Ajay Jain, PhD
Professor Emeritus
HDF Comprehensive Cancer Ctr
School of Medicine
Predictive computational modeling encompasses all of the work in the Jain Lab. This takes primary form in algorithmic approaches for drug discovery.
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The primary areas of research in the lab are: 1) methods for docking small molecules to proteins using empirically derived scoring functions, 2) methods for inducing the shape of a protein binding pocket given the structures and affinities of ligands that bind the pocket competitively, 3) generalized surface-based approaches to computing molecular similarity, both among small molecules and proteins, 4) approaches for modeling and prediction of polypharmacology based on molecular structure, and 5) applications of such methods for cancer drug discovery. All of the approaches share their roots in the use of sophisticated computational algorithms involving object representation, function optimization, and search.
History Following a long period of applied research in defense applications and in speech understanding, Prof. Jain began a research career exclusively focused on issues in computational chemistry and computational biology. His foundational work in computer-aided drug design was done in industry, beginning with the Compass and Hammerhead techniques (see papers from 1994-1997). Compass involved a new representational scheme for capturing the 3D surface-properties of small molecules that made it possible to systematically address a previously unaddressed aspect in modeling the activity of small molecules: choice of the relative alignment and conformation (or pose) of competitive ligands including the detailed relationship of their hydrophobic shapes. A key insight, made with colleagues, was that the choice of pose should be directly governed by the function being used to predict binding affinity (essentially a direct analogy to physics where the lowest energy state is sought). The difficulty was that the function to predict activity was being induced at the same time as the pose choice. The Compass method overcame this problem, and was one of the foundational methods in establishing the field of multiple-instance learning, as it has come to be known within the Computer Science community. This work lead to the development of one of the first molecular docking programs described that addressed ligand conformational flexibility. The Hammerhead docking system built upon the molecular representations, multiple-instance approach, and search strategy developed for Compass.
Advances in Molecular Docking and Ligand-Based Modeling Subsequent work built on the foundation laid by Compass and Hammerhead. These methods addressed problems in computation of molecular diversity and prediction of ADME properties (see papers from 1998-2000). Our most recent work in computational drug design (see the Surflex methodological papers from 2003 onward) is focused on pushing the frontiers of molecular docking and in constructing ligand-based models of protein active sites in cases where protein structure is unknown. The Surflex docking approach is unique, both with respect to scoring function and search methodology. Surflex-Dock is competitive with the best and most widely available methods in terms of docking accuracy and screening utility on publicly available benchmarks. We have recently made a substantial innovation to the multiple-instance parameter estimation process by generalizing our approach to now include negative training data. Putative inactive molecules have been added to a set of known active molecules in re-estimation of the scoring function for the Surflex docking method. We have continued our work in ligand-based modeling as well. The Surflex similarity method has been augmented, both in search strategy and in its objective function, to support the construction of ligand-based models of protein activity. The models are competitive with the best docking methods in terms of effectiveness in identifying novel ligands, generalizing remarkably well even across different chemical scaffolds. The Surflex QMOD approach takes QSAR to a new level, by transforming the problem into one of molecular docking. A protein binding site is induced given structure-activity data using the multiple-instance machine learning paradigm developed for Compass.
Rational and Predictive Pharmacology Research within the lab has branched out to encompass larger biological scales, with studies that contemplate the multiple effects of small molecules in the whole organism. Our earliest work in drug discovery focused exclusively on the therapeutically desired target. At least as important are off-targets: those that are not intended to be modulated by a therapeutic but are affected at relevant drug concentrations. We are interested in building accurate predictive models for promiscuous bad-actor targets such as hERG and cytochrome-p450 enzymes. More broadly, we are interested in building models for multitudes of human targets in order to help guide the design and selection of compounds during preclinical research. This is challenging, both in terms of the stringency on model accuracy and also in terms of information curation regarding the multiple effects of existing therapeutics and those that have undergone clinical testing.
