CBC-Funded Publications 2016

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2016

Alhasan AH, Scott AW, Wu JJ, Feng G, Meeks JJ, Thaxton CS, Mirkin CA. Circulating microRNA signature for the diagnosis of very high-risk prostate cancer. Proc Natl Acad Sci U S A. 2016 Sep 20;113(38):10655-60. (PubMed)

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Cherkezyan L, Stypula-Cyrus Y, Weinberg S, Zhang D, Thusgaard Ruhoff P, Roy HK, Subramanian H, Chandel NS, Szleifer I, Backman V. Label-free imaging of the native, living cellular nanoarchitecture using partial-wave spectroscopic microscopy. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6372-E6381. (PubMed)

Almassalha LM, Bauer GM, Chandler JE, Gladstein S, Szleifer I, Roy HK, Backman V. The Greater Genomic Landscape: The Heterogeneous Evolution of Cancer. Cancer Res. 2016 Oct 1;76(19):5605-5609. (PubMed)

Anderson LL, Berns EJ, Bugga P, George AL Jr, Mrksich M. Measuring Drug Metabolism Kinetics and Drug-Drug Interactions Using Self-Assembled Monolayers for Matrix-Assisted Laser Desorption-Ionization Mass SpectromAnal Chem. 2016 Sep 6;88(17):8604-9. (PubMed)

Anderson GM, Cook EH Jr. Commentary on “Platelet Studies in Autism Spectrum Disorder Patients and First-Degree Relatives”. Mol Autism. 2016 Mar 29;7:20. eCollection 2016. (PubMed)

Angeloni NL, McMahon KM, Swaminathan S, Plebanek MP, Osman I, Volpert OV, Thaxton CS. Pathways for Modulating Exosome Lipids Identified By High-Density Lipoprotein-Like Nanoparticle Binding to Scavenger Receptor Type B-1. Sci Rep. 2016 Mar 11;6:22915. (PubMed)

Antanasijevic A, Hafeman NJ, Tundup S, Kingsley CN, Mishra RK, Rong L, Manicassamy B, Wardrop DJ, Caffrey MS. Stabilization and improvement of a promising influenza antiviral: Making a PAIN PAINless. ACS Infect Dis. 2016 Sep 9;2(9):608-615. (PubMed)

Antanasijevic A, Kingsley C, Basu A, Bowlin TL, Rong L, Caffrey M. Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions. J Biomol NMR. 2016 Mar;64(3):255-65. (PubMed)

Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, Chlenski A, Dobratic M, Mariani CJ, Godley LA, Prabhakar N, White K, Stranger BE, Cohn SL. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget. 2016 Nov 22;7(47):76816-76826. (PubMed)

Aprison EZ, Ruvinsky I. Sexually Antagonistic Male Signals Manipulate Germline and Soma of C. elegans Hermaphrodites. Curr Biol. 2016 Oct 24;26(20):2827-2833. (PubMed)

Asada K, Canestrari E, Paroo Z. A druggable target for rescuing microRNA defects. Bioorg Med Chem Lett. 2016 Oct 15;26(20):4942-4946. (PubMed)

Bagley SC, Altman RB. Computing disease incidence, prevalence and comorbidity from electronic medical records. J Biomed Inform. 2016 Oct;63:108-111. (PubMed)

Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol. 2016 Apr 26;12(4):e1004885. doi: 10.1371/journal.pcbi.1004885. eCollection 2016 Apr. (PubMed)

Banigan EJ, Marko JF. Self-propulsion and interactions of catalytic particles in a chemically active medium. Phys Rev E. 2016 Jan;93(1):012611. (PubMed)

Barbeira A, Shah KP, Torres JM, Wheeler HE, Torstenson ES, Edwards T, Garcia T, Bell GI, Nicolae D, Cox NJ, Im HK. MetaXcan: Summary Statistics Based Gene-Level Association Method Infers Accurate PrediXcan Results. bioRxiv. Preprint first posted online Mar. 23, 2016. (biorxiv.org)

Barnaby SN, Perelman GA, Kohlstedt KL, Chinen AB, Schatz GC, Mirkin CA. Design Considerations for RNA Spherical Nucleic Acids (SNAs). Bioconjug Chem. 2016 Sep 21;27(9):2124-31. (PubMed)

Bass J. Targeting Time in Metabolic Therapeutics. Cell Metab. 2016 Apr 12;23(4):575-7. (PubMed)

Bass J, Lazar MA. Circadian time signatures of fitness and disease. Science. 2016 Nov 25;354(6315):994-999. Review. (PubMed)

Beiser D, Vu M, Gibbons R. Test-Retest Reliability of a Computerized Adaptive Depression Screener. Psychiatr Serv. 2016 Sep 1;67(9):1039-41. (PubMed)

Below JE, Parra EJ, Gamazon ER, Torres J, Krithika S, Candille S, Lu Y, Manichakul A, Peralta-Romero J, Duan Q, Li Y, Morris AP, Gottesman O, Bottinger E, Wang XQ, Taylor KD, Ida Chen YD, Rotter JI, Rich SS, Loos RJ, Tang H, Cox NJ, Cruz M, Hanis CL, Valladares-Salgado A. Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs. Sci Rep. 2016 Jan 19;6:19429. (PubMed)

Bercich RA, Wang A, Mei H, Hammer LH, Seburn KL, Hargrove LJ, Irazoqui PP. Enhancing the versatility of myoelectric prosthetic control through fully wireless chronic acquisition of biopotentials. J Neural Eng. 2016 13:4 046012. (PubMed)

Berni Canani R, Sangwan N, Stefka AT, Nocerino R, Paparo L, Aitoro R, Calignano A, Khan AA, Gilbert JA, Nagler CR. Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants. ISME J. 2016 Mar;10(3):742-50. (PubMed)

Berns EJ, Cabezas MD, Mrksich M. Cellular Assays with a Molecular Endpoint Measured by SAMDI Mass Spectrometry. Small. 2016 Jul;12(28):3811-8. (PubMed)

Berth SH, Mesnard-Hoaglin N, Wang B, Kim H, Song Y, Sapar M, Morfini G, Brady ST. HIV Glycoprotein Gp120 Impairs Fast Axonal Transport by Activating Tak1 Signaling Pathways. ASN Neuro. 2016 Nov 20;8(6). (PubMed)

Bertolino E, Reinitz J, Manu. The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Dev Biol. 2016 May 1;413(1):128-44. (PubMed)

Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal Biochem. 2016 Sep 15;509:50-9. (PubMed)

Brangwynne CP, Marko JF. Cell division: A sticky problem for chromosomes. Nature. 2016 Jul 14;535(7611):234-5. (PubMed)

Brickner DG, Sood V, Tutucci E, Coukos R, Viets K, Singer R, Brickner JH. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms. Mol Biol Cell. 2016 Oct 1;27(19):2980-93. (PubMed)

Brown AS, Kong SW, Kohane IS, Patel CJ. ksRepo: a generalized platform for computational drug repositioning. BMC Bioinformatics. 2016 Feb 9;17:78. (PubMed)

Burbulla LF, Beaumont KG, Mrksich M, Krainc D. Micropatterning Facilitates the Long-Term Growth and Analysis of iPSC-Derived Individual Human Neurons and Neuronal Networks. Adv Healthc Mater. 2016 Aug;5(15):1894-903. (PubMed)

