| Title | Authors (identified) | Published In | Identifier(s) | Topic | Published Date |
|---|
| WikiPathways 2024: next generation pathway database | [1]Ayushi Agrawal, [2]Hasan Balcı, [3]Kristina Hanspers, [4]Susan Coort, [5]Marvin Martens, [6]Denise Slenter, [7]Friederike Ehrhart, [8]Daniela Digles, [9]Andra Waagmeester, [10]Isabel Wassink, ..., [20]Egon Willighagen, [21]Martina Summer-Kutmon, [22]Alexander R. Pico [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKAD960
PubMed: 37941138 | WikiPathways [curation] | 2023-11-06 |
| BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms | [1]Alexander R. Pico, [2]Hiromasa Ono, [3]Ryo Nozu, [4]Naoya Oec, [5]Hidemasa U. Bono [Full author list] | BioHackrXiv [curation], DBCLS BioHackathon 2023 Reports [curation] | DOI: 10.37044/OSF.IO/4USKB
| optical character recognition [curation]; WikiPathways [curation] | 2023-07-12 |
| Introducing R as a smart version of calculators enables beginners to explore it on their own | [1]Krishna Choudhary, [2]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.54685.2
| | 2022-06-21 |
| Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science | [1]Deepak R. Unni, [9]Michel Dumontier, [10]Karamarie Fecho, ..., [2]Sierra Moxon, [3]Michael Bada, [4]Matthew Brush, [5]Richard Bruskiewich, [6]J Harry Caufield, [7]Paul A Clemons, [8]Vlado Dancik, ..., [131]Bria Persaud, [132]Emily R Pfaff, [133]Alexander R. Pico, [134]Elizabeth Pollard, [135]Guthrie Price, ... [Full author list] | Clinical and Translational Science [curation] | DOI: 10.1111/CTS.13302
| knowledge graph of science [curation] | 2022-06-06 |
| COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms | [1]Marek Ostaszewski, [2]Anna Niarakis, [3]Alexander Mazein, [4]Inna Kuperstein, [5]Robert Phair, [6]Aurelio Orta-Resendiz, [7]Vidisha Singh, [8]Sara Sadat Aghamiri, [9]Marcio Luis Acencio, [10]Enrico Glaab, ..., [124]Olaf Wolkenhauer, [125]Egon Willighagen, [126]Alexander R. Pico, [127]Chris T. Evelo, [128]Marc E Gillespie, ... [Full author list] | Molecular Systems Biology [curation] | DOI: 10.15252/MSB.202110387
PubMed: 34664389 | SARS-CoV-2 [curation]; COVID-19 [curation] | 2021-10-19 |
| Introducing R as a smart version of calculators enables beginners to explore it on their own | [1]Krishna Choudhary, [2]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.54685.1
| | 2021-08-26 |
| Ten simple rules for creating reusable pathway models for computational analysis and visualization | [1]Kristina Hanspers, [2]Martina Summer-Kutmon, [3]Susan Coort, [4]Daniela Digles, [5]Lauren J Dupuis, [6]Friederike Ehrhart, [7]Finterly Hu, [8]Elisson N. Lopes, [9]Marvin Martens, [10]Nhung Pham, [11]Woosub Shin, [12]Denise Slenter, [13]Andra Waagmeester, [14]Egon Willighagen, [15]Laurent Winckers, [16]Chris T. Evelo, [17]Alexander R. Pico [Full author list] | PLOS Computational Biology [curation] | DOI: 10.1371/JOURNAL.PCBI.1009226
| | 2021-08-19 |
| scNetViz: from single cells to networks using Cytoscape | [1]Krishna Choudhary, [2]Elaine C. Meng, [3]J Javier Diaz-Mejia, [4]Gary D. Bader, [5]Alexander R. Pico, [6]John "Scooter" Morris [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.52460.1
| Cytoscape [curation] | 2021-06-07 |
| WikiPathways: connecting communities | [1]Marvin Martens, [2]Ammar Ammar, [3]Anders Riutta, [4]Andra Waagmeester, [5]Denise Slenter, [6]Kristina Hanspers, [7]Ryan Miller, [8]Daniela Digles, [9]Elisson N. Lopes, [10]Friederike Ehrhart, [11]Lauren J Dupuis, [12]Laurent Winckers, [13]Susan Coort, [14]Egon Willighagen, [15]Chris T. Evelo, [16]Alexander R. Pico, [17]Martina Summer-Kutmon [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKAA1024
PubMed: 33211851 | collaboration [curation]; biological pathway [curation]; WikiPathways [curation] | 2021-01-08 |
| Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma | [1]Chen Huang, [2]Lijun Chen, [3]Sara R Savage, [4]Rodrigo Vargas Eguez, [5]Yongchao Dou, [6]Yize Li, [7]Felipe da Veiga Leprevost, [8]Eric J Jaehnig, [9]Jonathan T Lei, [10]Bo Wen, ..., [39]Jiang Qian, [40]Xi S Chen, [41]Alexander R. Pico, [42]Pei Wang, [43]Arul M Chinnaiyan, ... [Full author list] | Cancer Cell [curation] | DOI: 10.1016/J.CCELL.2020.12.007
PubMed: 33417831 | head and neck squamous cell carcinoma [curation] | 2021-01-05 |
| The Dynamic Platelet Transcriptome in Obesity and Weight Loss | [1]Marzieh Ezzaty Mirhashemi, [2]Ravi V Shah, [3]Robert R Kitchen, [4]Jian Rong, [5]Aferdita Spahillari, [6]Alexander R. Pico, [7]Olga Vitseva, [8]Daniel Levy, [9]Danielle Demarco, [10]Sajani Shah, [11]Mark D Iafrati, [12]Martin G Larson, [13]Kahraman Tanriverdi, [14]Jane E. Freedman [Full author list] | Arteriosclerosis, Thrombosis, and Vascular Biology [curation] | DOI: 10.1161/ATVBAHA.120.315186
PubMed: 33297754 | | 2020-12-10 |
| Pathway information extracted from 25 years of pathway figures | [1]Kristina Hanspers, [2]Anders Riutta, [3]Martina Summer-Kutmon, [4]Alexander R. Pico [Full author list] | Genome Biology [curation] | DOI: 10.1186/S13059-020-02181-2
PubMed: 33168034 | | 2020-11-09 |
| Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells | [1]Steven A Yukl, [2]Shahzada Khan, [3]Tsui-Hua Chen, [4]Martin Trapecar, [5]Frank Wu, [6]Guorui Xie, [7]Sushama Telwatte, [8]Daniel Fulop, [9]Alexander R. Pico, [10]Gregory M Laird, [11]Kristen D Ritter, [12]Norman G Jones, [13]Chuanyi M Lu, [14]Robert F Siliciano, [15]Nadia R Roan, [16]Jeffrey M Milush, [17]Ma Somsouk, [18]Steven G Deeks, [19]Peter W Hunt, [20]Shomyseh Sanjabi [Full author list] | Journal of Virology [curation] | DOI: 10.1128/JVI.01331-20
PubMed: 33115867 | | 2020-10-28 |
| COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms | [1]Marek Ostaszewski, [2]Anna Niarakis, [3]Alexander Mazein, [4]Inna Kuperstein, [5]Robert Phair, [6]Aurelio Orta-Resendiz, [7]Vidisha Singh, [8]Sara Sadat Aghamiri, [9]Marcio Luis Acencio, [10]Enrico Glaab, ..., [123]Olaf Wolkenhauer, [124]Egon L. Wilighagen, [125]Alexander R. Pico, [126]Chris T. Evelo, [127]Marc E. Gillespie, ... [Full author list] | | DOI: 10.1101/2020.10.26.356014
| systems biology [curation]; SARS-CoV-2 [curation]; COVID-19 [curation] | 2020-10-28 |
| Mir-30d Regulates Cardiac Remodeling by Intracellular And Paracrine Signaling | [1]Jin Li, [2]Ane M Salvador, [3]Guoping Li, [4]Nedyalka Valkov, [5]Olivia Ziegler, [6]Ashish Suresh Yeri, [7]Chun Yang Xiao, [8]Bessie Meechoovet, [9]Eric Alsop, [10]Rodosthenis S Rodosthenous, ..., [13]Daniel Levy, [14]John C Tigges, [15]Alexander R. Pico, [16]Ionita Ghiran, [17]Michael G Silverman, ... [Full author list] | Circulation Research [curation] | DOI: 10.1161/CIRCRESAHA.120.317244
PubMed: 33092465 | | 2020-10-22 |
| Comprehensive Metabolic Phenotyping Refines Cardiovascular Risk in Young Adults | [1]Venkatesh L. Murthy, [2]Jared P Reis, [3]Alexander R. Pico, [4]Robert Kitchen, [5]Joao A C Lima, [6]Donald Lloyd-Jones, [7]Norrina Allen, [8]Mercedes Carnethon, [9]Gregory D Lewis, [10]Matthew Nayor, [11]Ramachandran S. Vasan, [12]Jane E. Freedman, [13]Clary B Clish, [14]Ravi V Shah [Full author list] | Circulation [curation] | DOI: 10.1161/CIRCULATIONAHA.120.047689
PubMed: 33073606 | | 2020-10-19 |
| Metabolic Architecture of Acute Exercise Response in Middle-Aged Adults in the Community | [1]Matthew Nayor, [2]Ravi V Shah, [3]Patricia E Miller, [4]Jasmine B Blodgett, [5]Melissa Tanguay, [6]Alexander R. Pico, [7]Venkatesh L Murthy, [8]Rajeev Malhotra, [9]Nicholas E Houstis, [10]Amy Deik, ... [Full author list] | Circulation [curation] | DOI: 10.1161/CIRCULATIONAHA.120.050281
PubMed: 32927962 | | 2020-09-15 |
| Molecular Signature of Multisystem Cardiometabolic Stress and Its Association With Prognosis | [1]Venkatesh L Murthy, [2]Bing Yu, [3]Wenshuang Wang, [4]Xiuyan Zhang, [5]Taryn Alkis, [6]Alexander R. Pico, [7]Ashish Yeri, [8]Shilpa N Bhupathiraju, [9]Jan Bressler, [10]Christie M. Ballantyne, [11]Jane E. Freedman, [12]Jose Ordovas, [13]Eric Boerwinkle, [14]Katherine L Tucker, [15]Ravi Shah [Full author list] | JAMA cardiology [curation] | DOI: 10.1001/JAMACARDIO.2020.2686
PubMed: 32717046 | | 2020-07-22 |
| Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms | [1]Marek Ostaszewski, [2]Alexander Mazein, [3]Marc Gillespie, [4]Inna Kuperstein, [5]Anna Niarakis, [6]Henning Hermjakob, [7]Alexander R. Pico, [8]Egon Willighagen, [9]Chris T. Evelo, [10]Jan Hasenauer, ... [Full author list] | Scientific Data [curation] | DOI: 10.1038/S41597-020-00589-W
PubMed: 32678106 | SARS-CoV-2 [curation]; COVID-19 [curation] | 2020-07-17 |
| Author Correction: Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation | [1]Andrew S Mendiola, [2]Jae Kyu Ryu, [3]Sophia Bardehle, [4]Anke Meyer-Franke, [5]Kenny Kean-Hooi Ang, [6]Chris Wilson, [7]Kim M Baeten, [8]Kristina Hanspers, [9]Mario Merlini, [10]Sean Thomas, ..., [25]Ari J Green, [26]Scott S Zamvil, [27]Alexander R. Pico, [28]Benoit G. Bruneau, [29]Michelle R Arkin, ... [Full author list] | Nature Immunology [curation] | DOI: 10.1038/S41590-020-0754-X
PubMed: 32661365 | | 2020-07-13 |
| PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data | [1]Gabriel J Odom, [2]Yuguang Ban, [3]Antonio Colaprico, [4]Lizhong Liu, [5]Tiago Chedraoui Silva, [6]Xiaodian Sun, [7]Alexander R. Pico, [8]Bing Zhang, [9]Lily Wang, [10]Xi Chen [Full author list] | Proteomics [curation] | DOI: 10.1002/PMIC.201900409
PubMed: 32430990 | R package [curation] | 2020-05-20 |
| COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms | [1]Marek Ostaszewski, [2]Alexander Mazein, [3]Marc Gillespie, [4]Inna Kuperstein, [5]Anna Niarakis, [6]Henning Hermjakob, [7]Alexander R. Pico, [8]Egon Willighagen, [9]Chris T. Evelo, [10]Jan Hasenauer, ... [Full author list] | Scientific Data [curation] | DOI: 10.1038/S41597-020-0477-8
PubMed: 32371892 | SARS-CoV-2 [curation]; COVID-19 [curation]; COVID-19 Disease Map [curation] | 2020-05-05 |
| Transcriptional profiling and therapeutic targeting of oxidative stress in neuroinflammation | [1]Andrew S Mendiola, [2]Jae Kyu Ryu, [3]Sophia Bardehle, [4]Anke Meyer-Franke, [5]Kenny Kean-Hooi Ang, [6]Chris Wilson, [7]Kim M Baeten, [8]Kristina Hanspers, [9]Mario Merlini, [10]Sean Thomas, ..., [25]Ari J Green, [26]Scott S Zamvil, [27]Alexander R. Pico, [28]Benoit G. Bruneau, [29]Michelle R Arkin, ... [Full author list] | Nature Immunology [curation] | DOI: 10.1038/S41590-020-0654-0
PubMed: 32284594 | | 2020-04-13 |
