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Srinivasan Ramachandran

Title(s)RSCH DATA ANL 3, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    1. The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data. bioRxiv. 2025 Sep 04. Ahooyi TM, Stear B, Simmons JA, Metzger VT, Kumar P, Evangelista JE, Clarke DJB, Xie Z, Kim H, Jenkins SL, Maurya MR, Ramachandran S, Fahy E, Gillespie TH, Imam FT, Kokash N, Roth ME, Fullem R, Jevtic D, Mihajlovic A, Tiemeyer M, Bakker C, Schroeder AJ, Markowski J, Nedzel J, Hill DD, Terry J, Nemarich C, Boline J, Park PJ, Ardlie KG, Vora J, Mazumder R, Ranzinger R, de Bono B, Subramaniam S, Grethe JS, Yang JJ, Lambert CG, Resnick A, Milosavljevic A, Ma'ayan A, Silverstein JC, Taylor DM. PMID: 40832351; PMCID: PMC12363844.
      View in: PubMed   Mentions:
    2. Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput Biol. 2025 Apr; 21(4):e1012901. Clarke DJB, Evangelista JE, Xie Z, Marino GB, Byrd AI, Maurya MR, Srinivasan S, Yu K, Petrosyan V, Roth ME, Milinkov M, King CH, Vora JK, Keeney J, Nemarich C, Khan W, Lachmann A, Ahmed N, Agris A, Pan J, Ramachandran S, Fahy E, Esquivel E, Mihajlovic A, Jevtic B, Milinovic V, Kim S, McNeely P, Wang T, Wenger E, Brown MA, Sickler A, Zhu Y, Jenkins SL, Blood PD, Taylor DM, Resnick AC, Mazumder R, Milosavljevic A, Subramaniam S, Ma'ayan A. PMID: 40179105; PMCID: PMC11967941.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    3. Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease. Alzheimers Res Ther. 2025 Jan 04; 17(1):5. Valdes P, Caldwell AB, Liu Q, Fitzgerald MQ, Ramachandran S, Karch CM, Dominantly Inherited Alzheimer Network (DIAN), Galasko DR, Yuan SH, Wagner SL, Subramaniam S. PMID: 39754192; PMCID: PMC11699654.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    4. Limitations of the human iPSC-derived neuron model for early-onset Alzheimer's disease. Mol Brain. 2023 11 03; 16(1):75. Valdes P, Henry KW, Fitzgerald MQ, Muralidharan K, Caldwell AB, Ramachandran S, Goldstein LSB, Mobley WC, Galasko DR, Subramaniam S. PMID: 37924159; PMCID: PMC10623777.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    5. Endotype Characterization Reveals Mechanistic Differences Across Brain Regions in Sporadic Alzheimer's Disease. J Alzheimers Dis Rep. 2023; 7(1):957-972. Patel AO, Caldwell AB, Ramachandran S, Subramaniam S. PMID: 37849634; PMCID: PMC10578327.
      View in: PubMed   Mentions: 3  
    6. MetGENE: gene-centric metabolomics information retrieval tool. Gigascience. 2022 12 28; 12. Srinivasan S, Maurya MR, Ramachandran S, Fahy E, Subramaniam S. PMID: 37983749; PMCID: PMC10659118.
      View in: PubMed   Mentions: 2     Fields:    
    7. Transcriptomic profiling of sporadic Alzheimer's disease patients. Mol Brain. 2022 10 12; 15(1):83. Caldwell AB, Anantharaman BG, Ramachandran S, Nguyen P, Liu Q, Trinh I, Galasko DR, Desplats PA, Wagner SL, Subramaniam S. PMID: 36224601; PMCID: PMC9559068.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    8. ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. Exp Mol Med. 2022 06; 54(6):777-787. Azad P, Caldwell AB, Ramachandran S, Spann NJ, Akbari A, Villafuerte FC, Bermudez D, Zhao H, Poulsen O, Zhou D, Bafna V, Subramaniam S, Haddad GG. PMID: 35672450; PMCID: PMC9256584.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    9. Heme Oxygenase-1 at the Nexus of Endothelial Cell Fate Decision Under Oxidative Stress. Front Cell Dev Biol. 2021; 9:702974. Raghunandan S, Ramachandran S, Ke E, Miao Y, Lal R, Chen ZB, Subramaniam S. PMID: 34595164; PMCID: PMC8476872.
