HARMONY: a server for the assessment of protein structures. - Ganesan Pugalenthi; Khader Shameer; Narayanaswamy Srinivasan; Ramanathan Sowdhamini (Nucleic Acids Res., 2006)

PURE: A webserver for the prediction of domains in unassigned regions in proteins. - Chilamakuri Chandra Sekhar Reddy; Khader Shameer; Bernard O. Offmann; Ramanathan Sowdhamini (BMC Bioinform., 2008)

3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach. - Khader Shameer; Paramasivam Nagarajan; Kumar Gaurav; Ramanathan Sowdhamini (BioData Min., 2009)

A Sequence Data Mining Protocol to Identify Best Representative Sequence for Protein Domain Families. - V. S. Gowri; Khader Shameer; Chilamakuri Chandra Sekhar Reddy; Prashant Shingate; Ramanathan Sowdhamini (ICDM Workshops, 2010)

PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. - Khader Shameer; Lalima L. Madan; Shivamurthy Veeranna; Balasubramanian Gopal; Ramanathan Sowdhamini (BMC Bioinform., 2010)

HORI: a web server to compute Higher Order Residue Interactions in protein structures. - Pandurangan Sundaramurthy; Khader Shameer; Raashi Sreenivasan; Sunita Gakkhar; Ramanathan Sowdhamini (BMC Bioinform., 2010)

Poster: HORIBALFRE: Higher Order Residue Interactions Based ALgorithm for Fold REcognition. - Pandurangan Sundaramurthy; Raashi Sreenivasan; Khader Shameer; Sunita Gakkhar; Ramanathan Sowdhamini (ICCABS, 2011)

3DSwap: curated knowledgebase of proteins involved in 3D domain swapping. - Khader Shameer; Prashant Shingate; S. C. P. Manjunath; M. Karthika; Ganesan Pugalenthi; Ramanathan Sowdhamini (Database J. Biol. Databases Curation, 2011)

Ten Simple Rules for Getting Help from Online Scientific Communities. - Giovanni Marco Dall'Olio; Jacopo Marino; Michael Schubert; Kevin L. Keys; Melanie I. Stefan; Colin S. Gillespie; Pierre Poulain; Khader Shameer; Robert Sugar; Brandon M. Invergo; Lars Juhl Jensen; Jaume Bertranpetit; et al. (PLoS Comput. Biol., 2011)

BioStar: An Online Question & Answer Resource for the Bioinformatics Community. - Laurence D. Parnell; Pierre Lindenbaum; Khader Shameer; Giovanni Marco Dall'Olio; Daniel C. Swan; Lars Juhl Jensen; Simon J. Cockell; Brent S. Pedersen; Mary E. Mangan; Christopher A. Miller 002; István Albert (PLoS Comput. Biol., 2011)

Gene expression profiling of peripheral blood mononuclear cells in the setting of peripheral arterial disease. - Rizwan Masud; Khader Shameer; Aparna Dhar; Keyue Ding; Iftikhar J. Kullo (J. Clin. Bioinform., 2012)

Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. - Khader Shameer; Ramanathan Sowdhamini (J. Clin. Bioinform., 2012)

An Integrative Pipeline for Multi-Modal Discovery of Disease Relationships. - Benjamin S. Glicksberg; Li Li 062; Wei-Yi Cheng; Khader Shameer; Jörg Hakenberg; Rafael Castellanos; Meng Ma; Lisong Shi; Hardik Shah; Joel T. Dudley; Rong Chen 006 (Pacific Symposium on Biocomputing, 2015)

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment. - Khader Shameer; Lokesh P. Tripathi; Krishna R. Kalari; Joel T. Dudley; Ramanathan Sowdhamini (Briefings Bioinform., 2016)

Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. - Benjamin S. Glicksberg; Li Li 062; Marcus A. Badgeley; Khader Shameer; Roman Kosoy; Noam D. Beckmann; Nam Pho; Jörg Hakenberg; Meng Ma; Kristin L. Ayers; Gabriel E. Hoffman; Shuyu Dan Li; et al. (Bioinform., 2016)

Predictive Modeling of Hospital Readmission Rates Using Electronic Medical Record-Wide Machine Learning: A Case-Study Using Mount Sinai Heart Failure Cohort. - Khader Shameer; Kipp W. Johnson; Alexandre Yahi; Riccardo Miotto; Li Li 062; Doran Ricks; Jebakumar Jebakaran; Patricia H. Kovatch; Partho P. Sengupta; Annetine Gelijns; Alan Moskovitz; Bruce Darrow; et al. (PSB, 2017)

Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. - Khader Shameer; Marcus A. Badgeley; Riccardo Miotto; Benjamin S. Glicksberg; Joseph W. Morgan; Joel T. Dudley (Briefings Bioinform., 2017)

An Electronic Phenotyping Algorithm for Automated Cohorting of Patients with Severe Acute Respiratory Distress Syndrome. - Abhinav Agrawal; Molly Stewart; Jamie S. Hirsch; John Chelico; Shameer Khader; Negin Hajizadeh (AMIA, 2018)