| Wikidata as a knowledge graph for the life sciences | [1]Andra Waagmeester, [2]Gregory Stupp, [3]Sebastian Burgstaller-Muehlbacher, [4]Benjamin M. Good, [5]Malachi Griffith, [6]Obi Griffith, [7]Kristina Hanspers, [8]Henning Hermjakob, [9]Toby Hudson, [10]Kevin Hybiske, ..., [14]Daniel Mietchen, [15]Elvira Mitraka, [16]Alexander R. Pico, [17]Timothy Elliott Putman, [18]Anders Riutta, ... [Full author list] | eLife [curation] | DOI: 10.7554/ELIFE.52614
PubMed: 32180547 | biology [curation]; Wikidata [curation]; ontology [curation]; life sciences [curation]; semantic interoperability [curation]; FAIR data [curation]; knowledge graph [curation]; knowledge graph of science [curation] | 2020-03-17 |
| Proteogenomic Characterization of Endometrial Carcinoma | [1]Yongchao Dou, [2]Emily Kawaler, [3]Daniel Cui Zhou, [4]Marina A. Gritsenko, [5]Chen Huang, [6]Lili Blumenberg, [7]Alla Karpova, [8]Vladislav A Petyuk, [9]Sara R Savage, [10]Shankha Satpathy, ..., [33]Ramani Kothadia, [34]Yosef Maruvka, [35]Alexander R. Pico, [36]Amanda E Oliphant, [37]Emily L Hoskins, ... [Full author list] | Cell [curation] | DOI: 10.1016/J.CELL.2020.01.026
PubMed: 32059776 | endometrial carcinoma [curation] | 2020-02-13 |
| Author response: Wikidata as a knowledge graph for the life sciences | [1]Andra Waagmeester, [2]Gregory Stupp, [3]Sebastian Burgstaller-Muehlbacher, [4]Benjamin M. Good, [5]Malachi Griffith, [6]Obi Griffith, [7]Kristina Hanspers, [8]Henning Hermjakob, [9]Toby Hudson, [10]Kevin Hybiske, ..., [14]Daniel Mietchen, [15]Elvira Mitraka, [16]Alexander R. Pico, [17]Timothy Elliott Putman, [18]Anders Riutta, ... [Full author list] | eLife [curation] | DOI: 10.7554/ELIFE.52614.SA2
| Wikidata [curation]; life sciences [curation] | 2020-01-24 |
| Circulating miRNAs and Risk of Sudden Death in Patients With Coronary Heart Disease | [1]Michael G Silverman, [2]Ashish Yeri, [3]M Vinayaga Moorthy, [4]Fernando Camacho Garcia, [5]Neal A Chatterjee, [6]Charlotte S A Glinge, [7]Jacob Tfelt-Hansen, [8]Ane M Salvador, [9]Alexander R. Pico, [10]Ravi Shah, [11]Christine M. Albert, [12]Saumya Das [Full author list] | JACC. Clinical electrophysiology [curation] | DOI: 10.1016/J.JACEP.2019.08.011
PubMed: 31971908 | | 2019-10-30 |
| Wikidata as a FAIR knowledge graph for the life sciences | [1]Andra Waagmeester, [2]Gregory Stupp, [3]Sebastian Burgstaller-Muehlbacher, [4]Benjamin M. Good, [5]Malachi Griffith, [6]Obi Griffith, [7]Kristina Hanspers, [8]Henning Hermjakob, [9]Toby Hudson, [10]Kevin Hybiske, ..., [14]Daniel Mietchen, [15]Elvira Mitraka, [16]Alexander R. Pico, [17]Timothy Elliott Putman, [18]Anders Riutta, ... [Full author list] | | DOI: 10.1101/799684
| Wikidata [curation]; life sciences [curation]; knowledge graph [curation]; knowledge graph of science [curation] | 2019-10-21 |
| RCy3: Network biology using Cytoscape from within R | [1]Julia A Gustavsen, [2]Shraddha Pai, [3]Ruth Isserlin, [4]Barry Demchak, [5]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.20887.3
PubMed: 31819800 | Cytoscape [curation] | 2019-10-18 |
| Cytoscape Automation: empowering workflow-based network analysis | [1]David Otasek, [2]John H Morris, [3]Jorge Bouças, [4]Alexander R. Pico, [5]Barry Demchak [Full author list] | Genome Biology [curation] | DOI: 10.1186/S13059-019-1758-4
PubMed: 31477170 | Cytoscape [curation] | 2019-09-02 |
| exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids | [1]Oscar D Murillo, [2]William Thistlethwaite, [3]Joel Rozowsky, [4]Sai Lakshmi Subramanian, [5]Rocco Lucero, [6]Neethu Shah, [7]Andrew R Jackson, [8]Srimeenakshi Srinivasan, [9]Allen Chung, [10]Clara D Laurent, ..., [50]Saumya Das, [51]Kei-Hoi Cheung, [52]Alexander R. Pico, [53]Andrew I. Su, [54]Robert L Raffai, ... [Full author list] | Cell [curation] | DOI: 10.1016/J.CELL.2019.02.018
PubMed: 30951672 | RNA analysis [curation] | 2019-04-01 |
| Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data | [1]J Javier Diaz-Mejia, [2]Elaine C Meng, [3]Alexander R. Pico, [4]Sonya A MacParland, [5]Troy Ketela, [6]Trevor J Pugh, [7]Gary D. Bader, [8]John "Scooter" Morris [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.18490.3
PubMed: 31508207 | single-cell RNA-seq [curation] | 2019-03-15 |
| Proteins Altered by Surgical Weight Loss Highlight Biomarkers of Insulin Resistance in the Community | [1]Ravi V. Shah, [2]Shih-Jen Hwang, [3]Ashish Yeri, [4]Kahraman Tanriverdi, [5]Alexander R. Pico, [6]Chen Yao, [7]Venkatesh Murthy, [8]Jennifer Ho, [9]Olga Vitseva, [10]Danielle Demarco, [11]Sajani Shah, [12]Mark D. Iafrati, [13]Daniel Levy, [14]Jane E. Freedman [Full author list] | Arteriosclerosis, Thrombosis, and Vascular Biology [curation] | DOI: 10.1161/ATVBAHA.118.311928
PubMed: 30580566 | biomarker [curation]; insulin resistance [curation]; preproinsulin [curation] | 2019-01-01 |
| Fibrin-targeting immunotherapy protects against neuroinflammation and neurodegeneration | [1]Jae Kyu Ryu, [2]Victoria A Rafalski, [3]Anke Meyer-Franke, [4]Ryan A Adams, [5]Suresh B Poda, [6]Pamela E Rios Coronado, [7]Lars Østergaard Pedersen, [8]Veena Menon, [9]Kim M Baeten, [10]Shoana L Sikorski, ..., [28]Michelle R Arkin, [29]Stevin H Zorn, [30]Alexander R. Pico, [31]Lennart Mucke, [32]Stephen B Freedman, ... [Full author list] | Nature Immunology [curation] | DOI: 10.1038/S41590-018-0232-X
