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ORCIDRaja Mazumder
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2020 – today
- 2024
[j34]Karina Martinez
, Jon Agirre, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Cecilia N. Arighi, Kristian B. Axelsen, Evan Bolton, Emily Bordeleau, Nathan J. Edwards, Elisa Fadda, Ten Feizi, Catherine A. Hayes, Callum M. Ives, Hiren J. Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frédérique Lisacek, Yan Liu, Thomas Lütteke, Junfeng Ma, Adnan Malik, Maria Jesus Martin, Akul Y. Mehta, Sriram Neelamegham, Kalpana Panneerselvam, René Ranzinger, Sylvie Ricard-Blum, Gaoussou Sanou, Vijay Shanker, Paul D. Thomas, Michael Tiemeyer, James Urban, Randi Vita, Jeet Vora, Yasunori Yamamoto, Raja Mazumder:
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) - 2021
- [j33]John Torcivia-Rodriguez, Raja Mazumder:
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. Briefings Bioinform. 22(3) (2021) - [j32]Nikhita Gogate, Daniel Lyman, Amanda Bell, Edmund Cauley, Keith A. Crandall, Ashia Joseph, Robel Y. Kahsay, Darren A. Natale, Lynn M. Schriml, Sabyasach Sen, Raja Mazumder:
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. Briefings Bioinform. 22(6) (2021) - [j31]Janisha A. Patel, Dennis A. Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Y. Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney:
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, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder:
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, Claudia Wultsch, Konstantinos Krampis:
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, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker:
DEXTER: Disease-Expression Relation Extraction from Text. Database J. Biol. Databases Curation 2018: bay045 (2018) - [j27]Yu Hu, Hayley Dingerdissen, Samir Gupta, Robel Y. Kahsay, K. Vijay-Shanker, Quan Wan, Cheng Yan, Raja Mazumder:
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. Comput. Biol. Medicine 103: 183-197 (2018) - [j26]Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Y. Kahsay:
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, Vahan Simonyan, Raja Mazumder:
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, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan, Alexey Pschenichnov, Alexandre Rostovtsev, Luis V. Santana-Quintero, Krista Smith, Elaine E. Thompson, Valery Tkachenko, John Torcivia-Rodriguez, Alin Voskanian, Quan Wan, Jing Wang, Tsung-Jung Wu, Carolyn Wilson, Raja Mazumder:
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, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu:
Computational clustering for viral reference proteomes. Bioinform. 32(13): 2041-2043 (2016) - 2015
- [j22]Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder:
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, Qingrong Chen, Maureen Colbert, Daniel J. Crichton, Richard P. Finney, Ying Hu, Warren A. Kibbe, Heather Kincaid, Daoud M. Meerzaman, Elvira Mitraka, Yang Pan, Krista Smith, Sudhir Srivastava, Sari Ward, Cheng Yan, Raja Mazumder:
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, Vahan Simonyan, Konstantinos Krampis:
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, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder:
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, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder:
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, Tejas Narsule, Vahan Simonyan, Valerii Soika, Raja Mazumder:
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, Vahan Simonyan, Raja Mazumder:
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, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder:
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, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu:
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, Cathy H. Wu, Bruno W. S. Sobral:
An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. Nucleic Acids Res. 36(Database-Issue): 884-891 (2008) - [j12]Raja Mazumder, Sona Vasudevan:
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function. PLoS Comput. Biol. 4(9) (2008) - 2007
- [j11]Baris E. Suzek, Hongzhan Huang, Peter B. McGarvey, Raja Mazumder, Cathy H. Wu:
UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinform. 23(10): 1282-1288 (2007) - 2006
- [j10]Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek:
The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34(Database-Issue): 187-191 (2006) - 2005
- [j9]Raja Mazumder, Darren A. Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H. Wu:
Computational identification of strain-, species- and genus-specific proteins. BMC Bioinform. 6: 279 (2005) - 2004
- [j8]Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto:
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, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, Winona C. Barker:
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, Sergei L. Mekhedov, Anastasia N. Nikolskaya, B. Sridhar Rao, Sergei Smirnov, Alexander V. Sverdlov, Sona Vasudevan, Yuri I. Wolf, Jodie J. Yin, Darren A. Natale:
The COG database: an updated version includes eukaryotes. BMC Bioinform. 4: 41 (2003) - [j5]Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
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, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant:
MMDB: Entrez's 3D-structure database. Nucleic Acids Res. 31(1): 474-477 (2003) - 2002
- [j3]Nikhat Zafar, Raja Mazumder, Donald Seto:
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, Ashok S. Kolaskar, Donald Seto:
GeneOrder: comparing the order of genes in small genomes. Bioinform. 17(1): 162-166 (2001)
Coauthor Index
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