biblio manual

Manual/bib_manual.bib

+@Article{Plancherel,
+  Title                    = {{Contribution à l'étude de la représentation d'une fonction arbitraire par les intégrales définies}},
+  Author                   = {Plancherel, Michel and Mittag-Leffler},
+  Journal                  = {{Rendiconti del Circolo Matematico di Palermo}},
+  Year                     = {{1910}},
+  Number                   = {{1}},
+  Pages                    = {{289-335}},
+  Volume                   = {{30}},
+}
+@Article{Bai2015,
+  Title                    = {{How cryo-EM is revolutionizing structural biology}},
+  Author                   = {Bai, Xiao-Chen and McMullan, Greg and Scheres, Sjors H. W.},
+  Journal                  = {{Trends in Biochemical Sciences}},
+  Year                     = {{2015}},
+
+  Month                    = {{JAN}},
+  Number                   = {{1}},
+  Pages                    = {{49-57}},
+  Volume                   = {{40}},
+
+  Doi                      = {{10.1016/j.tibs.2014.10.005}},
+  ISSN                     = {{0968-0004}},
+  Unique-id                = {{ISI:000347862900007}}
+}
+
+@InCollection{NEwREV-ELad,
+  Title                    = {{Cryogenic Electron Microscopy and Single-Particle Analysis}},
+  Author                   = {Elmlund, Dominika and Elmlund, Hans},
+  Booktitle                = {{Annual Review of Biochemistry, Vol. 84}},
+  Year                     = {{2015}},
+  Editor                   = {{Kornberg, RD}},
+  Pages                    = {{499-517}},
+  Series                   = {{Annual Review of Biochemistry}},
+  Volume                   = {{84}},
+
+  Doi                      = {{10.1146/annurev-biochem-060614-034226}},
+  ISBN                     = {{978-0-8243-0884-1}},
+  ISSN                     = {{0066-4154}},
+  Orcid-numbers            = {{Elmlund, Hans/0000-0002-6992-0601}},
+  Researcherid-numbers     = {{Elmlund, Hans/}},
+  Unique-id                = {{ISI:000355765300019}}
+}
+
+@article{Penczek_2010,
+Author = {Penczek, Pawel A.},
+Title = {{Image Restoration in Cryo-Electron Microscopy}},
+Journal = {{Methods in Enzymology}},
+Year = {{2010}},
+Volume = {{482}},
+Pages = {{35-72}}
+}
+
+@Article{AllegrettiNAT2015,
+  Title                    = {{Horizontal membrane-intrinsic alpha-helices in the stator a-subunit of an F-type ATP synthase}},
+  Author                   = {Allegretti, Matteo and Klusch, Niklas and Mills, Deryck J. and Vonck, Janet and Kuehlbrandt, Werner and Davies, Karen M.},
+  Journal                  = {{Nature}},
+  Year                     = {{2015}},
+
+  Month                    = {{MAY 14}},
+  Number                   = {{7551}},
+  Pages                    = {{237+}},
+  Volume                   = {{521}},
+
+  Abstract                 = {{ATP, the universal energy currency of cells, is produced by F-type ATP synthases, which are ancient, membrane-bound nanomachines. F-type ATP synthases use the energy of a transmembrane electrochemical gradient to generate ATP by rotary catalysis. Protons moving across the membrane drive a rotor ring composed of 8-15 c-subunits(1). A central stalk transmits the rotation of the c-ring to the catalytic F-1 head, where a series of conformational changes results in ATP synthesis(2). A key unresolved question in this fundamental process is how protons pass through the membrane to drive ATP production. Mitochondrial ATP synthases form V-shaped homodimers in cristae membranes(3). Here we report the structure of a native and active mitochondrial ATP synthase dimer, determined by single-particle electron cryomicroscopy at 6.2 angstrom resolution. Our structure shows four long, horizontal membrane-intrinsic alpha-helices in the a-subunit, arranged in two hairpins at an angle of approximately 70 degrees relative to the c-ring helices. It has been proposed that a strictly conserved membrane-embedded arginine in the a-subunit couples proton translocation to c-ring rotation(4). A fit of the conserved carboxy-terminal a-subunit sequence places the conserved arginine next to a proton-binding c-subunit glutamate. The map shows a slanting solvent-accessible channel that extends from the mitochondrial matrix to the conserved arginine. Another hydrophilic cavity on the lumenal membrane surface defines a direct route for the protons to an essential histidine-glutamate pair(5). Our results provide unique new insights into the structure and function of rotary ATP synthases and explain how ATP production is coupled to proton translocation.}},