PubMed: 30323343 | immunotherapy [curation]; neurodegeneration [curation]; neuronitis [curation] | 2018-10-15 |
| Associations of Circulating Extracellular RNAs With Myocardial Remodeling and Heart Failure | [1]Ravi V Shah, [2]Jian Rong, [3]Martin G Larson, [4]Ashish Yeri, [5]Olivia Ziegler, [6]Kahraman Tanriverdi, [7]Venkatesh Murthy, [8]Xiaojun Liu, [9]Chunyang Xiao, [10]Alexander R. Pico, [11]Tianxiao Huan, [12]Daniel Levy, [13]Gregory D Lewis, [14]Anthony Rosenzweig, [15]Ramachandran S. Vasan, [16]Saumya Das, [17]Jane E. Freedman [Full author list] | JAMA cardiology [curation] | DOI: 10.1001/JAMACARDIO.2018.2371
PubMed: 30090932 | | 2018-09-01 |
| Identifying Genes in Published Pathway Figure Images | [1]Anders Riutta, [2]Kristina Hanspers, [3]Alexander R. Pico [Full author list] | | DOI: 10.1101/379446
| | 2018-07-29 |
| The Cytoscape Automation app article collection. | [1]Barry Demchak, [2]David Otasek, [3]Alexander R. Pico, [4]Gary D. Bader, [5]Keiichiro Ono, [6]Brett Settle, [7]Eric Sage, [8]John H Morris, [9]William Longabaugh, [10]Christian Lopes, [11]Michael Kucera, [12]Adam Treister, [13]Benno Schwikowski, [14]Piet Molenaar, [15]Trey Ideker [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.15355.1
PubMed: 29983926 | automation [curation]; Cytoscape [curation] | 2018-06-20 |
| MicroRNAs Associated With Reverse Left Ventricular Remodeling in Humans Identify Pathways of Heart Failure Progression. | [1]Ravi Shah, [2]Olivia Ziegler, [3]Ashish Yeri, [4]Xiaojun Liu, [5]Venkatesh Murthy, [6]Dustin Rabideau, [7]Chun Yang Xiao, [8]Kristina Hanspers, [9]Arianna Belcher, [10]Michael Tackett, [11]Anthony Rosenzweig, [12]Alexander R. Pico, [13]James Januzzi, [14]Saumya Das [Full author list] | Circulation: Heart Failure [curation] | DOI: 10.1161/CIRCHEARTFAILURE.117.004278
PubMed: 29438982 | microRNA [curation]; ventricular remodeling [curation] | 2018-02-01 |
| WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research | [1]Denise Slenter, [2]Martina Summer-Kutmon, [3]Kristina Hanspers, [4]Anders Riutta, [5]Jacob Windsor, [6]Nuno Nunes, [7]Jonathan Mélius, [8]Elisa Cirillo, [9]Susan Coort, [10]Daniela Digles, ..., [19]Lars Eijssen, [20]Chris T. Evelo, [21]Alexander R. Pico, [21-Q28530149]Alexander R. Pico, [22]Egon Willighagen, ... [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKX1064
PubMed: 29136241 | database [curation]; biological pathway [curation]; WikiPathways [curation]; metabolomics [curation] | 2018-01-04 |
| Identifier Mapping in Cytoscape | [1]Adam Treister, [2]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.14807.1
PubMed: 30079244 | Cytoscape [curation] | 2018-01-01 |
| Proteomic analysis of heart failure hospitalization among patients with chronic kidney disease: The Heart and Soul Study | [1]Ruth F Dubin, [2]Mary A. Whooley, [3]Alexander R. Pico, [4]Peter Ganz, [5]Nelson B Schiller, [6]Craig Meyer [Full author list] | PLOS One [curation] | DOI: 10.1371/JOURNAL.PONE.0208042
PubMed: 30557359 | heart failure [curation]; chronic renal insufficiency [curation]; hospitalization [curation] | 2018-01-01 |
| Research synergy and drug development: Bright stars in neighboring constellations | [1]Samet Keserci, [2]Eric Livingston, [3]Lingtian Wan, [4]Alexander R. Pico, [5]George Chacko [Full author list] | Heliyon [curation] | DOI: 10.1016/J.HELIYON.2017.E00442
PubMed: 29264408 | | 2017-11-15 |
| Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives | [1]Kenneth Daily, [2]Shannan J Ho Sui, [3]Lynn Schriml, [4]Phillip Dexheimer, [5]Nathan Salomonis, [6]Robin Schroll, [7]Stacy Bush, [8]Mehdi Keddache, [9]Christopher Mayhew, [10]Samad Lotia, ..., [12]Kristen Dang, [13]Lorena Pantano, [14]Alexander R. Pico, [15]Elke Grassman, [16]Diana Nordling, ... [Full author list] | Scientific Data [curation] | DOI: 10.1038/SDATA.2017.30
PubMed: 28350385 | pluripotency [curation]; RNA sequencing [curation] | 2017-03-28 |
| Extracellular RNAs Are Associated With Insulin Resistance and Metabolic Phenotypes. | [1]Ravi Shah, [2]Venkatesh Murthy, [3]Michael Pacold, [4]Kirsty Danielson, [5]Kahraman Tanriverdi, [6]Martin G Larson, [7]Kristina Hanspers, [8]Alexander R. Pico, [9]Eric Mick, [10]Jared Reis, [11]Sarah de Ferranti, [12]Elizaveta Freinkman, [13]Daniel Levy, [14]Udo Hoffmann, [15]Stavroula Osganian, [16]Saumya Das, [17]Jane E. Freedman [Full author list] | Diabetes Care [curation] | DOI: 10.2337/DC16-1354
PubMed: 28183786 | insulin resistance [curation] | 2017-02-09 |
| Translational Epidemiology: Entering a Brave New World of Team Science | [1]Ravi Shah, [2]Alexander R. Pico, [3]Jane E. Freedman [Full author list] | Circulation Research [curation] | DOI: 10.1161/CIRCRESAHA.116.309881
PubMed: 27789584 | team science [curation] | 2016-10-01 |
| Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources | [1]Andra Waagmeester, [2]Martina Summer-Kutmon, [3]Anders Riutta, [4]Ryan Miller, [5]Egon Willighagen, [6]Chris T. Evelo, [7]Alexander R. Pico [Full author list] | PLOS Computational Biology [curation] | DOI: 10.1371/JOURNAL.PCBI.1004989
PubMed: 27336457 | Semantic Web [curation]; SPARQL [curation]; WikiPathways [curation] | 2016-06-01 |
