Publications

( ) Open Access articles are available for download as PDF.
( ) For papers behind paywall, PDF versions prior to copy-editing can be made available on request.

Selected publications

• Huber ST, Sarajlic E, Huijjink R, Weis F, Evers WH, Jakobi AJ^#
  Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes
  eLife 11:e72629 (2022) | pdf | doi |  
  Associated data:     

• Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Johansen T, Brech A, Sachse C. Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake
  Nature Communications 11: 440 (2020) | pdf | doi |     
  Associated data:         

• Jakobi AJ, Wilmanns M, Sachse C.
  Model-based local density sharpening of cryo-EM maps.
  eLife 6: e27131 (2017) | pdf | doi |     
  Associated data:     

• Jakobi AJ^#*, Passon DM, Knoops K, Stellato F, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M^#.
  In cellulo X-ray Diffraction of Native Alcohol Oxidase Crystals in Yeast Cells by Serial Femtosecond Crystallography
  IUCrJ 3: 88-95 (2016) ^#corresponding author, ^*equal contribution | pdf | doi |  

       Highlighted in IUCrJ Editorial Notes, DESY Photon Science Highlights
       Featured in: DESY News, Femto, Research in Germany, CUI, chemie.de

• Jakobi AJ, Mashaghi A, Tans S, Huizinga EG.
  Calcium modulates force sensing by the von Willebrand Factor A2 domain
  Nature Communications 2: e385 (2011) | pdf | doi |    

       Featured in: Chemisch Weekblad C2W, NWO, AMOLF, NU.nl

Full publication list

orcid.org/0000-0002-7761-2027

2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2008

Preprints

• Huber ST, Terwiel D, Evers WH, Maresca D, Jakobi AJ^#
  Cryo-EM structure of gas vesicles for buoyancy-controlled motility
  bioRxiv 489936 (2022) | pdf | doi | Associated data:     

• Maan R^$, Reese L^$, Volkov VA^$, King MR, van der Sluis E, Andrea N, Evers WH, Jakobi AJ, Dogterom M
  Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus ends
  bioRxiv 460284 (2021) ^$equal contribution
  Associated data:   

• Ramlal K, Burt A, Martín Garrido N, Palmer CM^#, Jakobi AJ^#, Aylett CHS^#
  Direct information estimation from cryo-EM movies with CARYON
  bioRxiv 398891 (2020) | pdf | doi |  

Published articles

2022

• Bharadwaj A and Jakobi AJ^#
  Electron scattering properties of biological macromolecules and their use in cryo-EM map sharpening
  Faraday Discussions (2022) | pdf | doi |  
  Associated data:     

• Huber ST, Sarajlic E, Huijjink R, Weis F, Evers WH, Jakobi AJ^#
  Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes
  eLife 11:e72629 (2022) | pdf | doi |  
  Associated data:     

2021

• Klionsky D, Abdel-Aziz AK, Abdelfatah S, Abdoli A, Abel S, …, Jakobi AJ et al.
  Guidelines for the use and interpretation of assays for monitoring autophagy
  Autophagy 27: 1-240 (2021) | pdf | doi |  

2020

• Jakobi AJ
  Seeing with electrons
  Europhysics News 51: 20-23 (2020) | pdf | doi |  

• Joseph AP , Jakobi AJ, Burnley T, Patwardhan A, Topf M, Wynn M.
  Comparing Cryo-EM Reconstructions and Validating Atomic Model Fit using Difference Maps
  J Chem Inf Model 60: 2552–2560 (2020) | pdf | doi |  
  Associated source code:  

• Jakobi AJ, Huber ST, Mortensen SA, Schultz SW, Palara A, Kuhm T, Shrestha BK, Lamark T, Johansen T, Brech A, Sachse C. Structural basis of p62/SQSTM1 helical filaments and their role in cellular cargo uptake
  Nature Communications 11: 440 (2020) | pdf | doi |     
  Associated data:       

2019

• Koiwai K, Tsukimoto J, Higashi T, Mafune F, Miyajima K, Nakane T, Matsugaki N, Jakobi AJ, Sugahara M, Tanaka T, Tono K, Joti Y, Yabashi M, Nureki O, Mizohata E, Nakatsu T, Nango E, Iwata S, Chavas LMG, Senda T, Itoh K, Yumoto F.
  Improvement of production and isolation of human neuraminidase-1 in cellulo crystals
  ACS Appl. Bio Mater. 2: 4941-4952 (2019) | pdf | doi |  

2018

• Beckers M, Jakobi AJ, Sachse C.
  Thresholding of cryo-EM density maps by false discovery rate control
  IUCrJ 6: 1-16 (2018) | pdf | doi |       
  Highlighted in IUCrJ Editorial Notes

2017

• Jakobi AJ, Wilmanns M, Sachse C.
  Model-based local density sharpening of cryo-EM maps.
  eLife 6: e27131 (2017) | pdf | doi |       
  Highlighted in IUCrJ Editorial Notes

• Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJH, Beck M, Sachse C, Mueller CW.
  Molecular architecture of a minimal yeast Pol I pre-initiation complex.
  EMBO J 36: 2698-2709 (2017) | pdf | doi |  

