andrade‐Navarro, Gregorio Alanis-Lobato, Burkhard Rost
Software Mentions: 3
Published: almost 7 years ago

10.3390/jof4030081

Identification of Antifungal Targets Based on Computer Modeling
Cited by: 10
Author(s): Elena Bencúrová, Shishir Gupta, Edita Sarukhanyan, Thomas Dandekar
Software Mentions: 3
Published: over 6 years ago

10.1093/database/bau131

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
Cited by: 49
Author(s): José Villaveces, Rafael C. Jiménez, Pablo Porras, Noemi del-Toro, Margaret Duesbury, Marine Dumousseau, Sandra Orchard, Hongyoon Choi, Peipei Ping, Nansu Zong, Manor Askenazi, Bianca Habermann, Henning Hermjakob
Software Mentions: 3
Published: almost 10 years ago

10.1186/2041-1480-5-5

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains
Cited by: 47
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Kiyoko F. Aoki‐Kinoshita, Seiichiro Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano, Ono Hiromasa, Hidemasa Bono, Simon Kocbek, Jan Aerts, Yukie Akune, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Joachim Baran, Jerven Bolleman, Raoul Jean Pierre Bonnal, Pier Luigi Buttigieg, Matthew P. Campbell, Yi An Chen, Hirokazu Chiba, Peter J. A. Cock, K. Bretonnel Cohen, Alexandru Constantin, Geraint Duck, Michel Dumontier, Takatomo Fujisawa, Toyofumi Fujiwara, Naohisa Goto, Robert Hoehndorf, Yoshinobu Igarashi, Hidetoshi Itaya, Maori Ito, Wataru Iwasaki, Matúš Kalaš, Takeo Katoda, Taejoon Kim, Anna Kokubu, Yusuke Komiyama, Masaaki Kotera, Camille Laibe, Hilmar Lapp, Thomas Lütteke, M. Scott Marshall, Mori Takaaki, Hiroshi Mori, Mizuki Morita, Katsuhiko Murakami, Mitsuteru Nakao, Hisashi Narimatsu, Hiroyo Nishide, Yosuke Nishimura, Johan Nyström-Persson, Soichi Ogishima, Yasunobu Okamura, Shujiro Okuda, Kazuki Oshita, Nicolle H. Packer, Pjotr Prins, René Ranzinger, Philippe Rocca-Serra, Susanna Assunta Sansone, Hiromichi Sawaki, Sung Ho Shin, Andrea Splendiani, Francesco Strozzi, Shu Tadaka, Filip V. Toukach, Ikuo Uchiyama, Masahito Umezaki, Rutger A. Vos, Patricia L. Whetzel, Issaku Yamada, Chisato Yamasaki, Riu Yamashita, William S. York, Christian M. Zmasek, Shoko Kawamoto, Toshihisa Takagi
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12967-020-02405-w

COVID-19: viral–host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection
Cited by: 76
Author(s): Francesco Messina, Emanuela Giombini, Chiara Agrati, Francesco Vairo, Tommaso Ascoli Bartoli, Samir Al Moghazi, Mauro Piacentini, Franco Locatelli, Gary P. Kobinger, Markus Maeurer, Alimuddin Zumla, Maria Rosaria Capobianchi, F. Lauria, Giuseppe Ippolito, Isabella Abbate, Chiara Agrati, Samir Al Moghazi, Tommaso Ascoli Bartoli, Barbara Bartolini, Maria Rosaria Capobianchi, Alessandro Capone, Delia Goletti, Gabriella Rozera, Carla Nisii, Roberta Gagliardini, Fabiola Ciccosanti, Gian María Fimia, Emanuele Nicastri, Emanuela Giombini, Simone Lanini, Alessandra D’Abramo, Gabriele Rinonapoli, Enrico Gottardi, Chiara Montaldo, Raffaella Marconi, Antonio Addis, Bradley A. Maron, Ginestra Bianconi, Bertrand De Meulder, Jason Kennedy, Shabaana A. Khader, Francesca Luca, Markus Maeurer, Mauro Piacentini, Stefano Merler, Giuseppe Pantaleo, Rafick‐Pierre Sékaly, Serena Sanna, Nicola Segata, Alimuddin Zumla, Francesco Messina, Francesco Vairo, F. Lauria, Giuseppe Ippolito
Software Mentions: 3
Published: over 4 years ago

