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Raja Mazumder
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2020 – today
- 2024
- [j34]Karina Martinez
, Jon Agirre
Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. Database J. Biol. Databases Curation 2024 (2024) - [i2]Sean Kim, Raja Mazumder:
Enhancing Scientific Reproducibility Through Automated BioCompute Object Creation Using Retrieval-Augmented Generation from Publications. CoRR abs/2409.15076 (2024) - 2022
- [c4]Michelle G. Giglio, Suvarna Nadendla, Arthur Brady, Amanda Charbonneau, Karl Czajkowski, Jeremy Yang, Tom Gillespie, Philippe Rocca-Serra, Jeffrey S. Grethe, Raja Mazumder, Bernard de Bono, Jonathan C. Silverstein, Daniel Clark, Mark A. Musen, Owen White:
Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem. ICBO 2022: 1-7 - 2021
- [j33]John Torcivia-Rodriguez
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. Briefings Bioinform. 22(3) (2021) - [j32]Nikhita Gogate
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Briefings Bioinform. 22(6) (2021) - [j31]Janisha A. Patel
Bioinformatics tools developed to support BioCompute Objects. Database J. Biol. Databases Curation 2021 (2021) - [c3]Daniel Lyman, Darren A. Natale, Lynn M. Schriml, Kriston Anton, Daniel C. Crichton, Raja Mazumder:
Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. ICBO 2021: 99-103 - 2020
- [j30]Robel Y. Kahsay, Jeet Vora, Rahi Navelkar
GlyGen data model and processing workflow. Bioinform. 36(12): 3941-3943 (2020)
2010 – 2019
- 2019
- [j29]Baekdoo Kim, Thahmina Ali, Changsu Dong, Carlos Lijeron, Raja Mazumder
miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines. J. Comput. Biol. 26(3): 280-284 (2019) - [c2]Amanda Bell, Raja Mazumder, Daniel J. Crichton, Vijay K. Shanker, Frédéric B. Bastian, Hayley Dingerdissen, Samir Gupta, Evan Holmes, Robel Y. Kahsay, Heather L. Kincaid, A. S. M. Ashique Mahmood, Marc Robinson-Rechavi, Stephanie S. Singleton:
OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery. AMIA 2019 - 2018
- [j28]Samir Gupta
DEXTER: Disease-Expression Relation Extraction from Text. Database J. Biol. Databases Curation 2018: bay045 (2018) - [j27]Yu Hu
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. Comput. Biol. Medicine 103: 183-197 (2018) - [j26]Hayley Dingerdissen
BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. Nucleic Acids Res. 46(Database-Issue): D1128-D1136 (2018) - 2017
- [j25]Scott Goldweber, Jamal Theodore, John Torcivia-Rodriguez
Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices. IEEE ACM Trans. Comput. Biol. Bioinform. 14(2): 498-500 (2017) - 2016
- [j24]Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William J. Faison, Scott Goldweber, Anton Golikov, Naila Gulzar
High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. Database J. Biol. Databases Curation 2016 (2016) - [j23]Chuming Chen
Computational clustering for viral reference proteomes. Bioinform. 32(13): 2041-2043 (2016) - 2015
- [j22]Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar
BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. Database J. Biol. Databases Curation 2015 (2015) - [j21]Tsung-Jung Wu, Lynn M. Schriml
Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. Database J. Biol. Databases Curation 2015 (2015) - [i1]Priti Kumari, Raja Mazumder
Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. F1000Research 4: 20 (2015) - 2014
- [j20]Tsung-Jung Wu, Amirhossein Shamsaddini
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). Database J. Biol. Databases Curation 2014 (2014) - [j19]Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S. Almeida, William J. Faison, Mona Motwani
Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. BMC Bioinform. 15: 28 (2014) - 2013
- [j18]Phuc Vinh Nguyen Lam, Radoslav Goldman, Konstantinos Karagiannis
Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. Genom. Proteom. Bioinform. 11(2): 96-104 (2013) - [j17]Konstantinos Karagiannis
SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. Genom. Proteom. Bioinform. 11(2): 122-126 (2013) - 2012
- [j16]Pascale Gaudet, Cecilia N. Arighi
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation 2012 (2012) - [j15]Pascale Gaudet, Raja Mazumder
Biocuration Virtual Issue 2012. Database J. Biol. Databases Curation 2012 (2012) - 2011
- [j14]Hongzhan Huang, Peter B. McGarvey
A comprehensive protein-centric ID mapping service for molecular data integration. Bioinform. 27(8): 1190-1191 (2011)
2000 – 2009
- 2008
- [j13]C. Zhang, Oswald Crasta, Stephen A. Cammer, Rebecca Will, Ron Kenyon, Daniel E. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, Tian Xue, Y. Zhang, M. Moore, Peter B. McGarvey, Hongzhan Huang, Yongxing Chen, J. Zhang, Raja Mazumder
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. 36(Database-Issue): 884-891 (2008) - [j12]Raja Mazumder
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function. PLoS Comput. Biol. 4(9) (2008) - 2007
- [j11]Baris E. Suzek
UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinform. 23(10): 1282-1288 (2007) - 2006
- [j10]Cathy H. Wu
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34(Database-Issue): 187-191 (2006) - 2005
- [j9]Raja Mazumder
Computational identification of strain-, species- and genus-specific proteins. BMC Bioinform. 6: 279 (2005) - 2004
- [j8]Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder
GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes. BMC Bioinform. 5: 52 (2004) - [j7]Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, Cholanayakanahalli R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder
PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res. 32(Database-Issue): 112-114 (2004) - 2003
- [j6]Roman L. Tatusov, Natalie D. Fedorova, John D. Jackson, Aviva R. Jacobs, Boris Kiryutin, Eugene V. Koonin, Dmitri M. Krylov, Raja Mazumder
The COG database: an updated version includes eukaryotes. BMC Bioinform. 4: 41 (2003) - [j5]Aron Marchler-Bauer
CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31(1): 383-387 (2003) - [j4]Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31(1): 474-477 (2003) - 2002
- [j3]Nikhat Zafar, Raja Mazumder
CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinform. 3: 12 (2002) - [j2]Nikhat Zafar, Raja Mazumder, Donald Seto:
Application of global computational tools GeneOrder and CoreGenes to the comparative analyses of chordopoxvirus genomes. Inf. Sci. 146(1-4): 127-135 (2002) - [c1]Nikhat Zafar, Raja Mazumder, Donald Seto:
Application of Global Computational Tools GeneOrder and OrthologLocator to the Comparative Analyses of Chordopoxvirus Genomes. JCIS 2002: 1186-1192 - 2001
- [j1]Raja Mazumder
GeneOrder: comparing the order of genes in small genomes. Bioinform. 17(1): 162-166 (2001)
Coauthor Index
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