Cade BE, Chen H, Stilp AM, Gleason KJ, Sofer T, Ancoli-Israel S, Arens R, Bell GI, Below JE, Bjonnes AC, Chun S, Conomos MP, Evans DS, Johnson WC, Frazier-Wood AC, Lane JM, Larkin EK, Loredo JS, Post WS, Ramos AR, Rice K, Rotter JI, Shah NA, Stone KL, Taylor KD, Thornton TA, Tranah GJ, Wang C, Zee PC, Hanis CL, Sunyaev SR, Patel SR, Laurie CC, Zhu X, Saxena R, Lin X, Redline S. Genetic Associations with Obstructive Sleep Apnea Traits in Hispanic/Latino Americans. Am J Respir Crit Care Med. 2016 Oct 1;194(7):886-897. (PubMed)

Cannon DS, Medina TR, Mermelstein RJ, Hedeker D, Bakian AV, Coon H, Cook EH, Hamil C, Weiss RB. CYP2A6 Longitudinal Effects in Young Smokers. Nicotine Tob Res. 2016 Feb;18(2):196-203. (PubMed)

Cao Y, Terebus A, Liang J. Accurate Chemical Master Equation Solution Using Multi-Finite Buffers. Multiscale Model Simul. 2016;14(2):923-963. (PubMed)

Cao Y, Terebus A, Liang J. State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation. Bull Math Biol. 2016 Apr 22. (PubMed)

Caschera F, Lee JW, Ho KK, Liu AP, Jewett MC. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chem Commun (Camb). 2016 Apr 7;52(31):5467-9. (PubMed)

Castro VM, Kong SW, Clements CC, Brady R, Kaimal AJ, Doyle AE, Robinson EB, Churchill SE, Kohane IS, Perlis RH. Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study. Transl Psychiatry. 2016 Jan 5;6:e708. (PubMed)

Cassidy JJ, Straughn AJ, Carthew RW. Differential Masking of Natural Genetic Variation by miR-9a in Drosophila. Genetics. 2016 Feb;202(2):675-87. (PubMed)

Cavallo JS, Mayo LM, de Wit H. Acquisition of Conditioning between Methamphetamine and Cues in Healthy Humans. PLoS One. 2016 Aug 22;11(8):e0161541. eCollection 2016. (PubMed)

Cedernaes J, Bass J. Decoding obesity in the brainstem. Elife. 2016 May 9;5. (PubMed)

Chen Y, McClure RA, Kelleher NL. Screening for Expressed Nonribosomal Peptide Synthetases and Polyketide Synthases Using LC-MS/MS-Based Proteomics. Methods Mol Biol. 2016;1401:135-47. (PubMed)

Chinen AB, Ferrer JR, Merkel TJ, Mirkin CA. Relationships between Poly(ethylene glycol) Modifications on RNA-Spherical Nucleic Acid Conjugates and Cellular Uptake and Circulation Time. Bioconjug Chem. 2016 Nov 16;27(11):2715-2721. (PubMed)

Chuang Y, Hung ME, Cangelose BK, Leonard JN. Regulation of the IL-10-driven macrophage phenotype under incoherent stimuli. Innate Immun. 2016 Nov;22(8):647-657. (PubMed)

Ciryam P, Kundra R, Freer R, Morimoto RI, Dobson CM, Vendruscolo M. A transcriptional signature of Alzheimer’s disease is associated with a metastable subproteome at risk for aggregation. Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):4753-8. (PubMed)

Clevenger KD, Bok JW, Ye R, Miley GP, Velk T, Chen C, Yang K, Gao P, Lamprecht M, Thomas PM, Islam MN, Wu CC, Keller NP, Kelleher NL. Large scale discovery and deorphanization of natural products using fungal artificial chromosomes and untargeted metabolomics (FAC-MS). Planta Med. 2016 Dec;81(S 01):S1-S381. (PubMed)

Cone JJ, Fortin SM, McHenry JA, Stuber GD, McCutcheon JE, Roitman MF. Physiological state gates acquisition and expression of mesolimbic reward prediction signals. Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):1943-8. (PubMed)

Cook DC, Zdraljevic S, Tanny RE, Seo B, Riccardi DD, Noble LM, Rockman MV, Alkema MJ, Braendle C, Kammenga JE, Wang J, Kruglyak L, Félix MA, Lee J, Andersen EC. The genetic basis of natural variation in C. elegans telomere length. Genetics. 2016 Sep;204(1):371-83. (PubMed)

Cossairt O, He K, Shang R, Matsuda N, Sharma M, Huang X, Katsaggelos A, Spinoulas L, Yoo S. Compressive Reconstruction for 3D Incoherent Holographic Microscopy. International Conference on Image Processing (ICIP). September 2016. (ieeexplore.ieee.org)

Culver KS, Shin YJ, Rotz MW, Meade TJ, Hersam MC, Odom TW. Shape-Dependent Relaxivity of Nanoparticle-Based T1 Magnetic Resonance Imaging Contrast Agents. J Phys Chem C Nanomater Interfaces. 2016 Sep 29;120(38):22103-22109. (PubMed)

Czyż DM, Jain-Gupta N, Shuman HA, Crosson S. A dual-targeting approach to inhibit Brucella abortus replication in human cells. Sci Rep. 2016 Oct 21;6:35835. (PubMed)

D’Urso A, Takahashi YH, Xiong B, Marone J, Coukos R, Randise-Hinchliff C, Wang JP, Shilatifard A, Brickner JH. Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. Elife. 2016 Jun 23;5. (PubMed)

Das A, Shamirian A, T. Snee PT. Arsenic Silylamide: An Effective Precursor for Arsenide Semiconductor Nanocrystal Synthesis. Chem. Mater. Chem. Mater. 2016, 28 (11), pp 4058–4064. (pubs.acs.org)

DasGupta B, Liang J. Models and Algorithms for Biomolecules and Molecular Networks. (Book) IEEE Press Series in Biomedical Engineering. Metin Akay, Series Editor. 2016. (books.google.com)

Dekker J, Mirny L. The 3D Genome as Moderator of Chromosomal Communication. Cell. 2016 Mar 10;164(6):1110-21. Review. (PubMed)

Demeulemeester J, Kumar P, Møller EK, Nord S, Wedge DC, Peterson A, Mathiesen RR, Fjelldal R, Zamani Esteki M, Theunis K, Fernandez Gallardo E, Grundstad AJ, Borgen E, Baumbusch LO, Børresen-Dale AL, White KP, Kristensen VN, Van Loo P, Voet T, Naume B. Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing. Genome Biol. 2016 Dec 9;17(1):250. (PubMed)

Demissie RD, Kabre P, Tuntland ML, Fung LW. An Efficient and Economical Assay to Screen for Triclosan Binding to FabI. J Biomol Screen. 2016 Apr;21(4):391-8. (PubMed)

Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure. 2016 Feb 2;24(2):300-9. (PubMed)

Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, Zheng G, Pan T, Solomon O, Eyal E, Hershkovitz V, Han D, Doré LC, Amariglio N, Rechavi G, He C. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature. 2016 Feb 25;530(7591):441-6. (PubMed)

Dong B, Almassalha LM, Stypula-Cyrus Y, Urban BE, Chandler JE, Nguyen TQ, Sun C, Zhang HF, Backman V. Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9716-21. (PubMed)

Dong B, Almassalha L, Urban BE, Nguyen TQ, Khuon S, Chew TL, Backman V, Sun C, Zhang HF. Super-resolution spectroscopic microscopy via photon localization. Nat Commun. 2016 Jul 25;7:12290. (PubMed)

Dubash AD, Kam CY, Aguado BA, Patel DM, Delmar M, Shea LD, Green KJ. Plakophilin-2 loss promotes TGF-β1/p38 MAPK-dependent fibrotic gene expression in cardiomyocytes. J Cell Biol. 2016 Feb 15;212(4):425-38. (PubMed)

Durak LJ, Payne JT, Lewis JC. Late-Stage Diversification of Biologically Active Molecules via Chemoenzymatic C-H Functionalization. ACS Catal. 2016 Mar 4;6(3):1451-1454. (PubMed)