Unsupervised Learning of an Advanced Illness Cohort to Develop Patient Stratification Models. - Raj Brar; Shameer Khader; Abraham Saraya; Kevin Bock 002; Michael I. Oppenheim; John Chelico; Jamie S. Hirsch (AMIA, 2018)

MEWSCast: Predictive Forecasting of Modified Early Warning Scores for Preemptive Management of Clinical Acuity. - Jamie S. Hirsch; Raj Brar; Abraham Saraya; Kevin Bock 002; Michael I. Oppenheim; John Chelico; Shameer Khader (AMIA, 2018)

Discovering Drivers of Mortality in Severe Acute Respiratory Distress Syndrome: An Investigation using Machine Intelligence Methods. - Shameer Khader; Imroze Shaheen; Molly Stewart; Yalini Senathirajah; Jamie S. Hirsch; John Chelico; Negin Hajizadeh (AMIA, 2018)

Automated disease cohort selection using word embeddings from Electronic Health Records. - Benjamin S. Glicksberg; Riccardo Miotto; Kipp W. Johnson; Khader Shameer; Li Li 062; Rong Chen 006; Joel T. Dudley (PSB, 2018)

Causal inference on electronic health records to assess blood pressure treatment targets: An application of the parametric g formula. - Kipp W. Johnson; Benjamin S. Glicksberg; Rachel Hodos; Khader Shameer; Joel T. Dudley (PSB, 2018)

Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. - Khader Shameer; Benjamin S. Glicksberg; Rachel Hodos; Kipp W. Johnson; Marcus A. Badgeley; Ben Readhead; Max S. Tomlinson; Timothy O'Connor; Riccardo Miotto; Brian A. Kidd; Rong Chen 006; Avi Ma'ayan; et al. (Briefings Bioinform., 2018)

Mammography Assessment using Multi-Scale Deep Classifiers. - Ulzee An; Khader Shameer; Lakshmi Subramanian (CoRR, 2018)

Pharmacological risk factors associated with hospital readmission rates in a psychiatric cohort identified using prescriptome data mining. - Khader Shameer; M. Mercedes Perez-Rodriguez; Roy Bachar; Li Li 062; Amy Johnson; Kipp W. Johnson; Benjamin S. Glicksberg; Milo R. Smith; Ben Readhead; Joseph Scarpa; Jebakumar Jebakaran; Patricia H. Kovatch; et al. (BMC Medical Informatics Decis. Mak., 2018)

CANDI: an R package and Shiny app for annotating radiographs and evaluating computer-aided diagnosis. - Marcus A. Badgeley; Manway Liu; Benjamin S. Glicksberg; Mark M. Shervey; John R. Zech; Khader Shameer; Joseph Lehar; Eric K. Oermann; Michael V. McConnell; Thomas M. Snyder; Joel T. Dudley (Bioinform., 2019)

Uncovering Machine Learning-Ready Data from Public Clinical Trial Resources: A case-study on normalization across Aggregate Content of ClinicalTrials.gov. - Emmette R. Hutchison; Youyi Zhang; Sreenath Nampally; James Weatherall; Faisal M. Khan; Khader Shameer (BIBM, 2020)

Sepsis in the era of data-driven medicine: personalizing risks, diagnoses, treatments and prognoses. - Andrew C. Liu; Krishna Patel; Ramya Dhatri Vunikili; Kipp W. Johnson; Fahad Abdu; Shivani Kamath Belman; Benjamin S. Glicksberg; Pratyush Tandale; Roberto Fontanez; Oommen K. Mathew; Andrew Kasarskis; Priyabrata Mukherjee; et al. (Briefings Bioinform., 2020)

TrialGraph: Machine Intelligence Enabled Insight from Graph Modelling of Clinical Trials. - Christopher Yacoumatos; Stefano Bragaglia; Anshul Kanakia; Nils Svangård; Jonathan Mangion; Claire Donoghue; James Weatherall; Faisal M. Khan; Khader Shameer (CoRR, 2021)

High Precision Mammography Lesion Identification From Imprecise Medical Annotations. - Ulzee An; Ankit Bhardwaj; Khader Shameer; Lakshminarayanan Subramanian (Frontiers Big Data, 2021)

Predictive Modelling of Susceptibility to Substance Abuse, Mortality and Drug-Drug Interactions in Opioid Patients. - Ramya Dhatri Vunikili; Benjamin S. Glicksberg; Kipp W. Johnson; Joel T. Dudley; Lakshminarayanan Subramanian; Khader Shameer (Frontiers Artif. Intell., 2021)

Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning. - Sonish Sivarajkumar; Pratyush Tandale; Ankit Bhardwaj; Kipp W. Johnson; Anoop Titus; Benjamin S. Glicksberg; Shameer Khader; Kamlesh K. Yadav; Lakshminarayanan Subramanian (CoRR, 2023)

SciLinker: a large-scale text mining framework for mapping associations among biological entities. - Dongyu Liu; Cora Ames; Shameer Khader; Franck Rapaport (Frontiers Artif. Intell., 2025)