Ajay Jain, PhD

Title(s)Professor, HDF Comprehensive Cancer Ctr
SchoolSchool of Medicine
Address1450 Third St
San Francisco CA 94158
Phone415-502-7242
ORCID ORCID Icon0000-0003-4641-8501 Additional info
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    Collapse Overview 
    Collapse Overview
    Predictive computational modeling encompasses all of the work in the Jain Lab. This takes primary form in algorithmic approaches for drug discovery. 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.

    Collapse Research 
    Collapse Research Activities and Funding
    Binding-Site Modeling with Multiple-Instance Machine-Learning
    NIH R01GM101689Jan 1, 2013 - Mar 31, 2021
    Role: Principal Investigator
    Data-Driven Approaches for Molecular Docking
    NIH R01GM070481Jul 1, 2005 - Jun 30, 2015
    Role: Principal Investigator
    Cancer Center Support Grant
    NIH P30CA082103Aug 5, 1999 - May 31, 2023
    Role: Co-Investigator

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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. Advanced deep learning methodology for accurate, real-time segmentation of high-resolution intravascular ultrasound images. Int J Cardiol. 2021 Jun 18. Bajaj R, Huang X, Kilic Y, Ramasamy A, Jain A, Ozkor M, Tufaro V, Safi H, Erdogan E, Serruys PW, Moon J, Pugliese F, Mathur A, Torii R, Baumbach A, Dijkstra J, Zhang Q, Bourantas CV. PMID: 34153412.
      View in: PubMed   Mentions:    Fields:    
    2. NH787 EMS mutant of rice variety Nagina22 exhibits higher phosphate use efficiency. Sci Rep. 2021 Apr 28; 11(1):9156. Poli Y, Nallamothu V, Hao A, Goud MD, Wang X, Desiraju S, Mangrauthia SK, Jain A. PMID: 33911118.
      View in: PubMed   Mentions:    Fields:    
    3. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem. 2021 03 25; 64(6):3282-3298. Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. PMID: 33724820.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    4. COVID-19 and changes in activity and treatment of ST elevation MI from a UK cardiac centre. Int J Cardiol Heart Vasc. 2021 Apr; 33:100736. Chen Y, Rathod KS, 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. PMID: 33644297.
      View in: PubMed   Mentions:
    5. A deep learning methodology for the automated detection of end-diastolic frames in intravascular ultrasound images. Int J Cardiovasc Imaging. 2021 Jun; 37(6):1825-1837. Bajaj R, Huang X, Kilic Y, Jain A, Ramasamy A, Torii R, Moon J, Koh T, Crake T, Parker MK, Tufaro V, Serruys PW, Pugliese F, Mathur A, Baumbach A, Dijkstra J, Zhang Q, Bourantas CV. PMID: 33590430.
      View in: PubMed   Mentions: 1     Fields:    
    6. Reducing phenanthrene uptake and translocation, and accumulation in the seeds by overexpressing OsNRT2.3b in rice. Sci Total Environ. 2021 Mar 20; 761:143690. Wang X, Jain A, Huang X, Lan X, Xu L, Zhao G, Cong X, Zhang Z, Fan X, Hu F. PMID: 33348216.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimals
    7. XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps. J Med Chem. 2020 09 24; 63(18):10509-10528. Jain AN, Cleves AE, Brueckner AC, Lesburg CA, Deng Q, Sherer EC, Reibarkh MY. PMID: 32877178.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    8. Progression of Fatty Liver Disease in Children Receiving Standard of Care Lifestyle Advice. Gastroenterology. 2020 11; 159(5):1731-1751.e10. Xanthakos SA, Lavine JE, Yates KP, Schwimmer JB, Molleston JP, Rosenthal P, Murray KF, Vos MB, Jain AK, Scheimann AO, Miloh T, Fishbein M, Behling CA, Brunt EM, Sanyal AJ, Tonascia J, NASH Clinical Research Network . PMID: 32712103.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    9. Structure- and Ligand-Based Virtual Screening on DUD-E+: Performance Dependence on Approximations to the Binding Pocket. J Chem Inf Model. 