CBC-Funded Publications 2018

Updated: March 29, 2018

As of March 2018, over 2080 research papers have been published as a result of CBC funding.


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2018

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B. How many human proteoforms are there? Nat Chem Biol. 2018 Feb 14;14(3):206-214. (PubMed)

Bailey LJ, Sheehy KM, Dominik PK, Liang WG, Rui H, Clark M, Jaskolowski M, Kim Y, Deneka D, Tang WJ, Kossiakoff AA. Locking the Elbow: Improved Antibody Fab Fragments as Chaperones for Structure Determination. J Mol Biol. 2018 Feb 2;430(3):337-347. (PubMed)

Bhuripanyo K, Yiyang Wang Y, Liu X, Zhou L, Liu R, Duong D, Zhao B, Bi Y, Zhou H, Chen G, Seyfried NT, Chazin WJ, Kiyokawa H, Yin J. Identifying the substrate proteins of U-box E3s E4B and CHIP by orthogonal ubiquitin transfer. Sci Adv. 2018 Jan 3;4(1):e1701393. (PubMed)

Briscoe SD, Albertin CB, Rowell JJ, Ragsdale CW. Neocortical Association Cell Types in the Forebrain of Birds and Alligators. Curr Biol. 2018 Mar 5;28(5):686-696.e6. (PubMed)

Chen H, Cade BE, Gleason KJ, (…) Bell GI, (…) Redline S. Multi-ethnic Meta-analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea Related Quantitative Trait Locus in Men. Am J Respir Cell Mol Biol. 2018 Mar;58(3):391-401. (PubMed)

Chen J, Sathiyamoorthy K, Zhang X, Schaller S, Perez White BE, Jardetzky TS, Longnecker R. Ephrin receptor A2 is a functional entry receptor for Epstein-Barr virus. Nat Microbiol. 2018 Feb;3(2):172-180. (PubMed)

Chen Z, Notti RQ, Ueberheide BM, Ruthenburg AJ. Quantitative and structural assessment of histone methyllysine analog engagement by cognate binding proteins reveals affinity decrements relative to native counterparts. Biochemistry. 2018 Jan 23;57(3):300-304. (PubMed)

Chu BTT, Petrovich ML, Chaudhary A, Wright D, Murphy B, Wells G, Poretsky R. Metagenomic analysis reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments. Appl Environ Microbiol. 2018 Feb 14;84(5). (PubMed)

Clevenger KD, Ye R, Bok JW, Thomas PM, Islam MN, Miley GP, Robey M, Chen C, Yang K, Swyers M, Wu E, Gao P, Wu C, Keller NP, Kelleher NL. Interrogation of Benzomalvin Biosynthesis using FAC-MS: Discovery of a Benzodiazepine Synthase Activity. Biochemistry. 2018 Mar 13. [Epub ahead of print] (PubMed)

Cook LC, Hu H, Maienschein-Cline M, Federle MJ. A vaginal tract signal detected by the GBS SaeRS system elicits transcriptomic changes and enhances murine colonization. Infect Immun. 2018 Mar 22;86(4). (PubMed)

Davis RG, Park HM, Kim K, Greer JB, Fellers RT, LeDuc RD, Romanova EV, Rubakhin SS, Zombeck JA, Wu C, Yau PM, Gao P, van Nispen AJ, Patrie SM, Thomas PM, Sweedler JV, Rhodes JS, Kelleher NL. Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains. Anal Chem. 2018 Mar 20;90(6):3802-3810. (PubMed)

Dehn S, Thorp EB. Myeloid receptor CD36 is required for early phagocytosis of myocardial infarcts and induction of Nr4a1-dependent mechanisms of cardiac repair. FASEB J. 2018 Jan;32(1):254-264. (PubMed)

Dhiman VK, Bolt MJ, White KP. Nuclear receptors in cancer – uncovering new and evolving roles through genomic analysis. Nat Rev Genet. 2018 Mar;19(3):160-174. Review. (PubMed)

Fisher DW, Luu P, Agarwal N, Kurz JE, Chetkovich DM. Loss of HCN2 leads to delayed gastrointestinal motility and reduced energy intake in mice. PLoS One. 2018 Feb 21;13(2):e0193012. eCollection 2018. (PubMed)

