CBC-Funded Publications 2019

Updated: May 23, 2019

As of May 2019, over 2340 research papers have been published as a result of CBC funding.


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2019

Ahsan K, Singh N, Rocha M, Huang C, Prince VE. Prickle1 is required for EMT and migration of zebrafish cranial neural crest. Dev Biol. 2019 Feb 2. [Epub ahead of print] (PubMed)

Cassidy JJ, Bernasek S, Bakker R, Giri R, Peláez N, Eder B, Anna Bobowska A, Bagheri N, Amaral LAN, Carthew RW. Repressive gene regulation synchronizes development with cellular metabolism. bioRxiv preprint first posted online Feb. 12, 2019. (biorxiv.org)

Cedernaes J, Huang W, Ramsey KM, Waldeck N, Cheng L, Marcheva B, Omura C, Kobayashi Y, Peek CB, Levine DC, Dhir R, Awatramani R, Bradfield CA, Wang XA, Takahashi JS, Mokadem M, Ahima RS, Bass J. Transcriptional Basis for Rhythmic Control of Hunger and Metabolism within the AgRP Neuron. Cell Metab. 2019 Feb 18. [Epub ahead of print] (PubMed)

Chen S, Fan J, Zhang M, Qin L, Dominguez D, Long A, Wang G, Ma R, Li H, Zhang Y, Fang D, Sosman J, Zhang B. CD73 expression on effector T cells sustained by TGF-β facilitates tumor resistance to anti-4-1BB/CD137 therapy. Nat Commun. 2019 Jan 11;10(1):150. (PubMed)

Chen X, Cao G, Wu J, Wang X, Pan Z, Gao J, Tian Q, Xu L, Li Z, Hao Y, Huang Q, Wang P, Xiao M, Xie L, Tang S, Liu Z, Hu L, Tang J, He R, Wang L, Zhou X, Wu Y, Chen M, Sun B, Zhu B, Huang J, Ye L. The histone methyltransferase EZH2 primes the early differentiation of follicular helper T cells during acute viral infection. Cell Mol Immunol. 2019 Mar 6. [Epub ahead of print] (PubMed)

Cheng J, Demeulemeester J, Wedge DC, Vollan HKM, Pitt JJ, Russnes HG, Pandey BP, Nilsen G, Nord S, Bignell GR, White KP, Børresen-Dale AL, Campbell PJ, Kristensen VN, Stratton MR, Lingjærde OC, Moreau Y, Van Loo P. Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors. Nat Commun. 2019 Jan 28;10(1):525. (PubMed)

Chowdhury SR, Kennedy S, Zhu K, Mishra R, Chuong P, Nguyen AU, Kathman SG, Statsyuk AV. Discovery of covalent enzyme inhibitors using virtual docking of covalent fragments. Bioorg Med Chem Lett. 2019 Jan 1;29(1):36-39. (PubMed)

Cline EN, Das A, Bicca MA, Mohammad SN, Schachner LF, Kamel JM, DiNunno N, Weng A, Paschall JD, Lo Bu R, Khan FM, Rollins MG, Ives AN, Shekhawat G, Nunes-Tavares N, de Mello FG, Compton PD, Kelleher NL, Klein WL. A Novel Crosslinking Protocol Stabilizes Amyloid β Oligomers Capable of Inducing Alzheimer’s-Associated Pathologies. J Neurochem. 2019 Mar;148(6):822-836. (PubMed)

Curtis M, Kenny HA, Ashcroft B, Mukherjee A, Johnson A, Zhang Y, Helou Y, Batlle R, Liu X, Gutierrez N, Gao X, Yamada SD, Lastra R, Montag A, Ahsan N, Locasale JW, Salomon AR, Nebreda AR, Lengyel E. Fibroblasts Mobilize Tumor Cell Glycogen to Promote Proliferation and Metastasis. Cell Metab. 2019 Jan 8;29(1):141-155.e9. (PubMed)

Dam DHM, Zhao L, Jelsma SA, Zhao Y, Paller AS. Folic acid functionalized hollow nanoparticles for selective photodynamic therapy of cutaneous squamous cell carcinoma. Mater. Chem. Front., 2019, DOI: 10.1039/C9QM00144A. First posted online Apr. 29, 2019. [Epub ahead of print] (pubs.rsc.org)

Dan K, Veetil AT, Chakraborty K, Krishnan Y. DNA nanodevices map enzymatic activity in organelles. Nat Nanotechnol. 2019 Mar;14(3):252-259. (PubMed)

