2018

Riley NM, Sikora JW, Seckler HS, Greer JB, Fellers RT, LeDuc RD, et al. The Value of Activated Ion Electron Transfer Dissociation for High-Throughput Top-Down Characterization of Intact Proteins. Anal Chem. American Chemical Society; 2018 Jul 17;90(14):8553–60.
Rush MJP, Riley NM, Westphall MS, Coon JJ. Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Anal Chem. American Chemical Society; 2018 Jul 10;:acs.analchem.8b01113.
Hebert AS, Prasad S, Belford MW, Bailey DJ, McAlister GC, Abbatiello SE, et al. Rapid and Comprehensive Single Shot Proteomics with LC-FAIMS-MS/MS. Anal Chem. American Chemical Society; 2018 Jul 3;:acs.analchem.8b02233.
Turton KB, Wilkerson EM, Hebert AS, Fogerty FJ, Schira HM, Botros FE, et al. Expression of novel “LOCGEF” isoforms of ARHGEF18 in eosinophils. Rosenberg H, Foster PS, Fairfax K, Kaiko G, Munitz A, Spencer L, editors. J Leukoc Biol. Wiley-Blackwell; 2018 Jul;104(1):135–45.
Jha P, McDevitt MT, Gupta R, Quiros PM, Williams EG, Gariani K, et al. Systems Analyses Reveal Physiological Roles and Genetic Regulators of Liver Lipid Species. Cell Systems. 2018 Jun 27;6(6):722–6.
Jha P, McDevitt MT, Halilbasic E, Williams EG, Quiros PM, Gariani K, et al. Genetic Regulation of Plasma Lipid Species and Their Association with Metabolic Phenotypes. Cell Systems. 2018 Jun 27;6(6):709–721.e6.
Qian S, Lv X, Scheid RN, Lu L, Yang Z, Chen W, et al. Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun. Nature Publishing Group; 2018 Jun 21;9(1):2425.
Esnault S, Hebert AS, Jarjour NN, Coon JJ, Mosher DF. Proteomic and Phosphoproteomic Changes Induced by Prolonged Activation of Human Eosinophils with IL-3. Journal of proteome research. American Chemical Society; 2018 Jun 1;17(6):2102–11.
Hutchins PD, Russell JD, Coon JJ. LipiDex: An Integrated Software Package for High-Confidence Lipid Identification. Cell Systems. 2018 May 23;6(5):621–5.
MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, et al. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. Myers CL, editor. PLoS Comput Biol. Public Library of Science; 2018 May;13(5):e1006088.
MacGilvray ME, Shishkova E, Chasman D, Place M, Gitter A, Coon JJ, et al. Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response. Myers CL, editor. PLoS Comput Biol. Public Library of Science; 2018 May;13(5):e1006088.
Mitok KA, Freiberger EC, Schueler KL, Rabaglia ME, Stapleton DS, Kwiecien NW, et al. Islet proteomics reveals genetic variation in dopamine production resulting in altered insulin secretion. J Biol Chem. American Society for Biochemistry and Molecular Biology; 2018 Apr 20;293(16):5860–77.
Kontur WS, Bingman CA, Olmsted CN, Wassarman DR, Ulbrich A, Gall DL, et al. Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin. J Biol Chem. American Society for Biochemistry and Molecular Biology; 2018 Apr 6;293(14):4955–68.
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of The Royal Society Interface. The Royal Society; 2018 Apr;15(141):20170387.
Rhoads TW, Burhans MS, Chen VB, Hutchins PD, Rush MJP, Clark JP, et al. Caloric Restriction Engages Hepatic RNA Processing Mechanisms in Rhesus Monkeys. Cell Metab. 2018 Mar 6;27(3):677–688.e5.
Vakirlis N, Hebert AS, Opulente DA, Achaz G, Hittinger CT, Fischer G, et al. A Molecular Portrait of De Novo Genes in Yeasts. Mol Biol Evol. 2018 Mar 1;35(3):631–45.
Bucci MD, Weisenhorn E, Haws S, Yao Z, Zimmerman G, Gannon M, et al. An Autophagy-Independent Role for ATG41 in Sulfur Metabolism During Zinc Deficiency. Genetics. Genetics; 2018 Mar;208(3):1115–30.
Reidenbach AG, Kemmerer ZA, Aydin D, Jochem A, McDevitt MT, Hutchins PD, et al. Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family. Cell Chem Biol. 2018 Feb 15;25(2):154–165.e11.
Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, et al. Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem cell reports. 2018 Feb 13;10(2):627–41.
Lu L, Chen X, Qian S, Zhong X. The plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution. Nat Commun. Nature Publishing Group; 2018 Feb 12;9(1):630.
Hebert AS, Thöing C, Riley NM, Kwiecien NW, Shiskova E, Huguet R, et al. Improved Precursor Characterization for Data-Dependent Mass Spectrometry. Anal Chem. American Chemical Society; 2018 Feb 6;90(3):2333–40.
Lapointe CP, Stefely JA, Jochem A, Hutchins PD, Wilson GM, Kwiecien NW, et al. Multi-omics Reveal Specific Targets of the RNA-Binding Protein Puf3p and Its Orchestration of Mitochondrial Biogenesis. Cell Systems. 2018 Jan 24;6(1):125–6.
Bottoms S, Dickinson Q, McGee M, Hinchman L, Higbee A, HEBERT A, et al. Chemical genomic guided engineering of gamma-valerolactone tolerant yeast. Microbial Cell Factories 2016 15:1. BioMed Central; 2018 Jan 12;17(1):5.
Lee J-H, Mand MR, Kao C-H, Zhou Y, Ryu SW, Richards AL, et al. ATM directs DNA damage responses and proteostasis via genetically separable pathways. Sci Signal. American Association for the Advancement of Science; 2018 Jan 9;11(512):eaan5598.
Riley NM, Coon JJ. The Role of Electron Transfer Dissociation in Modern Proteomics. Anal Chem. American Chemical Society; 2018 Jan 2;90(1):40–64.
Overmyer KA, Tyanova S, Hebert AS, Westphall MS, Cox J, Coon JJ. Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice. Nature Protocols. Nature Publishing Group; 2018 Jan;13(1):293–306.
Riley NM, Westphall MS, Coon JJ. Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation. J Am Soc Mass Spectrom. Springer US; 2018 Jan;29(1):140–9.