| Reactome from a WikiPathways Perspective | [1]Anwesha Bohler, [2]Guanming Wu, [3]Martina Summer-Kutmon, [4]Leontius Adhika Pradhana, [5]Susan Coort, [6]Kristina Hanspers, [7]Robin Haw, [8]Alexander R. Pico, [9]Chris T. Evelo [Full author list] | PLOS Computational Biology [curation] | DOI: 10.1371/JOURNAL.PCBI.1004941
PubMed: 27203685 | Reactome [curation]; biological pathway [curation]; WikiPathways [curation] | 2016-05-01 |
| WikiPathways: capturing the full diversity of pathway knowledge | [1]Martina Summer-Kutmon, [2]Anders Riutta, [3]Nuno Nunes, [4]Kristina Hanspers, [5]Egon Willighagen, [6]Anwesha Bohler, [7]Jonathan Mélius, [8]Andra Waagmeester, [9]Sravanthi R Sinha, [10]Ryan Miller, [11]Susan Coort, [12]Elisa Cirillo, [13]Bart Smeets, [14]Chris T. Evelo, [15]Alexander R. Pico [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKV1024
PubMed: 26481357 | biological pathway [curation]; WikiPathways [curation] | 2016-01-04 |
| Longer genotypically-estimated leukocyte telomere length is associated with increased adult glioma risk | [1]Kyle M Walsh, [2]Veryan Codd, [3]Terri Rice, [4]Christopher P Nelson, [5]Ivan V Smirnov, [6]Lucie S McCoy, [7]Helen M Hansen, [8]Edward Elhauge, [9]Juhi Ojha, [10]Stephen S. Francis, [11]Nils R Madsen, [12]Paige M Bracci, [13]Alexander R. Pico, [14]Annette M Molinaro, [15]Tarik Tihan, ... [Full author list] | Oncotarget [curation] | DOI: 10.18632/ONCOTARGET.6468
PubMed: 26646793 | telomere length [curation] | 2015-12-04 |
| From scientific discovery to cures: bright stars within a galaxy | [1]R Sanders Williams, [2]Samad Lotia, [3]Alisha K Holloway, [4]Alexander R. Pico [Full author list] | Cell [curation] | DOI: 10.1016/J.CELL.2015.09.007
PubMed: 26406364 | | 2015-09-01 |
| Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies | [1]Sai Lakshmi Subramanian, [2]Robert R Kitchen, [3]Roger P Alexander, [4]Bob S Carter, [5]Kei-Hoi Cheung, [6]Louise C Laurent, [7]Alexander R. Pico, [8]Lewis R. Roberts, [9]Matthew E Roth, [10]Joel Rozowsky, [11]Andrew I. Su, [12]Mark Bender Gerstein, [13]Aleksandar Milosavljevic [Full author list] | Journal of extracellular vesicles [curation] | DOI: 10.3402/JEV.V4.27497
PubMed: 26320941 | metadata [curation]; ontology [curation] | 2015-08-28 |
| CyAnimator: Simple Animations of Cytoscape Networks | [1]John H Morris, [2]Dhameliya Vijay, [3]Steven Federowicz, [4]Alexander R. Pico, [5]Thomas E Ferrin [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.6852.2
PubMed: 26937268 | Cytoscape [curation] | 2015-08-05 |
| PSFC: a Pathway Signal Flow Calculator App for Cytoscape | [1]Lilit Nersisyan, [2]Graham Johnson, [3]Megan Riel-Mehan, [4]Alexander R. Pico, [5]Arsen Arakelyan [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.6706.2
PubMed: 26834984 | Cytoscape [curation] | 2015-08-05 |
| Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors | [1]Jeanette E Eckel-Passow, [2]Daniel H Lachance, [3]Annette M Molinaro, [4]Kyle M Walsh, [5]Paul A Decker, [6]Hugues Sicotte, [7]Melike Pekmezci, [8]Terri Rice, [9]Matt L Kosel, [10]Ivan V Smirnov, ..., [21]Shichun Zheng, [22]Gerald F Reis, [23]Alexander R. Pico, [24]Brian P O'Neill, [25]Jan C Buckner, ... [Full author list] | The New England Journal of Medicine [curation] | DOI: 10.1056/NEJMOA1407279
PubMed: 26061753 | | 2015-06-10 |
| PathVisio 3: an extendable pathway analysis toolbox | [1]Martina Summer-Kutmon, [2]Martijn P van Iersel, [3]Anwesha Bohler, [4]Thomas Kelder, [5]Nuno Nunes, [6]Alexander R. Pico, [7]Chris T. Evelo [Full author list] | PLOS Computational Biology [curation] | DOI: 10.1371/JOURNAL.PCBI.1004085
PubMed: 25706687 | PathVisio [curation]; pathway analysis [curation] | 2015-02-01 |
| Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions | [1]John "Scooter" Morris, [2]Giselle M Knudsen, [3]Erik Verschueren, [4]Jeffrey R Johnson, [5]Peter Cimermancic, [6]Alexander L. Greninger, [7]Alexander R. Pico [Full author list] | Nature Protocols [curation] | DOI: 10.1038/NPROT.2014.164
PubMed: 25275790 | protein-protein interaction [curation] | 2014-10-02 |
| WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization | [1]Martina Summer-Kutmon, [2]Samad Lotia, [3]Chris T. Evelo, [4]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.4254.2
PubMed: 25254103 | visualization [curation]; Cytoscape [curation]; WikiPathways [curation] | 2014-07-01 |
| BridgeDb app: unifying identifier mapping services for Cytoscape | [1]Jianjiong Gao, [2]Chao Zhang, [3]Martijn P van Iersel, [4]Li Zhang, [5]Dong Xu, [6]Nikolaus Schultz, [7]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.4521.1
PubMed: 25110584 | Cytoscape [curation]; BridgeDb [curation] | 2014-07-01 |
| The Cytoscape app article collection | [1]Alexander R. Pico, [2]Gary D. Bader, [3]Barry Demchak, [4]Oriol Guitart Pla, [5]Timothy Hull, [6]William Longabaugh, [7]Christian Lopes, [8]Samad Lotia, [9]Piet Molenaar, [10]Jason Montojo, [11]John "Scooter" Morris, [12]Keiichiro Ono, [13]Benno Schwikowski, [14]David Welker, [15]Trey Ideker [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.4642.1
PubMed: 25580224 | Cytoscape [curation] | 2014-07-01 |
| enhancedGraphics: a Cytoscape app for enhanced node graphics | [1]John "Scooter" Morris, [2]Allan Kuchinsky, [3]Thomas E Ferrin, [4]Alexander R. Pico [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.4460.1
PubMed: 25285206 | Cytoscape [curation] | 2014-07-01 |