Dickens LT, Letourneau LR, Sanyoura M, Greeley SAW, Philipson LH, Naylor RN. Management and pregnancy outcomes of women with GCK-MODY enrolled in the US Monogenic Diabetes Registry. Acta Diabetol. 2019 Apr;56(4):405-411. (PubMed)

Dorsey BW, Huang L, Mondragón A. Structural organization of a Type III-A CRISPR effector subcomplex determined by X-ray crystallography and cryo-EM. Nucleic Acids Res. 2019 Apr 23;47(7):3765-3783. (PubMed)

Firlar E, Ouy M, Bogdanowicz A, Covnot L, Song B, Nadkarni Y, Shahbazian-Yassar R, Shokuhfar T. Investigation of the magnetosome biomineralization in magnetotactic bacteria using graphene liquid cell – transmission electron microscopy. Nanoscale. 2019 Jan 3;11(2):698-705. (PubMed)

Gao X, Jing Xu1, Chen H, Xue D, Pan W, Zhou C, Ma YC, Ma L. Defective Expression of Mitochondrial, Vacuolar H+-ATPase and Histone Genes in a C. elegans Model of SMA. Front. Genet., 03 May 2019. (www.frontiersin.org)

Ghadge GD, Kay BK, Drigotas C, Roos RP. Single chain variable fragment antibodies directed against SOD1 ameliorate disease in mutant SOD1 transgenic mice. Neurobiol Dis. 2019 Jan;121:131-137. (PubMed)

Gladstein S, Almassalha LM, Cherkezyan L, Chandler JE, Eshein A, Eid A, Zhang D, Wu W, Bauer GM, Stephens AD, Morochnik S, Subramanian H, Marko JF, Ameer GA, Szleifer I, Backman V. Multimodal interference-based imaging of nanoscale structure and macromolecular motion uncovers UV induced cellular paroxysm. Nat Commun. 2019 Apr 10;10(1):1652. (PubMed)

Gomez CM. The cerebellum in health and disease. Neurosci Lett. 2019 Jan 1;688:1. (PubMed)

Graham WV, He W, Marchiando AM, Zha J, Singh G, Li HS, Biswas A, Ong MLDM, Jiang ZH, Choi W, Zuccola H, Wang Y, Griffith J, Wu J, Rosenberg HJ, Wang Y, Snapper SB, Ostrov D, Meredith SC, Miller LW, Turner JR. Intracellular MLCK1 diversion reverses barrier loss to restore mucosal homeostasis. Nat Med. 2019 Apr;25(4):690-700. (PubMed)

Guo Y, Crnkovic CM, Won KJ, Yang X, Lee JR, Orjala J, Lee H, Jeong H. Commensal Gut Bacteria Convert the Immunosuppressant Tacrolimus to Less PotentMetabolites. Drug Metab Dispos. 2019 Mar;47(3):194-202. (PubMed)

Haliyur R, Tong X, Sanyoura M, Shrestha S, Lindner J, Saunders DC, Aramandla R, Poffenberger G, Redick SD, Bottino R, Prasad N, Levy SE, Blind RD, Harlan DM, Philipson LH, Stein RW, Brissova M, Powers AC. Human islets expressing HNF1A variant have defective β cell transcriptional regulatory networks. J Clin Invest. 2019 Jan 2;129(1):246-251. (PubMed)

Heath CM, Wignall SM. Chromokinesin Kif4 promotes proper anaphase in mouse oocyte meiosis. Mol Biol Cell. 2019 May 8:mbcE18100666. [Epub ahead of print] (PubMed)

Hentchel KL, Reyes Ruiz LM, Curtis PD, Fiebig A, Coleman ML, Crosson S. Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater. ISME J. 2019 Feb;13(2):523-536. (PubMed)

Hogan PG, Mork RL, Boyle MG, Muenks CE, Morelli JJ, Thompson RM, Sullivan ML, Gehlert SJ, Merlo JR, McKenzie MG, Wardenburg JB, Rzhetsky A, Burnham CD, Fritz SA. Interplay of personal, pet, and environmental colonization in households affected by community-associated methicillin-resistant Staphylococcus aureus. J Infect. 2019 Mar;78(3):200-207. (PubMed)

Howe M, Ridouh I, Allegra Mascaro AL, Larios A, Azcorra M, Dombeck DA. Coordination of rapid cholinergic and dopaminergic signaling in striatum during spontaneous movement. Elife. 2019 Mar 28;8. (PubMed)

Iyamu ID, Lv W, Malik N, Mishra RK, Schiltz GE. Development of tetrahydroindazole-based potent and selective sigma-2 receptor ligands. ChemMedChem. 2019 May 9. [Epub ahead of print] (PubMed)