Fornelli L, Toby TK, Schachner LF, Doubleday PF, Srzentić K, DeHart CJ, Kelleher NL. Top-down proteomics: Where we are, where we are going? J Proteomics. 2018 Mar 20;175:3-4. (PubMed)

Galey MM, Sanchez LM. Spatial Analyses of Specialized Metabolites: The Key to Studying Function in Hosts. mSystems. Mar 2018, 3 (2) e00148-17. (PubMed)

Gandal MJ, Haney JR, Parikshak NN, Leppa V, Ramaswami G, Hartl C, Schork AJ, Appadurai V, Buil A, Werge TM, Liu C, White KP; CommonMind Consortium; PsychENCODE Consortium; iPSYCH-BROAD Working Group, Horvath S, Geschwind DH. Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. Science. 2018 Feb 9;359(6376):693-697. (PubMed)

Gatto RG, Li W, Magin RL. Diffusion Tensor Imaging Identifies Presymptomatic Axonal Degeneration in the Spinal Cord of ALS Mice. Brain Res. 2018 Jan 15;1679:45-52. (PubMed)

Harris D, Lukoyanov D, Shaw S, Compton PD, Tokmina-Lukaszewska M, Bothner B, Kelleher NL, Dean DR, Hoffman BM, Seefeldt LC. The Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2. Biochemistry. 2018 Feb 6;57(5):701-710. (PubMed)

Hong BJ, Iscen A, Chipre AJ, Li MM, Lee OS, Leonard JN, Schatz GC, Nguyen ST. Highly Stable, Ultra-Small Polymer-Grafted Nanobins (usPGNs) with Stimuli-Responsive Capability. J Phys Chem Lett. 2018 Mar 1;9(5):1133-1139. (PubMed)

Ishihara J, Ishihara A, Fukunaga K, Briquez PS, Hubbell JA. Laminin heparin-binding peptides promiscuously bind growth factors and enhance diabetic wound healing. bioRxiv. Online February 5, 2018. [Epub ahead of print] (biorxiv.org)

Jun G, Manning A, Almeida M, (…) Bell GI, (…) Blangero J. Evaluating the contribution of rare variants to type 2 diabetes and related traits using pedigrees. Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):379-384. (PubMed)

Karabin NB, Allen S, Kwon HK, Bobbala S, Firlar E, Shokuhfar T, Shull KR, Scott EA. Sustained micellar delivery via inducible transitions in nanostructure morphology. Nat Commun. 2018 Feb 12;9(1):624. (PubMed)

Kathayat RS, Cao Y, Elvira PD, Sandoz PA, Zaballa ME, Springer MZ, Drake LE, Macleod KF, van der Goot FG, Dickinson BC. Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Nat Commun. 2018 Jan 23;9(1):334. (PubMed)

Kenney GE, Dassama LMK, Pandelia ME, Gizzi AS, Martinie RJ, Gao P, DeHart CJ, Schachner LF, Skinner OS, Ro SY, Zhu X, Sadek M, Thomas PM, Almo SC, Bollinger JM Jr., Krebs C, Kelleher NL, Rosenzweig AC. The biosynthesis of methanobactin. Science. 2018 Mar 23;359(6382):1411-1416. (PubMed)

Koirala D, Shelke SA, Dupont M, Ruiz S, DasGupta S, Bailey LJ, Benner SA, Piccirilli JA. Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography. Nucleic Acids Res. 2018 Mar 16;46(5):2624-2635. (PubMed)

Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston R. The modERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics. 2018 Mar;208(3):937-949. (PubMed)

LeDuc RD, Schwämmle V, Shortreed MR, Cesnik AJ, Solntsev SK, Shaw JB, Martin MJ, Vizcaino JA, Alpi E, Danis P, Kelleher NL, Smith LM, Ge Y, Agar JN, Chamot-Rooke J, Loo JA, Pasa-Tolic L, Tsybin YO. ProForma: A Standard Proteoform Notation. J Proteome Res. 2018 Mar 2;17(3):1321-1325. (PubMed)

