GeneOrder: comparing the order of genes in small genomes. - Raja Mazumder; Ashok S. Kolaskar; Donald Seto (Bioinform., 2001)

Application of Global Computational Tools GeneOrder and OrthologLocator to the Comparative Analyses of Chordopoxvirus Genomes. - Nikhat Zafar; Raja Mazumder; Donald Seto (JCIS, 2002)

CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes. - Nikhat Zafar; Raja Mazumder; Donald Seto (BMC Bioinform., 2002)

Application of global computational tools GeneOrder and CoreGenes to the comparative analyses of chordopoxvirus genomes. - Nikhat Zafar; Raja Mazumder; Donald Seto (Inf. Sci., 2002)

The COG database: an updated version includes eukaryotes. - 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; et al. (BMC Bioinform., 2003)

MMDB: Entrez's 3D-structure database. - Jie Chen 039; 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 002; et al. (Nucleic Acids Res., 2003)

CDD: a curated Entrez database of conserved domain alignments. - 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 002; et al. (Nucleic Acids Res., 2003)

GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes. - Srikanth Celamkoti; Sashidhara Kundeti; Anjan Purkayastha; Raja Mazumder; Charles Buck; Donald Seto (BMC Bioinform., 2004)

PIRSF: family classification system at the Protein Information Resource. - 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; et al. (Nucleic Acids Res., 2004)

Computational identification of strain-, species- and genus-specific proteins. - Raja Mazumder; Darren A. Natale; Sudhir Murthy; Rathi Thiagarajan; Cathy H. Wu (BMC Bioinform., 2005)

The Universal Protein Resource (UniProt): an expanding universe of protein information. - 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; et al. (Nucleic Acids Res., 2006)

UniRef: comprehensive and non-redundant UniProt reference clusters. - Baris E. Suzek; Hongzhan Huang; Peter B. McGarvey; Raja Mazumder; Cathy H. Wu (Bioinform., 2007)

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data. - 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; et al. (Nucleic Acids Res., 2008)

Structure-Guided Comparative Analysis of Proteins: Principles, Tools, and Applications for Predicting Function. - Raja Mazumder; Sona Vasudevan (PLoS Comput. Biol., 2008)

A comprehensive protein-centric ID mapping service for molecular data integration. - Hongzhan Huang; Peter B. McGarvey; Baris E. Suzek; Raja Mazumder; Jian Zhang 051; Yongxing Chen; Cathy H. Wu (Bioinform., 2011)

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. - 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; et al. (Database J. Biol. Databases Curation, 2012)

Biocuration Virtual Issue 2012. - Pascale Gaudet; Raja Mazumder (Database J. Biol. Databases Curation, 2012)

SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways. - Konstantinos Karagiannis; Vahan Simonyan; Raja Mazumder (Genom. Proteom. Bioinform., 2013)

Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes. - Phuc Vinh Nguyen Lam; Radoslav Goldman; Konstantinos Karagiannis; Tejas Narsule; Vahan Simonyan; Valerii Soika; Raja Mazumder (Genom. Proteom. Bioinform., 2013)

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). - Tsung-Jung Wu; Amirhossein Shamsaddini; Yang Pan; Krista Smith; Daniel J. Crichton; Vahan Simonyan; Raja Mazumder (Database J. Biol. Databases Curation, 2014)

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data. - Charles Cole 002; Konstantinos Krampis; Konstantinos Karagiannis; Jonas S. Almeida; William J. Faison; Mona Motwani; Quan Wan; Anton Golikov; Yang Pan; Vahan Simonyan; Raja Mazumder (BMC Bioinform., 2014)

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. - Quan Wan; Hayley Dingerdissen; Yu Fan; Naila Gulzar; Yang Pan; Tsung-Jung Wu; Cheng Yan; Haichen Zhang; Raja Mazumder (Database J. Biol. Databases Curation, 2015)

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis. - 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; et al. (Database J. Biol. Databases Curation, 2015)

Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly. - Priti Kumari 005; Raja Mazumder; Vahan Simonyan; Konstantinos Krampis (F1000Research, 2015)

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. - 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; et al. (Database J. Biol. Databases Curation, 2016)

Computational clustering for viral reference proteomes. - Chuming Chen; Hongzhan Huang; Raja Mazumder; Darren A. Natale; Peter B. McGarvey; Jian Zhang 051; Shawn W. Polson; Yuqi Wang; Cathy H. Wu (Bioinform., 2016)

Pubcast and Genecast: Browsing and Exploring Publications and Associated Curated Content in Biology Through Mobile Devices. - Scott Goldweber; Jamal Theodore; John Torcivia-Rodriguez; Vahan Simonyan; Raja Mazumder (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

DEXTER: Disease-Expression Relation Extraction from Text. - Samir Gupta; Hayley Dingerdissen; Karen E. Ross; Yu Hu 015; Cathy H. Wu; Raja Mazumder; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2018)

Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. - Yu Hu 015; Hayley Dingerdissen; Samir Gupta; Robel Y. Kahsay; K. Vijay-Shanker; Quan Wan; Cheng Yan; Raja Mazumder (Comput. Biol. Medicine, 2018)

BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery. - Hayley Dingerdissen; John Torcivia-Rodriguez; Yu Hu 015; Ting-Chia Chang; Raja Mazumder; Robel Y. Kahsay (Nucleic Acids Res., 2018)

OncoMX: an Integrated Cancer Mutation and Expression Knowledgebase for Biomarker Evaluation and Discovery. - 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; et al. (AMIA, 2019)

miCloud: A Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines. - Baekdoo Kim; Thahmina Ali; Changsu Dong; Carlos Lijeron; Raja Mazumder; Claudia Wultsch; Konstantinos Krampis (J. Comput. Biol., 2019)

GlyGen data model and processing workflow. - 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; et al. (Bioinform., 2020)

Analysis of Biomarker Data Towards Development of a Molecular Biomarker Ontology. - Daniel Lyman; Darren A. Natale; Lynn M. Schriml; Kriston Anton; Daniel C. Crichton; Raja Mazumder (ICBO, 2021)

COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. - 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 (Briefings Bioinform., 2021)

Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. - John Torcivia-Rodriguez; Raja Mazumder (Briefings Bioinform., 2021)

Bioinformatics tools developed to support BioCompute Objects. - Janisha A. Patel; Dennis A. Dean; Charles Hadley King; Nan Xiao 002; Soner Koc; Ekaterina Minina; Anton Golikov; Phillip Brooks; Robel Y. Kahsay; Rahi Navelkar; Manisha Ray; Dave Roberson; et al. (Database J. Biol. Databases Curation, 2021)

Data Harmonization through Use of Community Standards in the Common Fund Data Ecosystem. - 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; et al. (ICBO, 2022)

Enhancing Scientific Reproducibility Through Automated BioCompute Object Creation Using Retrieval-Augmented Generation from Publications. - Sean Kim; Raja Mazumder (CoRR, 2024)

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. - 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; et al. (Database J. Biol. Databases Curation, 2024)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - Daniel J. B. Clarke; John Erol Evangelista; Zhuorui Xie; Giacomo B. Marino; Anna I. Byrd; Mano Ram Maurya; Sumana Srinivasan; Keyang Yu; Varduhi Petrosyan; Matthew E. Roth; Miroslav Milinkov; Charles Hadley King; et al. (PLoS Comput. Biol., 2025)