Iyamu D, Lv W, Malik N, Mishra RK, Schiltz GE. Discovery of a Novel Class of Potent and Selective Tetrahydroindazole-based Sigma-1 Receptor Ligands. Bioorganic & Medicinal Chemistry. Available online 16 March 2019. (sciencedirect.com)

Izquierdo J, Jain AD, Abdulkadir SA, Schiltz GE. Palladium-Catalyzed Coupling Reactions on Functionalized 2-Trifluoromethyl-4-chromenone Scaffolds: Synthesis of Highly Functionalized Trifluoromethyl Heterocycles. Synthesis. 2019; 51(06): 1342-1352. (Online)

Jani MS, Veetil AT, Krishnan Y. Precision immunomodulation with synthetic nucleic acid technologies. Nature Reviews Materials, 2019. Published online: 04 April 2019. [Epub ahead of print] (nature.com)

Jeffryes J, Strutz J, Henry C, Tyo KEJ. Metabolic In Silico Network Expansions to Predict and Exploit Enzyme Promiscuity. Methods Mol Biol. 2019;1927:11-21. (PubMed)

Jin Q, Martinez CA, Arcipowski KM, Zhu Y, Gutiérrez-Díaz BT, Wang KK, Johnson MR, Volk A, Wang F, Wu J, Grove C, Wang H, Sokirniy I, Thomas PM, Goo YA, Abshiru NA, Hijiya N, Peirs S, Vandamme N, Berx G, Goossens S, Marshall SA, Rendleman EJ, Takahashi YH, Wang L, Rawat R, Bartom ET, Collings CK, Van Vlierberghe P, Bourquin JP, Bornhauser B, Serafin V, Bresolin S, Paganin M, Accordi B, Basso G, Kelleher NL, Weinstock J, Suresh K, Crispino JD, Shilatifard A, Strikoudis A, Mantis C, Kandela I, Kelly S, Ueberheide B, Ntziachristos P. USP7 cooperates with NOTCH1 to drive the oncogenic transcriptional program in T cell leukemia. Clin Cancer Res. 2019 Jan 1;25(1):222-239. (PubMed)

Kafader JO, Melani RD, Senko MW, Makarov AA, Kelleher NL, Compton PD. Measurement of Individual Ions Sharply Increases the Resolution of Orbitrap Mass Spectra of Proteins. Anal Chem. 2019 Feb 19;91(4):2776-2783. (PubMed)

Klomp JE, Shaaya M, Jacob M, Rebiai R, Aaron JS, Collins KB, Huyot V, Gonzalez AM, Muller WA, Chew TL, Malik AB, Karginov AV. Time-Variant SRC Kinase Activation Determines Endothelial Permeability Response. Cell Chemical Biology 26, 1–14, August 15, 2019. [Epub ahead of print] (www.cell.com)

LeDuc RD, Fellers RT, Early BP, Greer JB, Shams DP, Thomas P, Kelleher NL. Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics. Mol Cell Proteomics. 2019 Jan 15. [Epub ahead of print] (PubMed)

Leung K, Chakraborty K, Saminathan A, Krishnan Y. A DNA nanomachine chemically resolves lysosomes in live cells. Nat Nanotechnol. 2019 Feb;14(2):176-183. (PubMed)

Levine MZ, Gregorio NE, Jewett MC, Watts KR, Oza JP. Escherichia coli-Based Cell-Free Protein Synthesis: Protocols for a robust, flexible, and accessible platform technology. J Vis Exp. 2019 Feb 25;(144). (PubMed)

Lue JK, Prabhu SA, Liu Y, Gonzalez Y, Verma A, Mundi PS, Abshiru NA, Camarillo JM, Mehta S, Chen EI, Qiao C, Nandakumar R, Cremers S, Kelleher NL, Elemento O, Amengual JE. Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas. Clin Cancer Res. 2019 Apr 12. [Epub ahead of print] (PubMed)

Mathew B, Ravindran S, Liu X, Torres L, Chennakesavalu M, Huang CC, Feng L, Zelka R, Lopez J, Sharma M, Roth S. Mesenchymal stem cell-derived extracellular vesicles and retinal ischemia-reperfusion. Biomaterials. 2019 Jan 9;197:146-160. (PubMed)

May JL, Kouri FM, Hurley LA, Liu J, Tommasini-Ghelfi S, Ji Y, Gao P, Calvert AE, Lee A, Chandel NS, Davuluri RV, Horbinski CM, Locasale JW, Stegh AH. IDH3α regulates one-carbon metabolism in glioblastoma. Sci Adv. 2019 Jan 2;5(1):eaat0456. eCollection 2019 Jan. (PubMed)