Durbin KR, Fornelli L, Fellers RT, Doubleday PF, Narita M, Kelleher NL. Quantitation and Identification of Thousands of Human Proteoforms below 30 kDa. J Proteome Res. 2016 Mar 4;15(3):976-82. (PubMed)

Eastland A, Hornick J, Kawamura R, Nanavati D, Marko JF. Dependence of the structure and mechanics of metaphase chromosomes on oxidized cysteines. Chromosome Res. 2016 Sep;24(3):339-53. (PubMed)

Ebel ME, Kansas GS. Functions of Smad Transcription Factors in TGF-β1-Induced Selectin Ligand Expression on Murine CD4 Th Cells. J Immunol. 2016 Oct 1;197(7):2627-34. (PubMed)

Eckert MA, Pan S, Hernandez KM, Loth RM, Andrade J, Volchenboum SL, Faber P, Montag A, Lastra R, Peter ME, Yamada SD, Lengyel E. Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube. Cancer Discov. 2016 Dec;6(12):1342-1351. (PubMed)

Efimova EV, Takahashi S, Shamsi NA, Wu D, Labay E, Ulanovskaya OA, Weichselbaum RR, Kozmin SA, Kron SJ. Linking Cancer Metabolism to DNA Repair and Accelerated Senescence. Mol Cancer Res. 2016 Feb;14(2):173-84. (PubMed)

Enjin A, Zaharieva EE, Frank DD, Mansourian S, Suh GS, Gallio M, Stensmyr MC. Humidity Sensing in Drosophila. Curr Biol. 2016 May 23;26(10):1352-8. (PubMed)

Estabrook R, Massey SH, Clark CA, Burns JL, Mustanski BS, Cook EH, O’Brien TC, Makowski B, Espy KA, Wakschlag LS. Separating Family-Level and Direct Exposure Effects of Smoking During Pregnancy on Offspring Externalizing Symptoms: Bridging the Behavior Genetic and Behavior Teratologic Divide. Behav Genet. 2016 May;46(3):389-402. (PubMed)

Farmer CA, Kaat AJ, Mazurek MO, Lainhart JE, DeWitt MB, Cook EH, Butter EM, Aman MG. Confirmation of the Factor Structure and Measurement Invariance of the Children’s Scale of Hostility and Aggression: Reactive/Proactive in Clinic-Referred Children With and Without Autism Spectrum Disorder. J Child Adolesc Psychopharmacol. 2016 Feb;26(1):10-8. (PubMed)

Foit L, Thaxton CS. Synthetic high-density lipoprotein-like nanoparticles potently inhibit cell signaling and production of inflammatory mediators induced by lipopolysaccharide binding Toll-like receptor 4. Biomaterials. 2016 Sep;100:67-75. (PubMed)

Francis SM, Kistner-Griffin E, Yan Z, Guter S, Cook EH, Jacob S. Variants in Adjacent Oxytocin/Vasopressin Gene Region and Associations with ASD Diagnosis and Other Autism Related Endophenotypes. Front Neurosci. 2016 May 12;10:195. eCollection 2016. (PubMed)

Fuchsberger C, Flannick J, Teslovich TM, (…) Bell GI, (…) McCarthy MI. The genetic architecture of type 2 diabetes. Nature. 2016 Aug 4;536(7614):41-7. (PubMed)

Geeleher P, Cox NJ, Huang RS. Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models. Genome Biol. 2016 Sep 21;17(1):190. (PubMed)

Gibbons RD, Weiss DJ, Frank E, Kupfer D. Computerized Adaptive Diagnosis and Testing of Mental Health Disorders. Annu Rev Clin Psychol. 2016;12:83-104. (PubMed)

Goering AW, McClure RA, Doroghazi JR, Albright JC, Haverland NA, Zhang Y, Ju KS, Thomson RJ, Metcalf WW, Kelleher NL. Metabologenomics: Correlation of Microbial Gene Clusters with Metabolites Drives Discovery of a Nonribosomal Peptide with an Unusual Amino Acid Monomer. ACS Cent Sci. 2016 Feb 24;2(2):99-108. (PubMed)

Goloborodko A, Imakaev MV, Marko JF, Mirny L. Compaction and segregation of sister chromatids via active loop extrusion. Elife. 2016 May 18;5. (PubMed)

Goloborodko A, Marko JF, Mirny LA. Chromosome Compaction by Active Loop Extrusion. Biophys J. 2016 May 24;110(10):2162-8. (PubMed)

Grossman RL, Heath AP, Ferretti V, Varmus HE, Lowy DR, Kibbe WA, Staudt LM. Toward a Shared Vision for Cancer Genomic Data. N Engl J Med. 2016 Sep 22;375(12):1109-12. (PubMed)

Grossman RL, Heath A, Murphy M, Patterson M, Wells W. A Case for Data Commons: Toward Data Science as a Service. Comput Sci Eng. 2016 Sep-Oct;18(5):10-20. (PubMed)

Gunn BM, Schneider JR, Shansab M, Bastian AR, Fahrbach KM, Smith AD 4th, Mahan AE, Karim MM, Licht AF, Zvonar I, Tedesco J, Anderson MR, Chapel A, Suscovich TJ, Malaspina DC, Streeck H, Walker BD, Kim A, Lauer G, Altfeld M, Pillai S, Szleifer I, Kelleher NL, Kiser PF, Hope TJ, Alter G. Enhanced binding of antibodies generated during chronic HIV infection to mucus component MUC16. Mucosal Immunol. 2016 Nov;9(6):1549-1558. (PubMed)

Gürsoy G, Liang J. Three-dimensional chromosome structures from energy landscape. Proc Natl Acad Sci U S A. 2016 Oct. 25. Vol. 113 no. 43 11991–11993. (www.pnas.org)

Gürsoy G, Terebus A, Cao Y, Liang J. Mechanisms of Stochastic Focusing and Defocusing in Biological Reaction Networks: Insight from Accurate Chemical Master Equation (ACME) Solutions. Conf Proc IEEE Eng Med Biol Soc. 2016. (gila.bioe.uic.edu)

Hadizadeh N, Johnson RC, Marko JF. Facilitated dissociation of a nucleoid protein from the bacterial chromosome. J Bacteriol. 2016 May 27;198(12):1735-42. (PubMed)

Han D, Lu X, Shih AH, Nie J, You Q, Xu MM, Melnick AM, Levine RL, He C. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations. Mol Cell. 2016 Aug 18;63(4):711-9. (PubMed)

Han Y, Lyman KA, Clutter M, Schiltz GE, Ismail QA, Cheng X, Luan CH, Chetkovich DM. Method for Identifying Small Molecule Inhibitors of the Protein-protein Interaction Between HCN1 and TRIP8b. J Vis Exp. 2016 Nov 11;(117). (PubMed)

Hanis CL, Redline S, Cade BE, Bell GI, Cox NJ, Below JE, Brown EL, Aguilar D. Beyond type 2 diabetes, obesity and hypertension: an axis including sleep apnea, left ventricular hypertrophy, endothelial dysfunction, and aortic stiffness among Mexican Americans in Starr County, Texas. Cardiovasc Diabetol. 2016 Jun 8;15:86. (PubMed)

Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A. 2016 Feb 23;113(8):2092-7. (PubMed)

Hedrick JL, Brown KA, Kluender EJ, Cabezas MD, Chen PC, Mirkin CA. Hard Transparent Arrays for Polymer Pen Lithography. ACS Nano. 2016 Mar 22;10(3):3144-8. (PubMed)