+  Address                  = {{MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND}},
+  Affiliation              = {{Kuhlbrandt, W (Reprint Author), Max Planck Inst Biophys, Dept Struct Biol, Max von Laue Str 3, D-60438 Frankfurt, Germany. Allegretti, Matteo; Klusch, Niklas; Mills, Deryck J.; Vonck, Janet; Kuehlbrandt, Werner; Davies, Karen M., Max Planck Inst Biophys, Dept Struct Biol, D-60438 Frankfurt, Germany.}},
+  Author-email             = {{werner.kuehlbrandt@biophys.mpg.de karen.davies@biophys.mpg.de}},
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+  Doc-delivery-number      = {{CH9SY}},
+  Doi                      = {{10.1038/nature14185}},
+  Eissn                    = {{1476-4687}},
+  Funding-acknowledgement  = {{Max Planck Society; Deutsche Forschungsgemeinschaft Cluster of Excellence Frankfurt `Macromolecular Complexes'}},
+  Funding-text             = {{We thank T. Meier and J. D. Faraldo-Gomez for discussions and reading the manuscript. O. Yildiz and J. F. Castillo-Hernandez provided computer support. This work was funded by the Max Planck Society (M.A., N.K., D.J.M., J.V., K.M.D., W.K.) and the Deutsche Forschungsgemeinschaft Cluster of Excellence Frankfurt `Macromolecular Complexes' (K.M.D., W.K.).}},
+  ISSN                     = {{0028-0836}},
+  Journal-iso              = {{Nature}},
+  Keywords-plus            = {{ESSENTIAL ARGININE RESIDUE; POLYTOMELLA SP; CROSS-LINKING; C-RING; CHLAMYDOMONAS-REINHARDTII; ELECTRON-MICROSCOPY; F0F1-ATP SYNTHASE; PROTON CHANNEL; CRYO-EM; RESOLUTION}},
+  Language                 = {{English}},
+  Number-of-cited-references = {{45}},
+  Publisher                = {{NATURE PUBLISHING GROUP}},
+  Research-areas           = {{Science \& Technology - Other Topics}},
+  Times-cited              = {{1}},
+  Type                     = {{Article}},
+  Unique-id                = {{ISI:000354377800062}},
+  Web-of-science-categories = {{Multidisciplinary Sciences}}
+}
+
+@Article{Yershova2010,
+  Title                    = {{Generating Uniform Incremental Grids on SO(3) Using the Hopf Fibration}},
+  Author                   = {Yershova, Anna and Jain, Swati and LaValle, Steven M. and Mitchell, Julie C.},
+  Journal                  = {{Int. J. Robot. Res.}},
+  Year                     = {{2010}},
+
+  Month                    = {{JUN}},
+  Number                   = {{7}},
+  Pages                    = {{801-812}},
+  Volume                   = {{29}},
+
+  Doi                      = {{10.1177/0278364909352700}},
+  ISSN                     = {{0278-3649}},
+  Unique-id                = {{ISI:000277911900003}}
+}
+
+@article{ E_doseCheng,
+Publication-Type = {{J}},
+Type = {{Journal Paper}},
+Title = {{Influence of electron dose rate on electron counting images recorded
+   with the K2 camera}},
+Author = {{Xueming Li} and Zheng, S.Q. and Egami, K. and Agard, D.A. and {Yifan
+   Cheng}},
+Journal = {{J. Struct. Biol.}},
+Month = {{Nov.}},
+Year = {{2013}},
+Volume = {{184}},
+Issue = {{2}},
+Pages = {{251-60}},
+Publisher = {{Academic Press Inc.}},
+Address = {{USA}},
+Language = {{English}},
+Affiliation = {{Xueming Li; Zheng, S.Q.; Egami, K.; Agard, D.A.; Yifan Cheng; Dept. of
+   Biochem. \& Biophys., Univ. of California San Francisco, San Francisco,
+   CA, USA..}},
+ISSN = {{1047-8477}},
+Number-of-References = {{30}},
+Identifying-Codes = {{[S1047-8477(13)00211-6],[10.1016/j.jsb.2013.08.005]}},
+Unique-ID = {{INSPEC:14249667}},
+}
+
+@article{ ResolRev_Kuelbrandt,
+Author = {K\"uhlbrandt, Werner},
+Title = {{The Resolution Revolution}},
+Journal = {{Science}},
+Year = {{2014}},
+Volume = {{343}},
+Number = {{6178}},
+Pages = {{1443-1444}},
+Month = {{MAR 28}},
+Publisher = {{AMER ASSOC ADVANCEMENT SCIENCE}},
+Address = {{1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA}},
+Type = {{Editorial Material}},
+Language = {{English}},
+Affiliation = {{Kuhlbrandt, W (Reprint Author), Max Planck Inst Biophys, Dept Biol Struct, D-60538 Frankfurt, Germany.
