Research Labs

Anczuków O and Krainer AR (2016). Splicing-factor alterations in cancers. RNA, 22:1285-301, 2016.

Anczuków O, Akerman M, Cléry A, Wu J, Shen C, Shirole NH, Raimer A, Sun S, Jensen MA, Hua Y, Allain FH, Krainer AR. SRSF1-Regulated Alternative Splicing in Breast Cancer. Molecular Cell. 60(1):105-17, 2015. 

Anczuków O, Rosenberg AZ, Akerman M, Das S, Zhan L, Karni R, Muthuswamy SK, Krainer AR. The splicing factor SRSF1 regulates apoptosis and proliferation to promote mammary epithelial cell transformation. Nat Struct Mol Biol. 19(2):220-8, 2012.

Anczuków O, Buisson M, Léoné M, Coutanson C, Lasset C, Calender A, Sinilnikova OM, Mazoyer S. BRCA2 deep intronic mutation causing activation of a cryptic exon: opening toward a new preventive therapeutic strategy. Clin Cancer Res. 18(18):4903-9, 2012.

Banchereau R, Hong S, Cantarel B, Baldwin N, Baisch J, Edens M, Cepika AM, Acs P, Turner J, Anguiano E, Vinod P, Khan S, Obermoser G, Blankenship D, Wakeland E, Nassi L, Gotte A, Punaro M, Liu YJ, Banchereau J, Rossello-Urgell J, Wright T, Pascual V.  Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients. Cell. 165(6):1548-1550. 2016.

Banchereau R, Baldwin N, Cepika AM, Athale S, Xue Y, Yu CI, Metang P, Cheruku A, Berthier I, Gayet I, Wang Y, Ohouo M, Snipes L, Xu H, Obermoser G, Blankenship D, Oh S, Ramilo O, Chaussabel D, Banchereau J, Palucka K, Pascual V. Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines. Nat Commun. 5:5283. 2014.

Schmitt N, Liu Y, Bentebibel SE, Munagala I, Bourdery L, Venuprasad K, Banchereau J, Ueno H. The cytokine TGF-β co-opts signaling via STAT3-STAT4 to promote the differentiation of human TFH cells. Nat Immunol. 15(9):856-65. 2014.

Obermoser G, Presnell S, Domico K, Xu H, Wang Y, Anguiano E, Thompson-Snipes L, Ranganathan R, Zeitner B, Bjork A, Anderson D, Speake C, Ruchaud E, Skinner J, Alsina L, Sharma M, Dutartre H, Cepika A, Israelsson E, Nguyen P, Nguyen QA, Harrod AC, Zurawski SM, Pascual V, Ueno H, Nepom GT, Quinn C, Blankenship D, Palucka K, Banchereau J, Chaussabel D. Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. Immunity.  38(4):831-44. 2013.

Banchereau J, Zurawski S, Thompson-Snipes L, Blanck JP, Clayton S, Munk A, Cao Y, Wang Z, Khandelwal S, Hu J, McCoy WH 4th, Palucka KA, Reiter Y, Fremont DH, Zurawski G, Colonna M, Shaw AS, Klechevsky E. Immunoglobulin-like transcript receptors on human dermal CD14+ dendritic cells act as a CD8-antagonist to control cytotoxic T cell priming. Proc Natl Acad Sci U S A.  109(46):18885-90. 2012.

Xu W, Joo H, Clayton S, Dullaers M, Herve MC, Blankenship D, De La Morena MT, Balderas R, Picard C, Casanova JL, Pascual V, Oh S, Banchereau J. Macrophages induce differentiation of plasma cells through CXCL10/IP-10. J Exp Med.  209(10):1813-23, S1-2. 2012.

Garcia-Romo GS, Caielli S, Vega B, Connolly J, Allantaz F, Xu Z, Punaro M, Baisch J, Guiducci C, Coffman RL, Barrat FJ, Banchereau J, Pascual V. Netting neutrophils are major inducers of type I IFN production in pediatric systemic lupus erythematosus. Sci Transl Med. 3(73):73ra20. 2011.

Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D, O'Garra A. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature.  466(7309):973-7. 2010.

