Publications – Technology Development




A cryogenic, coincident fluorescence, electron and ion beam microscope

Boltje DB, Hoogenboom JP, Jakobi AJ, Jensen GJ, Jonker CTH, Kaag MJ, Koster AJ, Last MGF, de Agrela Pinto C, Plitzko JM, Raunser S, Tacke S, Wang Z, van der Wee EB, Wepf R, den Hoedt S

Journal of Structural Biology: X

Subtomogram averaging for biophysical analysis and supramolecular context

Metskas LA, Wilfong R, Jensen GJ

Journal of Structural Biology

Montage electron tomography of vitrified specimens

Peck A, Carter SD, Mai H, Chen S, Burt A, Jensen GJ

Communications Biology

UVC inactivation of pathogenic samples suitable for cryo-EM analysis

Depelteau JS, Renault L, Althof N, Cassidy CK, Mendonça LM, Jensen GJ, Resch GP, Briegel A




Generation of ordered protein assemblies using rigid three-body fusion

Vulovic I, Yao Q*, Park Y-J*, Courbet A, Norris A, Busch F, Sahasrabuddhe A, Merten H, Sahtoe DD, Ueda G, Fallas JA, Weaver SJ, Hsia Y, Langan RA, Plückthun A, Wysocki VH, Veesler D, Jensen GJ, Baker D

Acta Crystallographica Section D

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Peck A, Yao Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ

Journal of Molecular Biology

Moltemplate: a tool for coarse-grained modeling of complex biological matter and soft condensed matter physics

Jewett AI+, Stelter D, Lambert J, Saladi SM, Roscioni OM, Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT, Shea J-E, Jensen GJ, Goodsell DS+



Gateways 2019 (Conference)

DDX-Interface: A factory of interoperable scientific gateways

James A, Chacon R, Buddenhagen J, Ortega DR, Rees-Lee P, Jensen G, James DR


Qualitative analyses of polishing and precoating FIB milled crystals for MicroED

Martynowycz MW, Zhao W, Hattne J, Jensen GJ, Gonen T


Fusion of DARPin to aldolase enables visualization of small protein by cryoEM

Yao Q*, Weaver SJ*, Mock J-Y, Jensen GJ


ETDB-Caltech: a blockchain-based distributed public database for electron tomography

Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Alexandria, Jensen GJ


De novo structural pattern mining in cellular electron cryotomograms

Xu M, Singla J, Tocheva EI, Chang Y-W, Stevens RC, Jensen GJ, Alber F


Collection of continuous rotation MicroED data from ion beam-milled crystals of any size

Martynowycz MW, Zhao W, Hattne J, Jensen GJ, Gonen T

Journal of Structural Biology

Rapid tilt-series acquisition for electron cryotomography

Chreifi G*, Chen S*, Metskas LA, Kaplan M, Jensen GJ



Journal of Structural Biology

Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells

Carter SD*, Mageswaran SK*, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z+, Jensen GJ+

Journal of Structural Biology

Best practices for managing large cryoEM facilities

Alewijnse B, Ashton AW, Chambers MG, Chen S, Cheng A, Ebrahim M, Eng E, Hagen WJH, Koster AJ, Lopez CS, Lukoyanova N, Ortega J, Renault L, Reyntjens S, Rice WJ, Scapin G, Schrijver R, Siebert A, Stagg SM, Grum-Tokars V, Wright ER, Wu S, Yu Z, Zhou ZH, Carragher B, Potter CS

Angewandte Chemie International Edition

Photon-induced near-field electron microscopy (PINEM) of eukaryotic cells

Kaplan M, Yoo BK, Tang J+, Karam T, Liao B, Majumdar D, Baltimore D, Jensen G+, Zewail A



Methods in Microbiology

Electron cryotomography

Oikonomou CM, Swulius MT, Briegel A, Beeby M, Yao Q, Chang Y-W, Jensen GJ

(proof available here)

Methods in Molecular Biology

Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall

Nguyen LT, Gumbart JC, Jensen GJ



Journal of Structural Biology

The Caltech Tomography Database and Automatic Processing Pipeline

Ding HJ, Oikonomou, CM, Jensen GJ



Nature Methods

Correlated cryogenic photoactivated localization microscopy and cryo-electron tomography

Chang YW, Chen S, Tocheva EI, Treuner-Lange A, Löbach S, Søgaard-Andersen L, Jensen GJ





Nature Structural and Molecular Biology

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, Mostronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-Garcia E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Keywegt GJ

Quarterly Reviews of Biophysics

Electron Tomography of Cells

Gan L, Jensen GJ



Methods in Enzymology

Correcting for the Ewald sphere in high-resolution single-particle reconstructions

Leong PA, Yu X, Zhou ZH, Jensen GJ

Methods in Enzymology

Cryo-EM, Part B: 3-D Reconstruction

Jensen GJ

Methods in Enzymology

Correlated light and electron cryo-microscopy

Briegel A, Chen S, Koster AJ, Plitzko JM, Schwartz CL, Jensen GJ

Methods in Enzymology

Plunge freezing for electron cryomicroscopy

Dobro MJ, Melanson LA, Jensen GJ, McDowall AW


Electron cryotomography of bacterial cells

Chen S, McDowall A, Dobro MJ, Briegel A, Ladinsky M, Shi J, Tocheva EI, Beeby M, Pilhofer M, Ding HJ, Li Z, Gan L, Morris DM, Jensen GJ



Microscopy and Microanalysis

Nanogold as a specific marker for electron cryotomography

He Y, Jensen GJ, Bjorkman PJ

Journal of Structural Biology

Fully automated, sequential tilt-series acquisition with Leginon

Suloway C, Shi J, Cheng A, Pulokas J, Carragher B, Potter CS, Zheng SQ, Agard DA, Jensen GJ



Microscopy and Microanalysis

An improved cryogen for plunge freezing

Tivol WF+, Briegel A, Jensen GJ

Journal of Structural Biology

Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography

Lee E*, Fahimian BP*, Iancu CV, Suloway C, Murphy GE, Wright ER, Castaño-Díez D, Jensen GJ, Miao J



Nature Protocols

Electron cryotomography sample preparation using the Vitrobot

Iancu CV, Tivol WF, Schooler JB, Dias DP, Henderson GP, Murphy GE, Wright ER, Li Z, Yu Z, Briegel A, Gan L, He Y, Jensen GJ

Journal of the American Chemical Society

Rigid, specific, and discrete gold nanoparticle/antibody conjugates

Ackerson CJ, Jadzinsky PD, Jensen GJ, Kornberg RD

Journal of Structural Biology

Observations on the behavior of vitreous ice at approximately 82 and approximately 12 K

Wright ER*, Iancu CV*, Tivol WF, Jensen GJ

Journal of Structural Biology

A comparison of liquid nitrogen and liquid helium as cryogens for electron cryotomography

Iancu CV, Wright ER, Heymann JB, Jensen GJ



Journal of Structural Biology

A “flip-flop” rotation stage for routine dual-axis electron cryotomography

Iancu CV*, Wright ER*, Benjamin J, Tivol WF, Dias DP, Murphy GE, Morrison RC, Heymann JB, Jensen GJ