2017

Lee J-H, Yang B, Lindahl AJ, Damaschke N, Boersma MD, Huang W, et al. Identifying Dysregulated Epigenetic Enzyme Activity in Castrate Resistant Prostate Cancer Development. ACS chemical biology. American Chemical Society; 2017 Oct 11;12(11):2804–14.
Zhang P, Wang X, Fan A, Zheng Y, Liu X, Wang S, et al. A cryptic pigment biosynthetic pathway uncovered by heterologous expression is essential for conidial development in Pestalotiopsis fici. Molecular microbiology. 2017 May 18;105(3):469–83.
Zhang X, Medow J, Iskandar B, Wang F, Shokoueinejad M, Koueik J, et al. Invasive and noninvasive means of measuring intracranial pressure: a review. Physiol Meas. IOP Publishing; 2017 May 10.
Wiemann P, Perevitsky A, Lim FY, Shadkchan Y, Knox BP, Landero Figueora JA, et al. Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense. Cell reports. 2017 May 2;19(5):1008–21.
Aguilar-Hernández V, Kim D-Y, Stankey RJ, Scalf M, Smith LM, Vierstra RD. Mass Spectrometric Analyses Reveal a Central
Role for Ubiquitylation in Remodeling the Arabidopsis Proteome During Photomorphogenesis. Mol Plant. 2017 Apr 28;10(6):846–65.
Tazeh NN, Canter DJ, Damodaran S, Rushmer T, Richards KA, Abel EJ, et al. Neutrophil to Lymphocyte Ratio (NLR) at the Time of Transurethral Resection of Bladder Tumor: A Large Retrospective Study and Analysis of Racial Differences. Bladder Cancer. IOS Press; 2017 Apr 27;3(2):89–94.
Iwahori S, Umaña AC, VanDeusen HR, Kalejta RF. Human cytomegalovirus-encoded viral cyclin-dependent kinase (v-CDK) UL97 phosphorylates and inactivates the retinoblastoma protein-related p107 and p130 proteins. J Biol Chem. American Society for Biochemistry and Molecular Biology; 2017 Apr 21;292(16):6583–99.
Price AM, Dai J, Bazot Q, Patel L, Nikitin PA, Djavadian R, et al. Epstein-Barr virus ensures B cell survival by uniquely modulating apoptosis at early and late times after infection. Elife. eLife Sciences Publications Limited; 2017 Apr 20;6:212.
Roy S, Sridharan R. Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes. Genome Res. Cold Spring Harbor Lab; 2017 Apr 19;27(7):gr.215004.116–262.
Drennan AC, Rui L. HiJAKing the epigenome in leukemia and lymphoma. Leuk Lymphoma. 2017 Apr 12;88(11):1–8.
Chang C-F, Gould M. Playing the odds: lung cancer surveillance after curative surgery. Curr Opin Pulm Med. 2017 Apr 11;23(4):1–304.  Duncan ID, Bugiani M, Radcliff AB, Moran JJ, Lopez-Anido C, Duong P, et al. A mutation in the Tubb4a gene leads to microtubule accumulation with hypomyelination and demyelination. Ann Neurol. 2017 Apr 10;81(5):690–702.
Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, et al. Global Post-Translational Modification Discovery. Journal of proteome research. American Chemical Society; 2017 Apr 7;16(4):1383–90.
Krautkramer KA, Rey FE, Denu JM. Chemical signaling between gut microbiota and host chromatin: What is your gut really saying? J Biol Chem. 2017 Apr 7;:jbc.R116.761577.
Moody LR, Barrett-Wilt GA, Sussman MR, Messing A. Glial fibrillary acidic protein exhibits altered turnover kinetics in a mouse model of Alexander disease. J Biol Chem. American Society for Biochemistry and Molecular Biology; 2017 Apr 7;292(14):5814–24.
Minkoff BB, Makino S-I, Haruta M, Beebe ET, Wrobel RL, Fox BG, et al. A cell-free method for expressing and reconstituting membrane proteins enables functional characterization of the plant receptor-like protein kinase FERONIA. J Biol Chem. American Society for Biochemistry and Molecular Biology; 2017 Apr 7;292(14):5932–42.
Kropp J, Carrillo JA, Namous H, Daniels A, Salih SM, Song J, et al. Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos. BMC genomics. BioMed Central; 2017 Apr 5;18(1):280.
Vargas-Muñiz JM, Renshaw H, Waitt G, Soderblom EJ, Moseley MA, Palmer JM, et al. Caspofungin exposure alters the core septin AspB interactome of Aspergillus fumigatus. Biochem Biophys Res Commun. 2017 Apr 1;485(2):221–6.
Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, et al. Histone Lysine-to-Methionine Mutations Reduce Histone Methylation and Cause Developmental Pleiotropy. Plant Physiol. American Society of Plant Biologists; 2017 Apr;173(4):2243–52.
Attie AD, Churchill GA, Nadeau JH. How mice are indispensable for understanding obesity and diabetes genetics. Current Opinion in Endocrinology & Diabetes and Obesity. 2017 Apr;24(2):83–91.
Tannous J, Keller NP, Atoui A, Khoury El A, Lteif R, Oswald IP, et al. Secondary Metabolism in Penicillium expansum: Emphasis on Recent Advances in Patulin Research. Crit Rev Food Sci Nutr. Taylor & Francis; 2017 Mar 31;207:0–00.
Xiao G, Cintron-Rosado GA, Glazier DA, Xi BM, Liu C, Liu P, et al. Catalytic Site-Selective Acylation of Carbohydrates Directed by Cation-n Interaction. Journal of the American Chemical Society. American Chemical Society; 2017 Mar 29;139(12):4346–9.
Deota S, Chattopadhyay T, Ramachandran D, Armstrong E, Camacho B, Maniyadath B, et al. Identification of a Tissue-Restricted Isoform of SIRT1 Defines a Regulatory Domain that Encodes Specificity. Cell reports. 2017 Mar 28;18(13):3069–77.
Song W, Wang S, Tang W. De Novo Synthesis of Mono- and Oligosaccharides via Dihydropyran Intermediates. Chem Asian J. 2017 Mar 20;12(10):1027–42.
Koo D-H, Singh B, Jiang J, Friebe B, Gill BS, Chastain PD, et al. Single molecule mtDNA fiber FISH for analyzing numtogenesis. Anal Biochem. 2017 Mar 18.
