Publications

• Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils.. Nature communications, 2023.
• Ryder BD, Boyer DR, Ustyantseva E, Mendoza-Oliva A, Kuska MI, Wydorski PM, Sawaya M, Diamond MI, Eisenberg DS, Kampinga HH, Joachimiak LA. DNAJB8 oligomerization is mediated by an aromatic-rich motif that is dispensable for substrate activity.. bioRxiv : the preprint server for biology, 2023.
• Murray KA, Hu CJ, Pan H, Lu J, Abskharon R, Bowler JT, Rosenberg GM, Williams CK, Elezi G, Balbirnie M, Faull KF, Vinters HV, Seidler PM, Eisenberg DS. Small molecules disaggregate alpha-synuclein and prevent seeding from patient brain-derived fibrils.. Proceedings of the National Academy of Sciences of the United States of America, 2023.
• Buxbaum JN, Dispenzieri A, Eisenberg DS, F?ndrich M, Merlini G, Saraiva MJM, Sekijima Y, Westermark P. Amyloid nomenclature 2022: update, novel proteins, and recommendations by the International Society of Amyloidosis (ISA) Nomenclature Committee.. Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis, 2022.
• Seidler PM, Murray KA, Boyer DR, Ge P, Sawaya MR, Hu CJ, Cheng X, Abskharon R, Pan H, DeTure MA, Williams CK, Dickson DW, Vinters HV, Eisenberg DS. Structure-based discovery of small molecules that disaggregate Alzheimer's disease tissue derived tau fibrils in vitro.. Nature communications, 2022.
• Bowler JT, Sawaya MR, Boyer DR, Cascio D, Bali M, Eisenberg DS. Micro-electron diffraction structure of the aggregation-driving N terminus of Drosophila neuronal protein Orb2A reveals amyloid-like β-sheets.. The Journal of biological chemistry, 2022.
• Murray KA, Hu CJ, Griner SL, Pan H, Bowler JT, Abskharon R, Rosenberg GM, Cheng X, Seidler PM, Eisenberg DS. De novo designed protein inhibitors of amyloid aggregation and seeding.. Proceedings of the National Academy of Sciences of the United States of America, 2022.
• Hazari A, Sawaya MR, Vlahakis N, Johnstone TC, Boyer D, Rodriguez J, Eisenberg D, Raskatov JA. The rippled β-sheet layer configuration-a novel supramolecular architecture based on predictions by Pauling and Corey.. Chemical science, 2022.
• Murray KA, Hughes MP, Hu CJ, Sawaya MR, Salwinski L, Pan H, French SW, Seidler PM, Eisenberg DS. Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies.. Nature structural & molecular biology, 2022.
• Rosenberg GM, Murray KA, Salwinski L, Hughes MP, Abskharon R, Eisenberg DS. Bioinformatic identification of previously unrecognized amyloidogenic proteins.. The Journal of biological chemistry, 2022.
• Abskharon R, Sawaya MR, Boyer DR, Cao Q, Nguyen BA, Cascio D, Eisenberg DS. Cryo-EM structure of RNA-induced tau fibrils reveals a small C-terminal core that may nucleate fibril formation.. Proceedings of the National Academy of Sciences of the United States of America, 2022.
• Jiang YX, Cao Q, Sawaya MR, Abskharon R, Ge P, DeTure M, Dickson DW, Fu JY, Ogorzalek Loo RR, Loo JA, Eisenberg DS. Amyloid fibrils in FTLD-TDP are composed of TMEM106B and not TDP-43.. Nature, 2022.
• Murray KA, Evans D, Hughes MP, Sawaya MR, Hu CJ, Houk KN, Eisenberg D. Extended β-Strands Contribute to Reversible Amyloid Formation.. ACS nano, 2022.
• Gray ALH, Sawaya MR, Acharyya D, Lou J, Edington EM, Best MD, Prosser RA, Eisenberg DS, Do TD. Atomic view of an amyloid dodecamer exhibiting selective cellular toxic vulnerability in acute brain slices.. Protein science : a publication of the Protein Society, 2022.
• Hughes MP, Goldschmidt L, Eisenberg DS. Prevalence and species distribution of the low-complexity, amyloid-like, reversible, kinked segment structural motif in amyloid-like fibrils.. The Journal of biological chemistry, 2021.
• Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis.. Cell, 2021.
• Cao Q, Boyer DR, Sawaya MR, Abskharon R, Saelices L, Nguyen BA, Lu J, Murray KA, Kandeel F, Eisenberg DS. Cryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril cores.. Nature structural & molecular biology, 2021.
• Tayeb-Fligelman E, Cheng X, Tai C, Bowler JT, Griner S, Sawaya MR, Seidler PM, Jiang YX, Lu J, Rosenberg GM, Salwinski L, Abskharon R, Zee CT, Hou K, Li Y, Boyer DR, Murray KA, Falcon G, Anderson DH, Cascio D, Saelices L, Damoiseaux R, Guo F, Eisenberg DS. Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2.. bioRxiv : the preprint server for biology, 2021.
• Shipps C, Kelly HR, Dahl PJ, Yi SM, Vu D, Boyer D, Glynn C, Sawaya MR, Eisenberg D, Batista VS, Malvankar NS. Intrinsic electronic conductivity of individual atomically resolved amyloid crystals reveals micrometer-long hole hopping via tyrosines.. Proceedings of the National Academy of Sciences of the United States of America, 2021.
• Benson MD, Buxbaum JN, Eisenberg DS, Merlini G, Saraiva MJM, Sekijima Y, Sipe JD, Westermark P. Amyloid nomenclature 2020: update and recommendations by the International Society of Amyloidosis (ISA) nomenclature committee.. Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis, 2020.
• Lu J, Cao Q, Hughes MP, Sawaya MR, Boyer DR, Cascio D, Eisenberg DS. CryoEM structure of the low-complexity domain of hnRNPA2 and its conversion to pathogenic amyloid.. Nature communications, 2020.
• Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future.. Chemical Society reviews, 2020.
• Cao Q, Boyer DR, Sawaya MR, Ge P, Eisenberg DS. Cryo-EM structure and inhibitor design of human IAPP (amylin) fibrils.. Nature structural & molecular biology, 2020.