Helenius IT, Nair A, Bittar HE, Sznajder JI, Sporn PH, Beitel GJ. Focused Screening Identifies Evoxine as a Small Molecule That Counteracts CO2-Induced Immune Suppression. J Biomol Screen. 2016 Apr;21(4):363-71. (PubMed)

Henke MT, Kelleher NL. Modern mass spectrometry for synthetic biology and structure-based discovery of natural products. Nat Prod Rep. 2016 Aug 27;33(8):942-50. (PubMed)

Henke MT, Soukup AA, Goering AW, McClure RA, Thomson RJ, Keller NP, Kelleher NL. New aspercryptins, lipopeptide natural products, revealed by HDAC inhibition in Aspergillus nidulans. ACS Chem Biol. 2016 Aug 19;11(8):2117-23. (PubMed)

Hlavaty KA, McCarthy DP, Saito E, Yap WT, Miller SD, Shea LD. Tolerance induction using nanoparticles bearing HY peptides in bone marrow transplantation. Biomaterials. 2016 Jan;76:1-10. (PubMed)

Hnisz D, Weintraub AS, Day DS, Valton AL, Bak RO, Li CH, Goldmann J, Lajoie BR, Fan ZP, Sigova AA, Reddy J, Borges-Rivera D, Lee TI, Jaenisch R, Porteus MH, Dekker J, Young RA. Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science. 2016 Mar 25;351(6280):1454-8. (PubMed)

Holbrook RJ, Rammohan N, Rotz MW, MacRenaris KW, Preslar AT, Meade TJ. Gd(III)-Dithiolane Gold Nanoparticles for T1-Weighted Magnetic Resonance Imaging of the Pancreas. Nano Lett. 2016 May 11;16(5):3202-9. (PubMed)

Horikoshi M, Pasquali L, Wiltshire S, (…) Bell GI, (…) Morris AP; T2D-GENES Consortium. Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms. Hum Mol Genet. 2016 May 15;25(10):2070-2081. (PubMed)

Howe MW, Dombeck DA. Rapid signalling in distinct dopaminergic axons during locomotion and reward. Nature. 2016 Jul 28;535(7613):505-10. (PubMed)

Huang W, Luan CH, Hjort EE, Bei L, Mishra R, Sakamoto KM, Platanias LC, Eklund EA. The role of Fas-associated phosphatase 1 in leukemia stem cell persistence during tyrosine kinase inhibitor treatment of chronic myeloid leukemia. Leukemia. 2016 Jul;30(7):1502-9. (PubMed)

Hung ME, Leonard JN. A platform for actively loading cargo RNA to elucidate limiting steps in EV-mediated delivery. J Extracell Vesicles. 2016 May 13;5:31027. eCollection 2016. (PubMed)

Im W, Liang J, Olson A, Zhou HX, Vajda S, Vakser IA. Challenges in structural approaches to cell modeling. J Mol Biol. 2016 Jul 31;428(15):2943-64. (PubMed)

Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP. Shared genetic signals of hypoxia adaptation in Drosophila and in high-altitude human populations. Mol Biol Evol. 2016 Feb;33(2):501-17. (PubMed)

Jiang B, Suen R, Wang JJ, Zhang ZJ, Wertheim JA, Ameer GA. Tissue Engineering: Mechanocompatible Polymer-Extracellular-Matrix Composites for Vascular Tissue Engineering (Adv. Healthcare Mater. 13/2016). Adv Healthc Mater. 2016 Jul;5(13):1593. (PubMed)

Jiang B, Suen RM, Wertheim JA, Ameer GA. Targeting Heparin to Collagen within Extracellular Matrix Significantly Reduces Thrombogenicity and Improves Endothelialization of Decellularized Tissues. Biomacromolecules. 2016 Dec 12;17(12):3940-3948. (PubMed)

Jiang Y, Carvalho-de-Souza JL, Wong RC, Luo Z, Isheim D, Zuo X, Nicholls AW, Jung IW, Yue J, Liu DJ, Wang Y, De Andrade V, Xiao X, Navrazhnykh L, Weiss DE, Wu X, Seidman DN, Bezanilla F, Tian B. Heterogeneous silicon mesostructures for lipid-supported bioelectric interfaces. Nat Mater. 2016 Sep;15(9):1023-30. (PubMed)

Kathman SG, Statsyuk AV. Covalent Tethering of Fragments For Covalent Probe Discovery. Medchemcomm. 2016 Apr 1;7(4):576-585. (PubMed)

Keenholtz RA, Grindley ND, Hatfull GF, Marko JF. Crossover-site sequence and DNA torsional stress control strand interchanges by the Bxb1 site-specific serine recombinase. Nucleic Acids Res. 2016 Oct 14;44(18):8921-8932. (PubMed)

Kenney GE, Goering AW, Ross MO, DeHart CJ, Thomas PM, Hoffman BM, Kelleher NL, Rosenzweig AC. Characterization of Methanobactin from Methylosinus sp. LW4. J Am Chem Soc. 2016 Sep 7;138(35):11124-7. (PubMed)

Khaja F, Jayawardena D, Kuzmis A, Önyüksel H. Targeted Sterically Stabilized Phospholipid siRNA Nanomedicine for Hepatic and Renal Fibrosis. Nanomaterials 2016, 6(1), 8. (mdpi.com)

Kharerin H, Bhat PJ, Marko JF, Padinhateeri R. Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression. Sci Rep. 2016 Feb 4;6:20319. Erratum in: Sci Rep. 2016;6:22220. (PubMed)

Kim JJ, Silver RK, Elue R, Adams MG, La Porte LM, Cai L, Kim JB, Gibbons RD. The experience of depression, anxiety, and mania among perinatal women. Arch Womens Ment Health. 2016 Oct;19(5):883-90. (PubMed)

Kim S, Cassidy JJ, Yang B, Carthew RW, Hilgenfeldt S. Hexagonal Patterning of the Insect Compound Eye: Facet Area Variation, Defects, and Disorder. Biophys J. 2016 Dec 20;111(12):2735-2746. (PubMed)

Kineman RD, Majumdar N, Subbaiah PV, Cordoba-Chacon J. Hepatic PPARγ is not essential for the rapid development of steatosis following loss of hepatic GH signaling, in adult male mice. Endocrinology. 2016 May;157(5):1728-35. (PubMed)

Klinger CM, Ramirez-Macias I, Herman EK, Turkewitz AP, Field MC, Dacks JB. Resolving the homology-function relationship through comparative genomics of membrane-trafficking machinery and parasite cell biology. Mol Biochem Parasitol. 2016 Sep – Oct;209(1-2):88-103. (PubMed)

Klomp JE, Huyot V, Ray AM, Collins KB, Malik AB, Karginov AV. Mimicking transient activation of protein kinases in living cells. Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):14976-14981. (PubMed)

Krist DT, Park S, Boneh GH, Rice SE, Statsyuk AV. UbFluor: A Mechanism-Based Probe for HECT E3 Ligases. Chem Sci. 2016 Aug 1;7(8):5587-5595. (PubMed)

Lambert G, Chew J, Rust MJ. Costs of Clock-Environment Misalignment in Individual Cyanobacterial Cells. Biophys J. 2016 Aug 23;111(4):883-91. (PubMed)

LaFave LM, Béguelin W, Koche R, Teater M, Spitzer B, Chramiec A, Papalexi E, Keller MD, Hricik T, Konstantinoff K, Micol JB, Durham B, Knutson SK, Campbell JE, Blum G, Shi X, Doud EH, Krivtsov AV, Chung YR, Khodos I, de Stanchina E, Ouerfelli O, Adusumilli PS, Thomas PM, Kelleher NL, Luo M, Keilhack H, Abdel-Wahab O, Melnick A, Armstrong SA, Levine RL. Reply to “Uveal melanoma cells are resistant to EZH2 inhibition regardless of BAP1 status”. Nat Med. 2016 Jun 7;22(6):578-9. (PubMed)