Johnson LM, Du J, Hale CJ, Bischof S, Feng S, Chodavarapu RK, et al. Corrigendum: SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature. Nature Research; 2017 Mar 2;543(7643):136–6.
Wille CK, Li Y, Rui L, Johannsen EC, Kenney SC. Restricted TET2 Expression in Germinal Center Type B Cells Promotes Stringent Epstein-Barr Virus Latency. Longnecker RM, editor. Journal of virology. American Society for Microbiology; 2017 Mar 1;91(5):e01987–16.
Jay R, Heckman JE, Hinshaw L, Best S, Lubner M, Jarrard DF, et al. Multi-quadrant biopsy technique improves diagnostic ability in large heterogeneous renal masses. Abel EJ, Heckman JE, Hinshaw L, Best S, Lubner M, Jarrard DF, Downs TM,
Nakada SY, Lee FT Jr, Huang W, Ziemlewicz T.J Urol. 2015 Oct;194(4):886-91. [Epub 2015 Mar 30]. doi: 10.1016/j.juro.2015.03.106. Urologic Oncology: Seminars and Original Investigations. 2017 Mar;35(3):119.
Sychev ZE, Hu A, DiMaio TA, Gitter A, Camp ND, Noble WS, et al. Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. Dittmer DP, editor. PLOS Pathogens. 2017 Mar;13(3):e1006256.
Soukup AA, Fischer GJ, Luo J, Keller NP. The Aspergillus nidulans Pbp1 homolog is required for normal sexual development and secondary metabolism. Fungal Genetics and Biology. 2017 Mar;100:13–21.
Keller NP. Heterogeneity Confounds Establishment of “a” Model Microbial Strain. MBio. American Society for Microbiology; 2017 Feb 21;8(1):e00135–17.
Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, et al. Histone lysine-to-methionine mutations reduce histone methylation and cause developmental pleiotropy. Plant Physiol. American Society of Plant Biologists; 2017 Feb 15;173(4):pp.01499.2016–252.
Katsumura KR, Bresnick EH. The GATA factor revolution in hematology. Blood. American Society of Hematology; 2017 Feb 8;129(15):blood–2016–09–687871–2102.
Nawandar DM, Ohashi M, Djavadian R, Barlow E, Makielski K, Ali A, et al. Differentiation-dependent LMP1 expression is required for efficient lytic EBV reactivation in epithelial cells. Longnecker RM, editor. Journal of virology. American Society for Microbiology; 2017 Feb 8;91(8):JVI.02438–16.
Garcia K, Chasman D, Roy S, Ané J-M. Physiological responses and gene co-expression network of mycorrhizal roots under K+ deprivation. Plant Physiol. American Society of Plant Biologists; 2017 Feb 3;173(3):pp.01959.2016–1823.
Chen G, Jaskula-Sztul R, Esquibel CR, Lou I, Zheng Q, Dammalapati A, et al. Neuroendocrine Tumor‐Targeted Upconversion Nanoparticle‐Based Micelles for Simultaneous NIR‐Controlled Combination Chemotherapy and Photodynamic Therapy, and Fluorescence Imaging. Advanced Functional Materials. 2017 Feb 1;27(8):1604671.
Rodriguez-Molina JF, Lopez-Anido C, Ma KH, Zhang C, Olson T, Muth KN, et al. Dual specificity phosphatase 15 regulates Erk activation in Schwann cells. Journal of Neurochemistry. 2017 Feb 1;140(3):368–82.
Papillon-Cavanagh S, Lu C, Gayden T, Mikael LG, Bechet D, Karamboulas C, et al. Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas. Nature genetics. Nature Research; 2017 Feb 1;49(2):180–5.
Papale LA, Madrid A, Li S, Alisch RS. Early-life stress links 5-hydroxymethylcytosine to anxiety-related behaviors. Epigenetics. 2017 Jan 27;:00–0.
Wang HY, Simmons CJ, Zhang Y, Smits AM, Balzer PG, Wang S, et al. Chiral Catalyst-Directed Dynamic Kinetic Diastereoselective Acylation of Anomeric Hydroxyl Groups and a Controlled Reduction of the Glycosyl Ester Products. Organic …. American Chemical Society; 2017 Jan 12;19(3):508–11.
Guo X, Niemi NM, Hutchins PD, Condon SGF, Jochem A, Ulbrich A, et al. Ptc7p Dephosphorylates Select Mitochondrial Proteins to Enhance Metabolic Function. Cell reports. 2017 Jan 10;18(2):307–13.
Amasino RM, Cheung AY, Dresselhaus T, Kuhlemeier C. Focus on Flowering and Reproduction. Plant Physiol. 2017 Jan 3;173(1):1–4.
Sanders D, Qian S, Fieweger R, Lu L, Dowell JA, Denu JM, et al. Histone lysine-to-methionine mutations reduce histone methylation and cause developmental pleiotropy. Plant Physiol. American Society of Plant Biologists; 2017 Jan 1;173(4):pp.01499.2016–252.
Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, et al. Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation. G3. G3: Genes, Genomes, Genetics; 2017 Jan 1;7(1):203–19.
Li M, Zhao H, Ananiev GE, Musser MT, Ness KH, Maglaque DL, et al. Establishment of Reporter Lines for Detecting Fragile X Mental Retardation (FMR1) Gene Reactivation in Human Neural Cells. Stem Cells. 2017 Jan 1;35(1):158–69.
Marand AP, Zhang T, Zhu B, Jiang J. Towards genome-wide prediction and characterization of enhancers in plants. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms. 2017 Jan;1860(1):131–9.
Gross N, Kropp J, Khatib H. Sexual Dimorphism of miRNAs Secreted by Bovine In vitro-produced Embryos. Frontiers in genetics. Frontiers; 2017;8(8689):39.
Haruta M, Sussman MR. Ligand Receptor-Mediated Regulation of Growth in Plants. Curr Top Dev Biol. Elsevier; 2017;123:331–63.
Jaskula-Sztul R, Chen G, Dammalapati A, Harrison A, Tang W, Gong S, et al. AB3-loaded and tumor-targeted unimolecular micelles for medullary thyroid cancer treatment. Journal of Materials Chemistry B. Royal Society of Chemistry; 2017;5(1):151–9.
Auger AP, McCarthy MM. Epigenetic Contribution to Sex Differences in Brain and Behavior. In: Hormones, Brain and Behavior. Elsevier; 2017. pp. 49–62.