Wet Applications The laboratory is purely a dry one. We rely upon our collaborators to test predictions made by our computational tools. In addition to the hundreds of laboratories that make use of our software, we have active collaborations with both academic and industrial partners. We are particularly interested in applications involving cancer.
Websites
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- Jain Lab Website (jainlab.org)
Grants and Projects
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Publications (127)
Top publication keywords:
Macrocyclic CompoundsPeptides, CyclicModels, MolecularQuantitative Structure-Activity RelationshipCyclin-Dependent Kinase 2ProteinsProtein ConformationMolecular Docking SimulationLigandsMolecular ConformationPharmaceutical PreparationsProtein BindingParenteral Nutrition, TotalDrug DesignCoronary Thrombosis
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Learning Curve of a Laparoscopic Pancreaticoduodenectomy Program at a Second Institution.
The American surgeon 2024 Martin WT, Bonds M, Fischer L, Morris KT, Sarwar Z, Stewart K, Garwe T, Paniccia A, Schulick RD, Jain A, Edil BH -
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.
Journal of computer-aided molecular design 2024 Jain AN, Brueckner AC, Jorge C, Cleves AE, Khandelwal P, Cortes JC, Mueller L -
Novel near-infrared spectroscopy-intravascular ultrasound-based deep-learning methodology for accurate coronary computed tomography plaque quantification and characterization.
European heart journal open 2023 Ramasamy A, Sokooti H, Zhang X, Tzorovili E, Bajaj R, Kitslaar P, Broersen A, Amersey R, Jain A, Ozkor M, Reiber JHC, Dijkstra J, Serruys PW, Moon JC, Mathur A, Baumbach A, Torii R, Pugliese F, … -
Expedited transfer to a cardiac arrest centre for non-ST-elevation out-of-hospital cardiac arrest (ARREST): a UK prospective, multicentre, parallel, randomised clinical trial.
Lancet (London, England) 2023 Patterson T, Perkins GD, Perkins A, Clayton T, Evans R, Dodd M, Robertson S, Wilson K, Mellett-Smith A, Fothergill RT, McCrone P, Dalby M, MacCarthy P, Firoozi S, Malik I, Rakhit R, Jain A, Nolan JP, … -
Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.
Journal of computer-aided molecular design 2023 Jain AN, Brueckner AC, Jorge C, Cleves AE, Khandelwal P, Cortes JC, Mueller L
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Unmasking the True Identity of Rapamycin's Minor Conformer.
Journal of natural products 2023 Crull EB, Jain AN, Hawkins PCD, Cleves AE, Graziani EI, Williamson RT -
Thrombus Burden and Outcomes in Patients With COVID-19 Presenting With STEMI Across the Pandemic.
Journal of the American College of Cardiology 2023 Rathod KS, Teoh Z, Tyrlis A, Choudry FA, Hamshere SM, Comer K, Guttmann O, Jain AK, Ozkor MA, Wragg A, Archbold RA, Baumbach A, Mathur A, Jones DA -
The safety of deferred coronary angiography in COVID-19 patients with acute coronary syndrome: the Barts COVID recovered pathway.
American journal of cardiovascular disease 2023 Teoh Z, Rathod KS, Comer K, Tyrlis A, Choudry FA, Ozkor M, Archbold RA, Guttmann O, Wragg A, Baumbach A, Jain AK, Mathur A, Jones DA -
Etiologic fractions in patients of hepatocellular carcinoma in India with and without a background of cirrhosis: a multi-centric study.
Hepatology international 2023 Prabhakar T, Kaushal K, Prasad M, Gupta E, Sood A, Jain AK, Shukla A, Goel A, Duseja A, Saraya A, Shah S, Kumar G, Sarin SK -
A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.
Journal of medicinal chemistry 2023 Jain AN, Brueckner AC, Cleves AE, Reibarkh M, Sherer EC -
Lower systemic inflammation is associated with gut firmicutes dominance and reduced liver injury in a novel ambulatory model of parenteral nutrition.