2020 09 28; 60(9):4296-4310. Cleves AE, Jain AN. PMID: 32271577.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    10. Electrostatic-field and surface-shape similarity for virtual screening and pose prediction. J Comput Aided Mol Des. 2019 10; 33(10):865-886. Cleves AE, Johnson SR, Jain AN. PMID: 31650386.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    11. Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen. J Comput Aided Mol Des. 2019 06; 33(6):531-558. Jain AN, Cleves AE, Gao Q, Wang X, Liu Y, Sherer EC, Reibarkh MY. PMID: 31054028.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    12. Quantitative surface field analysis: learning causal models to predict ligand binding affinity and pose. J Comput Aided Mol Des. 2018 07; 32(7):731-757. Cleves AE, Jain AN. PMID: 29934750.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    13. ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs. J Comput Aided Mol Des. 2017 May; 31(5):419-439. Cleves AE, Jain AN. PMID: 28289981.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    14. Extrapolative prediction using physically-based QSAR. J Comput Aided Mol Des. 2016 Feb; 30(2):127-52. Cleves AE, Jain AN. PMID: 26860112.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    15. Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock. J Comput Aided Mol Des. 2015 Jun; 29(6):485-509. Cleves AE, Jain AN. PMID: 25940276.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    16. 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 Cardiovasc Interv. 2015 Apr 20; 8(4):575-84. 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. PMID: 25907084.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    17. Ex vivo antibody-dependent cellular cytotoxicity inducibility predicts efficacy of cetuximab. Cancer Immunol Res. 2015 May; 3(5):567-74. 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. PMID: 25769300.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCellsCTClinical Trials
    18. Radial primary percutaneous coronary intervention is independently associated with decreased long-term mortality in high-risk ST-elevation myocardial infarction patients. J Cardiovasc Med (Hagerstown). 2015 Mar; 16(3):170-7. 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. PMID: 25634086.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    19. The impact of socio-economic status on all-cause mortality after percutaneous coronary intervention: an observational cohort study of 13,770 patients. EuroIntervention. 2015 Feb; 10(10):e1-8. Jones DA, Howard JP, Rathod KS, Gallagher SM, Knight CJ, Jain AK, Mathur A, Mohiddin SA, Mills PG, Timmis AD, Archbold RA, Wragg A. PMID: 25701263.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    20. Validating hyperbilirubinemia and gut mucosal atrophy with a novel ultramobile ambulatory total parenteral nutrition piglet model. Nutr Res. 2015 Feb; 35(2):169-74. Jain AK, Wen JX, Arora S, Blomenkamp KS, Rodrigues J, Blaufuss TA, Liou V, Burrin DG, Long JP, Teckman JH. PMID: 25649660.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    21. Chemical and protein structural basis for biological crosstalk between PPARa and COX enzymes. J Comput Aided Mol Des. 2015 Feb; 29(2):101-12. Cleves AE, Jain AN. PMID: 25428568.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    22. A preclinical murine model of hepatic metastases. J Vis Exp. 2014 Sep 27; (91):51677. Soares KC, Foley K, Olino K, Leubner A, Mayo SC, Jain A, Jaffee E, Schulick RD, Yoshimura K, Edil B, Zheng L. PMID: 25285458.
      View in: PubMed   Mentions: 52     Fields:    Translation:AnimalsCells
    23. Renal Sympathetic Denervation - A Review of Applications in Current Practice. Interv Cardiol. 2014 Mar; 9(1):54-61. Kapil V, Jain AK, Lobo MD. PMID: 29588780.
