Publications

Cryo-EM structure of a dimeric B-Raf:14-3-3 complex reveals asymmetry in the active sites of B-Raf kinases

Kondo, Y, Ognjenović, J, Banerjee, S, Karandur, D, Merk, A, Kulhanek, K, Wong, K, Roose, JP, Subramaniam, S, Kuriyan, J.

Science Vol. 366, Issue 6461, pp. 109-115 (2019)

Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9

Zhu, X, Clarke, R, Puppala, AK, Chittori, S, Merk, A, Merrill B.J, Simonovic, M, Subramaniam, S.

Nat Struct Mol Biol. 26(8):679-685. (2019)

A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex

Marabelli, C, Marrocco, B, Pilotto, S, Chittori, S, Picaud, S, Marchese, S, Ciossani, G, Forneris, F, Filippakopoulos, P, Schoehn, G, Rhodes, D, Subramaniam, S, Mattevi, A.

Cell Rep. 27(2):387-399.e7. (2019)

Single-particle cryo-EM structure of a voltage-activated potassium channel in lipid nanodiscs

Matthies, D, Bae, C, Toombes, G, Fox, T, Bartesaghi, A, Subramaniam, S, Swartz, K.

Elife 7, pii: e37558. (2018)

Atomic Resolution Cryo-EM Structure of β-Galactosidase

Bartesaghi, A, Aguerrebere, C, Falconieri, V, Banerjee, S, Earl, LA, Zhu, X, Grigorieff N, Milne, JLS, Sapiro, G, Wu, X, Subramaniam, S.

Structure 26(6), 848-856. (2018) 

Cryo-EM structure of human rhodopsin bound to an inhibitory G protein

Kang, Y, Kuybeda, O, de Waal, PW, Mukherjee, S, Van Eps, N, Dutka, P, Zhou, XE, Bartesaghi, A, Erramilli, S, Morizumi, T, Gu, X, Yin, Y, Liu, P, Jiang, Y, Meng, X, Zhao, G, Melcher, K, Ernst, OP, Kossiakoff, AA, Subramaniam, S, Xu, HE.

Nature 558(7711), 553-558. (2018) 

Deep-learning-assisted Volume Visualization

Cheng, H-C, Cardone, A, Jain, S, Krokos, E, Narayan, K, Subramaniam, S, Varshney, A.

IEEE Transactions on Visualization and Computer Graphics 25(2), 1378-1391. (2018) 

Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N

Chittori, S, Hong, J, Saunders, H, Feng, H, Ghirlando, R, Kelly, AE, Bai, Y, Subramaniam, S.

Science 359(6373), 339-343. (2018)

Cryo-EM structures reveal mechanism and inhibition of DNA targeting by a CRISPR-Cas surveillance complex

Guo, TW, Bartesaghi, A, Yang, H, Falconieri, V, Rao, P, Merk, A, Eng, ET, Raczkowski, AM, Fox, T, Earl, LA, Patel, D, Subramaniam, S.

Cell 171(2), 414-426. (2017)

Broadly protective murine monoclonal antibodies against influenza B virus target highly conserved neuraminidase epitopes

Wohlbold, TJ, Podolsky, KA, Chromikova, V, Kirkpatrick, E, Falconieri, V, Meade, P, Amanat, F, Tan, J, tenOever, BR, Tan, GS, Subramaniam, S, Palese, P, Krammer, F.

Nature Microbiology 2(10), 1415-1424. (2017)

Building bridges between cellular and molecular structural biology

Patwardhan, A, Brandt, R, Butcher, SJ, Collinson, L, Gault, D, Grünewald, K, Hecksel, C, Huiskonen, JT, Iudin, A, Jones, ML, Korir, PK, Koster, AJ, Lagerstedt, I, Lawson, CL, Mastronarde, D, McCormick, M, Parkinson, H, Rosenthal, PB, Saalfeld, S, Saibil, HR, Sarntivijai, S, Solanes Valero, I, Subramaniam, S, Swedlow, JR, Tudose, I, Winn, M, Kleywegt, GJ.

Elife 6, pii: e25835. (2017)

Power Grid Protection of the Muscle Mitochondrial Reticulum

Glancy, B, Hartnell, LM, Combs, CA, Fenmou, A, Sun, J, Murphy, E, Subramaniam, S, Balaban, RS.

Cell Reports 19(3), 487-496. (2017)

Structural basis of kainate subtype glutamate receptor desensitization

Meyerson, JR, Chittori, S, Merk, A, Rao, P, Han, TH, Serpe, M, Mayer, ML, Subramaniam

Nature 537(7621), 567-571. (2016)

Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery

Merk, A, Bartesaghi, A, Banerjee, S, Falconieri, V, Rao, P, Davis, M, Pragani, R, Boxer, M, Earl, LA, Milne, JLS, Subramaniam, S.

Cell 165(7), 1698-1707. (2016)

Cryo-EM analysis of the conformational landscape of human P-glycoprotein (ABCB1) during its catalytic cycle

Frank, GA, Shukla, S, Rao, P, Borgnia, MJ, Bartesaghi, A, Merk, A, Mobin, A, Esser, L, Earl, LA, Gottesman, MM, Xia, D, Ambudkar, SV, Subramaniam, S.

Molecular Pharmacology 90(1), 35-41. (2016)

Using cryo-EM to map small ligands on dynamic metabolic enzymes: studies with glutamate dehydrogenase

Borgnia, MJ, Banerjee, S, Merk, A, Matthies, D, Bartesaghi, A, Rao, P, Pierson, J, Earl, LA, Falconieri, V, Subramaniam, S, Milne, JLS.

Molecular Pharmacology 89(6), 645-51. (2016)

Cryo-electron microscopy structures of chimeric hemagglutinin displayed on a universal influenza vaccine candidate

Tran, EEH, Podolsky, KA, Bartesaghi, A, Kuybeda, O, Grandinetti, G, Wohlbold, TJ, Tan, GS, Nachbagauer, R, Palese, P, Krammer, F, Subramaniam, S.