Annals of medicine 2022 Samaddar A, van Nispen J, Armstrong A, Song E, Voigt M, Murali V, Krebs J, Manithody C, Denton C, Ericsson AC, Jain AK -
Implications of computed tomography reconstruction algorithms on coronary atheroma quantification: Comparison with intravascular ultrasound.
Journal of cardiovascular computed tomography 2022 Ramasamy A, Hamid A Khan A, Cooper J, Simon J, Maurovich-Horvat P, Bajaj R, Kitslaar P, Amersey R, Jain A, Deaner A, Reiber JH, Moon JC, Dijkstra J, Serruys PW, Mathur A, Baumbach A, Torii R, Pugliese… -
Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis.
Journal of natural products 2022 Gao Q, Cleves AE, Wang X, Liu Y, Bowen S, Williamson RT, Jain AN, Sherer E, Reibarkh M -
Early quantitative infrared pupillometry for prediction of neurological outcome in patients admitted to intensive care after out-of-hospital cardiac arrest.
British journal of anaesthesia 2022 Warren A, McCarthy C, Andiapen M, Crouch M, Finney S, Hamilton S, Jain A, Jones D, Proudfoot A -
Identification of Protein Drug Targets of Biofilm Formation and Quorum Sensing in Multidrug Resistant Enterococcus faecalis.
Current protein & peptide science 2022 Yadav J, Das S, Karthikeyan D, Chug R, Jyoti A, Srivastava VK, Jain A, Kumar S, Sharma V, Kaushik S -
Impact of COVID-19 pandemic on the management of nonculprit lesions in patients presenting with ST-elevation myocardial infarction: Outcomes from the pan-London heart attack centers.
Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions 2021 Demir OM, Little CD, Jabbour R, Rahman H, Sayers M, Ahmed A, Connolly MJ, Kanyal R, MacCarthy P, Wilson SJ, Dalby M, Jain A, Malik I, Rakhit R, Perera D -
Early Hospital Discharge Following PCI for Patients With STEMI.
Journal of the American College of Cardiology 2021 Rathod KS, Comer K, Casey-Gillman O, Moore L, Mills G, Ferguson G, Antoniou S, Patel R, Fhadil S, Damani T, Wright P, Ozkor M, Das D, Guttmann OP, Baumbach A, Archbold RA, Wragg A, Jain AK, Choudry FA… -
Validation of the CREST score for predicting circulatory-aetiology death in out-of-hospital cardiac arrest without STEMI.
American journal of cardiovascular disease 2021 Jones TN, Kelham M, Rathod KS, Knight CJ, Proudfoot A, Jain AK, Wragg A, Ozkor M, Rees P, Guttmann O, Baumbach A, Mathur A, Jones DA -
Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction.
Journal of chemical information and modeling 2021 Cleves AE, Johnson SR, Jain AN -
The impact of the COVID-19 pandemic on the delivery of primary percutaneous coronary intervention in STEMI.
American journal of cardiovascular disease 2021 Frain K, Rathod KS, Tumi E, Chen Y, Hamshere S, Choudry F, Akhtar MM, Curtis M, Amersey R, Guttmann O, O'Mahony C, Jain A, Wragg A, Baumbach A, Mathur A, Jones DA, Rees P -
The influence of biological age and sex on long-term outcome after percutaneous coronary intervention for ST-elevation myocardial infarction.
American journal of cardiovascular disease 2021 Rathod KS, Jones DA, Jain AK, Lim P, MacCarthy PA, Rakhit R, Lockie T, Kalra S, Dalby MC, Malik IS, Whitbread M, Firoozi S, Bogle R, Redwood S, Cooper J, Gupta A, Lansky A, Wragg A, Mathur A, … -
A Bioinformatics Approach for the Prediction of Immunogenic Properties and Structure of the SARS-COV-2 B.1.617.1 Variant Spike Protein.
BioMed research international 2021 Srivastava VK, Kaushik S, Bhargava G, Jain A, Saxena J, Jyoti A -
Renal Artery Variations in Patients With Mild-to-Moderate Hypertension From the RADIANCE-HTN SOLO Trial.