• Abskharon R, Seidler PM, Sawaya MR, Cascio D, Yang TP, Philipp S, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Felgner PL, Nakajima R, Glabe CG, Eisenberg DS. Crystal structure of a conformational antibody that binds tau oligomers and inhibits pathological seeding by extracts from donors with Alzheimer's disease.. The Journal of biological chemistry, 2020.
• Glynn C, Sawaya MR, Ge P, Gallagher-Jones M, Short CW, Bowman R, Apostol M, Zhou ZH, Eisenberg DS, Rodriguez JA. Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core.. Nature structural & molecular biology, 2020.
• Boyer DR, Li B, Sun C, Fan W, Zhou K, Hughes MP, Sawaya MR, Jiang L, Eisenberg DS. The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure.. Proceedings of the National Academy of Sciences of the United States of America, 2020.
• Sangwan S, Sahay S, Murray KA, Morgan S, Guenther EL, Jiang L, Williams CK, Vinters HV, Goedert M, Eisenberg DS. Inhibition of synucleinopathic seeding by rationally designed inhibitors.. eLife, 2020.
• Basavalingappa V, Bera S, Xue B, Azuri I, Tang Y, Tao K, Shimon LJW, Sawaya MR, Kolusheva S, Eisenberg DS, Kronik L, Cao Y, Wei G, Gazit E. Mechanically rigid supramolecular assemblies formed from an Fmoc-guanine conjugated peptide nucleic acid.. Nature communications, 2019.
• Boyer DR, Li B, Sun C, Fan W, Sawaya MR, Jiang L, Eisenberg DS. Structures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphs.. Nature structural & molecular biology, 2019.
• Griner SL, Seidler P, Bowler J, Murray KA, Yang TP, Sahay S, Sawaya MR, Cascio D, Rodriguez JA, Philipp S, Sosna J, Glabe CG, Gonen T, Eisenberg DS. Structure-based inhibitors of amyloid beta core suggest a common interface with tau.. eLife, 2019.
• Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Author Correction: Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.. Nature structural & molecular biology, 2019.
• Makam P, Yamijala SSRKC, Tao K, Shimon LJW, Eisenberg DS, Sawaya MR, Wong BM, Gazit E. Non-proteinaceous hydrolase comprised of a phenylalanine metallo-supramolecular amyloid-like structure.. Nature catalysis, 2019.
• Seidler PM, Boyer DR, Murray KA, Yang TP, Bentzel M, Sawaya MR, Rosenberg G, Cascio D, Williams CK, Newell KL, Ghetti B, DeTure MA, Dickson DW, Vinters HV, Eisenberg DS. Structure-based inhibitors halt prion-like seeding by Alzheimer's disease-and tauopathy-derived brain tissue samples.. The Journal of biological chemistry, 2019.
• Warmack RA, Boyer DR, Zee CT, Richards LS, Sawaya MR, Cascio D, Gonen T, Eisenberg DS, Clarke SG. Structure of amyloid-β (20-34) with Alzheimer's-associated isomerization at Asp23 reveals a distinct protofilament interface.. Nature communications, 2019.
• Cao Q, Boyer DR, Sawaya MR, Ge P, Eisenberg DS. Cryo-EM structures of four polymorphic TDP-43 amyloid cores.. Nature structural & molecular biology, 2019.
• Lu J, Cao Q, Wang C, Zheng J, Luo F, Xie J, Li Y, Ma X, He L, Eisenberg D, Nowick J, Jiang L, Li D. Structure-Based Peptide Inhibitor Design of Amyloid-β Aggregation.. Frontiers in molecular neuroscience, 2019.
• Saelices L, Nguyen BA, Chung K, Wang Y, Ortega A, Lee JH, Coelho T, Bijzet J, Benson MD, Eisenberg DS. A pair of peptides inhibits seeding of the hormone transporter transthyretin into amyloid fibrils.. The Journal of biological chemistry, 2019.
• Benson MD, Buxbaum JN, Eisenberg DS, Merlini G, Saraiva MJM, Sekijima Y, Sipe JD, Westermark P. Amyloid nomenclature 2018: recommendations by the International Society of Amyloidosis (ISA) nomenclature committee.. Amyloid : the international journal of experimental and clinical investigation : the official journal of the International Society of Amyloidosis, 2019.
• Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. Author Correction: Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design.. Nature chemistry, 2018.
• Tuukkanen AT, Freire D, Chan S, Arbing MA, Reed RW, Evans TJ, Zenkeviciute G, Kim J, Kahng S, Sawaya MR, Chaton CT, Wilmanns M, Eisenberg D, Parret AHA, Korotkov KV. Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems.. Journal of molecular biology, 2018.
• Vogler TO, Wheeler JR, Nguyen ED, Hughes MP, Britson KA, Lester E, Rao B, Betta ND, Whitney ON, Ewachiw TE, Gomes E, Shorter J, Lloyd TE, Eisenberg DS, Taylor JP, Johnson AM, Olwin BB, Parker R. TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle.. Nature, 2018.
• Brumshtein B, Esswein SR, Sawaya MR, Rosenberg G, Ly AT, Landau M, Eisenberg DS. Identification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosis.. The Journal of biological chemistry, 2018.
• Cao Q, Shin WS, Chan H, Vuong CK, Dubois B, Li B, Murray KA, Sawaya MR, Feigon J, Black DL, Eisenberg DS, Jiang L. Inhibiting amyloid-β cytotoxicity through its interaction with the cell surface receptor LilrB2 by structure-based design.. Nature chemistry, 2018.
• Saelices L, Pokrzywa M, Pawelek K, Eisenberg DS. Assessment of the effects of transthyretin peptide inhibitors in Drosophila models of neuropathic ATTR.. Neurobiology of disease, 2018.
• Li B, Ge P, Murray KA, Sheth P, Zhang M, Nair G, Sawaya MR, Shin WS, Boyer DR, Ye S, Eisenberg DS, Zhou ZH, Jiang L. Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel.. Nature communications, 2018.
• McPartland L, Heller DM, Eisenberg DS, Hochschild A, Sawaya MR. Atomic insights into the genesis of cellular filaments by globular proteins.. Nature structural & molecular biology, 2018.