10.1186/2041-1480-4-6

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Cited by: 27
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Seiichiro Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, François Belleau, Jerven Bolleman, Raoul Jean Pierre Bonnal, Brad Chapman, Peter J. A. Cock, Tore Eriksson, Paul M. Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Kyung Hoon Kwon, Alberto Labarga, Anna‐Lena Lamprecht, Yuling Lin, Pierre Livet, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun Joon Park, Pjotr Prins, Taro Saito, Matthias Samwald, Venkata Satagopam, Yasumasa Shigemoto, Richard N. Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A. Vos, David Withers, Chisato Yamasaki, Christian M. Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi
Software Mentions: 3
Published: almost 12 years ago

10.1002/pro.3978

The <scp>BioGRID</scp> database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
Cited by: 612
Author(s): Rose Oughtred, Jennifer Rust, Christie S. Chang, Bobby-Joe Breitkreutz, Chris Stark, Andrew Willems, Lorrie Boucher, Genie Leung, Nadine K. Kolas, Frederick Zhang, Sonam Dolma, Jasmin Coulombe-Huntington, Andrew Chatr‐aryamontri, Kara Dolinski, Mike Tyers
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-12-23

easyDAS: Automatic creation of DAS servers
Cited by: 5
Author(s): Bernat Gel, Andy Jenkinson, Rafael C. Jiménez, Xavier Messeguer, Henning Hermjakob
Software Mentions: 2
Published: almost 14 years ago

10.1186/1752-0509-7-22

Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
Cited by: 13
Author(s): Fatemeh Vafaee, Daniela Roşu, Fiona Broackes-Carter, Igor Jurišica
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12894-016-0129-7

Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases
Cited by: 30
Author(s): Zhaohui Chen, Jayoung Kim
Software Mentions: 2
Published: over 8 years ago

10.1093/bioinformatics/bty188

SPV: a JavaScript Signaling Pathway Visualizer
Cited by: 9
Author(s): Alberto Calderone, Gianni Cesareni
Software Mentions: 2
Published: over 6 years ago

10.1186/s13062-016-0112-y

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data
Cited by: 26
Author(s): Yeongjun Jang, Namhee Yu, Jihae Seo, Sun Kim, Sanghyuk Lee
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.1002530

Modelling the Structure and Dynamics of Biological Pathways
Cited by: 27
Author(s): Laura O’Hara, Alessandra Livigni, Thanos Theo, Benjamin Boyer, Tim Angus, Derek W. Wright, Sz-Hau Chen, Sobia Raza, Mark W. Barnett, Paul Digard, Lee B. Smith, Tom C. Freeman
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1002789

Teaching the Fundamentals of Biological Data Integration Using Classroom Games
Cited by: 19
Author(s): Maria Victoria Schneider, Rafael C. Jiménez
Software Mentions: 2
Published: almost 12 years ago

10.1093/database/baz133

The human DEPhOsphorylation Database DEPOD: 2019 update
Cited by: 39
Author(s): Nikhil P Damle, Maja Köhn
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2021.674613

Effect of MAP3K8 on Prognosis and Tumor-Related Inflammation in Renal Clear Cell Carcinoma
Cited by: 6
Author(s): Jiatao Hao, Yumeng Cao, Hui Yu, Lu Zong, Ruifang An, Yan Xue
Software Mentions: 2
Published: about 3 years ago

10.3389/fmicb.2015.00235

A review on computational systems biology of pathogen–host interactions
Cited by: 56
Author(s): Saliha Durmuş, Tunahan Çakır, Arzucan Özgür, Reinhard Guthke
Software Mentions: 2
Published: over 9 years ago

10.1093/jamia/ocv001

Development of data representation standards by the human proteome organization proteomics standards initiative
Cited by: 54
Author(s): Eric W. Deutsch, Juan Pablo Albar, Pierre Alain Binz, Martin Eisenacher, Andrew R. Jones, Gerhard Mayer, Gilbert S. Omenn, Sandra Orchard, Juan Antonio Vizcaíno, Henning Hermjakob
Software Mentions: 2
Published: over 9 years ago

10.1186/2041-1480-2-4

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
Cited by: 17
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Rutger A. Vos, Takeshi Kawashima, Seiichiro Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong‐Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F. Aoki‐Kinoshita, Kazuharu Arakawa, Bruno Aranda, Raoul Jean Pierre Bonnal, José Marı́a Fernández, Takatomo Fujisawa, Paul M. Gordon, Naohisa Goto, Syed Haider, Todd W. Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, Erin McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas H. Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi
Software Mentions: 2
Published: almost 14 years ago

10.3390/proteomes1010003

Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration
Cited by: 1
Author(s): Juan Casado‐Vela, Rune Matthiesen, Susana Sellés, José Ramón Naranjo
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-019-46415-1

Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia
Cited by: 9
Author(s): Luke W. Bonham, Natasha Z.R. Steele, Celeste M. Karch, Iris Broce, Ethan G. Geier, Natalie Wen, Parastoo Momeni, John Hardy, Zachary A. Miller, Maria Luisa Gorno‐Tempini, Christopher P. Hess, Patrick A. Lewis, Bruce L. Miller, William W. Seeley, Claudia Manzoni, Rahul S. Desikan, Sergio E. Baranzini, Raffaele Ferrari, Jennifer S. Yokoyama
Software Mentions: 2
Published: over 5 years ago

10.1093/database/bav009

Shared resources, shared costs—leveraging biocuration resources
Cited by: 13
Author(s): Sandra Orchard, Henning Hermjakob
Software Mentions: 1
Published: almost 10 years ago

10.1093/database/baw103

HPIDB 2.0: a curated database for host–pathogen interactions
Cited by: 187
Author(s): Mais Ammari, Cathy Gresham, Fiona M. McCarthy, Bindu Nanduri
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pcbi.1005885

Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway
Cited by: 19
Author(s): Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Software Mentions: 1
Published: almost 7 years ago

10.1093/database/baaa035

MIPPIE: the mouse integrated protein–protein interaction reference
Cited by: 11
Author(s): Gregorio Alanis-Lobato, Jannik S Möllmann, Martin H. Schaefer, Miguel A. Andrade‐Navarro
Software Mentions: 1
Published: almost 5 years ago

10.12688/f1000research.9118.2

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
Cited by: 15
Author(s): Tanja Muetze, Ivan H. Goenawan, Heather L. Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J. Lynn
Software Mentions: 1
Published: about 8 years ago

10.12688/f1000research.3-44.v1

PsicquicGraph, a BioJS component to visualize molecular interactions from PSICQUIC servers
Cited by: 4
Author(s): José Villaveces, Rafael C. Jiménez, Bianca Habermann
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1002860

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions
Cited by: 72
Author(s): Martin H. Schaefer, Tiago J. S. Lopes, Nancy Mah, Jason E. Shoemaker, Yoshikazu Matsuoka, Jean-Fred Fontaine, Caroline Louis-Jeune, Amie J. Eisfeld, Gabriele Neumann, Carolina Perez‐Iratxeta, Yoshihiro Kawaoka, Hiroaki Kitano, Miguel A. Andrade‐Navarro
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pcbi.1004941

Reactome from a WikiPathways Perspective
Cited by: 36
Author(s): Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. Evelo
Software Mentions: 1
Published: over 8 years ago

10.12688/f1000research.3-56.v1

The BioJS article collection of open source components for biological data visualisation
Cited by: 5
Author(s): Manuel Corpas
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pcbi.1004518

A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
Cited by: 121
Author(s): Eduard Porta-Pardo, Luz Garcia‐Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik
Software Mentions: 1
Published: about 9 years ago

10.3389/fgene.2021.688447

Mapping Transcriptome Data to Protein–Protein Interaction Networks of Inflammatory Bowel Diseases Reveals Disease-Specific Subnetworks
Cited by: 1
Author(s): Sefika Feyza Maden, Saliha Ece Acuner-Ozbabacan
Software Mentions: 1
Published: over 3 years ago

10.1038/srep12340

A Comprehensive Inter-Tissue Crosstalk Analysis Underlying Progression and Control of Obesity and Diabetes
Cited by: 20
Author(s): Pawan Samdani, Meet Singhal, Neeraj Sinha, Parul Tripathi, Sachin Sharma, Kamiya Tikoo, Kanury V. S. Rao, Dhiraj Kumar
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2018.00162

Identification of Central Regulators of Calcium Signaling and ECM–Receptor Interaction Genetically Associated With the Progression and Recurrence of Atrial Fibrillation
Cited by: 13
Author(s): Petra Büttner, Laura Ueberham, M. Benjamin Shoemaker, Dan M. Roden, Borislav Dinov, Gerhard Hindricks, Andreas Bollmann, Daniela Husser
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-12-289

Bio::Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping
Cited by: 18
Author(s): Giuseppe Gallone, T. Ian Simpson, J. Douglas Armstrong, Andrew P. Jarman
Software Mentions: 1
Published: over 13 years ago

10.3389/fphys.2015.00171

Relationships between predicted moonlighting proteins, human diseases, and comorbidities from a network perspective
Cited by: 12
Author(s): Andreas Zanzoni, Charles E. Chapple, Catherine Brun
Software Mentions: 1
Published: over 9 years ago