American Society for Microbiology 7(2), e00257-16. (2016)

Imaging cellular architecture with 3D SEM

Hartnell, LM, Earl, LA, Bliss, D, Moran, A, Subramaniam, S.

Encyclopedia of Cell Biology 2, 44-50. (2016)

Mitochondrial reticulum for cellular energy distribution in muscle

Glancy, B, Hartnell, LM, Malide, D, Yu, Z, Combs, CA, Connelly, PS, Subramaniam, S, Balaban, RS.

Nature 523, 617-620. (2015)

Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution

Sun, L, Zhang, X, Gao, S, Rao, PA, Padilla-Sanchez, V, Chen, Z, Sun, S, Xiang, Y, Subramaniam, S, Rao, VB, Rossmann, MG.

Nature Communications 6, 7548. (2015)

2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor

Bartesaghi, A, Merk, A, Banerjee, S, Matthies, D, Wu, X, Milne, J, Subramaniam, S.

Science 348, 1147-1151. (2015)

A versatile nano display platform from bacterial spore coat proteins

Wu, IL, Narayan, K, Castaing, JP, Tian, F, Subramaniam, S, Ramamurthi, KS.

Nature Communications 6, 6777. (2015)

Griffithsin tandemers: flexible and potent lectin inhibitors of the human immunodeficiency virus

Moulaei, T, Alexandre, KB, Shenoy, SR, Meyerson, J, Krumpe, LR, Constantine, B, Wilson, J, Buckheit, R, McMahon, JB, Subramaniam, S, Wlodawer, A, O’Keefe, BR.

Retrovirology 12, 6. (2015)

Maturation of the HIV-1 core by a non-diffusional phase transition

Frank, GA, Narayan, K, Bess, JW, Del Prete, GQ, Wu, X, Moran, A, Hartnell, LM, Earl, LA, Lifson, JD, Subramaniam, S.

Nature Communications 6, 5854. (2015)

Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

Meyerson, JR, Rao, P, Kumar, J, Chittori, S, Banerjee, S, Pierson, J, Mayer, ML, Subramaniam, S.

Scientific Reports 4, 7084. (2014)

A 3D cellular context for the macromolecular world

Patwardhan, A, Ashton, A, Brandt, R, Butcher, S, Carzaniga, R, Chiu, W, Collinson, L, Doux, P, Duke, E, Ellisman, MH, Franken, E, Grunewald, K, Heriche, JK, Koster, A, Kuhlbrandt, W, Lagerstedt, I, Larabell, C, Lawson, CL, Saibil, HR, Sanz-Garcia, E, Subramaniam, S, Verkade, P, Swedlow, JR, Kleywegt, GJ.

Nature Structural & Molecular Biology 21(10), 841- 845. (2014)

Three-dimensional imaging of viral infections

Risco, C, de Castro, IF, Sanz-Sanchez, L, Narayan, K, Grandinetti, G, Subramaniam, S.

Annual Review of Virology 1, 453-473. (2014)

Structural mechanism of glutamate receptor activation and desensitization

Meyerson, JR, Kumar, J, Chittori, S, Rao, P, Pierson, J, Bartesaghi, A, Mayer, ML, Subramaniam.

Nature 514, 328-334. (2014)

Spatial localization of the Ebola glycoprotein mucin-like domain using cryo-electron tomography

Tran, EEH, Simmons, JA, Bartesaghi, A, Shoemaker, CJ, Nelson, E, White, JM, Subramaniam, S.

Journal of Virology 88(18), 10958-10962. (2014)

3D imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission

Do, T, Murphy, G, Earl, LA, Del Prete, GQ, Grandinetti, G, Li, GH, Estes, JD, Rao, P, Trubey, CM, Thomas, J, Spector, J, Bliss, D, Nath, A, Lifson, JD, Subramaniam, S.

Journal of Virology 88(18), 10327-10339. (2014)

Multi-resolution correlative focused ion beam scanning electron microscopy: Applications to cell biology

Narayan, K, Danielson, CM, Lagarec, K, Lowekamp, BC, Coffman, P, Laquerre, A, Phaneuf, MW, Hope, TJ, Subramaniam, S.

Journal of Structural Biology 185(3), 278-284. (2014)

Single-Particle Cryo-Electron Microscopy (Cryo-EM): Progress, Challenges, and Perspectives for Further Improvement

Agard, D, Cheng YF, Glaeser RM, Subramaniam S
Advances in Imaging and Electron Physics, Vol 185 2014, 185:113-137.

Accelerating Discovery in 3D Microanalysis: Leveraging Open Source Software and Deskside High Performance Computing

Yoo, TS, Lowekamp BC, Kuybeda O, Narayan K, Frank GA, Bartesaghi A, Borgnia M, Subramaniam S, Sapiro G, Ackerman MJ

Microscopy and Microanalysis 2014, 20:774-775.

Structure of Beta-Galactosidase at 3.2 Å Resolution Obtained by Cryo-Electron Microscopy

Bartesaghi, A, Matthies D, Banerjee S, Merk A, Subramaniam S

Proc Natl Acad Sci U S A 2014, 111:11709-11714.

Multi-Resolution Correlative Focused Ion Beam Scanning Electron Microscopy: Applications to Cell Biology

Narayan, K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, Subramaniam S

J Struct Biol 2014, 185:278-284.

Three-Dimensional Imaging of Viral Infections

Risco, C, de Castro IF, Sanz-Sanchez L, Narayan K, Grandinetti G, Subramaniam S

Annu Rev Virol 2014, 1:453-473.

Self-Assembled Monolayers Improve Protein Distribution on Holey Carbon Cryo-EM Supports

Meyerson, JR, Rao P, Kumar J, Chittori S, Banerjee S, Pierson J, Mayer ML, Subramaniam S

Sci Rep 2014, 4:7084.