+   Max Planck Inst Biophys, Dept Biol Struct, D-60538 Frankfurt, Germany.}},
+DOI = {{10.1126/science.1251652}},
+ISSN = {{0036-8075}},
+EISSN = {{1095-9203}},
+Keywords-Plus = {{LARGE RIBOSOMAL-SUBUNIT; ANGSTROM RESOLUTION; CRYO-EM}},
+Research-Areas = {{Science \& Technology - Other Topics}},
+Web-of-Science-Categories  = {{Multidisciplinary Sciences}},
+Author-Email = {{werner.kuehlbrandt@biophys.mpg.de}},
+Number-of-Cited-References = {{11}},
+Times-Cited = {{9}},
+Journal-ISO = {{Science}},
+Doc-Delivery-Number = {{AD7TZ}},
+Unique-ID = {{ISI:000333471000024}},
+}
+
+@article{ DEDcamera,
+Author = {Faruqi, A. R. and Henderson, R.},
+Title = {{Electronic detectors for electron microscopy}},
+Journal = {{Curr. Opin. Struct. Biol.}},
+Year = {{2007}},
+Volume = {{17}},
+Number = {{5}},
+Pages = {{549-555}},
+Month = {{OCT}},
+DOI = {{10.1016/j.sbi.2007.08.014}},
+ISSN = {{0959-440X}},
+Unique-ID = {{ISI:000251348200009}},
+}
+
+@article{ Ribo_scheres,
+Author = {Brown, Alan and Amunts, Alexey and Bai, Xiao-chen and Sugimoto, Yoichiro
+   and Edwards, Patricia C. and Murshudov, Garib and Scheres, Sjors H. W.
+   and Ramakrishnan, V.},
+Title = {{Structure of the large ribosomal subunit from human mitochondria}},
+Journal = {{Science}},
+Year = {{2014}},
+Volume = {{346}},
+Number = {{6210}},
+Pages = {{718-722}},
+Month = {{NOV 7}},
+DOI = {{10.1126/science.1258026}},
+ISSN = {{0036-8075}},
+EISSN = {{1095-9203}},
+Unique-ID = {{ISI:000344690100032}},
+}
+
+@article{ Ionchannel_Cheng,
+Author = {Liao, Maofu and Cao, Erhu and Julius, David and Cheng, Yifan},
+Title = {{Structure of the TRPV1 ion channel determined by electron
+   cryo-microscopy}},
+Journal = {{Nature}},
+Year = {{2013}},
+Volume = {{504}},
+Number = {{7478}},
+Pages = {{107+}},
+Month = {{DEC 5}},
+DOI = {{10.1038/nature12822}},
+ISSN = {{0028-0836}},
+EISSN = {{1476-4687}},
+ResearcherID-Numbers = {{Albert, Joerg/C-3656-2009}},
+Unique-ID = {{ISI:000327851700040}},
+}
+
+@article{ RyR1_Yan,
+Author = {Yan, Zhen and Bai, Xiao-chen and Yan, Chuangye and Wu, Jianping and Li,
+   Zhangqiang and Xie, Tian and Peng, Wei and Yin, Chang-cheng and Li,
+   Xueming and Scheres, Sjors H. W. and Shi, Yigong and Yan, Nieng},
+Title = {{Structure of the rabbit ryanodine receptor RyR1 at near-atomic
+   resolution}},
+Journal = {{Nature}},
+Year = {{2015}},
+Volume = {{517}},
+Number = {{7532}},
+Pages = {{50+}},
+Month = {{JAN 1}},
+DOI = {{10.1038/nature14063}},
+ISSN = {{0028-0836}},
+EISSN = {{1476-4687}},
+Unique-ID = {{ISI:000347178400032}},
+}
+
+@article{ Riob2_scheres,
+Author = {Brown, Alan and Amunts, Alexey and Bai, Xiao-chen and Sugimoto, Yoichiro
+   and Edwards, Patricia C. and Murshudov, Garib and Scheres, Sjors H. W.