Narayanaswamy N, Chakraborty K, Saminathan A, Zeichner E, Leung K, Devany J, Krishnan Y. A pH-correctable, DNA-based fluorescent reporter for organellar calcium. Nat Methods. 2019 Jan;16(1):95-102. (PubMed)

Nath A, Geeleher P, Huang RS. Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. Brief Bioinform. 2019 Jan 17. [Epub ahead of print] (PubMed)

Patil A, Manzano M, Gottwein E. Genome-wide CRISPR Screens Reveal Genetic Mediators of Cereblon Modulator Toxicity in Primary Effusion Lymphoma. bioRxiv preprint first posted online Apr. 25, 2019. [Epub ahead of print] (www.biorxiv.org)

Petrovich ML, Rosenthal AF, Griffin JS, Wells GF. Spatially resolved abundances of antibiotic resistance genes and intI1 in wastewater treatment biofilms. Biotechnol Bioeng. 2019 Mar;116(3):543-554. (PubMed)

Pusec CM, De Jesus A, Khan MW, Terry AR, Ludvik AE, Xu K, Giancola N, Pervaiz H, Smith ED, Ding X, Harrison S, Chandel NS, Becker TC, Hay N, Ardehali H, Cordoba-Chacon J, Layden BT. Hepatic HKDC1 expression contributes to liver metabolism. Endocrinology. 2019 Feb 1;160(2):313-330. (PubMed)

Quesada V, Freitas-Rodríguez S, Miller J, Pérez-Silva JG, Jiang ZF, Tapia W, Santiago-Fernández O, Campos-Iglesias D, Kuderna LFK, Quinzin M, Álvarez MG, Carrero D, Beheregaray LB, Gibbs JP, Chiari Y, Glaberman S, Ciofi C, Araujo-Voces M, Mayoral P, Arango JR, Tamargo-Gómez I, Roiz-Valle D, Pascual-Torner M, Evans BR, Edwards DL, Garrick RC, Russello MA, Poulakakis N, Gaughran SJ, Rueda DO, Bretones G, Marquès-Bonet T, White KP, Caccone A, López-Otín C. Giant tortoise genomes provide insights into longevity and age-related disease. Nat Ecol Evol. 2019 Jan;3(1):87-95. (PubMed)

Robert A, Tian P, Adam SA, Kittisopikul M, Jaqaman K, Goldman RD, Gelfand VI. Kinesin-dependent transport of keratin filaments: a unified mechanism for intermediate filament transport. FASEB J. 2019 Jan;33(1):388-399. (PubMed)

Romero-Calvo I, Weber C, Ray M, Brown M, Kirby K, Nandi RK, Long TM, Sparrow SM, Ugolkov A, Qiang W, Zhang Y, Brunetti T, Kindler H, Segal JP, Rzhetsky A, Mazar AP, Buschmann MM, Weichselbaum R, Roggin K, White KP. Human Organoids Share Structural and Genetic Features with Primary Pancreatic Adenocarcinoma Tumors. Mol Cancer Res. 2019 Jan;17(1):70-83. (PubMed)

Rotman ER, Bultman KM, Brooks JF 2nd, Gyllborg MC, Burgos HL, Wollenberg MS, Mandel MJ. Natural Strain Variation Reveals Diverse Biofilm Regulation in Squid-Colonizing Vibrio fischeri. J Bacteriol. 2019 Apr 9;201(9). (PubMed)

Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL. Standard Proteoforms and Their Complexes for Native Mass Spectrometry. J Am Soc Mass Spectrom. 2019 Apr 8. [Epub ahead of print] (PubMed)

Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. Identification and Quantification of Proteoforms by Mass Spectrometry. Review. Proteomics. First published: 03 May 2019. [Epub ahead of print] (onlinelibrary.wiley.com)

Scheidt K, Deibler KK, Schiltz GE, Clutter MR, Mishra RK, Vagadia PP, O’Connor M, George MD, Gordon R, Fowler G, Bergan R. Synthesis and Biological Evaluation of 3-Arylindazoles as Selective MEK4 Inhibitors. ChemMedChem. 2019 Feb 1. [Epub ahead of print] (PubMed)

Sun M, Johnson AK, Nelakuditi V, Guidugli L, Fischer D, Arndt K, Ma L, Sandford E, Shakkottai V, Boycott K, Chardon JW, Li Z, Del Gaudio D, Burmeister M, Gomez CM, Waggoner DJ, Das S. Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes. Genet Med. 2019 Jan;21(1):195-206. (PubMed)