| setsApp for Cytoscape: Set operations for Cytoscape Nodes and Edges | [1]John "Scooter" Morris, [2]Samad Lotia, [3]Allan Wu, [4]Nadezhda Tsankova Doncheva, [5]Mario Albrecht, [6]Alexander R. Pico, [7]Thomas E Ferrin [Full author list] | F1000Research [curation] | DOI: 10.12688/F1000RESEARCH.4392.2
PubMed: 25352980 | Cytoscape [curation] | 2014-07-01 |
| TELOMERE LENGTH VARIANTS ARE ASSOCIATED WITH HIGH-GRADE GLIOMA RISK: IDENTIFICATION OF A NOVEL GLIOMA RISK LOCUS BY GENOME-WIDE ASSOCIATION STUDY | [1]Kyle M. Walsh, [2]Kyle M. Walsh, [3]Veryan Codd, [4]Ivan V. Smirnov, [5]Terri Rice, [6]Paul A. Decker, [7]Helen M. Hansen, [8]Thomas Kollmeyer, [9]Matthew L. Kosel, [10]Annette M. Molinaro, ..., [15]Shichun Zheng, [16]Joseph L. Wiemels, [17]Alexander R. Pico, [18]Tarik Tihan, [19]Mitchell S. Berger, ... [Full author list] | Neuro-Oncology [curation] | DOI: 10.1093/NEUONC/NOU206.4
| genome-wide association study [curation]; telomere length [curation] | 2014-07-01 |
| Variants near TERT and TERC influencing telomere length are associated with high-grade glioma risk | [1]Kyle M Walsh, [2]Veryan Codd, [3]Ivan V Smirnov, [4]Terri Rice, [5]Paul A Decker, [6]Helen M Hansen, [7]Thomas Kollmeyer, [8]Matthew L Kosel, [9]Annette M Molinaro, [10]Lucie S McCoy, ..., [14]Shichun Zheng, [15]Joseph L Wiemels, [16]Alexander R. Pico, [17]Tarik Tihan, [18]Mitchell S Berger, ... [Full author list] | Nature Genetics [curation] | DOI: 10.1038/NG.3004
PubMed: 24908248 | telomere length [curation] | 2014-06-08 |
| NOA: a cytoscape plugin for network ontology analysis | [1]Chao Zhang, [2]Jiguang Wang, [3]Kristina Hanspers, [4]Dong Xu, [5]Luonan Chen, [6]Alexander R. Pico [Full author list] | Bioinformatics [curation] | DOI: 10.1093/BIOINFORMATICS/BTT334
PubMed: 23749961 | ontology [curation]; Cytoscape [curation] | 2013-06-07 |
| Genetic variants in telomerase-related genes are associated with an older age at diagnosis in glioma patients: evidence for distinct pathways of gliomagenesis | [1]Kyle M Walsh, [2]Terri Rice, [3]Paul A Decker, [4]Matthew L Kosel, [5]Thomas Kollmeyer, [6]Helen M Hansen, [7]Shichun Zheng, [8]Lucie S McCoy, [9]Paige M Bracci, [10]Erik Anderson, [11]George Hsuang, [12]Joe L Wiemels, [13]Alexander R. Pico, [14]Ivan Smirnov, [15]Annette M Molinaro, ... [Full author list] | Neuro-Oncology [curation] | DOI: 10.1093/NEUONC/NOT051
PubMed: 23733245 | diagnosis [curation] | 2013-06-03 |
| Cytoscape app store | [1]Samad Lotia, [2]Jason Montojo, [3]Yue Dong, [4]Gary D. Bader, [5]Alexander R. Pico [Full author list] | Bioinformatics [curation] | DOI: 10.1093/BIOINFORMATICS/BTT138
PubMed: 23595664 | Cytoscape [curation] | 2013-04-16 |
| Inherited variant on chromosome 11q23 increases susceptibility to IDH-mutated but not IDH-normal gliomas regardless of grade or histology | [1]Terri Rice, [2]Shichun Zheng, [3]Paul A Decker, [4]Kyle M Walsh, [5]Paige Bracci, [6]Yuanyuan Xiao, [7]Lucie S McCoy, [8]Ivan Smirnov, [9]Joseph S Patoka, [10]Helen M Hansen, ..., [12]Joe L Wiemels, [13]Tarik Tihan, [14]Alexander R. Pico, [15]Michael D Prados, [16]Susan M Chang, ... [Full author list] | Neuro-Oncology [curation] | DOI: 10.1093/NEUONC/NOS324
PubMed: 23361564 | | 2013-01-29 |
| Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies | [1]Kyle M Walsh, [2]Erik Anderson, [3]Helen M Hansen, [4]Paul A Decker, [5]Matt L Kosel, [6]Thomas Kollmeyer, [7]Terri Rice, [8]Shichun Zheng, [9]Yuanyuan Xiao, [10]Jeffrey S Chang, ..., [12]Paige M Bracci, [13]Joe L Wiemels, [14]Alexander R. Pico, [15]Ivan Smirnov, [16]Daniel H Lachance, ... [Full author list] | Genetic Epidemiology [curation] | DOI: 10.1002/GEPI.21707
PubMed: 23280628 | genome-wide association study [curation] | 2012-12-31 |
| A travel guide to Cytoscape plugins | [1]Rintaro Saito, [2]Michael E Smoot, [3]Keiichiro Ono, [4]Johannes Ruscheinski, [5]Peng-Liang Wang, [6]Samad Lotia, [7]Alexander R. Pico, [8]Gary D. Bader, [9]Trey Ideker [Full author list] | Nature Methods [curation] | DOI: 10.1038/NMETH.2212
PubMed: 23132118 | Cytoscape [curation] | 2012-11-06 |
| Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage | [1]Joseph A Wamstad, [2]Jeffrey M Alexander, [3]Rebecca M Truty, [4]Avanti Shrikumar, [5]Fugen Li, [6]Kirsten E Eilertson, [7]Huiming Ding, [8]John N Wylie, [9]Alexander R. Pico, [10]John A Capra, [11]Genevieve Erwin, [12]Steven J Kattman, [13]Gordon M. Keller, [14]Deepak Srivastava, [15]Stuart S Levine, [16]Katherine Pollard, [17]Alisha K Holloway, [18]Laurie A. Boyer, [19]Benoit G. Bruneau [Full author list] | Cell [curation] | DOI: 10.1016/J.CELL.2012.07.035
PubMed: 22981692 | | 2012-09-12 |
| A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation | [1]Robert B Jenkins, [2]Yuanyuan Xiao, [3]Hugues Sicotte, [4]Paul A Decker, [5]Thomas M Kollmeyer, [6]Helen M Hansen, [7]Matthew L Kosel, [8]Shichun Zheng, [9]Kyle M Walsh, [10]Terri Rice, ..., [16]Joe L Wiemels, [17]Tarik Tihan, [18]Alexander R. Pico, [19]Michael D Prados, [20]Susan M Chang, ... [Full author list] | Nature Genetics [curation] | DOI: 10.1038/NG.2388
PubMed: 22922872 | oligodendrocyte [curation] | 2012-08-26 |