+   and Ramakrishnan, V.},
+Title = {{Structure of the large ribosomal subunit from human mitochondria}},
+Journal = {{Science}},
+Year = {{2014}},
+Volume = {{346}},
+Number = {{6210}},
+Pages = {{718-722}},
+Month = {{NOV 7}},
+DOI = {{10.1126/science.1258026}},
+ISSN = {{0036-8075}},
+EISSN = {{1095-9203}},
+Unique-ID = {{ISI:000344690100032}},
+}
+
+@article{ Gamma_sec_Scheres,
+Author = {Lu, Peilong and Bai, Xiao-chen and Ma, Dan and Xie, Tian and Yan,
+   Chuangye and Sun, Linfeng and Yang, Guanghui and Zhao, Yanyu and Zhou,
+   Rui and Scheres, Sjors H. W. and Shi, Yigong},
+Title = {{Three-dimensional structure of human gamma-secretase}},
+Journal = {{Nature}},
+Year = {{2014}},
+Volume = {{512}},
+Number = {{7513}},
+Pages = {{166+}},
+Month = {{AUG 14}},
+DOI = {{10.1038/nature13567}},
+ISSN = {{0028-0836}},
+EISSN = {{1476-4687}},
+Unique-ID = {{ISI:000340200700025}},
+}
+@incollection{ rev_ML-10,
+Author = {Sigworth, Fred J. and Doerschuk, Peter C. and Carazo, Jose-Maria and
+     Scheres, Sjors H. W.},
+Editor = {{Jensen, GJ}},
+Title = {{An introduction to maximum-likelihood methods in cryo-EM}},
+Booktitle = {{Methods in Enzymology}},
+Series = {{Methods in Enzymology}},
+Year = {{2010}},
+Volume = {{482}},
+Number = {{Part b}},
+Pages = {{263-294}},
+DOI = {{10.1016/S0076-6879(10)82011-7}},
+ISSN = {{0076-6879}},
+ISBN = {{978-0-12-384991-5}},
+Times-Cited = {{2}},
+Unique-ID = {{ISI:000283462200010}},
+}
+
+@article{ Mears_07,
+Author = {Mears, Jason A. and Ray, Pampa and Hinshaw, Jenny E.},
+Title = {{A corkscrew model for dynamin constriction}},
+Journal = {{Structure}},
+Year = {{2007}},
+Volume = {{15}},
+Number = {{10}},
+Pages = {{1190-1202}},
+Month = {{OCT}},
+DOI = {{10.1016/j.str.2007.08.012}},
+ISSN = {{0969-2126}},
+Times-Cited = {{49}},
+Unique-ID = {{ISI:000250235900007}},
+}
+
+@article{ Lindert_09,
+Author = {Lindert, Steffen and Staritzbichler, Rene and Woetzel, Nils and Karakas,
+   Mert and Stewart, Phoebe L. and Meiler, Jens},
+Title = {{EM-Fold: De Novo Folding of alpha-Helical Proteins Guided by
+   Intermediate-Resolution Electron Microscopy Density Maps}},
+Journal = {{Structure}},
+Year = {{2009}},
+Volume = {{17}},
+Number = {{7}},
+Pages = {{990-1003}},
+Month = {{JUL 15}},
+DOI = {{10.1016/j.str.2009.06.001}},
+ISSN = {{0969-2126}},
+Times-Cited = {{15}},
+Unique-ID = {{ISI:000268214500011}},
+}
+
+@article{ Heymann_04,
+Author = {Heymann, JB and Conway, JF and Steven, AC},
+Title = {{Molecular dynamics of protein complexes from four-dimensional
+   cryo-electron microscopy}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2004}},
+Volume = {{147}},
+Number = {{3}},
+Pages = {{291-301}},
+Month = {{SEP}},
+DOI = {{10.1016/j.jsb.2004.02.006}},
+ISSN = {{1047-8477}},
+ResearcherID-Numbers = {{Conway, James/A-2296-2010
+Heymann, Bernard/F-6825-2011}},
+Times-Cited = {{19}},
+Unique-ID = {{ISI:000223666400009}},
+}
+@article{ Bsoft_08,
+Author = {Heymann, J. Bernard and Cardone, Giovanni and Winkler, Dennis C. and
+   Steven, Alasdair. C.},
+Title = {{Computational resources for cryo-electron tomography in Bsoft}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2008}},
+Volume = {{161}},
+Number = {{3}},
+Pages = {{232-242}},
+}
+
+@article{ Samso_02,
+Author = {Samso, M and Palumbo, MJ and Radermacher, M and Liu, JS and Lawrence, CE},
+Title = {{A Bayesian method for classification of images from electron micrographs}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2002}},
+Volume = {{138}},