A 3D Cellular Context for the Macromolecular World

Patwardhan, A, Ashton A, Brandt R, Butcher S, Carzaniga R, Chiu W, Collinson L, Doux P, Duke E, Ellisman MH, Franken E, Grunewald K, Heriche JK, Koster A, Kuhlbrandt W, Lagerstedt I, Larabell C, Lawson CL, Saibil HR, Sanz-Garcia E, Subramaniam S, Verkade P, Swedlow JR, Kleywegt GJ

Nat Struct Mol Biol 2014, 21:841-845.

Structural Mechanism of Glutamate Receptor Activation and Desensitization

Meyerson, JR, Kumar J, Chittori S, Rao P, Pierson J, Bartesaghi A, Mayer ML, Subramaniam S

Nature 2014, 514:328-334.

Three-Dimensional Imaging of Hiv-1 Virological Synapses Reveals Membrane Architectures Involved in Virus Transmission

Do, T, Murphy G, Earl LA, Del Prete GQ, Grandinetti G, Li GH, Estes JD, Rao P, Trubey CM, Thomas J, Spector J, Bliss D, Nath A, Lifson JD, Subramaniam S

J Virol 2014, 88:10327-10339.

Spatial Localization of the Ebola Virus Glycoprotein Mucin-Like Domain Determined by Cryo-Electron Tomography

Tran, EE, Simmons JA, Bartesaghi A, Shoemaker CJ, Nelson E, White JM, Subramaniam S

J Virol 2014, 88:10958-10962.

Complexes of Neutralizing and Non-Neutralizing Affinity Matured fAbs with a Mimetic of the Internal Trimeric Coiled-Coil of HIV-1 gp41

Gustchina, E, Li M, Ghirlando R, Schuck P, Louis JM, Pierson J, Rao P, Subramaniam S, Gustchina A, Clore GM, Wlodawer A

PLoS ONE 2013, 8:e78187.

Derivation of Neural Stem Cells from Human Adult Peripheral CD34+ Cells for an Autologous Model of Neuroinflammation

Wang, T, Choi E, Monaco MC, Campanac E, Medynets M, Do T, Rao P, Johnson KR, Elkahloun AG, Von Geldern G, Johnson T, Subramaniam S, Hoffman DA, Major E, Nath A

PLoS ONE 2013, 8:e81720.

Chemotaxis Receptor Arrays

Venkatesh, MJ, Subramaniam S

Encyclopedia of Biophysics. 2013

HIV-1 Envelope Glycoprotein Structure

Merk, A, Subramaniam S

Curr Opin Struct Biol 2013, 23:268-276.

Glutamate Receptor Desensitization Is Mediated by Changes in Quaternary Structure of the Ligand Binding Domain

Schauder, DM, Kuybeda O, Zhang J, Klymko K, Bartesaghi A, Borgnia MJ, Mayer ML, Subramaniam S

Proc Natl Acad Sci U S A 2013, 110:5921-5926.

Catching HIV ‘in the Act’ with 3D Electron Microscopy

Earl, LA, Lifson JD, Subramaniam S

Trends Microbiol 2013, 21:397-404.

Prefusion Structure of Trimeric HIV-1 Envelope Glycoprotein Determined by Cryo-Electron Microscopy

Bartesaghi, A, Merk A, Borgnia MJ, Milne JL, Subramaniam S

Nat Struct Mol Biol 2013, 20:1352-1357.

A Collaborative Framework for 3D Alignment and Classification of Heterogeneous Subvolumes in Cryo-Electron Tomography

Kuybeda, O, Frank GA, Bartesaghi A, Borgnia M, Subramaniam S, Sapiro G

J Struct Biol 2013, 181:116-127.

Cryo-Electron Microscopy–a Primer for the Non-Microscopist

Milne, JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S

FEBS J 2013, 280:28-45.

Molecular Structures of Trimeric Hiv-1 Env in Complex with Small Antibody Derivatives

Meyerson, JR, Tran EE, Kuybeda O, Chen W, Dimitrov DS, Gorlani A, Verrips T, Lifson JD, Subramaniam S

Proc Natl Acad Sci U S A 2013, 110:513-518.

HIV-1 Envelope Glycoprotein Trimers Display Open Quaternary Conformation When Bound to the Gp41 Membrane-Proximal External-Region-Directed Broadly Neutralizing Antibody Z13e1

Harris, AK, Bartesaghi A, Milne JL, Subramaniam S

J Virol 2013, 87:7191-7196.

Structure and Accessibility of HA Trimers on Intact 2009 H1N1 Pandemic Influenza Virus to Stem Region-Specific Neutralizing Antibodies

Harris, AK, Meyerson JR, Matsuoka Y, Kuybeda O, Moran A, Bliss D, Das SR, Yewdell JW, Sapiro G, Subbarao K, Subramaniam S

Proc Natl Acad Sci U S A 2013, 110:4592-4597.

Structure of Trimeric HIV-1 Envelope Glycoproteins

Subramaniam, S

Proc Natl Acad Sci U S A 2013, 110:E4172-4174.

Targeted Conformational Search with Map-Restrained Self-Guided Langevin Dynamics: Application to Flexible Fitting into Electron Microscopic Density Maps

Wu, X, Subramaniam S, Case DA, Wu KW, Brooks BR

J Struct Biol 2013, 183:429-440.

There is No Overkill in Biochemistry

Karnik, S, Subramaniam S

Resonance 2012, 17:1157-1164.

Structural Mechanism of Trimeric HIV-1 Envelope Glycoprotein Activation

Tran, EE, Borgnia MJ, Kuybeda O, Schauder DM, Bartesaghi A, Frank GA, Sapiro G, Milne JL, Subramaniam S

PLoS Pathog 2012, 8:e1002797.