• Eisenberg DS. Paul D. Boyer (1918-2018).. Science (New York, N.Y.), 2018.
• Saelices L, Chung K, Lee JH, Cohn W, Whitelegge JP, Benson MD, Eisenberg DS. Amyloid seeding of transthyretin by ex vivo cardiac fibrils and its inhibition.. Proceedings of the National Academy of Sciences of the United States of America, 2018.
• Eisenberg DS. How Hard It Is Seeing What Is in Front of Your Eyes.. Cell, 2018.
• Saelices L, Sievers SA, Sawaya MR, Eisenberg DS. Crystal structures of amyloidogenic segments of human transthyretin.. Protein science : a publication of the Protein Society, 2018.
• Guenther EL, Cao Q, Trinh H, Lu J, Sawaya MR, Cascio D, Boyer DR, Rodriguez JA, Hughes MP, Eisenberg DS. Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.. Nature structural & molecular biology, 2018.
• Guenther EL, Ge P, Trinh H, Sawaya MR, Cascio D, Boyer DR, Gonen T, Zhou ZH, Eisenberg DS. Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2.. Nature structural & molecular biology, 2018.
• Sangwan S, Sawaya MR, Murray KA, Hughes MP, Eisenberg DS. Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.. Protein science : a publication of the Protein Society, 2018.
• Do TD, Sangwan S, de Almeida NEC, Ilitchev AI, Giammona M, Sawaya MR, Buratto SK, Eisenberg DS, Bowers MT. Distal amyloid β-protein fragments template amyloid assembly.. Protein science : a publication of the Protein Society, 2018.
• Hughes MP, Sawaya MR, Boyer DR, Goldschmidt L, Rodriguez JA, Cascio D, Chong L, Gonen T, Eisenberg DS. Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks.. Science (New York, N.Y.), 2018.
• Gallagher-Jones M, Glynn C, Boyer DR, Martynowycz MW, Hernandez E, Miao J, Zee CT, Novikova IV, Goldschmidt L, McFarlane HT, Helguera GF, Evans JE, Sawaya MR, Cascio D, Eisenberg DS, Gonen T, Rodriguez JA. Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp.. Nature structural & molecular biology, 2018.
• Hanczyc P, Mikhailovsky A, Boyer DR, Sawaya MR, Heeger A, Eisenberg D. Ultrafast Time-Resolved Studies on Fluorescein for Recognition Strands Architecture in Amyloid Fibrils.. The journal of physical chemistry. B, 2018.
• Krotee P, Griner SL, Sawaya MR, Cascio D, Rodriguez JA, Shi D, Philipp S, Murray K, Saelices L, Lee J, Seidler P, Glabe CG, Jiang L, Gonen T, Eisenberg DS. Common fibrillar spines of amyloid-β and human islet amyloid polypeptide revealed by microelectron diffraction and structure-based inhibitors.. The Journal of biological chemistry, 2017.
• Kurt TD, Aguilar-Calvo P, Jiang L, Rodriguez JA, Alderson N, Eisenberg DS, Sigurdson CJ. Asparagine and glutamine ladders promote cross-species prion conversion.. The Journal of biological chemistry, 2017.
• Rodriguez JA, Jiang L, Eisenberg DS. Toward the Atomic Structure of PrPSc.. Cold Spring Harbor perspectives in biology, 2017.
• Sangwan S, Zhao A, Adams KL, Jayson CK, Sawaya MR, Guenther EL, Pan AC, Ngo J, Moore DM, Soriaga AB, Do TD, Goldschmidt L, Nelson R, Bowers MT, Koehler CM, Shaw DE, Novitch BG, Eisenberg DS. Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS).. Proceedings of the National Academy of Sciences of the United States of America, 2017.
• Goedert M, Eisenberg DS, Crowther RA. Propagation of Tau Aggregates and Neurodegeneration.. Annual review of neuroscience, 2017.
• Eisenberg DS, Sawaya MR. Neurodegeneration: Taming tangled tau.. Nature, 2017.
• Rodriguez JA, Eisenberg DS, Gonen T. Taking the measure of MicroED.. Current opinion in structural biology, 2017.
• Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser.. Cytoskeleton (Hoboken, N.J.), 2017.
• de la Cruz MJ, Hattne J, Shi D, Seidler P, Rodriguez J, Reyes FE, Sawaya MR, Cascio D, Weiss SC, Kim SK, Hinck CS, Hinck AP, Calero G, Eisenberg D, Gonen T. Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.. Nature methods, 2017.
• Buchner J, Eisenberg D, Schmid F. In memoriam-Rainer Jaenicke.. Protein science : a publication of the Protein Society, 2017.
• Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity.. eLife, 2017.
• Eisenberg DS, Sawaya MR. Structural Studies of Amyloid Proteins at the Molecular Level.. Annual review of biochemistry, 2017.
• Riek R, Eisenberg DS. The activities of amyloids from a structural perspective.. Nature, 2016.
• Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure.. Nature, 2016.
• Sawaya MR, Rodriguez J, Cascio D, Collazo MJ, Shi D, Reyes FE, Hattne J, Gonen T, Eisenberg DS. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.. Proceedings of the National Academy of Sciences of the United States of America, 2016.
• Eisenberg DS, Sawaya MR. Implications for Alzheimer's disease of an atomic resolution structure of amyloid-β(1-42) fibrils.. Proceedings of the National Academy of Sciences of the United States of America, 2016.
• Wagner JM, Chan S, Evans TJ, Kahng S, Kim J, Arbing MA, Eisenberg D, Korotkov KV. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.. BMC structural biology, 2016.
• Soriaga AB, Sangwan S, Macdonald R, Sawaya MR, Eisenberg D. Crystal Structures of IAPP Amyloidogenic Segments Reveal a Novel Packing Motif of Out-of-Register Beta Sheets.. The journal of physical chemistry. B, 2016.
• Do TD, LaPointe NE, Nelson R, Krotee P, Hayden EY, Ulrich B, Quan S, Feinstein SC, Teplow DB, Eisenberg D, Shea JE, Bowers MT. Amyloid β-Protein C-Terminal Fragments: Formation of Cylindrins and β-Barrels.. Journal of the American Chemical Society, 2016.