10.1186/s12711-016-0205-1

Using biological networks to integrate, visualize and analyze genomics data
Cited by: 65
Author(s): Theodosia Charitou, Kenneth Bryan, David J. Lynn
Software Mentions: 1
Published: over 8 years ago

10.3233/JAD-200206

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer’s Disease Through Expert Curation of Key Protein Targets
Cited by: 5
Author(s): Lionel Breuza, Cecilia N. Arighi, Ghislaine Argoud-Puy, Cristina Casals-Casas, Anne Estreicher, Maria Livia Famiglietti, George P. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Nevila Hyka‐Nouspikel, Barbara Kramarz, Ruth C. Lovering, Yvonne C. Lussi, Michele Magrane, Patrick Masson, Livia Perfetto, Sylvain Poux, Milagros Rodrı́guez-López, Christian J. Stoeckert, Shyamala Sundaram, Li-San Wang, Elizabeth Wu, Sandra Orchard
Software Mentions: 1
Published: about 4 years ago

10.1093/bioinformatics/btaa622

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)
Cited by: 10
Author(s): Vasundra Touré, Steven Vercruysse, Márcio Luís Acencio, Ruth C. Lovering, Sandra Orchard, Glyn Bradley, Cristina Casals-Casas, Claudine Chaouiya, Noemi del-Toro, Åsmund Flobak, Pascale Gaudet, Henning Hermjakob, Charles Tapley Hoyt, Luana Licata, Astrid Lægreid, Christopher J. Mungall, Anne Niknejad, Simona Panni, Livia Perfetto, Pablo Porras, Dexter Pratt, Julio Sáez-Rodríguez, Denis Thieffry, Paul D. Thomas, Dénes Türei, Martin Kuiper
Software Mentions: 1
Published: over 4 years ago

10.1590/1678-775720150364

Liver proteome of mice with different genetic susceptibilities to the effects of fluoride
Cited by: 6
Author(s): Zohaib Nisar Khan, Aline de Lima Leite, Senda Charone, Isabela Tomazini Sabino, Tatiana Martini, Heloísa Aparecida Barbosa da Silva Pereira, Rodrigo Cardoso de Oliveira, Marília Afonso Rabelo Buzalaf
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pcbi.1002833

Visual Data Mining of Biological Networks: One Size Does Not Fit All
Cited by: 21
Author(s): Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize A. Shirdel, Igor Jurišica
Software Mentions: 1
Published: almost 12 years ago

10.1186/1741-7007-5-44

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
Cited by: 250
Author(s): Samuel Kerrien, Sandra Orchard, Luisa Montecchi-Palazzi, Bruno Aranda, Antony F. Quinn, Nisha Vinod, Gary D. Bader, Ioannis Xenarios, Jérôme Wojcik, David James Sherman, Mike Tyers, John J. Salama, Susan Moore, Arnaud Céol, Andrew Chatr‐aryamontri, Matthias Oesterheld, Volker Stümpflen, Łukasz Salwiński, Jason Nerothin, Ethan Cerami, Michael E. Cusick, Marc Vidal, Michael K. Gilson, J. T. Armstrong, Peter Woollard, Christopher W. V. Hogue, David Eisenberg, Gianni Cesareni, Rolf Apweiler, Henning Hermjakob
Software Mentions: 1
Published: about 17 years ago

10.7717/peerj.1525

Identifying communities from multiplex biological networks
Cited by: 55
Author(s): Gilles Didier, Catherine Brun, Anaı̈s Baudot
Software Mentions: 1
Published: almost 9 years ago

10.1186/s40168-017-0307-1

Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins
Cited by: 27
Author(s): Andreas Zanzoni, Lionel Spinelli, Shérazade Braham, Catherine Brun
Software Mentions: 1
Published: over 7 years ago

10.1111/jcmm.16146

COPD patients with chronic bronchitis and higher sputum eosinophil counts show increased type‐2 and PDE4 gene expression in sputum
Cited by: 13
Author(s): Dave Singh, Michele Bassi, Deborah Balzano, Germano Lucci, Aida Emirova, Marie Anna Nandeuil, Gera L. Jellema, Ebenezer Afolabi, Brian Leaker, Oliver Kornmann, Kai Michael Beeh, Henrik Watz, Mirco Govoni
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.ppat.1008593