Shape-Based Regularization of Electron Tomographic Reconstruction

Gopinath, A, Xu G, Ress D, Oktem O, Subramaniam S, Bajaj C

IEEE Trans Med Imaging 2012, 31:2241-2252.

Data Management Challenges in Three-Dimensional EM

Patwardhan, A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-Garcia E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ

Nat Struct Mol Biol 2012, 19:1203-1207.

Protein Secondary Structure Determination by Constrained Single-Particle Cryo-Electron Tomography

Bartesaghi, A, Lecumberry F, Sapiro G, Subramaniam S

Structure 2012, 20:2003-2013.

Computational Separation of Conformational Heterogeneity Using Cryo-Electron Tomography and 3D Sub-Volume Averaging

Frank, GA, Bartesaghi A, Kuybeda O, Borgnia MJ, White TA, Sapiro G, Subramaniam S

J Struct Biol 2012, 178:165-176.

Chemical Mapping of Mammalian Cells by Atom Probe Tomography

Narayan, K, Prosa TJ, Fu J, Kelly TF, Subramaniam S

J Struct Biol 2012, 178:98-107.

Visualizing Cells and Humans in 3D: Biomedical Image Analysis at Nanometer and Meter Scales

Yoo, TS, Bliss D, Lowekamp BC, Chen DT, Murphy GE, Narayan K, Hartnell LM, Do T, Subramaniam S

IEEE Comput Graph Appl 2012, 32:39-49.

Correlative 3D Imaging of Whole Mammalian Cells with Light and Electron Microscopy

Murphy, GE, Narayan K, Lowekamp BC, Hartnell LM, Heymann JA, Fu J, Subramaniam S

J Struct Biol 2011, 176:268-278.

Three-Dimensional Structures of Soluble CD4-Bound States of Trimeric Simian Immunodeficiency Virus Envelope Glycoproteins Determined by Using Cryo-Electron Tomography

White, TA, Bartesaghi A, Borgnia MJ, de la Cruz MJ, Nandwani R, Hoxie JA, Bess JW, Lifson JD, Milne JL, Subramaniam S

J Virol 2011, 85:12114-12123.

Determination of Molecular Structures of HIV Envelope Glycoproteins Using Cryo-Electron Tomography and Automated Sub-Tomogram Averaging

Meyerson, JR, White TA, Bliss D, Moran A, Bartesaghi A, Borgnia MJ, de la Cruz MJ, Schauder D, Hartnell LM, Nandwani R, Dawood M, Kim B, Kim JH, Sununu J, Yang L, Bhatia S, Subramaniam C, Hurt DE, Gaudreault L, Subramaniam S

J Vis Exp 2011, 10.3791/2770:e2770.

Chemotaxis Kinase Chea Is Activated by Three Neighbouring Chemoreceptor Dimers as Effectively as by Receptor Clusters

Li, M, Khursigara CM, Subramaniam S, Hazelbauer GL

Mol Microbiol 2011, 79:677-685.

Compositional Mapping of the Surface and Interior of Mammalian Cells at Submicrometer Resolution

Szakal, C, Narayan K, Fu J, Lefman J, Subramaniam S

Anal Chem 2011, 83:1207-1213.

Trimeric HIV-1 Glycoprotein gp140 Immunogens and Native HIV-1 Envelope Glycoproteins Display the Same Closed and Open Quaternary Molecular Architectures

Harris, A, Borgnia MJ, Shi D, Bartesaghi A, He H, Pejchal R, Kang YK, Depetris R, Marozsan AJ, Sanders RW, Klasse PJ, Milne JL, Wilson IA, Olson WC, Moore JP, Subramaniam S

Proc Natl Acad Sci U S A 2011, 108:11440-11445.

Structural Plasticity of a Transmembrane Peptide Allows Self-Assembly into Biologically Active Nanoparticles

Tarasov, SG, Gaponenko V, Howard OM, Chen Y, Oppenheim JJ, Dyba MA, Subramaniam S, Lee Y, Michejda C, Tarasova NI

Proc Natl Acad Sci U S A 2011, 108:9798-9803.

Spiral Architecture of the Nucleoid in Bdellovibrio Bacteriovorus

Butan, C, Hartnell LM, Fenton AK, Bliss D, Sockett RE, Subramaniam S, Milne JL

J Bacteriol 2011, 193:1341-1350.

Lateral Density of Receptor Arrays in the Membrane Plane Influences Sensitivity of the E. Coli Chemotaxis Response

Khursigara, CM, Lan G, Neumann S, Wu X, Ravindran S, Borgnia MJ, Sourjik V, Milne J, Tu Y, Subramaniam S

EMBO J 2011, 30:1719-1729.

HIV-1 Activates CDC42 and Induces Membrane Extensions in Immature Dendritic Cells to Facilitate Cell-to-Cell Virus Propagation

Nikolic, DS, Lehmann M, Felts R, Garcia E, Blanchet FP, Subramaniam S, Piguet V

Blood 2011, 118:4841-4852.

A Coiled-Coil-Repeat Protein ‘Ccrp’ in Bdellovibrio Bacteriovorus Prevents Cellular Indentation, but Is Not Essential for Vibroid Cell Morphology

Fenton, AK, Hobley L, Butan C, Subramaniam S, Sockett RE

FEMS Microbiology Letters 2010, 313:89-95.

Ion-Abrasion Scanning Electron Microscopy Reveals Distorted Liver Mitochondrial Morphology in Murine Methylmalonic Acidemia

Murphy, GE, Lowekamp BC, Zerfas PM, Chandler RJ, Narasimha R, Venditti CP, Subramaniam S

J Struct Biol 2010, 171:125-132.