2016

• Tafur L, Sadian Y, Hoffmann NA, Jakobi AJ Wetzel R, Hagen WJH, Sachse C, Muller CW
  Molecular structures of transcribing RNA polymerase I.
  Molecular Cell 64: 1135-1143 (2016) | pdf | doi |  

• Schur FKM, Obr M, Wan W, Jakobi AJ, Sachse C, Krausslich HG, Briggs JAG
  An atomic model of the HIV-1 capsid-SP1 layer reveals structures regulating assembly and maturation
  Science 353: 506-508 (2016) | pdf | doi |  

• Ohashi Y, Soler N, Garcia Ortegon M, Zhang L, Kirsten M, Perisic O, Masson, GR, Burke J, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL.
  Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34 complex.
  Autophagy 12: 2129-2144 (2016) | pdf | doi |  

• Bertipaglia C^#, Jakobi AJ, Tarafder AK, Bykov YS, Picco A, Kukulski W, Kosinski J, Hagen WJH, Wilmanns M, Kaksonen M, Briggs JAG, Sachse C. ^#equal contribution
  Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle.
  EMBO Rep. 17: 1044-1060 (2016) | pdf | doi |     Featured in EMBOpress Collection on Autophagy

• Hoffmann NA, Jakobi AJ, Vorlander MK, Sachse C, Muller CW.
  Transcribing RNA polymerase III observed by electron cryo-microscopy.
  FEBS J 283: 2811-19 (2016) | pdf | doi |  

• Jakobi AJ^#*, Passon DM, Knoops K, Stellato F, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M^#
  In cellulo X-ray Diffraction of Native Alcohol Oxidase Crystals in Yeast Cells by Serial Femtosecond Crystallography.
  IUCrJ 3: 88-95 (2016) | pdf | doi |     ^#corresponding author, ^*equal contribution

2015

• Hoffmann NA, Jakobi AJ, Morcillo-Moreno M, Glatt S, Sachse C, Mueller CW
  Molecular structures of unbound and transcribing RNA polymerase III.
  Nature 528: 231-236 (2015) | pdf | doi |  

• Skruzny M, Desfosses A, Prinz S, Dodonova S, Uetrecht C, Gieras A, Jakobi AJ, Abella M, Hagen WJH, Schulz J, Meijers R, Rybin V, Briggs JAG, Sachse C, Kaksonen M.
  An organized co-assembly of clathrin adaptors is essential for endocytosis.
  Developmental Cell 33: 150-162 (2015) | pdf | doi |  

• Ehebauer MT, Jakobi AJ, Noens EE, Laubitz D, Cichocki B, Marrakchi H, Laneelle MA, Daffe M, Sachse C, Dziembowski A, Sauer U, Wilmanns M
  Characterization of the mycobacterial Acyl-CoA carboxylase holo complexes reveals their functional expansion into amino acid catabolism.
  PLoS Pathogens 33: 150-162 (2015) | pdf | doi  

• Fromm SA, Bharat T, Jakobi AJ, Hagen W, Sachse C
  Seeing Tobacco Mosaic Virus through direct electron detectors.
  J Struct Biol 189: 87-97 (2015) | pdf | doi |  

2014

• Volokhina E, Jakobi AJ, Urbanus RT, Huizinga EG, Sluiter H, Dineke Westra D, van Heerde W, van de Kar N, van den Heuvel L
  Novel Sequence Variation affects GPIba in Post-diarrheal Hemolytic Uremic Syndrome.
  J Nephrol Therapeutic S11: 007 (2014) | pdf | doi |  

2013

• Popovic M, Jakobi AJ, Rensen-de Leeuw M, Rehmann H The guanine nucleotide exchange factor Rlf interacts with SH3 domain-containing proteins via a binding site with a preselected conformation.
  J Struct Biol 183: 312-319 (2013) | pdf | doi |  

2012

• Jakobi AJ, Mashaghi A, Tans S, Huizinga EG
  Calcium modulates force sensing by the von Willebrand Factor A2 domain
  Nature Communications 2: e385 (2011) | pdf | doi |  

• Jakobi AJ, Huizinga EG
  A rapid cloning method employing orthogonal end protection.
  PLoS One e37617 (2012) | pdf | doi |  

• Jose RA, Voet A, Broos K, Jakobi AJ, Bruylants G, Egle B, Zhang KY, De Maeyer M, Deckmyn H, De Borggraeve WM
  An integrated fragment based screening approach for the discovery of small molecule modulators of the VWF-GPIb interaction.
  Chem Commun 48: 11349-11351 (2012) | pdf | doi |  

2011

• Jakobi AJ, Lutz M
  Structure of Ammonium 2-aminopyrazine-3-carboxylate.
  Acta Cryst Section E: Crystallographic Communications 67: o984 (2011) | pdf | doi |  

2008

• Jakobi AJ, Mauser H, Clark T
  ParaFrag - a novel approach for surface-based similarity comparison of molecular fragments.
  J Mol Model 14: 547-558 (2008) | pdf | doi |