      View in: PubMed   Mentions: 7  
    10. The Efficacy of Plant-Based Ionizers in Removing Aerosol for COVID-19 Mitigation. Research (Wash D C). 2021; 2021:2173642. Suwardi A, Ooi CC, Daniel D, Tan CKI, Li H, Liang OYZ, Tang YK, Chee JY, Sadovoy A, Jiang SY, Ramachandran S, Ye E, Kang CW, Cheong WCD, Lim KH, Loh XJ. PMID: 33655212; PMCID: PMC7896556.
      View in: PubMed   Mentions:
    11. Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment. Int J Mol Sci. 2020 Oct 21; 21(20). Thakran S, Guin D, Singh P, Singh P, Kukal S, Rawat C, Yadav S, Kushwaha SS, Srivastava AK, Hasija Y, Saso L, Ramachandran S, Kukreti R. PMID: 33096746; PMCID: PMC7589654.
      View in: PubMed   Mentions:
    12. Direct DNA Methylation Profiling with an Electric Biosensor. ACS Nano. 2020 06 23; 14(6):6743-6751. Ban DK, Liu Y, Wang Z, Ramachandran S, Sarkar N, Shi Z, Liu W, Karkisaval AG, Martinez-Loran E, Zhang F, Glinsky G, Bandaru PR, Fan C, Lal R. PMID: 32407064.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    13. Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation. Int J Mol Sci. 2020 Mar 11; 21(6). Jiang L, Ramamoorthy R, Ramachandran S, Kumar PP. PMID: 32168953; PMCID: PMC7139402.
      View in: PubMed   Mentions:
    14. Generating Cyan Fluorescence with De Novo Tripeptides: An In Vitro Mutation Study on the Role of Single Amino Acid Residues and Their Sequence. Chembiochem. 2019 09 16; 20(18):2324-2330. Guo J, Ramachandran S, Zhong R, Lal R, Zhang F. PMID: 31013385.
      View in: PubMed   Mentions:    Fields:    
    15. Improved regression model to predict an impact of SOD1 mutations on ALS patients survival time based on analysis of hydrogen bond stability. J Mol Graph Model. 2019 01; 86:247-255. Alemasov NA, Ivanisenko NV, Taneja B, Taneja V, Ramachandran S, Ivanisenko VA. PMID: 30414557.
      View in: PubMed   Mentions:
    16. Micromachined Chip Scale Thermal Sensor for Thermal Imaging. ACS Nano. 2018 02 27; 12(2):1760-1767. Shekhawat GS, Ramachandran S, Jiryaei Sharahi H, Sarkar S, Hujsak K, Li Y, Hagglund K, Kim S, Aden G, Chand A, Dravid VP. PMID: 29401382.
      View in: PubMed   Mentions:
    17. Small molecule NPT-440-1 inhibits ionic flux through Aβ1-42 pores: Implications for Alzheimer's disease therapeutics. Nanomedicine. 2016 11; 12(8):2331-2340. Gillman AL, Lee J, Ramachandran S, Capone R, Gonzalez T, Wrasidlo W, Masliah E, Lal R. PMID: 27335341; PMCID: PMC5116404.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    18. Oligomerization of the microtubule-associated protein tau is mediated by its N-terminal sequences: implications for normal and pathological tau action. J Neurochem. 2016 06; 137(6):939-54. Feinstein HE, Benbow SJ, LaPointe NE, Patel N, Ramachandran S, Do TD, Gaylord MR, Huskey NE, Dressler N, Korff M, Quon B, Cantrell KL, Bowers MT, Lal R, Feinstein SC. PMID: 26953146; PMCID: PMC4899250.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimalsCells
    19. Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels. Methods Mol Biol. 2016; 1345:251-68. Jang H, Arce FT, Lee J, Gillman AL, Ramachandran S, Kagan BL, Lal R, Nussinov R. PMID: 26453217; PMCID: PMC7511997.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    20. Ion Channel Formation by Tau Protein: Implications for Alzheimer's Disease and Tauopathies. Biochemistry. 2015 Dec 22; 54(50):7320-5. Patel N, Ramachandran S, Azimov R, Kagan BL, Lal R. PMID: 26575330; PMCID: PMC4690196.