Cardiovascular revascularization medicine : including molecular interventions 2021 Sanghvi K, Wang Y, Daemen J, Mathur A, Jain A, Dohad S, Sapoval M, Azizi M, Mahfoud F, Lurz P, Sayer J, Levy T, Zagoria R, Loening AM, Coleman L, Craig D, Horesh-Bar M, Kirtane AJ -
Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers.
Journal of medicinal chemistry 2021 Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN -
XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps.
Journal of medicinal chemistry 2020 Jain AN, Cleves AE, Brueckner AC, Lesburg CA, Deng Q, Sherer EC, Reibarkh MY -
Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket.
Journal of chemical information and modeling 2020 Cleves AE, Jain AN -
Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.
Journal of computer-aided molecular design 2019 Cleves AE, Johnson SR, Jain AN -
Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.
Journal of computer-aided molecular design 2019 Jain AN, Cleves AE, Gao Q, Wang X, Liu Y, Sherer EC, Reibarkh MY -
Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose.
Journal of computer-aided molecular design 2018 Cleves AE, Jain AN -
ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs.
Journal of computer-aided molecular design 2017 Cleves AE, Jain AN -
Extrapolative prediction using physically-based QSAR.
Journal of computer-aided molecular design 2016 Cleves AE, Jain AN -
Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.
Journal of computer-aided molecular design 2015 Cleves AE, Jain AN -
Manual Thrombus Aspiration Is Not Associated With Reduced Mortality in Patients Treated With Primary Percutaneous Coronary Intervention: An Observational Study of 10,929 Patients With ST-Segment Elevation Myocardial Infarction From the London Heart Attack Group.
JACC. Cardiovascular interventions 2015 Jones DA, Rathod KS, Gallagher S, Jain AK, Kalra SS, Lim P, Crake T, Ozkor M, Rakhit R, Knight CJ, Iqbal MB, Dalby MC, Malik IS, Whitbread M, Mathur A, Redwood S, MacCarthy PA, Weerackody R, Wragg A -
Ex vivo antibody-dependent cellular cytotoxicity inducibility predicts efficacy of cetuximab.
Cancer immunology research 2015 Taylor RJ, Saloura V, Jain A, Goloubeva O, Wong S, Kronsberg S, Nagilla M, Silpino L, de Souza J, Seiwert T, Vokes E, Villaflor V, Cohen EE -
Radial primary percutaneous coronary intervention is independently associated with decreased long-term mortality in high-risk ST-elevation myocardial infarction patients.
Journal of cardiovascular medicine (Hagerstown, Md.) 2015 Rathod KS, Jones DA, Bromage DI, Gallagher SM, Rathod VS, Kennon S, Knight C, Rothman MT, Mathur A, Smith E, Jain AK, Archbold RA, Wragg A -
The impact of socio-economic status on all-cause mortality after percutaneous coronary intervention: an observational cohort study of 13,770 patients.
EuroIntervention : journal of EuroPCR in collaboration with the Working Group on Interventional Cardiology of the European Society of Cardiology 2015 Jones DA, Howard JP, Rathod KS, Gallagher SM, Knight CJ, Jain AK, Mathur A, Mohiddin SA, Mills PG, Timmis AD, Archbold RA, Wragg A -
Validating hyperbilirubinemia and gut mucosal atrophy with a novel ultramobile ambulatory total parenteral nutrition piglet model.
Nutrition research (New York, N.Y.) 2014 Jain AK, Wen JX, Arora S, Blomenkamp KS, Rodrigues J, Blaufuss TA, Liou V, Burrin DG, Long JP, Teckman JH -
Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes.
Journal of computer-aided molecular design 2014 Cleves AE, Jain AN -
A preclinical murine model of hepatic metastases.
Journal of visualized experiments : JoVE 2014 Soares KC, Foley K, Olino K, Leubner A, Mayo SC, Jain A, Jaffee E, Schulick RD, Yoshimura K, Edil B, Zheng L -
Renal Sympathetic Denervation - A Review of Applications in Current Practice.