Leech KA, Kim HE, Hornby TG. Strategies to augment volitional and reflex function may improve locomotor capacity following incomplete spinal cord injury. J Neurophysiol. 2018 Mar 1;119(3):894-903. (PubMed)

Lyon YA, Riggs D, Fornelli L, Compton PD, Julian RR. The Ups and Downs of Repeated Cleavage and Internal Fragment Production in Top-Down Proteomics. J Am Soc Mass Spectrom. 2018 Jan;29(1):150-157. (PubMed)

Malik N, Iyamu ID, Scheidt KA, Schiltz GE. Synthesis of a novel fused pyrrolodiazepine-based library with anti-cancer activity. Tetrahedron Letters, 2018. Available online 8 March 2018. [Epub ahead of print] (www.sciencedirect.com)

Martin RW, Des Soye BJ, Kwon YC, Kay J, Davis RG, Thomas PM, Majewska NI, Chen CX, Marcum RD, Weiss MG, Stoddart AE, Amiram M, Ranji Charna AK, Patel JR, Isaacs FJ, Kelleher NL, Hong SH, Jewett MC. Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids. Nat Commun. 2018 Mar 23;9(1):1203. (PubMed)

Miley GP, Rote JC, Silverman RB, Kelleher NL, Thomson RJ. Total Synthesis of Tambromycin Enabled by Indole C-H Functionalization. Org Lett. 2018 Mar 27. [Epub ahead of print] (PubMed)

Mukherjee S, Griffin DH, Horn JR, Rizk SS, Nocula-Lugowska M, Malmqvist M, Kim SS, Kossiakoff AA. Engineered synthetic antibodies as probes to quantify the energetic contributions of ligand binding to conformational changes in proteins. J Biol Chem. 2018 Feb 23;293(8):2815-2828. [Epub ahead of print] (PubMed)

Nekrasova O, Harmon RM, Broussard JA, Koetsier JL, Godsel LM, Fitz GN, Gardel ML, Green KJ. Desmosomal cadherin association with Tctex-1 and cortactin-Arp2/3 drives perijunctional actin polymerization to promote keratinocyte delamination. Nat Commun. 2018 Mar 13;9(1):1053. (PubMed)

Nguyen HA, Su Y, Zhang JY, Antanasijevic A, Caffrey M, Schalk AM, Liu L, Rondelli D, Oh A, Mahmud DL, Bosland MC, Kajdacsy-Balla A, Peirs S, Lammens T, Mondelaers V, De Moerloose B, Goossens S, Schlicht MJ, Kabirov KK, Lyubimov AV, Merrill BJ, Saunthararajah Y, Van Vlierberghe P, Lavie A. A Novel l-Asparaginase with low l-Glutaminase Coactivity Is Highly Efficacious against Both T- and B-cell Acute Lymphoblastic Leukemias In Vivo. Cancer Res. 2018 Mar 15;78(6):1549-1560. (PubMed)

Parameswaran R, Carvalho-de-Souza JL, Jiang Y, Burke MJ, Zimmerman JF, Koehler K, Phillips AW, Yi J, Adams EJ, Bezanilla F, Tian B. Photoelectrochemical modulation of neuronal activity with free-standing coaxial silicon nanowires. Nat Nanotechnol. 2018 Feb 19. [Epub ahead of print] (PubMed)

Parkinson EI, Tryon JH, Goering AW, Ju KS, McClure RA, Kemball JD, Zhukovsky S, Labeda DP, Thomson RJ, Kelleher NL, Metcalf WW. Discovery of the tyrobetaine natural products and their biosynthetic gene cluster via metabologenomics. ACS Chem Biol. 2018 Mar 6. [Epub ahead of print] (PubMed)

Payne JT, Butkovich PH, Gu YF, Kunze KN, Park HJ, Wang D, Lewis JC. Enantioselective Desymmetrization of Methylenedianilines via Enzyme-Catalyzed Remote Halogenation. J Am Chem Soc. 2018 Jan 17;140(2):546-549. (PubMed)

Pérez Morales TG, Ratia K, Wang DS, Gogos A, Driver TG, Federle MJ. A novel chemical inducer of Streptococcus quorum sensing acts by inhibiting the pheromone-degrading endopeptidase PepO. J Biol Chem. 2018 Jan 19;293(3):931-940. (PubMed)