      View in: PubMed   Mentions: 24     Fields:    
    21. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PLoS One. 2015; 10(6):e0128711. Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S, Scaria V, Ramachandran S. PMID: 26035208; PMCID: PMC4452720.
      View in: PubMed   Mentions:
    22. Engineering geminivirus resistance in Jatropha curcus. Biotechnol Biofuels. 2014; 7(1):149. Ye J, Qu J, Mao HZ, Ma ZG, Rahman NE, Bai C, Chen W, Jiang SY, Ramachandran S, Chua NH. PMID: 25352912; PMCID: PMC4210599.
      View in: PubMed   Mentions:
    23. Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs. Chem Soc Rev. 2014 Oct 07; 43(19):6750-64. Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. PMID: 24566672; PMCID: PMC4143503.
      View in: PubMed   Mentions: 41     Fields:    Translation:HumansCells
    24. Role of the fast kinetics of pyroglutamate-modified amyloid-β oligomers in membrane binding and membrane permeability. Biochemistry. 2014 Jul 22; 53(28):4704-14. Lee J, Gillman AL, Jang H, Ramachandran S, Kagan BL, Nussinov R, Teran Arce F. PMID: 24950761; PMCID: PMC4215883.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    25. Measuring localized redox enzyme electron transfer in a live cell with conducting atomic force microscopy. Anal Chem. 2014 Aug 05; 86(15):7674-80. Alfonta L, Meckes B, Amir L, Schlesinger O, Ramachandran S, Lal R. PMID: 24979064; PMCID: PMC4215851.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    26. Activity and architecture of pyroglutamate-modified amyloid-β (AβpE3-42) pores. J Phys Chem B. 2014 Jul 03; 118(26):7335-44. Gillman AL, Jang H, Lee J, Ramachandran S, Kagan BL, Nussinov R, Teran Arce F. PMID: 24922585; PMCID: PMC4096221.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    27. Structure and permeability of ion-channels by integrated AFM and waveguide TIRF microscopy. Sci Rep. 2014 Mar 21; 4:4424. Ramachandran S, Arce FT, Patel NR, Quist AP, Cohen DA, Lal R. PMID: 24651823; PMCID: PMC3961736.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    28. Familial Alzheimer's disease Osaka mutant (ΔE22) β-barrels suggest an explanation for the different Aβ1-40/42 preferred conformational states observed by experiment. J Phys Chem B. 2013 Oct 03; 117(39):11518-29. Jang H, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. PMID: 24000923; PMCID: PMC3946471.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    29. Alzheimer's disease: which type of amyloid-preventing drug agents to employ? Phys Chem Chem Phys. 2013 Jun 21; 15(23):8868-77. Jang H, Connelly L, Arce FT, Ramachandran S, Lal R, Kagan BL, Nussinov R. PMID: 23450150; PMCID: PMC3663909.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimals
    30. High performance, LED powered, waveguide based total internal reflection microscopy. Sci Rep. 2013; 3:2133. Ramachandran S, Cohen DA, Quist AP, Lal R. PMID: 23823601; PMCID: PMC3701166.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    31. Mechanisms for the Insertion of Toxic, Fibril-like β-Amyloid Oligomers into the Membrane. J Chem Theory Comput. 2013 Jan 08; 9(1):822-833. Jang H, Connelly L, Arce FT, Ramachandran S, Kagan BL, Lal R, Nussinov R. PMID: 23316126; PMCID: PMC3539805.