• Sangwan S, Eisenberg DS. Perspective on SOD1 mediated toxicity in Amyotrophic Lateral Sclerosis.. Postepy biochemii, 2016.
• Moshe A, Landau M, Eisenberg D. Preparation of Crystalline Samples of Amyloid Fibrils and Oligomers.. Methods in molecular biology (Clifton, N.J.), 2016.
• Soragni A, Janzen DM, Johnson LM, Lindgren AG, Thai-Quynh Nguyen A, Tiourin E, Soriaga AB, Lu J, Jiang L, Faull KF, Pellegrini M, Memarzadeh S, Eisenberg DS. A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian Carcinomas.. Cancer cell, 2015.
• Yin JX, Maalouf M, Han P, Zhao M, Gao M, Dharshaun T, Ryan C, Whitelegge J, Wu J, Eisenberg D, Reiman EM, Schweizer FE, Shi J. Ketones block amyloid entry and improve cognition in an Alzheimer's model.. Neurobiology of aging, 2015.
• Brumshtein B, Esswein SR, Salwinski L, Phillips ML, Ly AT, Cascio D, Sawaya MR, Eisenberg DS. Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.. eLife, 2015.
• Saelices L, Johnson LM, Liang WY, Sawaya MR, Cascio D, Ruchala P, Whitelegge J, Jiang L, Riek R, Eisenberg DS. Uncovering the Mechanism of Aggregation of Human Transthyretin.. The Journal of biological chemistry, 2015.
• Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS. Structure of the toxic core of α-synuclein from invisible crystals.. Nature, 2015.
• Kurt TD, Jiang L, Fernández-Borges N, Bett C, Liu J, Yang T, Spraker TR, Castilla J, Eisenberg D, Kong Q, Sigurdson CJ. Human prion protein sequence elements impede cross-species chronic wasting disease transmission.. The Journal of clinical investigation, 2015.
• Soragni A, Yousefi S, Stoeckle C, Soriaga AB, Sawaya MR, Kozlowski E, Schmid I, Radonjic-Hoesli S, Boutet S, Williams GJ, Messerschmidt M, Seibert MM, Cascio D, Zatsepin NA, Burghammer M, Riekel C, Colletier JP, Riek R, Eisenberg DS, Simon HU. Toxicity of eosinophil MBP is repressed by intracellular crystallization and promoted by extracellular aggregation.. Molecular cell, 2015.
• Kurt TD, Jiang L, Fernández-Borges N, Bett C, Liu J, Yang T, Spraker TR, Castilla J, Eisenberg D, Kong Q, Sigurdson CJ. Human prion protein sequence elements impede cross-species chronic wasting disease transmission.. The Journal of clinical investigation, 2015.
• Brewster AS, Sawaya MR, Rodriguez J, Hattne J, Echols N, McFarlane HT, Cascio D, Adams PD, Eisenberg DS, Sauter NK. Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns.. Acta crystallographica. Section D, Biological crystallography, 2015.
• Li D, Jones EM, Sawaya MR, Furukawa H, Luo F, Ivanova M, Sievers SA, Wang W, Yaghi OM, Liu C, Eisenberg DS. Structure-based design of functional amyloid materials.. Journal of the American Chemical Society, 2014.
• Eisenberg D, Ahn HS, Bard AJ. Enhanced photoelectrochemical water oxidation on bismuth vanadate by electrodeposition of amorphous titanium dioxide.. Journal of the American Chemical Society, 2014.
• Brumshtein B, Esswein SR, Landau M, Ryan CM, Whitelegge JP, Phillips ML, Cascio D, Sawaya MR, Eisenberg DS. Formation of amyloid fibers by monomeric light chain variable domains.. The Journal of biological chemistry, 2014.
• Sawaya MR, Cascio D, Gingery M, Rodriguez J, Goldschmidt L, Colletier JP, Messerschmidt MM, Boutet S, Koglin JE, Williams GJ, Brewster AS, Nass K, Hattne J, Botha S, Doak RB, Shoeman RL, DePonte DP, Park HW, Federici BA, Sauter NK, Schlichting I, Eisenberg DS. Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam.. Proceedings of the National Academy of Sciences of the United States of America, 2014.
• Do TD, LaPointe NE, Sangwan S, Teplow DB, Feinstein SC, Sawaya MR, Eisenberg DS, Bowers MT. Factors that drive peptide assembly from native to amyloid structures: experimental and theoretical analysis of [leu-5]-enkephalin mutants.. The journal of physical chemistry. B, 2014.
• Hochberg GK, Ecroyd H, Liu C, Cox D, Cascio D, Sawaya MR, Collier MP, Stroud J, Carver JA, Baldwin AJ, Robinson CV, Eisenberg DS, Benesch JL, Laganowsky A. The structured core domain of αB-crystallin can prevent amyloid fibrillation and associated toxicity.. Proceedings of the National Academy of Sciences of the United States of America, 2014.
• Korman TP, Sahachartsiri B, Li D, Vinokur JM, Eisenberg D, Bowie JU. A synthetic biochemistry system for the in vitro production of isoprene from glycolysis intermediates.. Protein science : a publication of the Protein Society, 2014.
• Kurt TD, Jiang L, Bett C, Eisenberg D, Sigurdson CJ. A proposed mechanism for the promotion of prion conversion involving a strictly conserved tyrosine residue in the β2-α2 loop of PrPC.. The Journal of biological chemistry, 2014.
• Goldschmidt L, Eisenberg D, Derewenda ZS. Salvage or recovery of failed targets by mutagenesis to reduce surface entropy.. Methods in molecular biology (Clifton, N.J.), 2014.
• Li D, Furukawa H, Deng H, Liu C, Yaghi OM, Eisenberg DS. Designed amyloid fibers as materials for selective carbon dioxide capture.. Proceedings of the National Academy of Sciences of the United States of America, 2013.
• Ivanova MI, Sievers SA, Guenther EL, Johnson LM, Winkler DD, Galaleldeen A, Sawaya MR, Hart PJ, Eisenberg DS. Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS.. Proceedings of the National Academy of Sciences of the United States of America, 2013.
• Arbing MA, Chan S, Harris L, Kuo E, Zhou TT, Ahn CJ, Nguyen L, He Q, Lu J, Menchavez PT, Shin A, Holton T, Sawaya MR, Cascio D, Eisenberg D. Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions.. PloS one, 2013.