| GO-Elite: a flexible solution for pathway and ontology over-representation | [1]Alexander C Zambon, [2]Stan Gaj, [2-Q55408105]Stan Gaj, [3]Isaac Ho, [4]Kristina Hanspers, [5]Karen Vranizan, [6]Chris T. Evelo, [7]Bruce R Conklin, [8]Alexander R. Pico, [9]Nathan Salomonis [Full author list] | Bioinformatics [curation] | DOI: 10.1093/BIOINFORMATICS/BTS366
PubMed: 22743224 | ontology [curation] | 2012-06-27 |
| Mosaic: making biological sense of complex networks | [1]Chao Zhang, [2]Kristina Hanspers, [3]Allan Kuchinsky, [4]Nathan Salomonis, [5]Dong Xu, [6]Alexander R. Pico [Full author list] | Bioinformatics [curation] | DOI: 10.1093/BIOINFORMATICS/BTS278
PubMed: 22576176 | complex network [curation] | 2012-05-09 |
| Erratum: Corrigendum: The BioPAX community standard for pathway data sharing | [1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [62]David Merberg, [63]Victoria Petri, [64]Alexander R. Pico, [65]Dean Ravenscroft, [66]Liya Ren, ... [Full author list] | Nature Biotechnology [curation] | DOI: 10.1038/NBT0412-365C
| data sharing [curation]; The BioPAX community standard for pathway data sharing [curation] | 2012-04-01 |
| WikiPathways: building research communities on biological pathways | [1]Thomas Kelder, [2]Martijn P van Iersel, [3]Kristina Hanspers, [4]Martina Summer-Kutmon, [5]Bruce R Conklin, [6]Chris T. Evelo, [7]Alexander R. Pico [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKR1074
PubMed: 22096230 | community [curation]; WikiPathways [curation] | 2012-01-01 |
| Erratum: Corrigendum: The BioPAX community standard for pathway data sharing | [1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [62]David Merberg, [63]Victoria Petri, [64]Alexander R. Pico, [65]Dean Ravenscroft, [66]Liya Ren, ... [Full author list] | Nature Biotechnology [curation] | DOI: 10.1038/NBT1210-1308C
| data sharing [curation]; The BioPAX community standard for pathway data sharing [curation] | 2010-12-07 |
| The BioPAX community standard for pathway data sharing | [1]Emek Demir, [2]Michael P Cary, [3]Suzanne Paley, [4]Ken Fukuda, [5]Christian Lemer, [6]Imre Vastrik, [7]Guanming Wu, [8]Peter D'Eustachio, [9]Carl Schaefer, [10]Joanne Luciano, ..., [63]David Merberg, [64]Victoria Petri, [65]Alexander R. Pico, [66]Dean Ravenscroft, [67]Liya Ren, ... [Full author list] | Nature Biotechnology [curation] | DOI: 10.1038/NBT.1666
PubMed: 20829833 | biotechnology [curation]; microbiology [curation]; BioPAX [curation]; data sharing [curation] | 2010-09-01 |
| Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets | [1]Thomas Kelder, [1-Q28865045]Thomas Kelder, [2]Bruce R Conklin, [3]Chris T. Evelo, [4]Alexander R. Pico [Full author list] | PLOS Biology [curation] | DOI: 10.1371/JOURNAL.PBIO.1000472
PubMed: 20824171 | data set [curation]; pathway analysis [curation] | 2010-08-31 |
| Structure of the human BK channel Ca2+-activation apparatus at 3.0 A resolution | [1]Peng Yuan, [2]Manuel D Leonetti, [3]Alexander R. Pico, [4]Yichun Hsiung, [5]Roderick MacKinnon [Full author list] | Science [curation] | DOI: 10.1126/SCIENCE.1190414
PubMed: 20508092 | | 2010-07-09 |
| Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation | [1]Nathan Salomonis, [2]Christopher R Schlieve, [3]Laura Pereira, [4]Christine Wahlquist, [5]Alexandre Colas, [6]Alexander C Zambon, [7]Karen Vranizan, [8]Matthew J Spindler, [9]Alexander R. Pico, [10]Melissa S Cline, [11]Tyson A Clark, [12]Alan Williams, [13]John E Blume, [14]Eva Samal, [15]Mark Mercola, [16]Bradley J Merrill, [17]Bruce R Conklin [Full author list] | Proceedings of the National Academy of Sciences of the United States of America [curation] | DOI: 10.1073/PNAS.0912260107
PubMed: 20498046 | pluripotency [curation]; alternative mRNA splicing, via spliceosome [curation] | 2010-05-24 |
| The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services | [1]Martijn P van Iersel, [2]Alexander R. Pico, [3]Thomas Kelder, [4]Jianjiong Gao, [5]Isaac Ho, [6]Kristina Hanspers, [7]Bruce R Conklin, [8]Chris T. Evelo [Full author list] | BMC Bioinformatics [curation] | DOI: 10.1186/1471-2105-11-5
PubMed: 20047655 | BridgeDb Webservices [curation]; BridgeDb [curation] | 2010-01-04 |
| Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors | [1]Nathan Salomonis, [2]Brandon Nelson, [3]Karen Vranizan, [4]Alexander R. Pico, [5]Kristina Hanspers, [6]Allan Kuchinsky, [7]Linda Ta, [8]Mark Mercola, [9]Bruce R Conklin [Full author list] | PLOS Computational Biology [curation] | DOI: 10.1371/JOURNAL.PCBI.1000553
PubMed: 19893621 | alternative mRNA splicing, via spliceosome [curation]; human embryonic stem cell [curation] | 2009-11-06 |
| Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility | [1]Margaret Wrensch, [2]Robert B Jenkins, [3]Jeffrey S Chang, [4]Ru-Fang Yeh, [5]Yuanyuan Xiao, [6]Paul A Decker, [7]Karla V Ballman, [8]Mitchel Berger, [9]Jan C Buckner, [10]Susan Chang, ..., [17]Brian P O'Neill, [18]Joe Patoka, [19]Alexander R. Pico, [20]Michael D Prados, [21]Charles Quesenberry, ... [Full author list] | Nature Genetics [curation] | DOI: 10.1038/NG.408
PubMed: 19578366 | | 2009-08-01 |
| Mining biological pathways using WikiPathways web services | [1]Thomas Kelder, [2]Alexander R. Pico, [3]Kristina Hanspers, [4]Martijn P van Iersel, [5]Chris T. Evelo, [6]Bruce R Conklin [Full author list] | PLOS One [curation] | DOI: 10.1371/JOURNAL.PONE.0006447