      View in: PubMed   Mentions: 63     Fields:    
    32. Magnetic targeting of nanoparticles across the intact blood-brain barrier. J Control Release. 2012 Nov 28; 164(1):49-57. Kong SD, Lee J, Ramachandran S, Eliceiri BP, Shubayev VI, Lal R, Jin S. PMID: 23063548; PMCID: PMC4440873.
      View in: PubMed   Mentions: 76     Fields:    Translation:HumansAnimalsCells
    33. Effects of point substitutions on the structure of toxic Alzheimer's β-amyloid channels: atomic force microscopy and molecular dynamics simulations. Biochemistry. 2012 Apr 10; 51(14):3031-8. Connelly L, Jang H, Arce FT, Ramachandran S, Kagan BL, Nussinov R, Lal R. PMID: 22413858; PMCID: PMC7512688.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    34. All-d-Enantiomer of β-Amyloid Peptide Forms Ion Channels in Lipid Bilayers. J Chem Theory Comput. 2012 Mar 13; 8(3):1143-1152. Capone R, Jang H, Kotler SA, Connelly L, Teran Arce F, Ramachandran S, Kagan BL, Nussinov R, Lal R. PMID: 22423218; PMCID: PMC3302213.
      View in: PubMed   Mentions: 22     Fields:    
    35. Atomic force microscopy and MD simulations reveal pore-like structures of all-D-enantiomer of Alzheimer's β-amyloid peptide: relevance to the ion channel mechanism of AD pathology. J Phys Chem B. 2012 Feb 09; 116(5):1728-35. Connelly L, Jang H, Arce FT, Capone R, Kotler SA, Ramachandran S, Kagan BL, Nussinov R, Lal R. PMID: 22217000; PMCID: PMC4342054.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    36. Antimicrobial properties of amyloid peptides. Mol Pharm. 2012 Apr 02; 9(4):708-17. Kagan BL, Jang H, Capone R, Teran Arce F, Ramachandran S, Lal R, Nussinov R. PMID: 22081976; PMCID: PMC3297685.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansAnimals
    37. DNA zipper-based tweezers. Langmuir. 2012 Jan 10; 28(1):534-40. Landon PB, Ramachandran S, Gillman A, Gidron T, Yoon D, Lal R. PMID: 21875130.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    38. Mutant SOD1 forms ion channel: implications for ALS pathophysiology. Neurobiol Dis. 2012 Mar; 45(3):831-8. Allen MJ, Lacroix JJ, Ramachandran S, Capone R, Whitlock JL, Ghadge GD, Arnsdorf MF, Roos RP, Lal R. PMID: 21930207; PMCID: PMC3384721.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    39. Potential role of atomic force microscopy in systems biology. Wiley Interdiscip Rev Syst Biol Med. 2011 Nov-Dec; 3(6):702-16. Ramachandran S, Teran Arce F, Lal R. PMID: 21766465; PMCID: PMC4353599.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    40. Polymorphism of amyloid β peptide in different environments: implications for membrane insertion and pore formation. Soft Matter. 2011 May 09; 7(11):5267-5273. Arce FT, Jang H, Ramachandran S, Landon PB, Nussinov R, Lal R. PMID: 21918653; PMCID: PMC3170770.