Sheets MD, Fox CA, Dowdle ME, Blaser SI, Chung A, Park S. Controlling the Messenger: Regulated Translation of Maternal mRNAs in Xenopus laevis Development. Adv Exp Med Biol. Cham: Springer International Publishing; 2017;953(Chapter 2):49–82.
Jaskula-Sztul R, Chen G, Dammalapati A, Harrison A, Tang W, Gong S, et al. AB3-loaded and tumor-targeted unimolecular micelles for medullary thyroid cancer treatment. Journal of Materials Chemistry B. Royal Society of Chemistry; 2017;5(1):151–9.
Blute ML, Damaschke N, Wagner J, Yang B, Gleave M, Fazli L, et al. Persistence of senescent prostate cancer cells following prolonged neoadjuvant androgen deprivation therapy. Kyprianou N, editor. PloS one. 2017;12(2):e0172048.

2016

Dhillon RS, Denu JM. Using comparative biology to understand how aging affects mitochondrial metabolism. Mol Cell Endocrinol. 2016 Dec 23.
Keller MP, Paul PK, Rabaglia ME, Stapleton DS, Schueler KL, Broman AT, et al. The Transcription Factor Nfatc2 Regulates β-Cell Proliferation and Genes Associated with Type 2 Diabetes in Mouse and Human Islets. Lusis AJ, editor. PLOS Genet. Public Library of Science; 2016 Dec 9;12(12):e1006466.
Kim YJ, Wang R, Gao L, Li D, Xu C, Mang H, et al. POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. Proc Natl Acad Sci USA. National Acad Sciences; 2016 Dec 5;:201618618.
Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, et al. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Mol Cell. 2016 Dec 1;64(5):982–92.
Krautkramer KA, Kreznar JH, Romano KA, Vivas EI, Barrett-Wilt GA, Rabaglia ME, et al. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Mol Cell. 2016 Dec;64(5):982–92.
Papale LA, Li S, Madrid A, Zhang Q, Chen L, Chopra P, et al. Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress. Neurobiology of Disease. 2016 Dec;96:54–66.
Ma KH, Svaren J. Epigenomic reprogramming in peripheral nerve injury. Neural Regen Res. Medknow Publications; 2016 Dec;11(12):1930–1.
Chen X, Lu L, Mayer KS, Scalf M, Qian S, Lomax A, et al. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in Arabidopsis. Elife. eLife Sciences Publications Limited; 2016 Nov 22;5:e17214.
Khatib H, Wisconsin Alumni Research Foundation. Non-invasive assays for embryo quality. US Patent Office; 2016 Nov 17;(15/155,068).
Hideshima T, Qi J, Paranal RM, Tang W, Greenberg E, West N, et al. Discovery of selective small-molecule HDAC6 inhibitor for overcoming proteasome inhibitor resistance in multiple myeloma. Proceedings of the National Academy of Sciences. National Acad Sciences; 2016 Nov 15;113(46):13162–7.
Rui L, Drennan AC, Ceribelli M, Zhu F, Wright GW, Huang DW, et al. Epigenetic gene regulation by Janus kinase 1 in diffuse large B-cell lymphoma. Proc Natl Acad Sci USA. National Acad Sciences; 2016 Nov 15;113(46):E7260–7.
Lee W-H, Higuchi H, Ikeda S, Macke EL, Takimoto T, Pattnaik BR, et al. Mouse Tmem135 mutation reveals a mechanism involving mitochondrial dynamics that leads to age-dependent retinal pathologies. Elife. eLife Sciences Publications Limited; 2016 Nov 15;5:7618.
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, et al. Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. PLOS Genet. Public Library of Science; 2016 Nov 9;12(11):e1006447.
Ong RG, Higbee A, Bottoms S, Dickinson Q, Xie D, Smith SA, et al. Inhibition of microbial biofuel production in drought-stressed switchgrass hydrolysate. Biotechnology for Biofuels 2016 9:1. BioMed Central; 2016 Nov 8;9(1):237.
Legare JM, Modaff P, Iskandar BJ, Pauli RM. Syringomyelia in hereditary multiple exostosis. American Journal of Medical Genetics Part A. 2016 Nov 1;170(11):2956–9.
Marx H, Minogue CE, Jayaraman D, Richards AL, Kwiecien NW, Siahpirani AF, et al. A proteomic atlas of the legume Medicago truncatula and its nitrogen-fixing endosymbiont Sinorhizobium meliloti. Nature biotechnology. Nature Research; 2016 Nov 1;34(11):1198–205.
Coon JJ, HEBERT A, Wisconsin Alumni Research Foundation. Neutron Encoded Mass Tags for Analyte Quantification. US Patent Office; 2016 Oct 20;(15/154,514).
Keller M, Attie A, Kimple M, Wisconsin Alumni Research Foundation. E-prostanoid receptor, ptger3, as a novel anti-diabetic therapeutic target. US Patent Office; 2016 Oct 20;(15/197,228).
Lee SH, Caviness K, Albright ER, Lee J-H, Gelbmann CB, Rak M, et al. Long and Short Isoforms of the Human Cytomegalovirus UL138 Protein Silence IE Transcription and Promote Latency. Sandri-Goldin RM, editor. Journal of virology. American Society for Microbiology; 2016 Oct 15;90(20):9483–94.
Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, et al. Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae. Caudy A, editor. PLOS Genet. Public Library of Science; 2016 Oct 14;12(10):e1006372.
Woods D, Bednarek R, Bouché F, Gordon S, Vogel JP, Garvin DF, et al. Genetic architecture of flowering-time variation in Brachypodium distachyon. Plant Physiol. American Society of Plant Biologists; 2016 Oct 14;:pp.01178.2016.
Kuny CV, Kalejta RF. Human Cytomegalovirus Can Procure Deoxyribonucleotides for Viral DNA Replication in the Absence of Retinoblastoma Protein Phosphorylation. Frueh K, editor. Journal of virology. American Society for Microbiology; 2016 Oct 1;90(19):8634–43.
Chennamsetty I, Coronado M, Contrepois K, Keller MP, Carcamo-Orive I, Sandin J, et al. Nat1 Deficiency Is Associated with Mitochondrial Dysfunction and Exercise Intolerance in Mice. Cell reports. 2016 Oct;17(2):527–40.
Shishkova E, Hebert AS, Coon JJ. Now, More Than Ever, Proteomics Needs Better Chromatography. Cell Systems. 2016 Oct;3(4):321–4.