Molecular Architectures of Trimeric SIV and HIV-1 Envelope Glycoproteins on Intact Viruses: Strain-Dependent Variation in Quaternary Structure

White, TA, Bartesaghi A, Borgnia MJ, Meyerson JR, de la Cruz MJ, Bess JW, Nandwani R, Hoxie JA, Lifson JD, Milne JL, Subramaniam S

PLoS Pathog 2010, 6:e1001249.

3D Visualization of HIV Transfer at the Virological Synapse between Dendritic Cells and T Cells

Felts, RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell LM, Ruthel GT, Schneider DK, Nagashima K, Bess JW, Jr., Bavari S, Lowekamp BC, Bliss D, Lifson JD, Subramaniam S

Proc Natl Acad Sci U S A 2010, 107:13336-13341.

3D Imaging of Mammalian Cells with Ion-Abrasion Scanning Electron Microscopy

Heymann, JA, Shi D, Kim S, Bliss D, Milne JL, Subramaniam S

J Struct Biol 2009, 166:1-7.

Membrane Protein Structure Determination Using Cryo-Electron Tomography and 3D Image Averaging

Bartesaghi, A, Subramaniam S

Curr Opin Struct Biol 2009, 19:402-407.

Structural Snapshots of Conformational Changes in a Seven-Helix Membrane Protein: Lessons from Bacteriorhodopsin

Hirai, T, Subramaniam S, Lanyi JK

Curr Opin Struct Biol 2009, 19:433-439.

Staphylococcal Enterotoxin a Induces Small Clusters of HLA-DR1 on B Cells

Narayan, K, Perkins EM, Murphy GE, Dalai SK, Edidin M, Subramaniam S, Sadegh-Nasseri S

PLoS ONE 2009, 4:e6188.

3D Imaging of Diatoms with Ion-Abrasion Scanning Electron Microscopy

Hildebrand, M, Kim S, Shi D, Scott K, Subramaniam S

J Struct Biol 2009, 166:316-328.

Automatic Joint Classification and Segmentation of Whole Cell 3D Images

Narasimha, R, Ouyang H, Gray A, McLaughlin SW, Subramaniam S

Pattern Recognition 2009, 42:1067-1079.

Protein Conformational Changes in the Bacteriorhodopsin Photocycle: Comparison of Findings from Electron and X-Ray Crystallographic Analyses

Hirai, T, Subramaniam S

PLoS ONE 2009, 4:e5769.

Ion-Abrasion Scanning Electron Microscopy Reveals Surface-Connected Tubular Conduits in HIV-Infected Macrophages

Bennett, AE, Narayan K, Shi D, Hartnell LM, Gousset K, He H, Lowekamp BC, Yoo TS, Bliss D, Freed EO, Subramaniam S

PLoS Pathog 2009, 5:e1000591.

Cryo-Electron Tomography of Bacteria: Progress, Challenges and Future Prospects

Milne, JL, Subramaniam S

Nat Rev Microbiol 2009, 7:666-675.

3D Imaging of Diatoms with Ion Abrasion Scanning Electron Microscopy

Hildebrand, M, Kim S, Shi D, Subramaniam S

Microscopy and Microanalysis 2008, 14:972-973.

Molecular Architecture of Native HIV-1 gp 120 Trimers

Liu, J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S

Nature 455, 109–113 (2008).

Three-Dimensional Imaging of the Highly Bent Architecture of Bdellovibrio Bacteriovorus by Using Cryo-Electron Tomography

Borgnia, MJ, Subramaniam S, Milne JL

J Bacteriol 2008, 190:2588-2596.

Electron Tomography in Nanoparticle Imaging and Analysis

Lengyel, JS, Milne JL, Subramaniam S

Nanomedicine (Lond) 2008, 3:125-131.

Stoichiometry and Absolute Quantification of Proteins with Mass Spectrometry Using Fluorescent and Isotope-Labeled Concatenated Peptide Standards

Nanavati, D, Gucek M, Milne JL, Subramaniam S, Markey SP

Mol Cell Proteomics 2008, 7:442-447.

Extended Polypeptide Linkers Establish the Spatial Architecture of a Pyruvate Dehydrogenase Multienzyme Complex

Lengyel, JS, Stott KM, Wu X, Brooks BR, Balbo A, Schuck P, Perham RN, Subramaniam S, Milne JL

Structure 2008, 16:93-103

Classification and 3D Averaging with Missing Wedge Correction in Biological Electron Tomography

Bartesaghi, A, Sprechmann P, Liu J, Randall G, Sapiro G, Subramaniam S

J Struct Biol 2008, 162:436-450.

Chemoreceptors in Caulobacter Crescentus: Trimers of Receptor Dimers in a Partially Ordered Hexagonally Packed Array

Khursigara, CM, Wu X, Subramaniam S

J Bacteriol 2008, 190:6805-6810.

Evaluation of Denoising Algorithms for Biological Electron Tomography

Narasimha, R, Aganj I, Bennett AE, Borgnia MJ, Zabransky D, Sapiro G, McLaughlin SW, Milne JL, Subramaniam S

J Struct Biol 2008, 164:7-17.

Role of HAMP Domains in Chemotaxis Signaling by Bacterial Chemoreceptors

Khursigara, CM, Wu X, Zhang P, Lefman J, Subramaniam S

Proc Natl Acad Sci U S A 2008, 105:16555-16560.