      View in: PubMed   Mentions:
    24. Prognostic impact of anaemia on patients with ST-elevation myocardial infarction treated by primary PCI. Coron Artery Dis. 2014 Jan; 25(1):52-9. 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. PMID: 24051679.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    25. Prediction of off-target drug effects through data fusion. Pac Symp Biocomput. 2014; 160-71. Yera ER, Cleves AE, Jain AN. PMID: 24297543.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    26. Protein function annotation by local binding site surface similarity. Proteins. 2014 Apr; 82(4):679-94. Spitzer R, Cleves AE, Varela R, Jain AN. PMID: 24166661.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    27. A structure-guided approach for protein pocket modeling and affinity prediction. J Comput Aided Mol Des. 2013 Nov; 27(11):917-34. Varela R, Cleves AE, Spitzer R, Jain AN. PMID: 24214361.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    28. Contemporary analysis of incidence and outcomes of stent thrombosis presenting as ST elevation myocardial infarction in a primary percutaneous coronary intervention cohort. Am J Cardiol. 2013 Nov 01; 112(9):1347-54. Jones DA, Gallagher S, Rathod KS, Akhtar M, Knight CJ, Rothman MT, Kapur A, Mathur A, Jain AK, Timmis AD, Smith EJ, Wragg A. PMID: 24012030.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    29. 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 Jun 28; 3(6). Rathod KS, Jones DA, Gallagher SM, Bromage DI, Whitbread M, Archbold AR, Jain AK, Mathur A, Wragg A, Knight CJ. PMID: 23811175.
      View in: PubMed   Mentions: 8     Fields:    
    30. 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. Eur Heart J. 2013 Oct; 34(37):2887-95. 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. PMID: 23677845.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    31. A high throughput method for enrichment of natural killer cells and lymphocytes and assessment of in vitro cytotoxicity. J Immunol Methods. 2013 Aug 30; 394(1-2):40-8. So EC, Sallin MA, Zhang X, Chan SL, Sahni L, Schulze DH, Davila E, Strome SE, Jain A. PMID: 23680234.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    32. Influence of female sex on long-term mortality after acute coronary syndromes treated by percutaneous coronary intervention: a cohort study of 7304 patients. Coron Artery Dis. 2013 May; 24(3):183-90. Pain TE, Jones DA, Rathod KS, Gallagher SM, Knight CJ, Mathur A, Rothman MT, Jain AK, Wragg A. PMID: 23299565.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    33. Management of cardiogenic shock complicating acute coronary syndromes. Heart. 2013 Nov; 99(21):1614-23. Tharmaratnam D, Nolan J, Jain A. PMID: 23468511.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    34. Assessment of neoadjuvant chemotherapy on operative parameters and outcome in patients with peritoneal dissemination from high-grade appendiceal cancer. Ann Surg Oncol. 2013 Apr; 20(4):1068-73. Turner KM, Hanna NN, Zhu Y, Jain A, Kesmodel SB, Switzer RA, Taylor LM, Richard Alexander H. PMID: 23456383.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    35. 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. Catheter Cardiovasc Interv. 2013 May; 81(6):E237-44. Jones DA, Rathod KS, Gallagher S, Weerackody R, Knight CJ, Rothman MT, Mathur A, Jain AK, Timmis AD, Wragg A. PMID: 22707383.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    36. Safety and feasibility of hospital discharge 2 days following primary percutaneous intervention for ST-segment elevation myocardial infarction. Heart. 2012 Dec; 98(23):1722-7. 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, Smith EJ, Wragg A. PMID: 23053711.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    37. Iterative refinement of a binding pocket model: active computational steering of lead optimization. J Med Chem. 2012 Oct 25; 55(20):8926-42. Varela R, Walters WP, Goldman BB, Jain AN. PMID: 23046104.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    38. Surflex-Dock: Docking benchmarks and real-world application. J Comput Aided Mol Des. 2012 Jun; 26(6):687-99. Spitzer R, Jain AN. PMID: 22569590.