+Number = {{3}},
+Pages = {{157-170}},
+Month = {{JUN}},
+DOI = {{10.1016/S1047-8477(02)00001-1}},
+ISSN = {{1047-8477}},
+Times-Cited = {{4}},
+Unique-ID = {{ISI:000178144400001}},
+}
+@article{ Jaitly_10,
+Author = {Jaitly, Navdeep and Brubaker, Marcus A. and Rubinstein, John L. and
+   Lilien, Ryan H.},
+Title = {{A Bayesian method for 3D macromolecular structure inference using class
+   average images from single particle electron microscopy}},
+Journal = {{Bioinformatics}},
+Year = {{2010}},
+Volume = {{26}},
+Number = {{19}},
+Pages = {{2406-2415}},
+Month = {{OCT}},
+DOI = {{10.1093/bioinformatics/btq456}},
+ISSN = {{1367-4803}},
+Times-Cited = {{3}},
+Unique-ID = {{ISI:000282170000007}},
+}
+@article{ Kucukelbir_12,
+Author = {Kucukelbir, Alp and Sigworth, Fred J. and Tagare, Hemant D.},
+Title = {{A Bayesian adaptive basis algorithm for single particle reconstruction}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2012}},
+Volume = {{179}},
+Number = {{1}},
+Pages = {{56-67}},
+Month = {{JUL}},
+DOI = {{10.1016/j.jsb.2012.04.012}},
+ISSN = {{1047-8477}},
+Times-Cited = {{0}},
+Unique-ID = {{ISI:000305775400007}},
+}
+@Article{Orlova:11,
+   author   = {E. V. Orlova and H. R. Saibil},
+   title    = {Structural analysis of macromolecular assemblies by
+electron microscopy},
+   journal  = {Chem. Rev.},
+   year     = {2011},
+   volume   = {111},
+   pages    = {7710--7748},
+   annote   = {},
+   abstract = {},
+   citations = {11Z911},
+   address  = {},
+}
+
+@Article{Tocheva:10,
+   author   = {E. I. Tocheva and Z. Li and G. J. Jensen},
+   title    = {Electron cryotomography},
+   journal  = {Cold Spring Harbor Persp. Biol.},
+   year     = {2010},
+   volume   = {2},
+   pages    = {a003442},
+   annote   = {},
+   abstract = {},
+   citations = {17Z917},
+   address  = {},
+}
+
+@article{Elmlund_09,
+Author = {Elmlund, Dominika and Elmlund, Hans},
+Title = {{High-resolution single-particle orientation refinement based on
+   spectrally self-adapting common lines}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2009}},
+Volume = {{167}},
+Pages = {{83-94}},
+DOI = {{10.1016/j.jsb.2009.04.009}},
+ISSN = {{1047-8477}},
+Times-Cited = {{5}},
+Unique-ID = {{ISI:000266819300011}},
+}
+@article{ Elad_08,
+Author = {Elad, Nadav and Clare, Daniel K. and Salbil, Helen R. and Orlova, Elena
+   V.},
+Title = {{Detection and separation of heterogeneity in molecular complexes by
+   statistical analysis of their two-dimensional projections}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2008}},
+Volume = {{162}},
+Pages = {{108-120}},
+DOI = {{10.1016/j.jsb.2007.11.007}},
+ISSN = {{1047-8477}},
+Times-Cited = {{26}},
+Unique-ID = {{ISI:000255295600010}},
+}
+@article{ Heumann_11,
+Author = {Heumann, John M. and Hoenger, Andreas and Mastronarde, David N.},
+Title = {{Clustering and variance maps for cryo-electron tomography using
+   wedge-masked differences}},
+Journal = {{J. Struct. Biol.}},
+Year = {{2011}},
+Volume = {{175}},
+Pages = {{288-299}},
+DOI = {{10.1016/j.jsb.2011.05.011}},
+ISSN = {{1047-8477}},
+Times-Cited = {{7}},
+Unique-ID = {{ISI:000293807000004}},
+}
+@article{ Nogales_95,
+Author = {Nogales, E and Wolf, SG and Khan, IA and Luduena, RF and Downing, KH},
+Title = {{Structure of tubulin at 6.5 Angstrom and location of the taxol-binding
+   site}},
+Journal = {{Nature}},
+Year = {{1995}},
+Volume = {{375}},
+Pages = {{424-427}},
+DOI = {{10.1038/375424a0}},
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