Hepatitis B virus Core protein nuclear interactome identifies SRSF10 as a host RNA-binding protein restricting HBV RNA production
Cited by: 26
Author(s): Hélène Chabrolles, H. Auclair, Serena Vegna, Thomas Lahlali, Caroline Pons, Maud Michelet, Yohann Couté, Lucid Belmudes, Gilliane Chadeuf, Yujin Kim, Ariel Di Bernardo, Pascal Jalaguier, François-Loı̈c Cosset, Floriane Fusil, Michel Rivoire, Lee D. Arnold, Uri Lopatin, Christophe Combet, Fabien Zoulim, David S. Grierson, Benoı̂t Chabot, Julie Lucifora, David Durantel, Anna Salvetti
Software Mentions: 1
Published: about 4 years ago

10.1098/rspb.2013.2607

Mating systems and protein–protein interactions determine evolutionary rates of primate sperm proteins
Cited by: 12
Author(s): Julia Schumacher, David Rosenkranz, Holger Herlyn
Software Mentions: 1
Published: almost 11 years ago

10.3390/membranes6010008

Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features
Cited by: 17
Author(s): Joana B. Serrano, Edgar F. da Cruz e Silva, Sandra Rebelo
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-018-2118-1

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions
Cited by: 44
Author(s): M. Sivade, Diego Alonso-López, Mais Ammari, Glyn Bradley, N.H. Campbell, Arnaud Céol, Gianni Cesareni, Colin Combe, Javier De Las Rivas, Noemi del-Toro, Joshua Heimbach, Henning Hermjakob, Igor Jurišica, Maximilian Koch, Luana Licata, Ruth C. Lovering, David J. Lynn, Birgit Meldal, Gos Micklem, Simona Panni, Pablo Porras, Sylvie Ricard‐Blum, Bernd Roechert, Łukasz Salwiński, Anjali Shrivastava, Julie Sullivan, Nicolas Thierry‐Mieg, Yo Yehudi, Kim Van Roey, Sandra Orchard
Software Mentions: 1
Published: over 6 years ago

10.1002/pmic.201400390

A visual review of the interactome of LRRK2: Using deep‐curated molecular interaction data to represent biology
Cited by: 38
Author(s): Pablo Porras, Margaret Duesbury, Antonio Fabregat, Marius Ueffing, Sandra Orchard, Christian Johannes Gloeckner, Henning Hermjakob
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0106646

Proteomic Analysis of Gastrocnemius Muscle in Rats with Streptozotocin-Induced Diabetes and Chronically Exposed to Fluoride
Cited by: 41
Author(s): Aline L. Leite, Janete Gualiume Vaz Madureira Lobo, Heloísa Aparecida Barbosa da Silva Pereira, Marcelo Adorna Fernandes, Tatiani Martini, Fernanda Zucki, Dóris Hissako Sumida, Alfredo Rigalli, Marília Afonso Rabelo Buzalaf
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0202537

Investigating genetic-and-epigenetic networks, and the cellular mechanisms occurring in Epstein–Barr virus-infected human B lymphocytes via big data mining and genome-wide two-sided NGS data identification
Cited by: 10
Author(s): Chengwei Li, Bo-Ren Jheng, Bor‐Sen Chen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0090904

A Method for Predicting Protein-Protein Interaction Types
Cited by: 16
Author(s): Yael Silberberg, Martin Kupiec, Roded Sharan
Software Mentions: 1
Published: over 10 years ago

10.1186/s12964-020-00554-5

PINOT: an intuitive resource for integrating protein-protein interactions
Cited by: 20
Author(s): James E. Tomkins, Raffaele Ferrari, Nikoleta Vavouraki, John Hardy, Ruth C. Lovering, Patrick A. Lewis, Liam J. McGuffin, Claudia Manzoni
Software Mentions: 1
Published: over 4 years ago

10.1038/s41419-021-03881-8

Looking for pathways related to COVID-19: confirmation of pathogenic mechanisms by SARS-CoV-2–host interactome
Cited by: 12
Author(s): Francesco Messina, Emanuela Giombini, Chiara Montaldo, Ashish Sharma, À. Zoccoli, Rafick Pierre Sékaly, Franco Locatelli, Alimuddin Zumla, Markus Maeurer, Maria Rosaria Capobianchi, F. Lauria, Giuseppe Ippolito
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0031826

HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
Cited by: 298
Author(s): Martin H. Schaefer, Jean-Fred Fontaine, Arunachalam Vinayagam, Pablo Porras, Erich E. Wanker, Miguel A. Andrade‐Navarro
Software Mentions: 1
Published: almost 13 years ago

10.1093/bioinformatics/btv431

The MI bundle: enabling network and structural biology in genome visualization tools
Cited by: 10
Author(s): Arnaud Céol, Heiko Müller
Software Mentions: 1
Published: over 9 years ago