Raja Mazumder

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 14

Top Topics

Gene Expression

Cancer Patients

Top Venues

Database J. Biol. Databases Curation

Briefings Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

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)
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)
John Torcivia-Rodriguez, Raja Mazumder
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. Briefings Bioinform. 22 (3) (2021)
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)
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)
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) (2020)
Baekdoo Kim, Thahmina Ali, Changsu Dong, Carlos Lijeron, Raja Mazumder, Claudia Wultsch, Konstantinos Krampis
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) (2019)
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)
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 (2018)
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) (2018)
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 (2018)
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) (2017)
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)
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) (2016)
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)
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)
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 (2015)
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 (2014)
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)
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) (2013)
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) (2013)
Pascale Gaudet, Raja Mazumder
Biocuration Virtual Issue 2012. Database J. Biol. Databases Curation 2012 (2012)
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)
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) (2011)
Raja Mazumder, Sona Vasudevan
Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function. PLoS Comput. Biol. 4 (9) (2008)
C. Zhang, Oswald Crasta, S. 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) (2008)
Baris E. Suzek, Hongzhan Huang, Peter B. McGarvey, Raja Mazumder, Cathy H. Wu
UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinform. 23 (10) (2007)
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) (2006)
Raja Mazumder, Darren A. Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H. Wu
Computational identification of strain-, species- and genus-specific proteins. BMC Bioinform. 6 (2005)
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 (2004)
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) (2004)
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 (2003)
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) (2003)
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) (2003)
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) (2002)
Nikhat Zafar, Raja Mazumder, Donald Seto
Application of Global Computational Tools GeneOrder and OrthologLocator to the Comparative Analyses of Chordopoxvirus Genomes. JCIS (2002)
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 (2002)
Raja Mazumder, Ashok S. Kolaskar, Donald Seto
GeneOrder: comparing the order of genes in small genomes. Bioinform. 17 (1) (2001)