Smith CL, Blake JA, Kadin JA, Richardson JE, Bult CJ.  Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse.  Nucleic Acids Research. 2017.

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.  Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics. 2017.

Blake JA, Eppig JT, Kadin JA, Richardson JE, Smith CL, Bult CJ; the Mouse Genome Database Group.  Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse.  Nucleic Acids Research. 45(D1):D723-D729.  2017.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH.  Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.  Nucleic Acids Research. 2017.

Eppig JT, Smith CL, Blake JA, Ringwald M, Kadin JA, Richardson JE, Bult CJ.  Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.  Methods in Molecular Biology. 2017

Jiang X, Ringwald M, Blake J, Shatkay H. Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).  Database:  The Journal of Biological Databases and Curation. 2017.

Terri L. Woodard, Ewelina Bolcun-Filas. Prolonging Reproductive Life after Cancer: The Need for Fertoprotective Therapies.  Trends in Cancer.  2016

Bolcun-Filas E, Rinaldi VD, White ME, Schimenti JC. Reversal of female infertility by Chk2 ablation reveals the oocyte DNA damage checkpoint pathway. Science. 2014 Jan 31;343(6170):533-6.

Ananda G, Mockus S, Lundquist M, Spotlow V, Simons A, Mitchell T, Stafford G, Philip V, Stearns T, Srivastava A, Barter M, Rowe L, Malcolm J, Bult C, Karuturi RK, Rasmussen K, Hinerfeld D. Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors. Exp Mol Pathol. 2015 Feb;98(1):106-12.

Bult CJ, Krupke DM, Begley DA, Richardson JE, Neuhauser SB, Sundberg JP, Eppig JT. Mouse Tumor Biology (MTB): a database of mouse models for human cancer. Nucleic Acids Res. 2015 Jan;43(Database issue):D818-24.

Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE; Mouse Genome Database Group. The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res. 2015 Jan;43(Database issue):D726-36.

Morelli KH, Seburn KL, Schroeder DG, Spaulding EL, Dionne LA, Cox GA, Burgess RW. Severity of Demyelinating and Axonal Neuropathy Mouse Models Is Modified by Genes Affecting Structure and Function of Peripheral Nodes.  Cell Rep. 18(13):3178-3191, 2017.

Spaulding EL, Sleigh JN, Morelli KH, Pinter MJ, Burgess RW, Seburn KL. Synaptic Deficits at Neuromuscular Junctions in Two Mouse Models of Charcot-Marie-Tooth Type 2d. J Neurosci. 36(11):3254-67, 2016.

Garrett AM, Tadenev AL, Hammond YT, Fuerst PG, Burgess RW. Replacing the PDZ-interacting C-termini of DSCAM and DSCAML1 with epitope tags causes different phenotypic severity in different cell populations. Elife. 5, 2016.

He W, Bai G, Zhou H, Wei N, White NM, Lauer J, Liu H, Shi Y, Dumitru CD, Lettieri K, Shubayev V, Jordanova A, Guergueltcheva V, Griffin PR, Burgess RW, Pfaff SL, Yang XL (2015) CMT2D neuropathy is linked to the neomorphic binding activity of glycyl-tRNA synthetase. Nature.  526:710-714, 2015.

Motley WW, Seburn KL, Nawaz MH, Miers KE, Cheng J, Antonellis A, Green ED, Talbot K, Yang XL, Fischbeck KH, Burgess RW (2011) Charcot-Marie-Tooth-Linked mutant GARS is toxic to peripheral neurons independent of wild-type GARS levels. PLoS Genet.  7:e1002399, 2011.

Fuerst PG, Bruce F, Tian M, Wei W, Elstrott J, Feller MB, Erskine L, Singer JH, Burgess RW (2009) DSCAM and DSCAML1 function in self-avoidance in multiple cell types in the developing mouse retina. Neuron. 64:484-497, 2009.

Fuerst PG, Koizumi A, Masland RH, Burgess RW (2008) Neurite arborization and mosaic spacing in the mouse retina require DSCAM. Nature. 451:470-474, 2008.