Chang C-F, Gould MK. The Importance of Being Adaptable: Developing Guidelines for Lung Nodule Evaluation in Asia. Chest. 2016 Oct;150(4):763–5.
Kuang MC, Hutchins PD, Russell JD, Coon JJ, Hittinger CT, Kruglyak L. Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. Elife. eLife Sciences Publications Limited; 2016 Sep 30;5:e19027.
Hua R, Roy S. Organocatalytic Transformation of Carbon Dioxide. In: Recent Advances in Organocatalysis. InTech; 2016.
Gitter A, Huang F, Valluvan R, Fraenkel E, Anandkumar A. Unsupervised learning of transcriptional regulatory networks via latent tree graphical models. 2016.
Albright ER, Kalejta RF. Canonical and variant forms of histone H3 are deposited onto the human cytomegalovirus genome during lytic and latent infections. Frueh K, editor. Journal of virology. American Society for Microbiology; 2016 Sep 7;90(22):10309–20.
Hewitt K, Devadas P, Zemelko L, Keleş S, Bresnick E. SAMD14 enhancer-mediated hematopoietic stress signaling. Experimental Hematology. Elsevier; 2016 Sep 1;44(9):S79.
Blute ML Jr., Ziemlewicz TJ, Lang JM, Kyriakopoulos C, Jarrard DF, Downs TM, et al. Metastatic Tumor Burden Does Not Predict Overall Survival Following Cytoreductive Nephrectomy for Renal Cell Carcinoma: a Novel 3-Dimensional Volumetric Analysis. Urology. 2016 Sep.
Kalejta RF. Sifting and Winnowing through Human Cytomegalovirus Lytic Replication and Latency. Rall GF, editor. PLOS Pathogens. Public Library of Science; 2016 Sep;12(9):e1005607.
Hahn EE, Gould MK. Surveillance Imaging in Patients with Resected Non-Small Cell Lung Cancer: Too Much, Not Enough, or Just Right? Ann Am Thorac Soc. American Thoracic Society; 2016 Sep;13(9):1446–7.
Khatib H, Wisconsin Alumni Research Foundation. Genetic testing for improved cattle fertility. US Patent Office; 2016 Aug 18;(15/138,221).
Keller N, Wiemann P, Wisconsin Alumni Research Foundation. Methods and systems for producing fungal secondary metabolites. US Patent Office; 2016 Aug 18;(15/044,408).
Katsumura KR, Ong IM, DeVilbiss AW, Sanalkumar R, Bresnick EH. GATA Factor-Dependent Positive-Feedback Circuit in Acute Myeloid Leukemia Cells. Cell reports. 2016 Aug;16(9):2428–41.
Liu P, Sanalkumar R, Bresnick EH, Keleş S, Dewey CN. Integrative analysis with ChIP-seq advances the limits of transcript quantification from RNA-seq. Genome Res. Cold Spring Harbor Lab; 2016 Aug;26(8):1124–33.
Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, et al. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Mol Cell. 2016 Aug;63(4):608–20.
Floyd BJ, Wilkerson EM, Veling MT, Minogue CE, Xia C, Beebe ET, et al. Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Mol Cell. 2016 Aug;63(4):621–32.
Bilinski P, Han Y, Hufford MB, Lorant A, Zhang P, Jiang J, et al. Diverse origins of high copy tandem repeats in grass genomes. PeerJ Inc; 2016 Jul 22.
Riley NM, Bern M, Westphall MS, Coon JJ. Full-Featured Search Algorithm for Negative Electron-Transfer Dissociation. Journal of proteome research. American Chemical Society; 2016 Jul 22;15(8):2768–76.
Li X, Xie H, Fu X, Liu JT, Wang HY, Xi BM, et al. Rhodium(I)‐Catalyzed Benzannulation of Heteroaryl Propargylic Esters: Synthesis of Indoles and Related Heterocycles. Chemistry – A European Journal. 2016 Jul 18;22(30):10410–4.
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Riley NM, Hebert AS, Coon JJ. Proteomics Moves into the Fast Lane. Cell Systems. 2016 Mar;2(3):142–3.
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Zhu X, Gong H, He Q, Zeng Z, Busse JS, Jin W, et al. Silencing of vacuolar invertase and asparagine synthetase genes and its impact on acrylamide formation of fried potato products. Plant Biotechnology Journal. 2016 Feb 1;14(2):709–18.
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Khrustaleva L, Jiang J, Havey MJ. High-resolution tyramide-FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion. Theor Appl Genet. Springer Berlin Heidelberg; 2016;129(3):535–45.
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2015

Papale, L. A. Zhang, Q., Li, S., Chen, K., Keles, S., Alisch, R.S., 2015, Genome-wide disruption of 5-hydroxymethylcytosine in a mouse model of autism. Hum Mol Genet, Dec 15;24(24):7121-31. PMID: 26423458
Sisi Li; Ligia A Papale, Ph.D.; Qi Zhang, Ph.D.; Andy Madrid; Li Chen;Pankaj Chopra, Ph.D.; Sunduz Keles, Ph.D.; Peng Jin, Ph.D, Alisch, R.S., 2015, Genome-wide alterations in hippocampal 5-hydroxymethylcytosine links plasticity genes to acute stress. Neurobiol Dis., Nov 17. pii: S0969-9961(15)30089-9. doi:10.1016/j.nbd.2015.11.010. [Epub ahead of print] PMID:26598390.
Ma, K.H., Hung, H.A. Srinivasan, R., Xie, H., Orkin, S.H., Svaren, J. Regulation of peripheral nerve myelin maintenance by gene repression through Polycomb Repressive Complex 2, J. Neuroscience 2015, 35(22):8640-52. PubMed PMID: 26041929, PMC Journal In Process
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Turton, K. B., Annis, D. S., Rui, L., Esnault, S. & Mosher, D. F. Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells. PLoS ONE 10, e0127243 (2015).