Interventional cardiology (London, England) 2014 Kapil V, Jain AK, Lobo MD -
Prediction of off-target drug effects through data fusion.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2014 Yera ER, Cleves AE, Jain AN -
Prognostic impact of anaemia on patients with ST-elevation myocardial infarction treated by primary PCI.
Coronary artery disease 2014 Rathod KS, Jones DA, Rathod VS, Bromage D, Guttmann O, Gallagher SM, Mohiddin S, Rothman MT, Knight C, Jain AK, Kapur A, Mathur A, Timmis AD, Amersey R, Wragg A -
Protein function annotation by local binding site surface similarity.
Proteins 2013 Spitzer R, Cleves AE, Varela R, Jain AN -
A structure-guided approach for protein pocket modeling and affinity prediction.
Journal of computer-aided molecular design 2013 Varela R, Cleves AE, Spitzer R, Jain AN -
Contemporary analysis of incidence and outcomes of stent thrombosis presenting as ST elevation myocardial infarction in a primary percutaneous coronary intervention cohort.
The American journal of cardiology 2013 Jones DA, Gallagher S, Rathod KS, Akhtar M, Knight CJ, Rothman MT, Kapur A, Mathur A, Jain AK, Timmis AD, Smith EJ, Wragg A -
Out-of-hours primary percutaneous coronary intervention for ST-elevation myocardial infarction is not associated with excess mortality: a study of 3347 patients treated in an integrated cardiac network.
BMJ open 2013 Rathod KS, Jones DA, Gallagher SM, Bromage DI, Whitbread M, Archbold AR, Jain AK, Mathur A, Wragg A, Knight CJ -
Clinical outcomes after myocardial revascularization according to operator training status: cohort study of 22,697 patients undergoing percutaneous coronary intervention or coronary artery bypass graft surgery.
European heart journal 2013 Jones DA, Gallagher S, Rathod K, Jain AK, Mathur A, Uppal R, Westwood M, Wong K, Rothman MT, Shipolini A, Smith EJ, Mills PG, Timmis AD, Knight CJ, Archbold RA, Wragg A -
A high throughput method for enrichment of natural killer cells and lymphocytes and assessment of in vitro cytotoxicity.
Journal of immunological methods 2013 So EC, Sallin MA, Zhang X, Chan SL, Sahni L, Schulze DH, Davila E, Strome SE, Jain A -
Influence of female sex on long-term mortality after acute coronary syndromes treated by percutaneous coronary intervention: a cohort study of 7304 patients.
Coronary artery disease 2013 Pain TE, Jones DA, Rathod KS, Gallagher SM, Knight CJ, Mathur A, Rothman MT, Jain AK, Wragg A -
Management of cardiogenic shock complicating acute coronary syndromes.
Heart (British Cardiac Society) 2013 Tharmaratnam D, Nolan J, Jain A -
Assessment of neoadjuvant chemotherapy on operative parameters and outcome in patients with peritoneal dissemination from high-grade appendiceal cancer.
Annals of surgical oncology 2013 Turner KM, Hanna NN, Zhu Y, Jain A, Kesmodel SB, Switzer RA, Taylor LM, Richard Alexander H -
Deployment of drug-eluting stents for isolated proximal lad disease is associated with lower major adverse cardiac events and no increase in stent thrombosis when compared with bare metal stents: a 5-year observational cohort study.
Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions 2012 Jones DA, Rathod KS, Gallagher S, Weerackody R, Knight CJ, Rothman MT, Mathur A, Jain AK, Timmis AD, Wragg A -
Safety and feasibility of hospital discharge 2 days following primary percutaneous intervention for ST-segment elevation myocardial infarction.
Heart (British Cardiac Society) 2012 Jones DA, Rathod KS, Howard JP, Gallagher S, Antoniou S, De Palma R, Guttmann O, Cliffe S, Colley J, Butler J, Ferguson E, Mohiddin S, Kapur A, Knight CJ, Jain AK, Rothman MT, Mathur A, Timmis AD, … -
Iterative refinement of a binding pocket model: active computational steering of lead optimization.