      View in: PubMed   Mentions: 64     Fields:    Translation:Cells
    39. 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. Catheter Cardiovasc Interv. 2012 Nov 15; 80(6):885-92. Rothman MT, Jain AK, E-Five Registry Investigators . PMID: 22517785.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    40. Successful recanalization of chronic total occlusions is associated with improved long-term survival. JACC Cardiovasc Interv. 2012 Apr; 5(4):380-8. 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. PMID: 22516393.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    41. Intracoronary thrombolytic therapy: a treatment option for failed mechanical thrombectomy. Catheter Cardiovasc Interv. 2012 Nov 01; 80(5):835-7. Gallagher S, Jain AK, Archbold RA. PMID: 22109966.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    42. Does your model weigh the same as a duck? J Comput Aided Mol Des. 2012 Jan; 26(1):57-67. Jain AN, Cleves AE. PMID: 22187141.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    43. Percutaneous balloon pericardiotomy for recurrent malignant pericardial effusion. J Thorac Oncol. 2011 Dec; 6(12):2138-9. Jones DA, Jain AK. PMID: 22088990.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    44. Thrombus entrapment by a novel mesh-covered stent in ST-segment elevation myocardial infarction. J Am Coll Cardiol. 2011 Nov 22; 58(22):e39. Jain AK, Rothman MT. PMID: 22093516.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    45. Enteral bile acid treatment improves parenteral nutrition-related liver disease and intestinal mucosal atrophy in neonatal pigs. Am J Physiol Gastrointest Liver Physiol. 2012 Jan 15; 302(2):G218-24. Jain AK, Stoll B, Burrin DG, Holst JJ, Moore DD. PMID: 22094603.
      View in: PubMed   Mentions: 34     Fields:    Translation:Animals
    46. Chemical structural novelty: on-targets and off-targets. J Med Chem. 2011 Oct 13; 54(19):6771-85. Yera ER, Cleves AE, Jain AN. PMID: 21916467.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    47. Surface-based protein binding pocket similarity. Proteins. 2011 Sep; 79(9):2746-63. Spitzer R, Cleves AE, Jain AN. PMID: 21769944.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCells
    48. Clinical outcomes by geographic region for patients implanted with the zotarolimus-eluting stent. Arq Bras Cardiol. 2011 May; 96(5):353-62. Lotan C, Meredith IT, Jain A, Feres F, Firszt A, Garcia AF, Rothman MT. PMID: 21468534.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    49. Percutaneous occlusion of the left atrial appendage in non-valvular atrial fibrillation for the prevention of thromboembolism: NICE guidance. Heart. 2011 May; 97(9):762-5. Jain AK, Gallagher S. PMID: 21378010.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    50. Primary percutaneous coronary intervention for ST-elevation myocardial infarction in a patient with a single coronary artery arising from the right aortic sinus. J Invasive Cardiol. 2011 Mar; 23(3):E61-2. Gallagher SM, Jain AK, Archbold RA. PMID: 21364254.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    51. Acute myocarditis presenting as acute coronary syndrome: role of early cardiac magnetic resonance in its diagnosis. Heart. 2011 Aug; 97(16):1312-8. 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. PMID: 21106555.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    52. QMOD: physically meaningful QSAR. J Comput Aided Mol Des. 2010 Oct; 24(10):865-78. Jain AN. PMID: 20721601.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    53. Twelve-month outcomes in patients with diabetes implanted with a zotarolimus-eluting stent: results from the E-Five Registry. Heart. 2010 Jun; 96(11):848-53. Jain AK, Lotan C, Meredith IT, Feres F, Zambahari R, Sinha N, Rothman MT, E-Five Registry Investigators . PMID: 20478863.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    54. Molecular shape and medicinal chemistry: a perspective. J Med Chem. 2010 May 27; 53(10):3862-86. 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. PMID: 20158188.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansCells
    55. Histopathologic basis for the favorable survival after resection of intraductal papillary mucinous neoplasm-associated invasive adenocarcinoma of the pancreas. Ann Surg. 2010 Mar; 251(3):470-6. Poultsides GA, Reddy S, Cameron JL, Hruban RH, Pawlik TM, Ahuja N, Jain A, Edil BH, Iacobuzio-Donahue CA, Schulick RD, Wolfgang CL. PMID: 20142731.