• Jiang L, Liu C, Leibly D, Landau M, Zhao M, Hughes MP, Eisenberg DS. Structure-based discovery of fiber-binding compounds that reduce the cytotoxicity of amyloid beta.. eLife, 2013.
• Miallau L, Jain P, Arbing MA, Cascio D, Phan T, Ahn CJ, Chan S, Chernishof I, Maxson M, Chiang J, Jacobs WR, Eisenberg DS. Comparative proteomics identifies the cell-associated lethality of M. tuberculosis RelBE-like toxin-antitoxin complexes.. Structure (London, England : 1993), 2013.
• Liu C, Zhao M, Jiang L, Cheng PN, Park J, Sawaya MR, Pensalfini A, Gou D, Berk AJ, Glabe CG, Nowick J, Eisenberg D. Out-of-register β-sheets suggest a pathway to toxic amyloid aggregates.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
• Min AB, Miallau L, Sawaya MR, Habel J, Cascio D, Eisenberg D. The crystal structure of the Rv0301-Rv0300 VapBC-3 toxin-antitoxin complex from M. tuberculosis reveals a Mg²⁺ ion in the active site and a putative RNA-binding site.. Protein science : a publication of the Protein Society, 2012.
• Cheng PN, Liu C, Zhao M, Eisenberg D, Nowick JS. Amyloid β-sheet mimics that antagonize protein aggregation and reduce amyloid toxicity.. Nature chemistry, 2012.
• Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels.. Cell, 2012.
• Stroud JC, Liu C, Teng PK, Eisenberg D. Toxic fibrillar oligomers of amyloid-β have cross-β structure.. Proceedings of the National Academy of Sciences of the United States of America, 2012.
• Eisenberg D, Jucker M. The amyloid state of proteins in human diseases.. Cell, 2012.
• Laganowsky A, Liu C, Sawaya MR, Whitelegge JP, Park J, Zhao M, Pensalfini A, Soriaga AB, Landau M, Teng PK, Cascio D, Glabe C, Eisenberg D. Atomic view of a toxic amyloid small oligomer.. Science (New York, N.Y.), 2012.
• Teng PK, Anderson NJ, Goldschmidt L, Sawaya MR, Sambashivan S, Eisenberg D. Ribonuclease A suggests how proteins self-chaperone against amyloid fiber formation.. Protein science : a publication of the Protein Society, 2011.
• Colletier JP, Laganowsky A, Landau M, Zhao M, Soriaga AB, Goldschmidt L, Flot D, Cascio D, Sawaya MR, Eisenberg D. Molecular basis for amyloid-beta polymorphism.. Proceedings of the National Academy of Sciences of the United States of America, 2011.
• Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H. PSICQUIC and PSISCORE: accessing and scoring molecular interactions.. Nature methods, 2011.
• Sievers SA, Karanicolas J, Chang HW, Zhao A, Jiang L, Zirafi O, Stevens JT, Münch J, Baker D, Eisenberg D. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation.. Nature, 2011.
• Landau M, Sawaya MR, Faull KF, Laganowsky A, Jiang L, Sievers SA, Liu J, Barrio JR, Eisenberg D. Towards a pharmacophore for amyloid.. PLoS biology, 2011.
• Zhao M, Cascio D, Sawaya MR, Eisenberg D. Structures of segments of α-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation.. Protein science : a publication of the Protein Society, 2011.
• Liu C, Sawaya MR, Cheng PN, Zheng J, Nowick JS, Eisenberg D. Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics.. Journal of the American Chemical Society, 2011.
• Apostol MI, Wiltzius JJ, Sawaya MR, Cascio D, Eisenberg D. Atomic structures suggest determinants of transmission barriers in mammalian prion disease.. Biochemistry, 2011.
• Zheng J, Liu C, Sawaya MR, Vadla B, Khan S, Woods RJ, Eisenberg D, Goux WJ, Nowick JS. Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide.. Journal of the American Chemical Society, 2011.
• Chim N, Habel JE, Johnston JM, Krieger I, Miallau L, Sankaranarayanan R, Morse RP, Bruning J, Swanson S, Kim H, Kim CY, Li H, Bulloch EM, Payne RJ, Manos-Turvey A, Hung LW, Baker EN, Lott JS, James MN, Terwilliger TC, Eisenberg DS, Sacchettini JC, Goulding CW. The TB Structural Genomics Consortium: a decade of progress.. Tuberculosis (Edinburgh, Scotland), 2011.
• Liu C, Sawaya MR, Eisenberg D. β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.. Nature structural & molecular biology, 2010.
• Arbing MA, Kaufmann M, Phan T, Chan S, Cascio D, Eisenberg D. The crystal structure of the Mycobacterium tuberculosis Rv3019c-Rv3020c ESX complex reveals a domain-swapped heterotetramer.. Protein science : a publication of the Protein Society, 2010.
• Khakshoor O, Lin AJ, Korman TP, Sawaya MR, Tsai SC, Eisenberg D, Nowick JS. X-ray crystallographic structure of an artificial beta-sheet dimer.. Journal of the American Chemical Society, 2010.
• Apostol MI, Sawaya MR, Cascio D, Eisenberg D. Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease.. The Journal of biological chemistry, 2010.
• Eisenberg D, Shenhar R, Rabinovitz M. Synthetic approaches to aromatic belts: building up strain in macrocyclic polyarenes.. Chemical Society reviews, 2010.
• Ostapchenko VG, Sawaya MR, Makarava N, Savtchenko R, Nilsson KP, Eisenberg D, Baskakov IV. Two amyloid States of the prion protein display significantly different folding patterns.. Journal of molecular biology, 2010.
• Wang L, Schubert D, Sawaya MR, Eisenberg D, Riek R. Multidimensional structure-activity relationship of a protein in its aggregated states.. Angewandte Chemie (International ed. in English), 2010.
• Laganowsky A, Benesch JL, Landau M, Ding L, Sawaya MR, Cascio D, Huang Q, Robinson CV, Horwitz J, Eisenberg D. Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function.. Protein science : a publication of the Protein Society, 2010.