Leech KA, Kinnaird CR, Holleran CL, Kahn J, Hornby TG. Effects of Locomotor Exercise Intensity on Gait Performance in Individuals With Incomplete Spinal Cord Injury. Phys Ther. 2016 Dec;96(12):1919-1929. (PubMed)

Lek M, Karczewski KJ, Minikel EV, (…) MacArthur DG; Exome Aggregation Consortium: (…) Bell GI, (…). Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 18;536(7616):285-91. (PubMed)

Li J, Chauve L, Phelps G, Brielmann RM, Morimoto RI. E2F coregulates an essential HSF developmental program that is distinct from the heat-shock response. Genes Dev. 2016 Sep 15;30(18):2062-2075. (PubMed)

Li R, Yan Z, Ye J, Huang H, Wang Z, Wei Q, Wang J, Zhao L, Lu S, Wang X, Tang S, Fan J, Zhang F, Zou Y, Song D, Liao J, Lu M, Liu F, Shi LL, Athiviraham A, Lee MJ, He TC. The Prodomain-Containing BMP9 Produced from a Stable Line Effectively Regulates the Differentiation of Mesenchymal Stem Cells. Int J Med Sci 2016; 13(1):8-18. (PubMed)

Li YF, Xin F, Altman RB. Separating the causes and consequences in disease transcriptome. Pac Symp Biocomput. 2016;21:381-92. (PubMed)

Liang WG, Triandafillou CG, Huang TY, Zulueta MM, Banerjee S, Dinner AR, Hung SC, Tang WJ. Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Proc Natl Acad Sci U S A. 2016 May 3;113(18):5000-5. (PubMed)

Lin M, Gessmann D, Naveed H, Liang J. Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale. J Am Chem Soc. 2016 Mar 2;138(8):2592-601. (PubMed)

Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. A systems proteomics view of the endogenous human claudin protein family. J Proteome Res. 2016 Feb 5;15(2):339-59. (PubMed)

Liu J, Zhu Y, Luo GZ, Wang X, Yue Y, Wang X, Zong X, Chen K, Yin H, Fu Y, Han D, Wang Y, Chen D, He C. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nat Commun. 2016 Oct 7;7:13052. (PubMed)

Liu JM, Zhang J, Zhang X, Hlavaty KA, Ricci CF, Leonard JN, Shea LD, Gower RM. Transforming growth factor-beta 1 delivery from microporous scaffolds decreases inflammation post-implant and enhances function of transplanted islets. Biomaterials. 2016 Feb;80:11-9. (PubMed)

Lu S, Wang J, Ye J, Zou Y, Zhu Y, Wei Q, Wang X, Tang S, Liu H, Fan J, Zhang F, Farina EM, Mohammed MM, Song D, Liao J, Huang J, Guo D, Lu M, Liu F, Liu J, Li L, Ma C, Hu X, Lee MJ, Reid RR, Ameer GA, Zhou D, He T. Bone morphogenetic protein 9 (BMP9) induces effective bone formation from reversibly immortalized multipotent adipose-derived (iMAD) mesenchymal stem cells. Am J Transl Res. 2016 Sep 15;8(9):3710-3730. (PubMed)

Luo GZ, Wang F, Weng X, Chen K, Hao Z, Yu M, Deng X, Liu J, He C. Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing. Nat Commun. 2016 Apr 15;7:11301. (PubMed)

Lykins J, Wang K, Wheeler K, Clouser F, Dixon A, El Bissati K, Zhou Y, Lyttle C, Rzhetsky A, McLeod R. Understanding Toxoplasmosis in the United States Through “Large Data” Analyses. Clin Infect Dis. 2016 Aug 15;63(4):468-75. (PubMed)

MacRenaris KW, Ma Z, Krueger RL, Carney CE, Meade TJ. Cell-Permeable Esterase-Activated Ca(II)-Sensitive MRI Contrast Agent. Bioconjug Chem. 2016 Feb 17;27(2):465-73. (PubMed)

Mallory EK, Zhang C, Ré C, Altman RB. Large-scale extraction of gene interactions from full-text literature using DeepDive. Bioinformatics. 2016 Jan 1;32(1):106-13. (PubMed)

Manrai AK, Funke BH, Rehm HL, Olesen MS, Maron BA, Szolovits P, Margulies DM, Loscalzo J, Kohane IS. Genetic Misdiagnoses and the Potential for Health Disparities. N Engl J Med. 2016 Aug 18;375(7):655-65. (PubMed)

Mansukhani ND, Guiney LM, Kim PJ, Zhao Y, Alducin D, Ponce A, Larios E, Yacaman MJ, Hersam MC. High-Concentration Aqueous Dispersions of Nanoscale 2D Materials Using Nonionic, Biocompatible Block Copolymers. Small. 2016 Jan;12(3):294-300. (PubMed)

Mayo LM, de Wit H. Acquisition of Conditioned Responses to a Novel Alcohol-Paired Cue in Social Drinkers. J Stud Alcohol Drugs. 2016 Mar;77(2):317-26. (PubMed)

McClure RA, Goering AW, Ju KS, Baccile JA, Schroeder FC, Metcalf WW, Thomson RJ, Kelleher NL. Elucidating the rimosamide-detoxin natural product families and their biosynthesis using metabolite/gene cluster correlations. ACS Chem Biol. 2016 Dec 16;11(12):3452-3460. (PubMed)

McConnell SC, Hernandez KM, Wcisel DJ, Kettleborough RN, Stemple DL, Yoder JA, Andrade J, de Jong JL. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):E5014-23. (PubMed)

Mehta SB, McQuilken M, La Riviere PJ, Occhipinti P, Verma A, Oldenbourg R, Gladfelter AS, Tani T. Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells. Proc Natl Acad Sci U S A. 2016 Oct 18;113(42):E6352-E6361. (PubMed)

Melani RD, Seckler HS, Skinner OS, Do Vale LH, Catherman AD, Havugimana PC, Valle de Sousa M, Domont GB, Kelleher NL, Compton PD. CN-GELFrEE – Clear Native Gel-eluted Liquid Fraction Entrapment Electrophoresis. J Vis Exp. 2016 Feb 29;(108). (PubMed)

Melani RD, Skinner OS, Fornelli L, Domont GB, Compton PD, Kelleher NL. Mapping Proteoforms and Protein Complexes From King Cobra Venom Using Both Denaturing and Native Top-down Proteomics. Mol Cell Proteomics. 2016 Jul;15(7):2423-34. (PubMed)

Mishra RK, Shum AK, Platanias LC, Miller RJ, Schiltz GE. Discovery and characterization of novel small-molecule CXCR4 receptor agonists and antagonists. Sci Rep. 2016 Jul 26;6:30155. (PubMed)

Miyazaki Y, Du X, Muramatsu S, Gomez CM. An miRNA-mediated therapy for SCA6 blocks IRES-driven translation of the CACNA1A second cistron. Sci Transl Med. 2016 Jul 13;8(347):347ra94. (PubMed)

Möhl BS, Chen J, Sathiyamoorthy K, Jardetzky TS, Longnecker R. Structural and Mechanistic Insights into the Tropism of Epstein-Barr Virus. Mol Cells. 2016 Apr 30;39(4):286-91. Review. (PubMed)

Montefiori L, Wuerffel R, Roqueiro D, Lajoie B, Guo C, Gerasimova T, De S, Wood W, Becker KG, Dekker J, Liang J, Sen R, Kenter AL. Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire. Cell Rep. 2016 Feb 2;14(4):896-906. (PubMed)