Zhang, T., Marand, A. P. & Jiang, J. PlantDHS: a database for DNase I hypersensitive sites in plants. NAR) 36(Database-Issue (2015). doi:10.1093/nar/gkv962
Zhu, B., Zhang, W., Zhang, T., Liu, B. & Jiang, J. Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures. Plant Cell (2015). doi:10.1105/tpc.15.00537
Hoffman, E. A., Frey, B. L., Smith, L. M. & Auble, D. T. Formaldehyde crosslinking: a tool for the study of chromatin complexes. J. Biol. Chem. (2015). doi:10.1074/jbc.R115.651679
Roy, S. et al. A predictive modeling approach for cell line-specific long-range regulatory interactions. NAR) 36(Database-Issue (2015). doi:10.1093/nar/gkv865
Thompson, D., Regev, A. & Roy, S. Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution. Annu. Rev. Cell Dev. Biol. (2015). doi:10.1146/annurev-cellbio-100913-012908
Kropp, J. & Khatib, H. Characterization of microRNA in bovine in vitro culture media associated with embryo quality and development. J. Dairy Sci. 98, 6552–6563 (2015).
Krautkramer, K. A., Reiter, L., Denu, J. M. & Dowell, J. A. Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry. J. Proteome Res. 14, 3252–3262 (2015).
Gent, J. I., Wang, K., Jiang, J. & Dawe, R. K. Stable Patterns of CENH3 Occupancy Through Maize Lineages Containing Genetically Similar Centromeres. Genetics 200, 1105–1116 (2015).
Zhang, T., Zhang, W. & Jiang, J. Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants. Plant Physiol. 168, 1406–1416 (2015).
Wang, H.-Y., Yang, K., Bennett, S. R., Guo, S.-R. & Tang, W. Iridium-Catalyzed Dynamic Kinetic Isomerization: Expedient Synthesis of Carbohydrates from Achmatowicz Rearrangement Products. Angew. Chem. Int. Ed. Engl. 54, 8756–8759 (2015).
Zhong, X. Comparative epigenomics: a powerful tool to understand the evolution of DNA methylation. New Phytol. (2015). doi:10.1111/nph.13540
Chow, C. L., Guo, W., Trivedi, P., Zhao, X. & Gubbels, S. P. Characterization of a unique cell population marked by transgene expression in the adult cochlea of nestin-CreER(T2)/tdTomato-reporter mice. J. Comp. Neurol. 523, 1474–1487 (2015).
Han, Y., Zhang, T., Thammapichai, P., Weng, Y. & Jiang, J. Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. Genetics 200, 771–779 (2015).
Iruretagoyena, J. I., Heiser, T., Iskandar, B. & Shah, D. A Rare Malignant Fetal Brain Tumor. Fetal. Diagn. Ther. (2015). doi:10.1159/000430911
Zuo, C., Hewitt, K., Bresnick, E. & Keles, S. A Hierarchical Framework for State Space Matrix Inference and Clustering. arXiv.org stat.ME, (2015).
Charoensuksai, P., Kuhn, P., Wang, L., Sherer, N. & Xu, W. O-GlcNAcylation of co-activator-associated arginine methyltransferase 1 regulates its protein substrate specificity. Biochem. J. 466, 587–599 (2015).
Hung, H. A., Sun, G., Keles, S. & Svaren, J. Dynamic regulation of Schwann cell enhancers after peripheral nerve injury. J. Biol. Chem. 290, 6937–6950 (2015).
Lee, J., Yun, J.-Y., Zhao, W., Shen, W.-H. & Amasino, R. M. A methyltransferase required for proper timing of the vernalization response in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 112, 2269–2274 (2015).
Iovene, M., Yu, Q., Ming, R. & Jiang, J. Evidence for emergence of sex-determining gene(s) in a centromeric region in Vasconcellea parviflora. Genetics 199, 413–421 (2015).
Zhong, X. et al. Domains rearranged methyltransferase3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 112, 911–916 (2015).
Baeza, J., Smallegan, M. J. & Denu, J. M. Site-specific reactivity of nonenzymatic lysine acetylation. ACS Chem. Biol. 10, 122–128 (2015).
Fan, J., Krautkramer, K. A., Feldman, J. L. & Denu, J. M. Metabolic regulation of histone post-translational modifications. ACS Chem. Biol. 10, 95–108 (2015).
Romens, S. E., McDonald, J., Svaren, J. & Pollak, S. D. Associations between early life stress and gene methylation in children. Child Dev 86, 303–309 (2015).
Su, Z. & Denu, J. M. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications. Curr Protoc Mol Biol 111, 21.32.1–21.32.21 (2015).
Gao, D., Jiang, N., Wing, R. A., Jiang, J. & Jackson, S. A. Transposons play an important role in the evolution and diversification of centromeres among closely related species. Front Plant Sci 6, 216 (2015).
Zhang, W. & Jiang, J. Genome-wide mapping of DNase I hypersensitive sites in plants. Methods Mol. Biol. 1284, 71–89 (2015).
Sarikaya-Bayram, Ö., Palmer, J. M., Keller, N., Braus, G. H. & Bayram, Ö. One Juliet and four Romeos: VeA and its methyltransferases. Front Microbiol 6, 1 (2015).
Kropp, J. & Khatib, H. mRNA fragments in in vitro culture media are associated with bovine preimplantation embryonic development. Front Genet 6, 273 (2015).

2014

Liu, N., Song, W., Schienebeck, C. M., Zhang, M. & Tang, W. Synthesis of Naturally Occurring Tropones and Tropolones. Tetrahedron 70, 9281–9305 (2014).
Wu, C.-H., Holden, M. T. & Smith, L. M. Enzymatic fabrication of high-density RNA arrays. Angew. Chem. Int. Ed. Engl. 53, 13514–13517 (2014).
Jain, S., Gitter, A. & Bar-Joseph, Z. Multitask learning of signaling and regulatory networks with application to studying human response to flu. PLoS Comput. Biol. 10, e1003943 (2014).
Baeza, J., Denu, J. M. & Smallegan, M. J. Site-specific reactivity of non-enzymatic lysine acetylation. Mol. Biol. Cell 25, (2014).
Kennedy-Darling, J., Holden, M. T., Shortreed, M. R. & Smith, L. M. Multiplexed programmable release of captured DNA. Chembiochem 15, 2353–2356 (2014).
Svaren, J. MicroRNA and transcriptional crosstalk in myelinating glia. Neurochem. Int. 77, 50–57 (2014).
Li, H. & Chang, Q. Regulation and function of stimulus-induced phosphorylation of MeCP2. Front Biol (Beijing) 9, 367–375 (2014).
Woods, D. P., Ream, T. S., Minevich, G., Hobert, O. &
Amasino, R. M. PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon. Genetics 198, 397–408 (2014).