Regularization for Inverting the Radon Transform with Wedge Consideration

Aganj, L, Bartesaghi A, Borgnia M, Liao HY, Sapiro G, Subramaniam S

2007 4th IEEE International Symposium on Biomedical Imaging : Macro to Nano, Vols 1-3 2007

Classification, Averaging and Reconstruction of Macromolecules in Electron Tomography

Bartesaghi, A, Sprechmann P, Randall G, Sapiro G, Subramaniam S

2007 4th IEEE International Symposium on Biomedical Imaging : Macro to Nano, Vols 1-3 2007, 

From Gigabytes to Bytes: Automated Denoising and Feature Identification in Electron Tomograms of Intact Bacterial Cells

Narasimha, R, Aganj I, Borgnia M, Sapiro G, McLaughlin S, Milne J, Subramaniamo S

2007 4th IEEE International Symposium on Biomedical Imaging : Macro to Nano, Vols 1-3 2007

Gigabytes to Bytes: Automated Denoising and Feature Extraction as Applied to the Analysis of HIV Architecture and Variability Using Electron Tomography

Narasimha, R, Bennett A, Zabransky D, Sougrat R, McLaughlin S, Subramaniam S

2007 IEEE International Conference on Acoustics, Speech, and Signal Processing, Vol I, Pts 1-3, Proceedings 2007

Determination of Protein Structures in Situ: Electron Tomography of Intact Viruses and Cells

Subramaniam, S

2007 4th IEEE International Symposium on Biomedical Imaging : Macro to Nano, Vols 1-3 2007

Electron Tomography of Bacterial Chemotaxis Receptor Assemblies

Zhang, P, Weis RM, Peters PJ, Subramaniam S

Methods Cell Biol 2007, 79:373-384.

Automated 100-Position Specimen Loader and Image Acquisition System for Transmission Electron Microscopy

Lefman, J, Morrison R, Subramaniam S

J Struct Biol 2007, 158:318-326.

Direct Visualization of Escherichia Coli Chemotaxis Receptor Arrays Using Cryo-Electron Microscopy

Zhang, P, Khursigara CM, Hartnell LM, Subramaniam S

Proc Natl Acad Sci U S A 2007, 104:3777-3781.

Electron Tomography of the Contact between T Cells and SIV/HIV-1: Implications for Viral Entry

Sougrat, R, Bartesaghi A, Lifson JD, Bennett AE, Bess JW, Zabransky DJ, Subramaniam S

PLoS Pathog 2007, 3:e63.

Cell Surface Filaments of the Gliding Bacterium Flavobacterium Johnsoniae Revealed by Cryo-Electron Tomography

Liu, J, McBride MJ, Subramaniam S

J Bacteriol 2007, 189:7503-7506.

Electron Tomography of Viruses

Subramaniam, S, Bartesaghi A, Liu J, Bennett AE, Sougrat R

Curr Opin Struct Biol 2007, 17:596-602.

Cryoelectron Tomographic Analysis of an HIV-Neutralizing Protein and Its Complex with Native Viral gp120

Bennett, A, Liu J, Van Ryk D, Bliss D, Arthos J, Henderson RM, Subramaniam S

J Biol Chem 2007, 282:27754-27759.

Automated, 100-Specimen Loading and Imaging System for Transmission Electron Microscopy

Lefman, J, Morrison R, Subramaniam S

Microscopy and Microanalysis 2006, 12:1100-1101.

Structure and Function of Icosahedral Pyruvate Dehydrogenase Complexes

Milne J, Wu X, Borgnia M, Lengyel J, Shi D, Perham R, Subramaniam S

Microscopy and Microanalysis. Cambridge University Press; 2006;12(S02):26–27.

Bridging the Imaging Gap in Nanobiology with Three-Dimensional Electron Microscopy

Subramaniam, S

2006 Bio- Micro- and Nanosystems Conference 2006

The SIV Surface Spike Imaged by Electron Tomography: One Leg or Three?

Subramaniam, S

PLoS Pathog 2006, 2:e91.

Molecular Structure of a 9-MDa Icosahedral Pyruvate Dehydrogenase Subcomplex Containing the E2 and E3 Enzymes Using Cryoelectron Microscopy

Milne, JL, Wu X, Borgnia MJ, Lengyel JS, Brooks BR, Shi D, Perham RN, Subramaniam S

J Biol Chem 2006, 281:4364-4370.

Site-Specific 3D Imaging of Cells and Tissues with a Dual Beam Microscope

Heymann, JA, Hayles M, Gestmann I, Giannuzzi LA, Lich B, Subramaniam S

J Struct Biol 2006, 155:63-73.

Bridging the Imaging Gap: Visualizing Subcellular Architecture with Electron Tomography

Subramaniam, S

Curr Opin Microbiol 2005, 8:316-322.

Electron Tomography of Degenerating Neurons in Mice with Abnormal Regulation of Iron Metabolism

Zhang, P, Land W, Lee S, Juliani J, Lefman J, Smith SR, Germain D, Kessel M, Leapman R, Rouault TA, Subramaniam S

J Struct Biol 2005, 150:144-153.

An Energy-Based Three-Dimensional Segmentation Approach for the Quantitative Interpretation of Electron Tomograms

Bartesaghi, A, Sapiro G, Subramaniam S

IEEE Trans Image Process 2005, 14:1314-1323.

A New Approach for 3D Segmentation of Cellular Tomograms Obtained Using Three-Dimensional Electron Microscopy

Bartesaghi, A, Sapiro G, Lee S, Lefman J, Wahl S, Orenstein J, Subramaniam S

2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821), Arlington, VA, USA, 2004, pp. 5-8 Vol. 1,

Site-Specific 3D Imaging of Cells and Tissues Using Dualbeam Technology

Gestmann, I, Hayles M, Shi D, Kumar G, Giannuzzi L, Lich B, Subramaniam S

Microscopy and Microanalysis 2004, 10:1124-1125.

Structure and Transport Mechanism of the Bacterial Oxalate Transporter OxIT

Hirai, T, Subramaniam S

Biophysical Journal 2004, 87:3600-3607.

A Template-Propagation Method for Segmentation of Filamentous Structures in Electron Tomograms

Shen, WC, Zhang PJ, Germain D, Rouault T, Subramaniam S

2004 2nd IEEE International Symposium on Biomedical Imaging: Nano to Macro (IEEE Cat No. 04EX821), Arlington, VA, USA, 2004, pp. 1-4 Vol. 1

Three-Dimensional Electron Microscopy at Molecular Resolution

Subramaniam, S, Milne JL

Annu Rev Biophys Biomol Struct 2004, 33:141-155.