• Goldschmidt L, Teng PK, Riek R, Eisenberg D. Identifying the amylome, proteins capable of forming amyloid-like fibrils.. Proceedings of the National Academy of Sciences of the United States of America, 2010.
• Sprinzak E, Cokus SJ, Yeates TO, Eisenberg D, Pellegrini M. Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression.. BMC systems biology, 2009.
• Salwinski L, Licata L, Winter A, Thorneycroft D, Khadake J, Ceol A, Aryamontri AC, Oughtred R, Livstone M, Boucher L, Botstein D, Dolinski K, Berardini T, Huala E, Tyers M, Eisenberg D, Cesareni G, Hermjakob H. Recurated protein interaction datasets.. Nature methods, 2009.
• Ivanova MI, Sievers SA, Sawaya MR, Wall JS, Eisenberg D. Molecular basis for insulin fibril assembly.. Proceedings of the National Academy of Sciences of the United States of America, 2009.
• Wiltzius JJ, Landau M, Nelson R, Sawaya MR, Apostol MI, Goldschmidt L, Soriaga AB, Cascio D, Rajashankar K, Eisenberg D. Molecular mechanisms for protein-encoded inheritance.. Nature structural & molecular biology, 2009.
• Teng PK, Eisenberg D. Short protein segments can drive a non-fibrillizing protein into the amyloid state.. Protein engineering, design & selection : PEDS, 2009.
• Wiltzius JJ, Sievers SA, Sawaya MR, Eisenberg D. Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process.. Protein science : a publication of the Protein Society, 2009.
• Maji SK, Perrin MH, Sawaya MR, Jessberger S, Vadodaria K, Rissman RA, Singru PS, Nilsson KP, Simon R, Schubert D, Eisenberg D, Rivier J, Sawchenko P, Vale W, Riek R. Functional amyloids as natural storage of peptide hormones in pituitary secretory granules.. Science (New York, N.Y.), 2009.
• Zhang K, Sawaya MR, Eisenberg DS, Liao JC. Expanding metabolism for biosynthesis of nonnatural alcohols.. Proceedings of the National Academy of Sciences of the United States of America, 2008.
• Llewellyn R, Eisenberg DS. Annotating proteins with generalized functional linkages.. Proceedings of the National Academy of Sciences of the United States of America, 2008.
• Medrano-Soto A, Pal D, Eisenberg D. Inferring molecular function: contributions from functional linkages.. Trends in genetics : TIG, 2008.
• Miallau L, Faller M, Chiang J, Arbing M, Guo F, Cascio D, Eisenberg D. Structure and proposed activity of a member of the VapBC family of toxin-antitoxin systems. VapBC-5 from Mycobacterium tuberculosis.. The Journal of biological chemistry, 2008.
• Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.. Cell, 2008.
• Riley R, Pellegrini M, Eisenberg D. Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.. PLoS computational biology, 2008.
• Wang L, Maji SK, Sawaya MR, Eisenberg D, Riek R. Bacterial inclusion bodies contain amyloid-like structure.. PLoS biology, 2008.
• Cruz D, Watson AD, Miller CS, Montoya D, Ochoa MT, Sieling PA, Gutierrez MA, Navab M, Reddy ST, Witztum JL, Fogelman AM, Rea TH, Eisenberg D, Berliner J, Modlin RL. Host-derived oxidized phospholipids and HDL regulate innate immunity in human leprosy.. The Journal of clinical investigation, 2008.
• Guo Z, Eisenberg D. The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.. Protein science : a publication of the Protein Society, 2008.
• Wiltzius JJ, Sievers SA, Sawaya MR, Cascio D, Popov D, Riekel C, Eisenberg D. Atomic structure of the cross-beta spine of islet amyloid polypeptide (amylin).. Protein science : a publication of the Protein Society, 2008.
• Miller CS, Eisenberg D. Using inferred residue contacts to distinguish between correct and incorrect protein models.. Bioinformatics (Oxford, England), 2008.
• Kuriyan J, Eisenberg D. The origin of protein interactions and allostery in colocalization.. Nature, 2007.
• Anderson DH, Kickhoefer VA, Sievers SA, Rome LH, Eisenberg D. Draft crystal structure of the vault shell at 9-A resolution.. PLoS biology, 2007.
• Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.. BMC biology, 2007.
• Kim SM, Bowers PM, Pal D, Strong M, Terwilliger TC, Kaufmann M, Eisenberg D. Functional linkages can reveal protein complexes for structure determination.. Structure (London, England : 1993), 2007.
• Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H. The minimum information required for reporting a molecular interaction experiment (MIMIx).. Nature biotechnology, 2007.
• Goldschmidt L, Cooper DR, Derewenda ZS, Eisenberg D. Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.. Protein science : a publication of the Protein Society, 2007.
• Salwinski L, Eisenberg D. The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.. Bioinformatics (Oxford, England), 2007.
• Sawaya MR, Sambashivan S, Nelson R, Ivanova MI, Sievers SA, Apostol MI, Thompson MJ, Balbirnie M, Wiltzius JJ, McFarlane HT, Madsen AØ, Riekel C, Eisenberg D. Atomic structures of amyloid cross-beta spines reveal varied steric zippers.. Nature, 2007.
• Guo Z, Eisenberg D. The mechanism of the amyloidogenic conversion of T7 endonuclease I.. The Journal of biological chemistry, 2007.
• Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.. PLoS biology, 2007.
• Tsemekhman K, Goldschmidt L, Eisenberg D, Baker D. Cooperative hydrogen bonding in amyloid formation.. Protein science : a publication of the Protein Society, 2007.
• Strong M, Eisenberg D. The protein network as a tool for finding novel drug targets.. Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques, 2007.
• White EL, Southworth K, Ross L, Cooley S, Gill RB, Sosa MI, Manouvakhova A, Rasmussen L, Goulding C, Eisenberg D, Fletcher TM. A novel inhibitor of Mycobacterium tuberculosis pantothenate synthetase.. Journal of biomolecular screening, 2006.
• Abdallah AM, Verboom T, Hannes F, Safi M, Strong M, Eisenberg D, Musters RJ, Vandenbroucke-Grauls CM, Appelmelk BJ, Luirink J, Bitter W. A specific secretion system mediates PPE41 transport in pathogenic mycobacteria.. Molecular microbiology, 2006.