Winston-McPherson, G. N., Shu, D. & Tang, W. Synthesis and biological evaluation of 2,3′-diindolylmethanes as agonists of aryl hydrocarbon receptor. Bioorg. Med. Chem. Lett. 24, 4023–4025 (2014).
Liu, R., Li, Q. & Smith, L. M. Detection of large ions in time-of-flight mass spectrometry: effects of ion mass and acceleration voltage on microchannel plate detector response. J. Am. Soc. Mass Spectrom. 25, 1374–1383 (2014).
Guillen-Ahlers, H., Shortreed, M. R., Smith, L. M. & Olivier, M. Advanced methods for the analysis of chromatin-associated proteins. Physiol. Genomics 46, 441–447 (2014).
Li, Y. & Zhao, X. Concise review: Fragile X proteins in stem cell maintenance and differentiation. Stem Cells 32, 1724–1733 (2014).
Kennedy-Darling, J. & Smith, L. M. Measuring the formaldehyde Protein-DNA cross-link reversal rate. Anal. Chem. 86, 5678–5681 (2014).
Zhong, X. et al. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157, 1050–1060 (2014).
Wu, Y., Zhang, W. & Jiang, J. Genome-wide nucleosome positioning is orchestrated by genomic regions associated with DNase I hypersensitivity in rice. PLoS Genet. 10, e1004378 (2014).
Schienebeck, C. M., Li, X., Shu, X.-Z. & Tang, W. 3-Acyloxy-1,4-enyne: a New Five-carbon Synthon for Rhodium-Catalyzed (5+2) Cycloadditions. Pure Appl. Chem. 86, 409–417 (2014).
Prolla, T. A. & Denu, J. M. NAD+ deficiency in age-related mitochondrial dysfunction. Cell Metab. 19, 178–180 (2014).
Wang, L., Zeng, Z., Zhang, W. & Jiang, J. Three potato centromeres are associated with distinct haplotypes with or without megabase-sized satellite repeat arrays. Genetics 196, 397–401 (2014).
Sheynkman, G. M., Shortreed, M. R., Frey, B. L., Scalf, M. & Smith, L. M. Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J. Proteome Res. 13, 228–240 (2014).
Wang, K., Wu, Y., Zhang, W., Dawe, R. K. & Jiang, J. Maize centromeres expand and adopt a uniform size in the genetic background of oat. Genome Res. 24, 107–116 (2014).
Gitter, A. et al. Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput 39–50 (2014).
Brinkman, A. M., Wu, J., Ersland, K. & Xu, W. Estrogen receptor α and aryl hydrocarbon receptor independent growth inhibitory effects of aminoflavone in breast cancer cells. BMC Cancer 14, 344 (2014).
Zhang, W., Zhang, T., Wu, Y. & Jiang, J. Open chromatin in plant genomes. Cytogenet. Genome Res. 143, 18–27 (2014).
Peñagaricano, F., Wang, X., Rosa, G. J., Radunz, A. E. & Khatib, H. Maternal nutrition induces gene expression changes in fetal muscle and adipose tissues in sheep. BMC Genomics 15, 1034 (2014).
Kropp, J., Salih, S. M. & Khatib, H. Expression of microRNAs in bovine and human pre-implantation embryo culture media. Front Genet 5, 91 (2014).
Woods, D. P., Ream, T. S. & Amasino, R. M. Memory of the vernalized state in plants including the model grass Brachypodium distachyon. Front Plant Sci 5, 99 (2014).
Knaack, S. A., Siahpirani, A. F. & Roy, S. A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. Cancer Inform 13, 69–84 (2014).

2013

Shu, X.-Z., Schienebeck, C. M., Song, W., Guzei, I. A. & Tang, W. Transfer of chirality in the rhodium-catalyzed intramolecular [5+2] cycloaddition of 3-acyloxy-1,4-enynes (ACEs) and alkynes: synthesis of enantioenriched bicyclo[5.3.0]decatrienes. Angew. Chem. Int. Ed. Engl. 52, 13601–13605 (2013).
Amasino, R. M. My favourite flowering image: Maryland Mammoth tobacco. J. Exp. Bot. 64, 5817–5818 (2013).
Li, X., Song, W. & Tang, W. Rhodium-catalyzed tandem annulation and (5 + 1) cycloaddition: 3-hydroxy-1,4-enyne as the 5-carbon component. J. Am. Chem. Soc. 135, 16797–16800 (2013).
Feldman, J. L., Baeza, J. & Denu, J. M. Activation of the protein deacetylase SIRT6 by long-chain fatty acids and widespread deacylation by mammalian sirtuins. J. Biol. Chem. 288, 31350–31356 (2013).
Johannsen, E. & Lambert, P. F. Epigenetics of human papillomaviruses. Virology 445, 205–212 (2013).
Duangpan, S., Zhang, W., Wu, Y., Jansky, S. H. & Jiang, J. Insertional mutagenesis using Tnt1 retrotransposon in potato. Plant Physiol. 163, 21–29 (2013).
Zhang, M., Liu, N. & Tang, W. Stereoselective total synthesis of hainanolidol and harringtonolide via oxidopyrylium-based [5 + 2] cycloaddition. J. Am. Chem. Soc. 135, 12434–12438 (2013).
Shu, D., Winston-McPherson, G. N., Song, W. & Tang, W. Platinum-catalyzed tandem indole annulation/arylation for the synthesis of diindolylmethanes and indolo[3,2-b]carbazoles. Org. Lett. 15, 4162–4165 (2013).
Sheynkman, G. M., Shortreed, M. R., Frey, B. L. & , Smith, L. M. Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-Seq. Mol. Cell Proteomics 12, 2341–2353 (2013).
Sridharan, R. et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1 gamma in reprogramming to pluripotency. Nat. Cell Biol. 15, 872–882 (2013).
Iovene, M., Zhang, T., Lou, Q., Buell, C. R. & Jiang, J. Copy number variation in potato – an asexually propagated autotetraploid species. Plant J. 75, 80–89 (2013).
Liu, R., Zhang, M., Winston-McPherson, G. & Tang, W. Ring expansion of alkynyl cyclopropanes to highly substituted cyclobutenes via a N-sulfonyl-1,2,3-triazole intermediate. Chem. Commun. (Camb.) 49, 4376–4378 (2013).
Kim, D.-Y., Scalf, M., Smith, L. M. & Vierstra, R. D. Advanced proteomic analyses yield a deep catalog of ubiquitylation targets in Arabidopsis. Plant Cell 25, 1523–1540 (2013).