Journal of medicinal chemistry 2012 Varela R, Walters WP, Goldman BB, Jain AN -
Surflex-Dock: Docking benchmarks and real-world application.
Journal of computer-aided molecular design 2012 Spitzer R, Jain AN -
Outcomes in patients with renal impairment undergoing percutaneous coronary intervention and implantation of the Endeavor zotarolimus-eluting stent: 1- and 2-year data from the E-Five Registry.
Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions 2012 Rothman MT, Jain AK, E-Five Registry Investigators -
Successful recanalization of chronic total occlusions is associated with improved long-term survival.
JACC. Cardiovascular interventions 2012 Jones DA, Weerackody R, Rathod K, Behar J, Gallagher S, Knight CJ, Kapur A, Jain AK, Rothman MT, Thompson CA, Mathur A, Wragg A, Smith EJ -
Intracoronary thrombolytic therapy: a treatment option for failed mechanical thrombectomy.
Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions 2012 Gallagher S, Jain AK, Archbold RA -
Does your model weigh the same as a duck?
Journal of computer-aided molecular design 2011 Jain AN, Cleves AE -
Percutaneous balloon pericardiotomy for recurrent malignant pericardial effusion.
Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer 2011 Jones DA, Jain AK -
Thrombus entrapment by a novel mesh-covered stent in ST-segment elevation myocardial infarction.
Journal of the American College of Cardiology 2011 Jain AK, Rothman MT -
Enteral bile acid treatment improves parenteral nutrition-related liver disease and intestinal mucosal atrophy in neonatal pigs.
American journal of physiology. Gastrointestinal and liver physiology 2011 Jain AK, Stoll B, Burrin DG, Holst JJ, Moore DD -
Chemical structural novelty: on-targets and off-targets.
Journal of medicinal chemistry 2011 Yera ER, Cleves AE, Jain AN -
Surface-based protein binding pocket similarity.
Proteins 2011 Spitzer R, Cleves AE, Jain AN -
Clinical outcomes by geographic region for patients implanted with the zotarolimus-eluting stent.
Arquivos brasileiros de cardiologia 2011 Lotan C, Meredith IT, Jain A, Feres F, Firszt A, Garcia AF, Rothman MT -
Percutaneous occlusion of the left atrial appendage in non-valvular atrial fibrillation for the prevention of thromboembolism: NICE guidance.
Heart (British Cardiac Society) 2011 Jain AK, Gallagher S -
Primary percutaneous coronary intervention for ST-elevation myocardial infarction in a patient with a single coronary artery arising from the right aortic sinus.
The Journal of invasive cardiology 2011 Gallagher SM, Jain AK, Archbold RA -
Acute myocarditis presenting as acute coronary syndrome: role of early cardiac magnetic resonance in its diagnosis.
Heart (British Cardiac Society) 2010 Monney PA, Sekhri N, Burchell T, Knight C, Davies C, Deaner A, Sheaf M, Baithun S, Petersen S, Wragg A, Jain A, Westwood M, Mills P, Mathur A, Mohiddin SA -
QMOD: physically meaningful QSAR.
Journal of computer-aided molecular design 2010 Jain AN -
Twelve-month outcomes in patients with diabetes implanted with a zotarolimus-eluting stent: results from the E-Five Registry.
Heart (British Cardiac Society) 2010 Jain AK, Lotan C, Meredith IT, Feres F, Zambahari R, Sinha N, Rothman MT, E-Five Registry Investigators -
Molecular shape and medicinal chemistry: a perspective.
Journal of medicinal chemistry 2010 Nicholls A, McGaughey GB, Sheridan RP, Good AC, Warren G, Mathieu M, Muchmore SW, Brown SP, Grant JA, Haigh JA, Nevins N, Jain AN, Kelley B -
Histopathologic basis for the favorable survival after resection of intraductal papillary mucinous neoplasm-associated invasive adenocarcinoma of the pancreas.