Seburn KL, Nangle LA, Cox GA, Schimmel P, Burgess RW (2006) An active dominant mutation of glycyl-tRNA synthetase causes neuropathy in a Charcot-Marie-Tooth 2D mouse model. Neuron. 51:715-726, 2006.

Wang X, Philip VM, Ananda G, White CC, Malhotra A, Michalski PJ, Karuturi KRM, Chintalapudi SR, Acklin C, Sasner M, Bennett DA, De Jager PL, Howell GR, Carter GW. A Bayesian Framework for Generalized Linear Mixed Modeling Identifies New Candidate Loci for Late-Onset Alzheimer's Disease. Genetics. 2018 Mar

Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, and Gregory W. Carter. CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis. PLoS Comput Biol. 2013 Oct; 9

Anna L. Tyler, Leah Rae Donahue, Gary A. Churchill, and Gregory W. Carter. Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross. PLoS Genet. 2016 Feb

Anna L. Tyler, Tracy C. McGarr, Barbara J. Beyer, Wayne N. Frankel, and Gregory W. Carter. A Genetic Interaction Network Model of a Complex Neurological Disease. Genes Brain Behav. 2014 Nov

Tyler AL, Ji B, Gatti DM, Munger SC, Churchill GA, Svenson KL, Carter GW, Epistatic Networks Jointly Influence Phenotypes Related to Metabolic Disease and Gene Expression in Diversity Outbred Mice. Genetics. 2017 Jun;206(2):621-639.

Ball RL, Fujiwara Y, Sun F, Hu J, Hibbs MA, Handel MA, Carter GW, Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. BMC Genomics. 2016 Aug 12;17(1):628.

Wu, X., Scott, D.A., Kriz, A.J., Chiu, A.C., Hsu, P.D., Dadon, D.B., Cheng, A.W., Trevino, A.E., Konermann, S., Chen, S., Jaenisch, R., Zhang, F., Sharp, P.A. (2014) Genome-wide binding of CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32(7):670-6. 2014.

Cheng, A.W.*, Shi, J.*, Wong P.*, Luo, K.L., Trepman, P., Wang, E.T., Choi, H., Burge, C.B., Lodish, H.F. Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood. 124(4):598-610. 2014.

Cheng, A.W.*, Wang, H.*, Yang, H, Shi, L., Katz, Y., Theunissen, T.W., Rangarajan, S., Shivalila, C.S., Dadon, D.B., Jaenisch, R. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res.   23(10):1163-71.  2013.

Wang, H.*, Yang, H.*, Shivalila, C.S.*, Dawlaty, M.M., Cheng, A.W., Zhang, F., Jaenisch, R. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell.  153(4):910-8. 2013.

Yang, H.*, Wang, H.*, Shivalila, C.S.*, Cheng, A.W., Shi, L., Jaenisch, R. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell.  154(6):1370-9. 2013.

Buganim, Y.*, Faddah D.A.*, Cheng, A.W., Itskovich, E., Markoulaki, S., Gantz, K., Klemm S.L., van Oudenaarden A., Jaenisch, R. Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase. Cell.  150(6):1209-22. 2012.

Shapiro, I.M. *, Cheng, A.W. *, Flytzanis, N.C., Balsamo, M., Condeelis, J.S., Oktay, M.H., Burge, C.B., Gertler, F.B. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet.  7(8):e1002218. 2011.

Creyghton, M.P.*, Cheng A.W.*, Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., Hanna, J., Lodato, M.A., Frampton, G.M., Sharp, P.A., Boyer, L.A., Young, R.A., Jaenisch, R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U.S.A. 107(50):21931-6. 2010.

Bubier JA, Jay JJ, Baker CL, Bergeson SE, Ohno H, Metten P, Crabbe JC, Chesler EJ. Identification of a QTL in Mus musculus for alcohol preference, withdrawal, and Ap3m2 expression using integrative functional genomics and precision genetics. Genetics. 197(4):1377-93. 2014.

 Baker E, Bubier JA, Reynolds T, Langston MA, Chesler EJ. GeneWeaver: data driven alignment of cross-species genomics in biology and disease. Nucleic Acids Res. 44(D1):D555-9. 2016.