      View in: PubMed   Mentions: 65     Fields:    Translation:Humans
    56. Physical binding pocket induction for affinity prediction. J Med Chem. 2009 Oct 08; 52(19):6107-25. Langham JJ, Cleves AE, Spitzer R, Kirshner D, Jain AN. PMID: 19754201.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    57. Prevention of thrombus embolization during primary percutaneous intervention using a novel mesh covered stent. Catheter Cardiovasc Interv. 2009 Jul 01; 74(1):88-93. Jain A, Weerackody R, Kennon S, Rothman M. PMID: 19360871.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    58. Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J Comput Aided Mol Des. 2009 Jun; 23(6):355-74. Jain AN. PMID: 19340588.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    59. Successful exclusion of large post-surgical pseudoaneurysms of the ascending aorta by a percutaneous approach. Ann Thorac Surg. 2009 Apr; 87(4):1281-4. Kannan BR, Jain AK, Qureshi SA, Rothman MT, Rosenthal E, Mathur A. PMID: 19324175.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    60. Image of the month. Gastrohepatic fistula following TACE for HCC. Arch Surg. 2009 Mar; 144(3):285-6. Jain A, Smith C, Geschwind JF, Pawlik TM. PMID: 19289671.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    61. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model. 2008 Sep; 48(9):1833-9. Langham JJ, Jain AN. PMID: 18771257.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    62. Recommendations for evaluation of computational methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):133-9. Jain AN, Nicholls A. PMID: 18338228.
      View in: PubMed   Mentions: 81     Fields:    Translation:HumansAnimals
    63. Customizing scoring functions for docking. J Comput Aided Mol Des. 2008 May; 22(5):269-86. Pham TA, Jain AN. PMID: 18273558.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    64. Bias, reporting, and sharing: computational evaluations of docking methods. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):201-12. Jain AN. PMID: 18075713.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    65. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des. 2008 Mar-Apr; 22(3-4):147-59. Cleves AE, Jain AN. PMID: 18074107.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    66. The role of ultrasound-guided fine-needle aspiration of axillary nodes in the staging of breast cancer. Ann Surg Oncol. 2008 Feb; 15(2):462-71. Jain A, Haisfield-Wolfe ME, Lange J, Ahuja N, Khouri N, Tsangaris T, Zhang Z, Balch C, Jacobs LK. PMID: 17985188.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    67. Real-world safety and efficacy of the endeavor zotarolimus-eluting stent: early data from the E-Five Registry. Am J Cardiol. 2007 Oct 22; 100(8B):77M-83M. Jain AK, Meredith IT, Lotan C, Rothman MT, Pateraki S, E-Five Investigators . PMID: 17950836.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCTClinical Trials
    68. Update on drug-eluting stents: as good as it gets? Clin Med (Lond). 2007 Aug; 7(4):401-4. Jain AK, Mathur A. PMID: 17882862.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    69. Complete removal of extensive right coronary artery thrombus by the use of an aspiration catheter to facilitate primary angioplasty. EuroIntervention. 2007 May; 3(1):166. Jain AK, Archbold RA. PMID: 19737704.
      View in: PubMed   Mentions:    Fields:    
    70. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J Comput Aided Mol Des. 2007 May; 21(5):281-306. Jain AN. PMID: 17387436.
      View in: PubMed   Mentions: 157     Fields:    
    71. 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 Inform. 2007 Feb 05; 2:10-21. Kingsley CB, Kuo WL, Polikoff D, Berchuck A, Gray JW, Jain AN. PMID: 19458754.
      View in: PubMed   Mentions:
    72. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006 Dec; 10(6):529-41. 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, Esserman L, Albertson DG, Waldman FM, Gray JW. PMID: 17157792.
      View in: PubMed   Mentions: 546     Fields:    Translation:HumansCells
    73. New developments in coronary stent technology. J Interv Cardiol. 2006 Dec; 19(6):493-9. Smith EJ, Jain AK, Rothman MT. PMID: 17107363.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    74. the coronary venous system: an alternative route of access to the myocardium. J Invasive Cardiol. 2006 Nov; 18(11):563-8. Jain AK, Smith EJ, Rothman MT. PMID: 17090824.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    75. Parameter estimation for scoring protein-ligand interactions using negative training data. J Med Chem. 2006 Oct 05; 49(20):5856-68. Pham TA, Jain AN. PMID: 17004701.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    76. Scoring functions for protein-ligand docking. Curr Protein Pept Sci. 2006 Oct; 7(5):407-20. Jain AN. PMID: 17073693.