Petrovich M, Chu B, Wright D, Griffin J, Elfeki M, Murphy BT, Poretsky R, Wells G. Antibiotic resistance genes show enhanced mobilization through suspended growth and biofilm-based wastewater treatment processes. FEMS Microbiol Ecol. 2018 Mar 9. [Epub ahead of print] (PubMed)

Radvansky BA, Dombeck DA. An olfactory virtual reality system for mice. Nat Commun. 2018 Feb 26;9(1):839. (PubMed)

Schoborg JA, Jewett MC. Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems. In: Synthetic Biology: Parts, Devices and Applications. 2018. Sven Panke and Christina Smolke, editors. Wiley Biotechnology Series. (books.google.com)

Skinner OS, Haverland NA, Fornelli L, Melani RD, Do Vale LHF, Seckler HS, Doubleday PF, Schachner LF, Srzentić K, Kelleher NL, Compton PD. Top-down characterization of endogenous protein complexes with native proteomics. Nat Chem Biol. 2018 Jan;14(1):36-41. (PubMed)

Smith LM, Kelleher NL. Proteoforms as the next proteomics currency. Science. 2018 Mar 9;359(6380):1106-1107. (PubMed)

Speltz TE, Danes JM, Stender JD, Frasor J, Moore TW. A Cell-Permeable Stapled Peptide Inhibitor of the Estrogen Receptor/Coactivator Interaction. ACS Chem Biol. 2018 Mar 16;13(3):676-684. (PubMed)

Stephens AD, Banigan EJ, Marko JF. Separate roles for chromatin and lamins in nuclear mechanics. Nucleus. 2018 Jan 1;9(1):119-124. (PubMed)

Stephens AD, Liu PZ, Banigan EJ, Almassalha LM, Backman V, Adam SA, Goldman RD, Marko JF. Chromatin histone modifications and rigidity affect nuclear morphology independent of lamins. Mol Biol Cell. 2018 Jan 15;29(2):220-233. (PubMed)

Tocco VJ, Li Y, Christopher KG, Matthews JH, Aggarwal V, Paschall L, Luesch H, Licht JD, Dickinson RB, Lele TP. The nucleus is irreversibly shaped by motion of cell boundaries in cancer and non-cancer cells. J Cell Physiol. 2018 Feb;233(2):1446-1454. (PubMed)

Turcan S, Makarov V, Taranda J, Wang Y, Fabius AWM, Wu W, Zheng Y, El-Amine N, Haddock S, Nanjangud G, LeKaye HC, Brennan C, Cross J, Huse JT, Kelleher NL, Osten P, Thompson CB, Chan TA. Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence. Nat Genet. 2018 Jan;50(1):62-72. (PubMed)

Urban BE, Xiao L, Chen S, Yang H, Dong B, Kozorovitskiy Y, Zhang HF. In vivo super-resolution imaging of neuronal structure in the mouse brain. IEEE Trans Biomed Eng. 2018 Jan;65(1):232-238. (PubMed)

Urban BE, Xiao L, Dong B, Chen S, Kozorovitskiy Y, Zhang HF. Imaging neuronal structure dynamics using two-photon super-resolution patterned excitation reconstruction (SuPER) microscopy. J Biophotonics. 2018 Mar;11(3). (PubMed)

Van Hedger K, Keedy SK, Mayo LM, Heilig M, de Wit H. Neural responses to cues paired with methamphetamine in healthy volunteers. Neuropsychopharmacology. 2018 Jan 30. [Epub ahead of print] (PubMed)

Wytock TP, Fiebig A, Willett JW, Herrou J, Fergin A, Motter AE, Crosson S. Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. Published online: March 27, 2018. [Epub ahead of print] (doi.org)

Yao Y, Delgado-Rivera L, Samareh Afsari H, Yin L, Thatcher GRJ, Moore TW, Miller LW. Time-Gated Luminescence Detection of Enzymatically Produced Hydrogen Sulfide: Design, Synthesis, and Application of a Lanthanide-Based Probe. Inorg Chem. 2018 Jan 16;57(2):681-688. (PubMed)