Moore L, Yang J, Lan TT, Osawa E, Lee DK, Johnson WD, Xi J, Chow EK, Ho D. Biocompatibility Assessment of Detonation Nanodiamond in Non-Human Primates and Rats Using Histological, Hematologic, and Urine Analysis. ACS Nano. 2016 Aug 23;10(8):7385-400. (PubMed)

Moussazadeh N, Berman SH, Laufer I, Gounder M, Zheng Y, Sommer J, Bilsky MH, Kelleher NL, Brennan C. Epigenetic Profiling Reveals a Unique Histone Code in Chordoma. Neurosurgery. 2016 Aug;63 Suppl 1:208. (PubMed)

Moyle-Heyrman G, Schipma MJ, Dean M, Davis DA, Burdette JE. Genome-wide transcriptional regulation of estrogen receptor targets in fallopian tube cells and the role of selective estrogen receptor modulators. J Ovarian Res. 2016 Feb 15;9(1):5. (PubMed)

Mutharasan RK, Foit L, Thaxton CS. High-Density Lipoproteins for Therapeutic Delivery Systems. J Mater Chem B Mater Biol Med. 2016 Jan 14;4(2):188-197. (PubMed)

Nandwana V, Ryoo SR, Kanthala S, De M, Chou SS, Prasad PV, Dravid VP. Engineered Theranostic Magnetic Nanostructures: Role of Composition and Surface Coating on Magnetic Resonance Imaging Contrast and Thermal Activation. ACS Appl Mater Interfaces. 2016 Mar 23;8(11):6953-61. (PubMed)

Nath A, Wang F, Lenkala D, LaCroix B, Glavin N, Kipping-Johnson K, Geeleher P, Rich E, Thirman M, Godley L, Raca G, Larson R, Huang R. Exploring the Longitudinal Transcriptomic Landscape of Tyrosine Kinase Inhibitor Treatment Response in Chronic Myeloid Leukemia Patients. JIM. 2016 Mar;64(4) ID: 26. (jim.bmj.com)

Nazeen S, Palmer NP, Berger B, Kohane IS. Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biol. 2016 Nov 14;17(1):228. (PubMed)

Ntai I, LeDuc RD, Fellers RT, Erdmann-Gilmore P, Davies SR, Rumsey J, Early BP, Thomas PM, Li S, Compton PD, Ellis MJ, Ruggles KV, Fenyo D, Boja ES, Rodriguez H, Townsend RR, Kelleher NL. Integrated Bottom-up and Top-down Proteomics of Patient-derived Breast Tumor Xenografts. Mol Cell Proteomics. 2016 Jan;15(1):45-56. (PubMed)

Ntai I, Toby TK, LeDuc RD, Kelleher NL. A Method for Label-Free, Differential Top-Down Proteomics. Methods Mol Biol. 2016;1410:121-33. (PubMed)

Ong TH, Romanova EV, Roberts-Galbraith RH, Yang N, Zimmerman TA, Collins JJ 3rd, Lee JE, Kelleher NL, Newmark PA, Sweedler JV. Mass Spectrometry Imaging and Identification of Peptides Associated with Cephalic Ganglia Regeneration in Schmidtea mediterranea. J Biol Chem. 2016 Apr 8;291(15):8109-20. (PubMed)

Pan Y, Sackmann EK, Wypisniak K, Hornsby M, Datwani SS, Herr AE. Determination of equilibrium dissociation constants for recombinant antibodies by high-throughput affinity electrophoresis. Sci Rep. 2016 Dec 23;6:39774. (PubMed)

Park MJ, Sheng R, Silkov A, Jung DJ, Wang ZG, Xin Y, Kim H, Thiagarajan-Rosenkranz P, Song S, Yoon Y, Nam W, Kim I, Kim E, Lee DG, Chen Y, Singaram I, Wang L, Jang MH, Hwang CS, Honig B, Ryu S, Lorieau J, Kim YM, Cho W. SH2 Domains Serve as Lipid-Binding Modules for pTyr-Signaling Proteins. Mol Cell. 2016 Apr 7;62(1):7-20. (PubMed)

Payne JT, Andorfer MC, Lewis JC. Engineering Flavin-Dependent Halogenases. Methods Enzymol. 2016;575:93-126. (PubMed)

Peisert S, Barnett W, Dart E, Cuff J, Grossman RL, Balas E, Berman A, Shankar A, Tierney B. The Medical Science DMZ. J Am Med Inform Assoc. 2016 Nov;23(6):1199-1201. (PubMed)

Perelis M, Ramsey KM, Marcheva B, Bass J. Circadian Transcription from Beta Cell Function to Diabetes Pathophysiology. J Biol Rhythms. 2016 Aug;31(4):323-36. Review. (PubMed)

Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol. 2016 Dec 1;8(12). Review. (PubMed)

Priyadarshini M, Wicksteed B, Schiltz GE, Gilchrist A, Layden BT. SCFA Receptors in Pancreatic β Cells: Novel Diabetes Targets? Review. Trends Endocrinol Metab. 2016 Sep;27(9):653-64. (PubMed)

Qin D, Huang L, Wlodaver A, Andrade J, Staley JP. Sequencing of lariat termini in S. cerevisiae reveals 5′ splice sites, branch points, and novel splicing events. RNA. 2016 Feb;22(2):237-53. (PubMed)

Rammohan N, MacRenaris KW, Moore LK, Parigi G, Mastarone DJ, Manus LM, Lilley LM, Preslar AT, Waters EA, Filicko A, Luchinat C, Ho D, Meade TJ. Nanodiamond-Gadolinium(III) Aggregates for Tracking Cancer Growth In Vivo at High Field. Nano Lett. 2016 Dec 14;16(12):7551-7564. (PubMed)

Rehman T, Khan MM, Shad MA, Hussain M, Oyler BL, Goo YA, Goodlett DR. Detection of Carbofuran-Protein Adducts in Serum of Occupationally Exposed Pesticide Factory Workers in Pakistan. Chem Res Toxicol. Chem. Res. Toxicol. 2016, 29 (10);1720-28. (PubMed)

Roy A, Kundu M, Jana M, Mishra RK, Yung Y, Luan CH, Gonzalez FJ, Pahan K. Identification and characterization of PPARα ligands in the hippocampus. Nat Chem Biol. 2016 Dec;12(12):1075-1083. (PubMed)

Ryczko D, Cone JJ, Alpert MH, Goetz L, Auclair F, Dubé C, Parent M, Roitman MF, Alford S, Dubuc R. A descending dopamine pathway conserved from basal vertebrates to mammals. Proc Natl Acad Sci U S A. 2016 Apr 26;113(17):E2440-9. (PubMed)

Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. Nanoscale. 2016 Dec 8;8(48):19928-19944. Review. (PubMed)

Savaryn JP, Skinner OS, Fornelli L, Fellers RT, Compton PD, Terhune SS, Abecassis MM, Kelleher NL. Targeted analysis of recombinant NF kappa B (RelA/p65) by denaturing and native top down mass spectrometry. J Proteomics. 2016 Feb 16;134:76-84.(PubMed)

Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. Nanoscale. 2016 Dec 8;8(48):19928-19944. Review. (PubMed)27883140

Savaryn JP, Toby TK, Catherman AD, Fellers RT, LeDuc RD, Thomas PM, Friedewald JJ, Salomon DR, Abecassis MM, Kelleher NL. Comparative top down proteomics of peripheral blood mononuclear cells from kidney transplant recipients with normal kidney biopsies or acute rejection. Proteomics. 2016 Feb 16;134:76-84. (PubMed)

Savaryn JP, Toby TK, Kelleher NL. A researcher’s guide to mass spectrometry-based proteomics. Proteomics. 2016 Sep;16(18):2435-43. (PubMed)