Swaroop A, Oyer JA, Will CM, Huang X, Yu W, Troche C, Bulic M, Durham BH, Wen QJ, Crispino JD, MacKerell AD Jr, Bennett RL, Kelleher NL, Licht JD. An activating mutation of the NSD2 histone methyltransferase drives oncogenic reprogramming in acute lymphocytic leukemia. Oncogene. 2019 Jan;38(5):671-686. (PubMed)

Tanaka KJ, Pinkett HW. Oligopeptide-binding protein from nontypeable Haemophilus influenzae has ligand-specific sites to accommodate peptides and heme in the binding pocket. J Biol Chem. 2019 Jan 18;294(3):1070-1082. (PubMed)

Terry AR, Hay N. Fuelling cancer cells. Nat Rev Endocrinol. 2019 Feb;15(2):71-72. (PubMed)

Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc. 2019 Jan;14(1):119-152. (PubMed)

Uraizee I, Varma VK, Sreedhar H, Gambacorta F, Nazeer S, Husain A, Walsh MJ. Label-free Identification of Antibody-mediated Rejection in Cardiac Allograft Biopsies Using Infrared Spectroscopic Imaging. Transplantation. 2019 Apr;103(4):698-704. (PubMed)

Warrier V, Cluzeau C, Chen BC, Green-Saxena A, Bergey DE, Betzig E, Saxena A. Rule-governed Dynamic Stochastic Equilibration of Multicellular Motion In Vivo During Olfactory Neurogenesis. biorxiv.org. Online Mar 28, 2019. (biorxiv.org)

Wolf S, Feng X, Schreiber K, Cao G, Weichselbaum R, Huang J, Leisegang M, Schreiber H. T-cell based immunotherapy and the tumor microenvironment. 10th International Symposium on the Clinical Use of Cellular Products. Cellular Therapy 2019. March 22-23, 2019, Erlangen, Germany. (cellular-therapy.de)

Xia Y, Dai R, Wang K, Jiao C, Zhang C, Xu Y, Li H, Jing X, Chen Y, Jiang Y, Kopp RF, Giase G, Chen C, Liu C. Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders. Mol Psychiatry. 2019 Apr 11. (PubMed)

Zayner JP, Mathes T, Sosnick TR, Kennis JTM. Helical Contributions Mediate Light-Activated Conformational Change in the LOV2 Domain of Avena sativa Phototropin 1. ACS Omega 2019, 4, 1, 1238-1243. (pubs.acs.org)

Zdraljevic S, Fox BW, Strand C, Panda O, Tenjo-Castano FJ, Brady SC, Crombie TA, John G. Doench JG, Schroeder FC, Andersen EC. Natural variation in arsenic toxicity is explained by differences in branched chain amino acid catabolism. Posted February 07, 2019. (biorxiv.org)

Zhang L, Luo Q, Shu Y, Zeng Z, Huang B, Feng Y, Zhang B, Xi Wang X, Lei Y, Ye Z, Zhao L, Cao D, Yang L, Chen X, Liu B, Wagstaff W, Reid RR, Luu HH, Haydon RC, Lee MJ, Moriatis Wolf J, Fu Z, He TC, Kang Q. Transcriptomic landscape regulated by the 14 types of bone morphogenetic proteins (BMPs) in lineage commitment and differentiation of mesenchymal stem cells (MSCs). Genes & Diseases, Available online 8 May 2019. [Epub ahead of print] (www.sciencedirect.com)

Zhang S, Weinberg S, DeBerge M, Gainullina A, Schipma M, Kinchen JM, Ben-Sahra I, Gius DR, Charvet LY, Chandel NS, Schumacker PT, Thorp EB. Efferocytosis Fuels Requirements of Fatty Acid Oxidation and the Electron Transport Chain to Polarize Macrophages for Tissue Repair. Cell Metab. 2019 Feb 5;29(2):443-456.e5. (PubMed)

Zhao B, Liu H, Mei Y, Liu Y, Han X, Yang J, Wickrema A, Ji P. Disruption of erythroid nuclear opening and histone release in myelodysplastic syndromes. Cancer Med. 2019 Jan 30. [Epub ahead of print] (PubMed)

Zhao Z, Wang L, Volk AG, Birch NW, Stoltz KL, Bartom ET, Marshall SA, Rendleman EJ, Nestler CM, Shilati J, Schiltz GE, Crispino JD, Shilatifard A. Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia. Genes Dev. 2019 Jan 1;33(1-2):61-74. (PubMed)

Zink KE, Dean M, Burdette JE, Sanchez LM. Capturing Small Molecule Communication Between Tissues and Cells Using Imaging Mass Spectrometry. J. Vis. Exp. (146), e59490, doi:10.3791/59490 (2019). (www.jove.com)