• Goulding CW, Bowers PM, Segelke B, Lekin T, Kim CY, Terwilliger TC, Eisenberg D. The structure and computational analysis of Mycobacterium tuberculosis protein CitE suggest a novel enzymatic function.. Journal of molecular biology, 2006.
• Eisenberg D, Nelson R, Sawaya MR, Balbirnie M, Sambashivan S, Ivanova MI, Madsen AØ, Riekel C. The structural biology of protein aggregation diseases: Fundamental questions and some answers.. Accounts of chemical research, 2006.
• Guo Z, Eisenberg D. Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I.. Proceedings of the National Academy of Sciences of the United States of America, 2006.
• Strong M, Sawaya MR, Wang S, Phillips M, Cascio D, Eisenberg D. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.. Proceedings of the National Academy of Sciences of the United States of America, 2006.
• Bennett MJ, Sawaya MR, Eisenberg D. Deposition diseases and 3D domain swapping.. Structure (London, England : 1993), 2006.
• Eisenberg D, Marcotte E, McLachlan AD, Pellegrini M. Bioinformatic challenges for the next decade(s).. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2006.
• Nelson R, Eisenberg D. Recent atomic models of amyloid fibril structure.. Current opinion in structural biology, 2006.
• Ivanova MI, Thompson MJ, Eisenberg D. A systematic screen of beta(2)-microglobulin and insulin for amyloid-like segments.. Proceedings of the National Academy of Sciences of the United States of America, 2006.
• Thompson MJ, Sievers SA, Karanicolas J, Ivanova MI, Baker D, Eisenberg D. The 3D profile method for identifying fibril-forming segments of proteins.. Proceedings of the National Academy of Sciences of the United States of America, 2006.
• Liu PT, Stenger S, Li H, Wenzel L, Tan BH, Krutzik SR, Ochoa MT, Schauber J, Wu K, Meinken C, Kamen DL, Wagner M, Bals R, Steinmeyer A, Zügel U, Gallo RL, Eisenberg D, Hewison M, Hollis BW, Adams JS, Bloom BR, Modlin RL. Toll-like receptor triggering of a vitamin D-mediated human antimicrobial response.. Science (New York, N.Y.), 2006.
• Wang S, Eisenberg D. Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action.. Biochemistry, 2006.
• Rachman H, Strong M, Ulrichs T, Grode L, Schuchhardt J, Mollenkopf H, Kosmiadi GA, Eisenberg D, Kaufmann SH. Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis.. Infection and immunity, 2006.
• Rachman H, Strong M, Schaible U, Schuchhardt J, Hagens K, Mollenkopf H, Eisenberg D, Kaufmann SH. Mycobacterium tuberculosis gene expression profiling within the context of protein networks.. Microbes and infection, 2006.
• Nelson R, Eisenberg D. Structural models of amyloid-like fibrils.. Advances in protein chemistry, 2006.
• Conboy L, Patel S, Kaptchuk TJ, Gottlieb B, Eisenberg D, Acevedo-Garcia D. Sociodemographic determinants of the utilization of specific types of complementary and alternative medicine: an analysis based on a nationally representative survey sample.. Journal of alternative and complementary medicine (New York, N.Y.), 2005.
• Bowers PM, O'Connor BD, Cokus SJ, Sprinzak E, Yeates TO, Eisenberg D. Utilizing logical relationships in genomic data to decipher cellular processes.. The FEBS journal, 2005.
• Riley R, Lee C, Sabatti C, Eisenberg D. Inferring protein domain interactions from databases of interacting proteins.. Genome biology, 2005.
• Sambashivan S, Liu Y, Sawaya MR, Gingery M, Eisenberg D. Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure.. Nature, 2005.
• Aprahamian I, Eisenberg D, Hoffman RE, Sternfeld T, Matsuo Y, Jackson EA, Nakamura E, Scott LT, Sheradsky T, Rabinovitz M. Ball-and-socket stacking of supercharged geodesic polyarenes: bonding by interstitial lithium ions.. Journal of the American Chemical Society, 2005.
• Nelson R, Sawaya MR, Balbirnie M, Madsen AØ, Riekel C, Grothe R, Eisenberg D. Structure of the cross-beta spine of amyloid-like fibrils.. Nature, 2005.
• Li H, Sawaya MR, Tabita FR, Eisenberg D. Crystal structure of a RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum.. Structure (London, England : 1993), 2005.
• Goulding CW, Apostol MI, Sawaya MR, Phillips M, Parseghian A, Eisenberg D. Regulation by oligomerization in a mycobacterial folate biosynthetic enzyme.. Journal of molecular biology, 2005.
• Müller P, Sawaya MR, Pashkov I, Chan S, Nguyen C, Wu Y, Perry LJ, Eisenberg D. The 1.70 angstroms X-ray crystal structure of Mycobacterium tuberculosis phosphoglycerate mutase.. Acta crystallographica. Section D, Biological crystallography, 2005.
• Li H, Pellegrini M, Eisenberg D. Detection of parallel functional modules by comparative analysis of genome sequences.. Nature biotechnology, 2005.
• Pal D, Eisenberg D. Inference of protein function from protein structure.. Structure (London, England : 1993), 2005.
• Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. Use of logic relationships to decipher protein network organization.. Science (New York, N.Y.), 2004.
• Reinhardt A, Eisenberg D. DPANN: improved sequence to structure alignments following fold recognition.. Proteins, 2004.
• Bennett MJ, Eisenberg D. The evolving role of 3D domain swapping in proteins.. Structure (London, England : 1993), 2004.
• Ivanova MI, Sawaya MR, Gingery M, Attinger A, Eisenberg D. An amyloid-forming segment of beta2-microglobulin suggests a molecular model for the fibril.. Proceedings of the National Academy of Sciences of the United States of America, 2004.
• Salwinski L, Eisenberg D. In silico simulation of biological network dynamics.. Nature biotechnology, 2004.
• Strong M, Cascio D, Eisenberg D. A web-based comparative genomics tutorial for investigating microbial genomes.. Microbiology education, 2004.
• Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution.. Genome biology, 2004.
• Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.. Nature biotechnology, 2004.