Schienebeck, C. M., Robichaux, P. J., Li, X., Chen, L. & Tang, W. Effect of ester on rhodium-catalyzed intermolecular [5+2] cycloaddition of 3-acyloxy-1,4-enynes and alkynes. Chem. Commun. (Camb.) 49, 2616–2618 (2013).
Sievers, C. K., Shanle, E. K., Bradfield, C. A. & Xu, W. Differential action of monohydroxylated polycyclic aromatic hydrocarbons with estrogen receptors α and β. Toxicol. Sci. 132, 359–367 (2013).
Shu, D., Song, W., Li, X. & Tang, W. Rhodium- and platinum-catalyzed [4+3] cycloaddition with concomitant indole annulation: synthesis of cyclohepta[b]indoles. Angew. Chem. Int. Ed. Engl. 52, 3237–3240 (2013).
Broderick, A. H., Carter, M. C. D., Lockett, M. R., , Smith, L. M. & Lynn, D. M. Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers. ACS Appl Mater Interfaces 5, 351–359 (2013).
Welham, N. V., Chang, Z., , Smith, L. M. & Frey, B. L. Proteomic analysis of a decellularized human vocal fold mucosa scaffold using 2D electrophoresis and high-resolution mass spectrometry. Biomaterials 34, 669–676 (2013).
Walling, J. G., Zhang, W. & Jiang, J. Fluorescence in situ hybridization techniques for cytogenetic and genomic analyses. Methods Mol. Biol. 956, 13–27 (2013).
Jackson, S. A. & Sridharan, R. The Nexus of Tet1 and the Pluripotency Network. Cell Stem Cell 12, 387–388 (2013).
Driver, A. M., Huang, W., Kropp, J., Peñagaricano, F. & Khatib, H. Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos. PLoS ONE 8, e69490 (2013).
Lee, J. & Amasino, R. M. Two FLX family members are non-redundantly required to establish the vernalization requirement in Arabidopsis. Nat Commun 4, 2186 (2013).
Schwartz, C. & Amasino, R. Nitrogen recycling and flowering time in perennial bioenergy crops. Front Plant Sci 4, 76 (2013).
Roy, S. et al. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PLoS Comput. Biol. 9, e1003252 (2013).

2012

Denu, J. M. & Gottesfeld, J. M. Minireview series on sirtuins: from biochemistry to health and disease. J. Biol. Chem. 287, 42417–42418 (2012).
Feldman, J. L., Dittenhafer-Reed, K. E. & Denu, J. M. Sirtuin catalysis and regulation. J. Biol. Chem. 287, 42419–42427 (2012).
Shu, X.-Z., Shu, D., Schienebeck, C. M. & Tang, W. Rhodium-catalyzed acyloxy migration of propargylic esters in cycloadditions, inspiration from the recent “gold rush”. Chem Soc Rev 41, 7698–7711 (2012).
Huang, W., Long, N. & Khatib, H. Genome-wide identification and initial characterization of bovine long non-coding RNAs from EST data. Anim. Genet. 43, 674–682 (2012).
Wollenberg, A. C. & Amasino, R. M. Natural variation in the temperature range permissive for vernalization in accessions of Arabidopsis thaliana. Plant Cell Environ. 35, 2181–2191 (2012).
Guo, W., Patzlaff, N. E., Jobe, E. M. & Zhao, X. Isolation of multipotent neural stem or progenitor cells from both the dentate gyrus and subventricular zone of a single adult mouse. Nat Protoc 7, 2005–2012 (2012).
Wagner, E. K., Nath, N., Flemming, R., Feltenberger, J. B. & Denu, J. M. Identification and Characterization of Small Molecule Inhibitors of a Plant Homeodomain Finger. Biochemistry (2012). doi:10.1021/bi3009278
Zhong, X., Li, H. & Chang, Q. MeCP2 phosphorylation is required for modulating synaptic scaling through mGluR5. J. Neurosci. 32, 12841–12847 (2012).
Zhong, X. et al. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat. Struct. Mol. Biol. 19, 870–875 (2012).
Zhang, M. & Tang, W. Synthesis of functionalized cyclohexenone core of welwitindolinones via rhodium-catalyzed [5 + 1]cycloaddition. Org. Lett. 14, 3756–3759 (2012).
Zhang, W., Zhang, T., Wu, Y. & Jiang, J. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24, 2719–2731 (2012).
Wu, C.-H., Lockett, M. R. & Smith, L. M. RNA-mediated gene assembly from DNA arrays. Angew. Chem. Int. Ed. Engl. 51, 4628–4632 (2012).
Denu, J. M. Fortifying the link between SIRT1, resveratrol, and mitochondrial function. Cell Metab. 15, 566–567 (2012).
Yun, J.-Y., Tamada, Y., Kang, Y. E. & Amasino, R. M. Arabidopsis trithorax-related3/SET domain GROUP2 is required for the winter-annual habit of Arabidopsis thaliana. Plant Cell Physiol. 53, 834–846 (2012).
Yu, W., Dittenhafer-Reed, K. E. & Denu, J. M. SIRT3 protein deacetylates isocitrate dehydrogenase 2 (IDH2) and regulates mitochondrial redox status. J. Biol. Chem. 287, 14078–14086 (2012).
Wu, J. & Xu, W. Histone H3R17me2a mark recruits human RNA polymerase-associated factor 1 complex to activate transcription. Proc. Natl. Acad. Sci. U.S.A. 109, 5675–5680 (2012).
Li, X., Huang, S., Schienebeck, C. M., Shu, D. & Tang, W. Rhodium-catalyzed carbonylation of 3-acyloxy-1,4-enynes for the synthesis of cyclopentenones. Org. Lett. 14, 1584–1587 (2012).
Hallows, W. C., Yu, W. &Denu, J. M. Regulation of glycolytic enzyme phosphoglycerate mutase-1 by Sirt1 protein-mediated deacetylation. J. Biol. Chem. 287, 3850–3858 (2012).
Hung, H., Kohnken, R. & Svaren, J. The nucleosome remodeling and deacetylase chromatin remodeling (NuRD) complex is required for peripheral nerve myelination. J. Neurosci. 32, 1517–1527 (2012).
Peñagaricano, F. & Khatib, H. Association of milk protein genes with fertilization rate and early embryonic development in Holstein dairy cattle. J. Dairy Res. 79, 47–52 (2012).