PubMed: 19649250 | web service [curation]; WikiPathways [curation] | 2009-07-30 |
| SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system | [1]Alexander R. Pico, [2]Ivan V Smirnov, [3]Jeffrey S Chang, [4]Ru-Fang Yeh, [5]Joseph L Wiemels, [6]John K Wiencke, [7]Tarik Tihan, [8]Bruce R Conklin, [9]Margaret Wrensch [Full author list] | Nucleic Acids Research [curation] | DOI: 10.1093/NAR/GKN756
PubMed: 18984625 | single-nucleotide polymorphism [curation]; prioritization [curation] | 2008-11-04 |
| The public road to high-quality curated biological pathways | [1]Michiel E. Adriaens, [2]Magali Jaillard, [3]Andra Waagmeester, [4]Susan Coort, [5]Alexander R. Pico, [6]Chris T. Evelo [Full author list] | Drug Discovery Today [curation] | DOI: 10.1016/J.DRUDIS.2008.06.013
PubMed: 18652912 | drug discovery [curation] | 2008-10-01 |
| WikiPathways: pathway editing for the people | [1]Alexander R. Pico, [2]Thomas Kelder, [3]Martijn P van Iersel, [4]Kristina Hanspers, [5]Bruce R Conklin, [6]Chris T. Evelo [Full author list] | PLOS Biology [curation] | DOI: 10.1371/JOURNAL.PBIO.0060184
PubMed: 18651794 | WikiPathways [curation]; Graphical Pathway Markup Language [curation] | 2008-07-22 |
| The emerging world of wikis | [1]James C Hu, [2]Rodolfo Aramayo, [3]Dan Bolser, [4]Tyrrell Conway, [5]Christine G Elsik, [6]Michael Gribskov, [7]Thomas Kelder, [11]Deborah A Siegele, [12]Barry L Wanner, [13]Roy D Welch, [7-Q28865045]Thomas Kelder, [8]Daisuke Kihara, [9]Tom Knight, [10]Alexander R. Pico [Full author list] | Science [curation] | DOI: 10.1126/SCIENCE.320.5881.1289B
PubMed: 18535227 | | 2008-06-06 |
| Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests | [1]Jeffrey S Chang, [2]Ru-Fang Yeh, [3]John K Wiencke, [4]Joseph L Wiemels, [5]Ivan Smirnov, [6]Alexander R. Pico, [7]Tarik Tihan, [8]Joe Patoka, [9]Rei Miike, [10]Jennette D Sison, [11]Terri Rice, [12]Margaret R Wrensch [Full author list] | Cancer Epidemiology, Biomarkers & Prevention [curation] | DOI: 10.1158/1055-9965.EPI-07-2830
PubMed: 18559551 | random forest [curation]; glioblastoma [curation]; single-nucleotide polymorphism [curation]; pathway analysis [curation] | 2008-06-01 |
| An Introduction to Pathway Analysis with GenMAPP | [1]Kristina Hanspers, [2]Alexander R. Pico, [3]Nathan Salomonis, [4]Alexander C Zambon, [5]Karen Vranizan, [6]Steven C. Lawlor, [7]Kam D Dahlquist, [8]Scott W. Doniger, [9]Bruce R Conklin [Full author list] | | DOI: 10.1038/PID.2008.1
| pathway analysis [curation] | 2008-04-08 |
| Presenting and exploring biological pathways with PathVisio | [1]Martijn P van Iersel, [2]Thomas Kelder, [3]Alexander R. Pico, [4]Kristina Hanspers, [5]Susan Coort, [6]Bruce R Conklin, [7]Chris T. Evelo [Full author list] | BMC Bioinformatics [curation] | DOI: 10.1186/1471-2105-9-399
PubMed: 18817533 | biological pathway [curation]; PathVisio [curation]; Graphical Pathway Markup Language [curation] | 2008-01-01 |
| GenMAPP 2: new features and resources for pathway analysis | [1]Nathan Salomonis, [2]Kristina Hanspers, [3]Alexander C Zambon, [4]Karen Vranizan, [5]Steven C. Lawlor, [6]Kam D Dahlquist, [7]Scott W. Doniger, [8]Josh Stuart, [9]Bruce R Conklin, [10]Alexander R. Pico [Full author list] | BMC Bioinformatics [curation] | DOI: 10.1186/1471-2105-8-217
PubMed: 17588266 | pathway analysis [curation] | 2007-06-24 |
| Integration of biological networks and gene expression data using Cytoscape | [1]Melissa S Cline, [2]Michael Smoot, [3]Ethan Cerami, [4]Allan Kuchinsky, [5]Nerius Landys, [6]Christopher T. Workman, [7]Rowan Christmas, [8]Iliana Avila-Campilo, [9]Michael Creech, [10]Benjamin Gross, ..., [18]Keiichiro Ono, [19]Vuk Pavlovic, [20]Alexander R. Pico, [21]Aditya Vailaya, [22]Peng-Liang Wang, ... [Full author list] | Nature Protocols [curation] | DOI: 10.1038/NPROT.2007.324
PubMed: 17947979 | Cytoscape [curation]; gene expression data [curation] | 2007-01-01 |
| Structure of the RCK domain from the E. coli K+ channel and demonstration of its presence in the human BK channel | [1]Y Jiang, [2]Alexander R. Pico, [3]Martine Cadene, [4]B T Chait, [5]Roderick MacKinnon [Full author list] | Neuron [curation] | DOI: 10.1016/S0896-6273(01)00236-7
PubMed: 11301020 | Escherichia coli [curation] | 2001-03-01 |
| Local cortical injections of glutamate and noradrenaline alter high-frequency (245Hz) neuronal activity in rat cortex | [1]Brent A Field, [2]Alexander R. Pico, [3]Richard T Marrocco [Full author list] | Neurocomputing [curation] | DOI: 10.1016/S0925-2312(99)00069-7
| norepinephrine [curation] | 1999-06-01 |
| Crystal structure of Hck in complex with a Src family-selective tyrosine kinase inhibitor | [1]T Schindler, [2]F Sicheri, [3]Alexander R. Pico, [4]A Gazit, [5]A Levitzki, [6]J Kuriyan [Full author list] | Molecular Cell [curation] | DOI: 10.1016/S1097-2765(00)80357-3
PubMed: 10360180 | crystal structure [curation] | 1999-05-01 |
| Intramolecular regulatory interactions in the Src family kinase Hck probed by mutagenesis of a conserved tryptophan residue | [1]M LaFevre-Bernt, [2]F Sicheri, [3]Alexander R. Pico, [4]M Porter, [5]J Kuriyan, [6]W T Miller [Full author list] | Journal of Biological Chemistry [curation] | DOI: 10.1074/JBC.273.48.32129
PubMed: 9822689 | | 1998-11-01 |