Three-Dimensional Electron Microscopic Imaging of Membrane Invaginations in Escherichia Coli Overproducing the Chemotaxis Receptor Tsr

Lefman, J, Zhang P, Hirai T, Weis RM, Juliani J, Bliss D, Kessel M, Bos E, Peters PJ, Subramaniam S

J Bacteriol 2004, 186:5052-5061.

Direct Visualization of Receptor Arrays in Frozen-Hydrated Sections and Plunge-Frozen Specimens of E. Coli Engineered to Overproduce the Chemotaxis Receptor Tsr

Zhang, P, Bos E, Heymann J, Gnaegi H, Kessel M, Peters PJ, Subramaniam S

J Microsc 2004, 216:76-83.

3D Imaging of Membrane Networks in a Bacterial Cell Using Electron Tomography

Zhang, P, Lefman J, Kessel M, Juliani J, Hirai T, Weis RM, Peters P, Subramaniam S

Microscopy and Microanalysis 2003, 9:1168-1169.

Automated Image Acquisition and Processing Using a New Generation of 4k×4k CCD Cameras for Cryo Electron Microscopic Studies of Macromolecular Assemblies

Zhang, P, Borgnia MJ, Mooney P, Shi D, Pan M, O’Herron P, Mao A, Brogan D, Milne JLS, Subramaniam S

Journal of Structural Biology 2003, 143:135-144.

Projection Structure of the Bacterial Oxalate Transporter Oxlt at 3.4 Å Resolution

Heymann, JA, Hirai T, Shi D, Subramaniam S

J Struct Biol 2003, 144:320-326.

A Core-Weighted Fitting Method for Docking Atomic Structures into Low-Resolution Maps: Application to Cryo-Electron Microscopy

Wu, X, Milne JLS, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR

Journal of Structural Biology 2003, 141:63-76.

Electron Microscopic Analysis of Membrane Assemblies Formed by the Bacterial Chemotaxis Receptor Tsr

Weis, RM, Hirai T, Chalah A, Kessel M, Peters PJ, Subramaniam S

J Bacteriol 2003, 185:3636-3643.

Structural Insights into the Mechanism of Proton Pumping by Bacteriorhodopsin

Hirai, T, Subramaniam S

FEBS Letters 2003, 545:2-8.

Structural Model for 12-Helix Transporters Belonging to the Major Facilitator Superfamily

Hirai, T, Heymann JA, Maloney PC, Subramaniam S

J Bacteriol 2003, 185:1712-1718.

Molecular Structure of an Icosahedral Pyruvate Dehydrogenase Complex

Subramaniam, S, Shi D, Perham RN, Milne JLS

Microscopy and Microanalysis 2002, 8:214-215.

Three-Dimensional Structure of a Bacterial Oxalate Transporter

Hirai, T, Heymann JA, Shi D, Sarker R, Maloney PC, Subramaniam S

Nat Struct Biol 2002, 9:597-600.

From Structure to Mechanism: Electron Crystallographic Studies of Bacteriorhodopsin

Subramaniam, S, Hirai T, Henderson R

Philos Trans A Math Phys Eng Sci 2002, 360:859-874.

Proton Translocation by Bacteriorhodopsin in the Absence of Substantial Conformational Changes

Tittor, J, Paula S, Subramaniam S, Heberle J, Henderson R, Oesterhelt D

J Mol Biol 2002, 319:555-565.

Molecular Architecture and Mechanism of an Icosahedral Pyruvate Dehydrogenase Complex: A Multifunctional Catalytic Machine

Milne, JL, Shi D, Rosenthal PB, Sunshine JS, Domingo GJ, Wu X, Brooks BR, Perham RN, Henderson R, Subramaniam S

EMBO J 2002, 21:5587-5598.

Projection Structure and Molecular Architecture of Oxlt, a Bacterial Membrane Transporter

Heymann, JA, Sarker R, Hirai T, Shi D, Milne JL, Maloney PC, Subramaniam S

EMBO J 2001, 20:4408-4413.

Automated Data Collection with a Tecnai 12 Electron Microscope: Applications for Molecular Imaging by Cryomicroscopy

Zhang, P, Beatty A, Milne JL, Subramaniam S

J Struct Biol 2001, 135:251-261.

Crystallographic Analysis of Protein Conformational Changes in the Bacteriorhodopsin Photocycle

Subramaniam, S, Henderson R

Biochim Biophys Acta 2000, 1460:157-165.

CCD Detectors in High-Resolution Biological Electron Microscopy

Faruqi, AR, Subramaniam S

Q Rev Biophys 2000, 33:1-27.

Integration of Deletion Mutants of Bovine Rhodopsin into the Membrane of the Endoplasmic Reticulum

Heymann, JAW, Subramaniam S

Molecular Membrane Biology 2000, 17:165-174.

The Structure of Bacteriorhodopsin: An Emerging Consensus

Subramaniam, S

Curr Opin Struct Biol 1999, 9:462-468.

Electron Crystallography of Bacteriorhodopsin with Millisecond Time Resolution

Subramaniam, S, Henderson R

J Struct Biol 1999, 128:19-25.

Cooled CCD Detector with Tapered Fibre Optics for Recording Electron Diffraction Patterns

Faruqi, AR, Henderson R, Subramaniam S

Ultramicroscopy 1999, 75:235-250.

Protein Conformational Changes in the Bacteriorhodopsin Photocycle

Subramaniam, S, Lindahl M, Bullough P, Faruqi AR, Tittor J, Oesterhelt D, Brown L, Lanyi J, Henderson R

J Mol Biol 1999, 287:145-161.

Evidence for a Long-Lived 13-Cis-Containing Intermediate in the Photocycle of the Leu 93 ->Ala Bacteriorhodopsin Mutant

Delaney, JK, Schmidt P, Atkinson GH, Subramaniam S

Journal of Physical Chemistry B 1997, 101.