Annals of surgery 2010 Poultsides GA, Reddy S, Cameron JL, Hruban RH, Pawlik TM, Ahuja N, Jain A, Edil BH, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL -
Physical binding pocket induction for affinity prediction.
Journal of medicinal chemistry 2009 Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN -
Prevention of thrombus embolization during primary percutaneous intervention using a novel mesh covered stent.
Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions 2009 Jain A, Weerackody R, Kennon S, Rothman M -
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation.
Journal of computer-aided molecular design 2009 Jain AN -
Successful exclusion of large post-surgical pseudoaneurysms of the ascending aorta by a percutaneous approach.
The Annals of thoracic surgery 2009 Kannan BR, Jain AK, Qureshi SA, Rothman MT, Rosenthal E, Mathur A -
Image of the month. Gastrohepatic fistula following TACE for HCC.
Archives of surgery (Chicago, Ill. : 1960) 2009 Jain A, Smith C, Geschwind JF, Pawlik TM -
Accurate and interpretable computational modeling of chemical mutagenicity.
Journal of chemical information and modeling 2008 Langham JJ, Jain AN -
Recommendations for evaluation of computational methods.
Journal of computer-aided molecular design 2008 Jain AN, Nicholls A -
Customizing scoring functions for docking.
Journal of computer-aided molecular design 2008 Pham TA, Jain AN -
Bias, reporting, and sharing: computational evaluations of docking methods.
Journal of computer-aided molecular design 2007 Jain AN -
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery.
Journal of computer-aided molecular design 2007 Cleves AE, Jain AN -
The role of ultrasound-guided fine-needle aspiration of axillary nodes in the staging of breast cancer.
Annals of surgical oncology 2007 Jain A, Haisfield-Wolfe ME, Lange J, Ahuja N, Khouri N, Tsangaris T, Zhang Z, Balch C, Jacobs LK -
Real-world safety and efficacy of the endeavor zotarolimus-eluting stent: early data from the E-Five Registry.
The American journal of cardiology 2007 Jain AK, Meredith IT, Lotan C, Rothman MT, Pateraki S, E-Five Investigators -
Update on drug-eluting stents: as good as it gets?
Clinical medicine (London, England) 2007 Jain AK, Mathur A -
Complete removal of extensive right coronary artery thrombus by the use of an aspiration catheter to facilitate primary angioplasty.
EuroIntervention : journal of EuroPCR in collaboration with the Working Group on Interventional Cardiology of the European Society of Cardiology 2007 Jain AK, Archbold RA -
Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search.
Journal of computer-aided molecular design 2007 Jain AN -
Magellan: a web based system for the integrated analysis of heterogeneous biological data and annotations; application to DNA copy number and expression data in ovarian cancer.
Cancer informatics 2007 Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN -
Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.
Cancer cell 2006 Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, … -
New developments in coronary stent technology.
Journal of interventional cardiology 2006 Smith EJ, Jain AK, Rothman MT -
the coronary venous system: an alternative route of access to the myocardium.
The Journal of invasive cardiology 2006 Jain AK, Smith EJ, Rothman MT -
Parameter estimation for scoring protein-ligand interactions using negative training data.
Journal of medicinal chemistry 2006 Pham TA, Jain AN -
Scoring functions for protein-ligand docking.
Current protein & peptide science 2006 Jain AN -
Robust ligand-based modeling of the biological targets of known drugs.
Journal of medicinal chemistry 2006 Cleves AE, Jain AN -
Breast tumor copy number aberration phenotypes and genomic instability.
BMC cancer 2006 Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG -
Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel.
Molecular cancer therapeutics 2006 Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, … -
A deterministic motif finding algorithm with application to the human genome.
Bioinformatics (Oxford, England) 2006 Hon LS, Jain AN -
Selective targeting of antitumor immune responses with engineered live-attenuated Listeria monocytogenes.