      View in: PubMed   Mentions: 22     Fields:    
    41. Antimicrobial protegrin-1 forms amyloid-like fibrils with rapid kinetics suggesting a functional link. Biophys J. 2011 Apr 06; 100(7):1775-83. Jang H, Arce FT, Mustata M, Ramachandran S, Capone R, Nussinov R, Lal R. PMID: 21463591; PMCID: PMC3072611.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    42. β-Barrel topology of Alzheimer's β-amyloid ion channels. J Mol Biol. 2010 Dec 17; 404(5):917-34. Jang H, Arce FT, Ramachandran S, Capone R, Lal R, Nussinov R. PMID: 20970427; PMCID: PMC7291702.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansAnimalsCells
    43. Multidimensional atomic force microscopy: a versatile novel technology for nanopharmacology research. AAPS J. 2010 Dec; 12(4):716-28. Lal R, Ramachandran S, Arnsdorf MF. PMID: 20957528; PMCID: PMC2976997.
      View in: PubMed   Mentions: 10     Fields:    
    44. Scope of atomic force microscopy in the advancement of nanomedicine. Indian J Exp Biol. 2010 Oct; 48(10):1020-36. Ramachandran S, Lal R. PMID: 21299045.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimals
    45. Structural convergence among diverse, toxic beta-sheet ion channels. J Phys Chem B. 2010 Jul 29; 114(29):9445-51. Jang H, Teran Arce F, Ramachandran S, Capone R, Lal R, Nussinov R. PMID: 20608696; PMCID: PMC2908347.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    46. Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A. 2010 Apr 06; 107(14):6538-43. Jang H, Arce FT, Ramachandran S, Capone R, Azimova R, Kagan BL, Nussinov R, Lal R. PMID: 20308552; PMCID: PMC2851998.
      View in: PubMed   Mentions: 112     Fields:    Translation:HumansCells
    47. Misfolded amyloid ion channels present mobile beta-sheet subunits in contrast to conventional ion channels. Biophys J. 2009 Dec 02; 97(11):3029-37. Jang H, Arce FT, Capone R, Ramachandran S, Lal R, Nussinov R. PMID: 19948133; PMCID: PMC2784570.
      View in: PubMed   Mentions: 40     Fields:    Translation:Cells
    48. K3 fragment of amyloidogenic beta(2)-microglobulin forms ion channels: implication for dialysis related amyloidosis. J Am Chem Soc. 2009 Oct 21; 131(41):14938-45. Mustata M, Capone R, Jang H, Arce FT, Ramachandran S, Lal R, Nussinov R. PMID: 19824733; PMCID: PMC2782653.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    49. A novel role for connexin hemichannel in oxidative stress and smoking-induced cell injury. PLoS One. 2007 Aug 08; 2(8):e712. Ramachandran S, Xie LH, John SA, Subramaniam S, Lal R. PMID: 17684558; PMCID: PMC1933596.
      View in: PubMed   Mentions: 71     Fields:    Translation:AnimalsCells
    50. Atomic force microscopy imaging and electrical recording of lipid bilayers supported over microfabricated silicon chip nanopores: lab-on-a-chip system for lipid membranes and ion channels. Langmuir. 2007 Jan 30; 23(3):1375-80. Quist AP, Chand A, Ramachandran S, Daraio C, Jin S, Lal R. PMID: 17241061.
      View in: PubMed   Mentions: 9     Fields:    
    51. Cisplatin nanoliposomes for cancer therapy: AFM and fluorescence imaging of cisplatin encapsulation, stability, cellular uptake, and toxicity. Langmuir. 2006 Sep 12; 22(19):8156-62. Ramachandran S, Quist AP, Kumar S, Lal R. PMID: 16952256.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    52. Piezoresistive cantilever based nanoflow and viscosity sensor for microchannels. Lab Chip. 2006 Nov; 6(11):1450-4. Quist A, Chand A, Ramachandran S, Cohen D, Lal R. PMID: 17066169.
      View in: PubMed   Mentions: 6     Fields:    Translation:Animals
    53. Nanomechanics of hemichannel conformations: connexin flexibility underlying channel opening and closing. J Biol Chem. 2006 Aug 11; 281(32):23207-17. Liu F, Arce FT, Ramachandran S, Lal R. PMID: 16769719.
      View in: PubMed   Mentions: 26     Fields:    Translation:AnimalsCells
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