      View in: PubMed   Mentions: 48     Fields:    Translation:AnimalsCells
    77. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem. 2006 May 18; 49(10):2921-38. Cleves AE, Jain AN. PMID: 16686535.
      View in: PubMed   Mentions: 31     Fields:    
    78. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006 Apr 18; 6:96. 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. PMID: 16620391.
      View in: PubMed   Mentions: 111     Fields:    Translation:HumansCells
    79. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. . 2006 Apr; 5(4):853-67. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay , Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN. PMID: 16648555.
      View in: PubMed   Mentions:
    80. A deterministic motif finding algorithm with application to the human genome. Bioinformatics. 2006 May 01; 22(9):1047-54. Hon LS, Jain AN. PMID: 16455748.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    81. Selective targeting of antitumor immune responses with engineered live-attenuated Listeria monocytogenes. Cancer Res. 2006 Jan 15; 66(2):1096-104. 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. PMID: 16424046.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    82. Pathway recognition and augmentation by computational analysis of microarray expression data. Bioinformatics. 2006 Jan 15; 22(2):233-41. Novak BA, Jain AN. PMID: 16278238.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    83. Success of a multidisciplinary heart failure clinic for initiation and up-titration of key therapeutic agents. Eur J Heart Fail. 2005 Mar 16; 7(3):405-10. Jain A, Mills P, Nunn LM, Butler J, Luddington L, Ross V, Cliffe P, Ranjadayalan K, Timmis AD. PMID: 15718181.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    84. Fractional genomic alteration detected by array-based comparative genomic hybridization independently predicts survival after hepatic resection for metastatic colorectal cancer. Clin Cancer Res. 2005 Mar 01; 11(5):1791-7. Mehta KR, Nakao K, Zuraek MB, Ruan DT, Bergsland EK, Venook AP, Moore DH, Tokuyasu TA, Jain AN, Warren RS, Terdiman JP, Waldman FM. PMID: 15756001.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    85. Mapping segmental and sequence variations among laboratory mice using BAC array CGH. Genome Res. 2005 Feb; 15(2):302-11. 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. PMID: 15687294.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    86. Expression of the tumor suppressor gene ARHI in epithelial ovarian cancer is associated with increased expression of p21WAF1/CIP1 and prolonged progression-free survival. Clin Cancer Res. 2004 Oct 01; 10(19):6559-66. Rosen DG, Wang L, Jain AN, Lu KH, Luo RZ, Yu Y, Liu J, Bast RC. PMID: 15475444.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    87. Virtual screening in lead discovery and optimization. Curr Opin Drug Discov Devel. 2004 Jul; 7(4):396-403. Jain AN. PMID: 15338948.
      View in: PubMed   Mentions: 37     Fields:    Translation:Cells
    88. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet. 2004 Jul 01; 13(13):1303-13. 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, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H. PMID: 15138198.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    89. High-resolution analysis of DNA copy number alterations in colorectal cancer by array-based comparative genomic hybridization. Carcinogenesis. 2004 Aug; 25(8):1345-57. Nakao K, Mehta KR, Fridlyand J, Moore DH, Jain AN, Lafuente A, Wiencke JW, Terdiman JP, Waldman FM. PMID: 15001537.
      View in: PubMed   Mentions: 71     Fields:    Translation:HumansCells
    90. Ligand-based structural hypotheses for virtual screening. J Med Chem. 2004 Feb 12; 47(4):947-61. Jain AN. PMID: 14761196.
      View in: PubMed   Mentions: 41     Fields:    Translation:Cells
    91. Determinants of BRAF mutations in primary melanomas. J Natl Cancer Inst. 2003 Dec 17; 95(24):1878-90. Maldonado JL, Fridlyand J, Patel H, Jain AN, Busam K, Kageshita T, Ono T, Albertson DG, Pinkel D, Bastian BC. PMID: 14679157.