Cancer research 2006 Yoshimura K, Jain A, Allen HE, Laird LS, Chia CY, Ravi S, Brockstedt DG, Giedlin MA, Bahjat KS, Leong ML, Slansky JE, Cook DN, Dubensky TW, Pardoll DM, Schulick RD -
Pathway recognition and augmentation by computational analysis of microarray expression data.
Bioinformatics (Oxford, England) 2005 Novak BA, Jain AN -
Success of a multidisciplinary heart failure clinic for initiation and up-titration of key therapeutic agents.
European journal of heart failure 2005 Jain A, Mills P, Nunn LM, Butler J, Luddington L, Ross V, Cliffe P, Ranjadayalan K, Timmis AD -
Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005 Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM -
Mapping segmental and sequence variations among laboratory mice using BAC array CGH.
Genome research 2005 Snijders AM, Nowak NJ, Huey B, Fridlyand J, Law S, Conroy J, Tokuyasu T, Demir K, Chiu R, Mao JH, Jain AN, Jones SJ, Balmain A, Pinkel D, Albertson DG -
Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival.
Clinical cancer research : an official journal of the American Association for Cancer Research 2004 Rosen DG, Wang L, Jain AN, Lu KH, Luo RZ, Yu Y, Liu J, Bast RC -
Virtual screening in lead discovery and optimization.
Current opinion in drug discovery & development 2004 Jain AN -
Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors.
Human molecular genetics 2004 Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, … -
High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization.
Carcinogenesis 2004 Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM -
Ligand-based structural hypotheses for virtual screening.
Journal of medicinal chemistry 2004 Jain AN -
Determinants of BRAF mutations in primary melanomas.
Journal of the National Cancer Institute 2003 Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC -
Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs.
Journal of molecular biology 2003 Hon LS, Jain AN -
Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors.
Cancer research 2003 Hackett CS, Hodgson JG, Law ME, Fridlyand J, Osoegawa K, de Jong PJ, Nowak NJ, Pinkel D, Albertson DG, Jain A, Jenkins R, Gray JW, Weiss WA -
Synergistic effect of a granulocyte-macrophage colony-stimulating factor-transduced tumor vaccine and systemic interleukin-2 in the treatment of murine colorectal cancer hepatic metastases.
Annals of surgical oncology 2003 Jain A, Slansky JE, Matey LC, Allen HE, Pardoll DM, Schulick RD -
Shaping of tumor and drug-resistant genomes by instability and selection.
Oncogene 2003 Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG -
Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma.
Oncogene 2003 Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG -
Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors.
Cancer research 2003 Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, DeVries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM -
High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays.
The American journal of pathology 2003 Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H -
Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine.
Journal of medicinal chemistry 2003 Jain AN -
Deriving quantitative conclusions from microarray expression data.
Bioinformatics (Oxford, England) 2002 Olshen AB, Jain AN -
Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway.
Cancer research 2002 Massion PP, Kuo WL, Stokoe D, Olshen AB, Treseler PA, Chin K, Chen C, Polikoff D, Jain AN, Pinkel D, Albertson DG, Jablons DM, Gray JW -
Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer.
Cancer research 2002 Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM -
Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules.
Journal of medicinal chemistry 1999 Ghuloum AM, Sage CR, Jain AN -
IcePick: a flexible surface-based system for molecular diversity.
Journal of medicinal chemistry 1999 Mount J, Ruppert J, Welch W, Jain AN -
Automatic identification and representation of protein binding sites for molecular docking.
Protein science : a publication of the Protein Society 1997 Ruppert J, Welch W, Jain AN -
Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities.
Journal of computer-aided molecular design 1996 Jain AN -
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.
Chemistry & biology 1996 Welch W, Ruppert J, Jain AN -
Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor.
Journal of medicinal chemistry 1995 Jain AN, Harris NL, Park JY -
A shape-based machine learning tool for drug design.
Journal of computer-aided molecular design 1994 Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE, Bauer BE, Webster TA, Lozano-Perez T -
Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark.
Journal of medicinal chemistry 1994 Jain AN, Koile K, Chapman D