Schaefer ZP, Bailey LJ, Kossiakoff AA. A polar ring endows improved specificity to an antibody fragment.  Protein Sci. 2016 Jul;25(7):1290-8. (PubMed)

Schalk AM, Antanasijevic A, Caffrey M, Lavie A. Experimental Data in Support of a Direct Displacement Mechanism for Type I/II L-Asparaginases. J Biol Chem. 2016 Mar 4;291(10):5088-100. (PubMed)

Schroeter ER, DeHart CJ, Schweitzer MH, Thomas PM, Kelleher NL. Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics. PeerJ. 2016 Oct 27;4:e2603. (PubMed)

Semlow DR, Blanco MR, Walter NG, Staley JP. Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites. Cell. 2016 Feb 25;164(5):985-98. (PubMed)

Seo SE, Wang MX, Shade CM, Rouge JL, Brown KA, Mirkin CA. Modulating the Bond Strength of DNA-Nanoparticle Superlattices. ACS Nano. 2016 Feb 23;10(2):1771-9. (PubMed)

Serebryannyy LA, Cruz CM, de Lanerolle P. A Role for Nuclear Actin in HDAC 1 and 2 Regulation. Sci Rep. 2016 Jun 27;6:28460. (PubMed)

Serebryannyy LA, Parilla M, Annibale P, Cruz CM, Laster K, Gratton E, Kudryashov D, Kosak ST, Gottardi CJ, de Lanerolle P. Persistent nuclear actin filaments inhibit transcription by RNA polymerase II. J Cell Sci. 2016 Sep 15;129(18):3412-25. (PubMed)

Serebryannyy L, Yuen M, Parilla M, Cooper ST, and de Lanerolle, P. The effects of disease models of nuclear actin polymerization on the nucleus. Front. Physiol. 2016 Oct 7;7:454. eCollection 2016. (PubMed)

Shamirian A, Samareh Afsari H, Hassan A, Miller LW, Snee PT. In vitro Detection of Hypoxia using a Ratiometric Quantum Dot-based Oxygen Sensor. ACS Sens. 2016. Publication Date (Web): 20 Sep 2016. (PubMed)

Shamirian A, Samareh Afsari H, Wu D, Miller LW, Snee PT. Ratiometric QD-FRET Sensing of Aqueous H2S in Vitro. Anal Chem. 2016 Jun 7;88(11):6050-6. (PubMed)

Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment. J Mol Biol. 2016 Oct 9;428(20):4100-4114. (PubMed)

Sheng R, Jung DJ, Silkov A, Kim H, Singaram I, Wang ZG, Xin Y, Kim E, Park MJ, Thiagarajan-Rosenkranz P, Smrt S, Honig B, Baek K, Ryu S, Lorieau J, Kim YM, Cho W. Lipids Regulate Lck Protein Activity through Their Interactions with the Lck Src Homology 2 Domain. J Biol Chem. 2016 Aug 19;291(34):17639-50. (PubMed)

Shy BR, MacDougall MS, Clarke R, Merrill BJ. Co-incident insertion enables high efficiency genome engineering in mouse embryonic stem cells. Nucleic Acids Res. 2016 Sep 19;44(16):7997-8010. (PubMed)

Singer BF, Bubula N, Li D, Przybycien-Szymanska MM, Bindokas VP, Vezina P. Drug-Paired Contextual Stimuli Increase Dendritic Spine Dynamics in Select Nucleus Accumbens Neurons. Neuropsychopharmacology. 2016 Jul;41(8):2178-87. (PubMed)

Singer BF, Bubula N, Przybycien-Szymanska MM, Li D, Vezina P. Stimuli associated with the presence or absence of amphetamine regulate cytoskeletal signaling and behavior. Eur Neuropsychopharmacol. 2016 Nov;26(11):1836-1842. (PubMed)

Skinner OS, Havugimana PC, Haverland NA, Fornelli L, Early BP, Greer JB, Fellers RT, Durbin KR, Do Vale LH, Melani RD, Seckler HS, Nelp MT, Belov ME, Horning SR, Makarov AA, LeDuc RD, Bandarian V, Compton PD, Kelleher NL. An informatic framework for decoding protein complexes by top-down mass spectrometry. Nat Methods. 2016 Mar;13(3):237-40. (PubMed)

Skinner OS, Schachner LF, Kelleher NL. The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes. Curr Protoc Bioinformatics. 2016 Dec 8;56:13.30.1-13.30.11. (PubMed)

Smarr CB, Yap WT, Neef TP, Pearson RM, Hunter ZN, Ifergan I, Getts DR, Bryce PJ, Shea LD, Miller SD. Biodegradable antigen-associated PLG nanoparticles tolerize Th2-mediated allergic airway inflammation pre- and postsensitization. Proc Natl Acad Sci U S A. 2016 May 3;113(18):5059-64. (PubMed)

Smith E, Greeley SA, Ye H, Torgerson TR, Dimmitt R, Atkinson P, Philips J, Goldman F. Extremely Early Onset IPEX Syndrome Caused by a Novel Small Exonic Deletion in FOXP3. J Pediatr Gastroenterol Nutr. 2016 Apr 26. (PubMed)

Smith L, Kuiken T, Hargrove L. Evaluation of linear regression simultaneous myoelectric control using intramuscular EMG. IEEE Trans Biomed Eng. 2016 Apr;63(4):737-46. (PubMed)

Smith L, Kuiken T, Hargrove L. Myoelectric control system and task-specific characteristics affect voluntary use of simultaneous control. IEEE Trans Neural Syst Rehabil Eng. 2016 Jan;24(1):109-16. (PubMed)

Snee PT, Das A. Synthetic Developments of Nontoxic Quantum Dots. Chemphyschem. 2016 Mar 3;17(5):598-617. (PubMed)

Somekh J, Peleg M, Eran A, Koren I, Feiglin A, Demishtein A, Shiloh R, Heiner M, Kong SW, Elazar Z, Kohane I. A model-driven methodology for exploring complex disease comorbidities applied to autism spectrum disorder and inflammatory bowel disease. J Biomed Inform. 2016 Oct;63:366-378. (PubMed)

Speltz TE, Fanning SW, Mayne CG, Fowler C, Tajkhorshid E, Greene GL, Moore TW. Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction. Angew Chem Int Ed Engl. 2016 Mar 18;55(13):4252-5. (PubMed)

Thaner RV, Eryazici I, Macfarlane RJ, Brown KA, Lee B, Nguyen ST, Mirkin CA. The Significance of Multivalent Bonding Motifs and “Bond Order” in DNA-Directed Nanoparticle Crystallization. J Am Chem Soc. 2016 May 18;138(19):6119-22. (PubMed)

Thaxton CS, Rink JS, Naha PC, Cormode DP. Lipoproteins and lipoprotein mimetics for imaging and drug delivery. Adv Drug Deliv Rev. 2016 Nov 15;106(Pt A):116-131. Review. (PubMed)

Toby TK, Fornelli L, Kelleher NL. Progress in Top-Down Proteomics and the Analysis of Proteoforms. Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):499-519. (PubMed)

Tollemar V, Collier ZJ, Mohammed MK, Lee MJ, Ameer GA, Reid RR. Stem cells, growth factors and scaffolds in craniofacial regenerative medicine. Review. Genes Dis. 2016 Mar;3(1):56-71. (PubMed)

Uchiyama K, Sakiyama T, Hasebe T, Musch MW, Miyoshi H, Nakagawa Y, He TC, Lichtenstein L, Naito Y, Itoh Y, Yoshikawa T, Jabri B, Stappenbeck T, Chang EB. Butyrate and bioactive proteolytic form of Wnt-5a regulate colonic epithelial proliferation and spatial development. Sci Rep. 2016 Aug 26;6:32094. (PubMed)