• Kleiger G, Panina EM, Mallick P, Eisenberg D. PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence.. Protein science : a publication of the Protein Society, 2004.
• Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update.. Nucleic acids research, 2004.
• Strong M, Graeber TG, Beeby M, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps.. Nucleic acids research, 2003.
• Lee S, Sawaya MR, Eisenberg D. Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.. Acta crystallographica. Section D, Biological crystallography, 2003.
• Ivanova MI, Gingery M, Whitson LJ, Eisenberg D. Role of the C-terminal 28 residues of beta2-microglobulin in amyloid fibril formation.. Biochemistry, 2003.
• Goulding CW, Apostol MI, Gleiter S, Parseghian A, Bardwell J, Gennaro M, Eisenberg D. Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis.. The Journal of biological chemistry, 2003.
• Hsu T, Hingley-Wilson SM, Chen B, Chen M, Dai AZ, Morin PM, Marks CB, Padiyar J, Goulding C, Gingery M, Eisenberg D, Russell RG, Derrick SC, Collins FM, Morris SL, King CH, Jacobs WR. The primary mechanism of attenuation of bacillus Calmette-Guerin is a loss of secreted lytic function required for invasion of lung interstitial tissue.. Proceedings of the National Academy of Sciences of the United States of America, 2003.
• Bleharski JR, Li H, Meinken C, Graeber TG, Ochoa MT, Yamamura M, Burdick A, Sarno EN, Wagner M, Röllinghoff M, Rea TH, Colonna M, Stenger S, Bloom BR, Eisenberg D, Modlin RL. Use of genetic profiling in leprosy to discriminate clinical forms of the disease.. Science (New York, N.Y.), 2003.
• Eisenberg D. The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.. Proceedings of the National Academy of Sciences of the United States of America, 2003.
• Goulding CW, Perry LJ, Anderson D, Sawaya MR, Cascio D, Apostol MI, Chan S, Parseghian A, Wang SS, Wu Y, Cassano V, Gill HS, Eisenberg D. Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA.. Biophysical chemistry, 2003.
• Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach.. Genome biology, 2003.
• Lee S, Eisenberg D. Seeded conversion of recombinant prion protein to a disulfide-bonded oligomer by a reduction-oxidation process.. Nature structural biology, 2003.
• Diaz-Avalos R, Long C, Fontano E, Balbirnie M, Grothe R, Eisenberg D, Caspar DL. Cross-beta order and diversity in nanocrystals of an amyloid-forming peptide.. Journal of molecular biology, 2003.
• Salwinski L, Eisenberg D. Computational methods of analysis of protein-protein interactions.. Current opinion in structural biology, 2003.
• Freedland SJ, Pantuck AJ, Paik SH, Zisman A, Graeber TG, Eisenberg D, McBride WH, Nguyen D, Tso CL, Belldegrun AS. Heterogeneity of molecular targets on clonal cancer lines derived from a novel hormone-refractory prostate cancer tumor system.. The Prostate, 2003.
• Wang S, Eisenberg D. Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate.. Protein science : a publication of the Protein Society, 2003.
• Cech TR, Eddy SR, Eisenberg D, Hersey K, Holtzman SH, Poste GH, Raikhel NV, Scheller RH, Singer DB, Waltham MC, National Academics Committee on Responsibilities of Authorship in the Biological Sciences. Sharing publication-related data and materials: responsibilities of authorship in the life sciences.. Plant physiology, 2003.
• Mura C, Kozhukhovsky A, Gingery M, Phillips M, Eisenberg D. The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs).. Protein science : a publication of the Protein Society, 2003.
• Mura C, Phillips M, Kozhukhovsky A, Eisenberg D. Structure and assembly of an augmented Sm-like archaeal protein 14-mer.. Proceedings of the National Academy of Sciences of the United States of America, 2003.
• Mura C, Katz JE, Clarke SG, Eisenberg D. Structure and function of an archaeal homolog of survival protein E (SurEalpha): an acid phosphatase with purine nucleotide specificity.. Journal of molecular biology, 2003.
• McCarty AS, Kleiger G, Eisenberg D, Smale ST. Selective dimerization of a C2H2 zinc finger subfamily.. Molecular cell, 2003.
• Anderson DH, Sawaya MR, Cascio D, Ernst W, Modlin R, Krensky A, Eisenberg D. Granulysin crystal structure and a structure-derived lytic mechanism.. Journal of molecular biology, 2003.
• Eisenberg D. John T. Edsall as tutor and teacher.. Biophysical chemistry, 2003.
• Gill HS, Pfluegl GM, Eisenberg D. Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation.. Biochemistry, 2002.
• Mallick P, Boutz DR, Eisenberg D, Yeates TO. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds.. Proceedings of the National Academy of Sciences of the United States of America, 2002.
• Goulding CW, Sawaya MR, Parseghian A, Lim V, Eisenberg D, Missiakas D. Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD.. Biochemistry, 2002.
• Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap.. Protein science : a publication of the Protein Society, 2002.
• Kleiger G, Grothe R, Mallick P, Eisenberg D. GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles.. Biochemistry, 2002.
• Deane CM, Salwinski L, Xenarios I, Eisenberg D. Protein interactions: two methods for assessment of the reliability of high throughput observations.. Molecular & cellular proteomics : MCP, 2002.
• Wang S, Mura C, Sawaya MR, Cascio D, Eisenberg D. Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets.. Acta crystallographica. Section D, Biological crystallography, 2002.
• Duan XJ, Xenarios I, Eisenberg D. Describing biological protein interactions in terms of protein states and state transitions: the LiveDIP database.. Molecular & cellular proteomics : MCP, 2002.
• Liu Y, Gotte G, Libonati M, Eisenberg D. Structures of the two 3D domain-swapped RNase A trimers.. Protein science : a publication of the Protein Society, 2002.
• Xenarios I, Salwínski L, Duan XJ, Higney P, Kim SM, Eisenberg D. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.. Nucleic acids research, 2002.
• Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era.. Nature, 2000.
• Eisenberg D, Gill HS, Pfluegl GM, Rotstein SH. Structure-function relationships of glutamine synthetases.. Biochimica et biophysica acta, 2000.
• Eisenberg D. How chaperones protect virgin proteins.. Science (New York, N.Y.), 1999.