      View in: PubMed   Mentions: 158     Fields:    Translation:Humans
    92. Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs. J Mol Biol. 2003 Sep 12; 332(2):305-10. Hon LS, Jain AN. PMID: 12948482.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    93. Genome-wide array CGH analysis of murine neuroblastoma reveals distinct genomic aberrations which parallel those in human tumors. Cancer Res. 2003 Sep 01; 63(17):5266-73. 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. PMID: 14500357.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansAnimalsCells
    94. 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. Ann Surg Oncol. 2003 Aug; 10(7):810-20. Jain A, Slansky JE, Matey LC, Allen HE, Pardoll DM, Schulick RD. PMID: 12900373.
      View in: PubMed   Mentions: 23     Fields:    Translation:Animals
    95. Shaping of tumor and drug-resistant genomes by instability and selection. Oncogene. 2003 Jul 10; 22(28):4370-9. Snijders AM, Fridlyand J, Mans DA, Segraves R, Jain AN, Pinkel D, Albertson DG. PMID: 12853973.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    96. Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma. Oncogene. 2003 Jul 03; 22(27):4281-6. Snijders AM, Nowee ME, Fridlyand J, Piek JM, Dorsman JC, Jain AN, Pinkel D, van Diest PJ, Verheijen RH, Albertson DG. PMID: 12833150.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCells
    97. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res. 2003 Jun 01; 63(11):2872-80. 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. PMID: 12782593.
      View in: PubMed   Mentions: 68     Fields:    Translation:HumansCells
    98. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol. 2003 Mar; 162(3):763-70. 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. PMID: 12598311.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCells
    99. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem. 2003 Feb 13; 46(4):499-511. Jain AN. PMID: 12570372.
      View in: PubMed   Mentions: 299     Fields:    Translation:Cells
    100. Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway. Cancer Res. 2002 Jul 01; 62(13):3636-40. 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. PMID: 12097266.
      View in: PubMed   Mentions: 67     Fields:    Translation:HumansCells
    101. Deriving quantitative conclusions from microarray expression data. Bioinformatics. 2002 Jul; 18(7):961-70. Olshen AB, Jain AN. PMID: 12117794.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    102. Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer. Cancer Res. 2002 Feb 15; 62(4):957-60. Wilhelm M, Veltman JA, Olshen AB, Jain AN, Moore DH, Presti JC, Kovacs G, Waldman FM. PMID: 11861363.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    103. Fully automatic quantification of microarray image data. Genome Res. 2002 Feb; 12(2):325-32. Jain AN, Tokuyasu TA, Snijders AM, Segraves R, Albertson DG, Pinkel D. PMID: 11827952.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansCells
    104. Molecular hashkeys: a novel method for molecular characterization and its application for predicting important pharmaceutical properties of molecules. J Med Chem. 1999 May 20; 42(10):1739-48. Ghuloum AM, Sage CR, Jain AN. PMID: 10346926.
      View in: PubMed   Mentions: 13     Fields:    
    105. IcePick: a flexible surface-based system for molecular diversity. J Med Chem. 1999 Jan 14; 42(1):60-6. Mount J, Ruppert J, Welch W, Jain AN. PMID: 9888833.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    106. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 1997 Mar; 6(3):524-33. Ruppert J, Welch W, Jain AN. PMID: 9070435.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    107. Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des. 1996 Oct; 10(5):427-40. Jain AN. PMID: 8951652.
      View in: PubMed   Mentions: 146     Fields:    Translation:Cells
    108. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol. 1996 Jun; 3(6):449-62. Welch W, Ruppert J, Jain AN. PMID: 8807875.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    109. Quantitative binding site model generation: compass applied to multiple chemotypes targeting the 5-HT1A receptor. J Med Chem. 1995 Apr 14; 38(8):1295-308. Jain AN, Harris NL, Park JY. PMID: 7731016.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    110. A shape-based machine learning tool for drug design. J Comput Aided Mol Des. 1994 Dec; 8(6):635-52. Jain AN, Dietterich TG, Lathrop RH, Chapman D, Critchlow RE, Bauer BE, Webster TA, Lozano-Perez T. PMID: 7738601.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    111. Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. J Med Chem. 1994 Jul 22; 37(15):2315-27. Jain AN, Koile K, Chapman D. PMID: 8057280.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
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