Valton AL, Dekker J. TAD disruption as oncogenic driver. Curr Opin Genet Dev. 2016 Feb;36:34-40. Review. (PubMed)

Voong LN, Xi L, Sebeson AC, Xiong B, Wang JP, Wang X. Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell. 2016 Dec 1;167(6):1555-1570.e15. (PubMed)

Wagner E, Glotzer M. Local RhoA activation induces cytokinetic furrows independent of spindle position and cell cycle stage. J Cell Biol. 2016 Jun 20;213(6):641-9. (PubMed)

Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. Am J Hum Genet. 2016 Apr 7;98(4):697-708. (PubMed)

Wang X, Chow CR, Ebine K, Lee J, Rosner MR, Pan T, Munshi HG. Interaction of tRNA with MEK2 in pancreatic cancer cells. Sci Rep. 2016 Jun 15;6:28260. (PubMed)

Wang X, Hao L, Bu HF, Scott AW, Tian K, Liu F, De Plaen IG, Liu Y, Mirkin CA, Tan XD. Spherical nucleic acid targeting microRNA-99b enhances intestinal MFG-E8 gene expression and restores enterocyte migration in lipopolysaccharide-induced septic mice. Sci Rep. 2016 Aug 19;6:31687. (PubMed)

Wheeler HE, Shah KP, Brenner J, Garcia T, Aquino-Michaels K, GTEx Consortium, Cox NJ, Nicolae DL, Im HK. Survey of the Heritability and Sparsity of Gene Expression Traits Across Human Tissues. bioRxiv preprint first posted online Mar. 15, 2016. (biorxiv.org)

Winkelman JD, Suarez C, Hocky GM, Harker AJ, Morganthaler AN, Christensen JR, Voth GA, Bartles JR, Kovar DR. Fascin- and α-Actinin-Bundled Networks Contain Intrinsic Structural Features that Drive Protein Sorting. Curr Biol. 2016 Oct 24;26(20):2697-2706. (PubMed)

Winter PB, Brielmann RM, Timkovich NP, Navarro HT, Teixeira-Castro A, Morimoto RI, Amaral LA. A network approach to discerning the identities of C. elegans in a free moving population. Sci Rep. 2016 Oct 11;6:34859. (PubMed)

Wolff ID, Tran MV, Mullen TJ, Villeneuve AM, Wignall SM. Assembly of C. elegans acentrosomal spindles occurs without evident MTOCs and requires microtubule sorting by KLP-18/kinesin-12 and MESP-1. Mol Biol Cell. 2016 Oct 15;27(20):3122-3131. (PubMed)

Xiao B, McLean MM, Lei X, Marko JF, Johnson RC. Controlled rotation mechanism of DNA strand exchange by the Hin serine recombinase. Sci Rep. 2016 Apr 1;6:23697. (PubMed)

Xie Z, Zhang D, Chung D, Tang Z, Huang H, Dai L, Qi S, Li J, Colak G, Chen Y, Xia C, Peng C, Ruan H, Kirkey M, Wang D, Jensen LM, Kwon OK, Lee S, Pletcher SD, Tan M, Lombard DB, White KP, Zhao H, Li J, Roeder RG, Yang X, Zhao Y. Metabolic Regulation of Gene Expression by Histone Lysine β-Hydroxybutyrylation. Mol Cell. 2016 Apr 21;62(2):194-206. (PubMed)

Yan Q, Chen R, Sutcliffe JS, Cook EH, Weeks DE, Li B, Chen W. The impact of genotype calling errors on family-based studies. Sci Rep. 2016 Jun 22;6:28323. (PubMed)

Ye J, Wang J, Zhu Y, Wei Q, Wang X, Yang J, Tang S, Liu H, Fan J, Zhang F, Farina EM, Mohammed MK, Zou Y, Song D, Liao J, Huang J, Guo D, Lu M, Liu F, Liu J, Li L, Ma C, Hu X, Haydon RC, Lee MJ, Reid RR, Ameer GA, Yang L, He TC. A thermoresponsive polydiolcitrate-gelatin scaffold and delivery system mediates effective bone formation from BMP9-transduced mesenchymal stem cells. Biomed Mater. 2016 Apr 21;11(2):025021. (PubMed)

Yoo SP, Pineda F, Barrett JC, Poon C, Tirrell M, Chung EJ. Gadolinium-Functionalized Peptide Amphiphile Micelles for Multimodal Imaging of Atherosclerotic Lesions. ACS Omega. 2016 Nov 30;1(5):996-1003. (PubMed)

Zarrinpar A, Lee DK, Silva A, Datta N, Kee T, Eriksen C, Weigle K, Agopian V, Kaldas F, Farmer D, Wang SE, Busuttil R, Ho CM, Ho D. Individualizing liver transplant immunosuppression using a phenotypic personalized medicine platform. Sci Transl Med. 2016 Apr 6;8(333):333ra49. (PubMed)

Zhang Y, Buhrman JS, Liu Y, Rayahin JE, Gemeinhart RA. Reducible Micelleplexes are Stable Systems for Anti-miRNA Delivery in Cerebrospinal Fluid. Mol Pharm. 2016 Jun 6;13(6):1791-1799. (PubMed)

Zhang Y, Sriraman SK, Kenny HA, Luther E, Torchilin V, Lengyel E. Reversal of Chemoresistance in Ovarian Cancer by Co-Delivery of a P-Glycoprotein Inhibitor and Paclitaxel in a Liposomal Platform. Mol Cancer Ther. 2016 Oct;15(10):2282-2293. (PubMed)

Zhao B, Mei Y, Schipma MJ, Roth EW, Bleher R, Rappoport JZ, Wickrema A, Yang J, Ji P. Nuclear Condensation during Mouse Erythropoiesis Requires Caspase-3-Mediated Nuclear Opening. Dev Cell. 2016 Mar 7;36(5):498-510. (PubMed)

Zhao B, Mei Y, Yang J, Ji P. Erythropoietin-regulated oxidative stress negatively affects enucleation during terminal erythropoiesis. Exp Hematol. 2016 Oct;44(10):975-81. (PubMed)

Zhao B, Yang J, Ji P. Chromatin condensation during terminal erythropoiesis. Nucleus. 2016 Sep 2;7(5):425-429. (PubMed)

Zheng Y, Fornelli L, Compton PD, Sharma S, Canterbury J, Mullen C, Zabrouskov V, Fellers RT, Thomas PM, Licht JD, Senko MW, Kelleher NL. Unabridged Analysis of Human Histone H3 by Differential Top-Down Mass Spectrometry Reveals Hypermethylated Proteoforms from MMSET/NSD2 Overexpression. Mol Cell Proteomics. 2016 Mar;15(3):776-90. (PubMed)

Zheng Y, Huang X, Kelleher NL. Epiproteomics: quantitative analysis of histone marks and codes by mass spectrometry. Curr Opin Chem Biol. 2016 Jun 29;33:142-150. Review. (PubMed)

Zimmerman JF, Parameswaran R, Murray G, Wang Y, Burke M, Tian B. Cellular uptake and dynamics of unlabeled freestanding silicon nanowires. Sci Adv. 2016 Dec 16;2(12):e1601039. (PubMed)

Zimnicka AM, Husain YS, Shajahan AN, Sverdlov M, Chaga O, Chen Z, Toth PT, Klomp J, Karginov AV, Tiruppathi C, Malik AB, Minshall RD. Src-dependent phosphorylation of caveolin-1 Tyr-14 promotes swelling and release of caveolae. Mol Biol Cell. 2016 Jul 1;27(13):2090-106. (PubMed)