Expression of Bacteriorhodopsin in Sf9 and Cos-1 Cells

Heymann, J, Jager R, Subramaniam S

J Bioenerg Biomembr 1997, 29:55-59.

Studies of Rh1 Metarhodopsin Stabilization in Wild-Type Drosophila and in Mutants Lacking One or Both Arrestins

Kiselev, A, Subramaniam S

Biochemistry 1997, 36:2188-2196.

Structural Changes Underlying Proton Pumping by Bacteriorhodopsin

Henderson, R, Bullough P, Lindahl M, Subramaniam S

FASEB Journal 1997, 11:A992-A992.

Electron Diffraction Studies of Light-Induced Conformational Changes in the Leu-93 to Ala Bacteriorhodopsin Mutant

Subramaniam, S, Faruqi AR, Oesterhelt D, Henderson R

Proc Natl Acad Sci U S A 1997, 94:1767-1772.

Reducing the Flexibility of Retinal Restores a Wild-Type-Like Photocycle in Bacteriorhodopsin Mutants Defective in Protein-Retinal Coupling

Delaney, JK, Yahalom G, Sheves M, Subramaniam S

Proc Natl Acad Sci U S A 1997, 94:5028-5033.

Expression, Stability, and Membrane Integration of Truncation Mutants of Bovine Rhodopsin

Heymann, JA, Subramaniam S

Proc Natl Acad Sci U S A 1997, 94:4966-4971.

The Residues Leu 93 and Asp 96 Act Independently in the Bacteriorhodopsin Photocycle: Studies with the Leu 93-to Ala, Asp 96 to Asn Double Mutant

Delaney, JK, Subramaniam S

Biophysical Journal 1996, 70:2366-2372.

Modulation of Arrestin Release in the Light-Driven Regeneration of Rh1 Drosophila Rhodopsin

Kiselev, A, Subramaniam S

Biochemistry 1996, 35:1848-1855.

Molecular Mechanism of Protein-Retinal Coupling in Bacteriorhodopsin

Delaney, JK, Schweiger U, Subramaniam S

Proc Natl Acad Sci U S A 1995, 92:11120-11124.

Activation and Regeneration of Rhodopsin in the Insect Visual Cycle

Kiselev, A, Subramaniam S

Science 1994, 266:1369-1373.

Electron Diffraction Analysis of Structural Changes in the Photocycle of Bacteriorhodopsin

Subramaniam, S, Gerstein M, Oesterhelt D, Henderson R

EMBO J 1993, 12:1-8.

Hydrophobic Amino Acids in the Retinal-Binding Pocket of Bacteriorhodopsin

Greenhalgh, DA, Farrens DL, Subramaniam S, Khorana HG

J Biol Chem 1993, 268:20305-20311.

Effect of Introducing Different Carboxylate-Containing Side-Chains at Position-85 on Chromophore Formation and Proton Transport in Bacteriorhodopsin

Greenhalgh, DA, Subramaniam S, Alexiev U, Otto H, Heyn MP, Khorana HG

Journal of Biological Chemistry 1992, 267:25734-25738.

Aspartic Acid-85 in Bacteriorhodopsin Functions Both as Proton Acceptor and Negative Counterion to the Schiff-Base

Subramaniam, S, Greenhalgh DA, Khorana HG

Journal of Biological Chemistry 1992, 267:25730-25733.

Replacement of Leucine-93 by Alanine or Threonine Slows Down the Decay of the N and O Intermediates in the Photocycle of Bacteriorhodopsin: Implications for Proton Uptake and 13-Cis-Retinal—-All-Trans-Retinal Reisomerization

Subramaniam, S, Greenhalgh DA, Rath P, Rothschild KJ, Khorana HG

Proc Natl Acad Sci U S A 1991, 88:6873-6877.

The Reaction of Hydroxylamine with Bacteriorhodopsin Studied with Mutants That Have Altered Photocycles: Selective Reactivity of Different Photointermediates

Subramaniam, S, Marti T, Rosselet SJ, Rothschild KJ, Khorana HG

Proc Natl Acad Sci U S A 1991, 88:2583-2587.

Protonation State of Asp (Glu)-85 Regulates the Purple-to-Blue Transition in Bacteriorhodopsin Mutants Arg-82—-Ala and Asp-85—-Glu: The Blue Form Is Inactive in Proton Translocation

Subramaniam, S, Marti T, Khorana HG

Proc Natl Acad Sci U S A 1990, 87:1013-1017.

Ultraviolet-Visible Transient Spectroscopy of Bacteriorhodopsin Mutants. Evidence for Two Forms of Tyrosine-185—-Phenylalanine

Dunach, M, Berkowitz S, Marti T, He YW, Subramaniam S, Khorana HG, Rothschild KJ

J Biol Chem 1990, 265:16978-16984.

Replacement of Aspartic Residues 85, 96, 115, or 212 Affects the Quantum Yield and Kinetics of Proton Release and Uptake by Bacteriorhodopsin

Marinetti, T, Subramaniam S, Mogi T, Marti T, Khorana HG

Proc Natl Acad Sci U S A 1989, 86:529-533.

Critical Mixing in Monolayer Mixtures of Phospholipid and Cholesterol

Subramaniam, S, McConnell HM

The Journal of Physical Chemistry 1987, 91:1715-1718.

Lateral Diffusion of Specific Antibodies Bound to Lipid Monolayers on Alkylated Substrates

Subramaniam, S, Seul M, McConnell HM

Proc Natl Acad Sci U S A 1986, 83:1169-1173.

Mono- and Bilayers of Phospholipids at Interfaces: Interlayer Coupling and Phase Stability

Seul, M, Subramaniam S, McConnell HM

Journal of Physical Chemistry 1985, 89:3592-3595.