Dickson PE, Miller MM, Calton MA, Bubier JA, Cook MN, Goldowitz D, Chesler EJ, Mittleman G. Systems genetics of intravenous cocaine self-administration in the BXD recombinant inbred mouse panel. Psychopharmacology (Berl). 2015. 

Chesler EJ, Gatti DM, Morgan AP, Strobel M, Trepanier L, Oberbeck D, McWeeney S, Hitzemann R, Ferris M, McMullan R, Clayshultle A, Bell TA, Manuel de Villena FP, Churchill GA. Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection. G3 (Bethesda). 6(12):3893-3902. 2016.

Bogue MA, Peters LL, Paigen B, Korstanje R, Yuan R, Ackert-Bicknell C, Grubb SC, Churchill GA, Chesler EJ. Accessing Data Resources in the Mouse Phenome Database for Genetic Analysis of Murine Life Span and Health Span. J Gerontol A Biol Sci Med Sci. 71(2):170-7. 2016.

Karp NA, Mason J, Beaudet AL, Benjamini Y, Bower L, Braun RE, Brown SDM, Chesler EJ, Dickinson ME, Flenniken AM, Fuchs H, Angelis MH, Gao X, Guo S, Greenaway S, Heller R, Herault Y, Justice MJ, Kurbatova N, Lelliott CJ, Lloyd KCK, Mallon AM, Mank JE, Masuya H, McKerlie C, Meehan TF, Mott RF, Murray SA, Parkinson H, Ramirez-Solis R, Santos L, Seavitt JR, Smedley D, Sorg T, Speak AO, Steel KP, Svenson KL; International Mouse Phenotyping Consortium, Wakana S, West D, Wells S, Westerberg H, Yaacoby S, White JK. Prevalence of sexual dimorphism in mammalian phenotypic traits. Nat Commun. 8:15475.  2017.

Ivan Dotu, Scott Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, and Jeffrey H Chuang. SARNAclust: Semi-Automatic Detection Of RNA Protein Binding Motifs From Immunoprecipitation Data. PLoS Comput Biol 14 (3): e1006078. (2018)

Young Kwang Chae, Jonathan F. Anker, Preeti Bais, Sandeep Namburi, Francis J. Giles and Jeffrey H. Chuang. Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. Oncotarget. 9:7949-7960 (2018)

Javad Noorbakhsh and Jeffrey H Chuang. Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures. Nature Genetics 49, 1288–1289 (2017).

Preeti Bais, Sandeep Namburi, Daniel M. Gatti, Xinyu Zhang, Jeffrey H. Chuang. CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens. Bioinformatics, 33:3110-3112 (2017)

Menghi F, Inaki K, Woo X, Kumar PA, Grzeda KR, Malhotra A, Yadav V, Kim H, Marquez EJ, Ucar D, Shreckengast PT, Wagner JP, MacIntyre G, Murthy Karuturi KR, Scully R, Keck J, Chuang JH, Liu ET. The tandem duplicator phenotype as a distinct genomic configuration in cancer.  Proc Natl Acad Sci U S A. 2016.

Ishimura R, Nagy G, Dotu I, Chuang JH, and Ackerman S. Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation. 2016. 10.7554/eLife.14295.

Menghi F, Inaki K, Woo X, Kumar PA, Grzeda KR, Malhotra A, Kim H, Marquez EJ, Ucar D, Shreckengast PT, Wagner JP, Murthy Karuturi KR, Scully R, Keck J, Chuang JH, Liu ET. The Tandem Duplicator Phenotype as a Distinct Genomic Configuration in Cancer. 2016. PNAS 113:17:E2373-82.

RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Ishimura R, Nagy G, Dotu I, Zhou H, Yang XL, Schimmel P, Senju S, Nishimura Y, Chuang JH, Ackerman SL. 2014. Science. 345(6195):455–459.

Grzeda KR, Royer-Bertrand B, Inaki K, Kim H, Hillmer AM, Liu ET, Chuang JH. Functional chromatin features are associated with structural mutations in cancer. BMC Genomics. 2014.15:1013.

Ritter DI, Dong Z, Guo S, Chuang JH. Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes. 2012. PLoS ONE 7(5):e35202.

French JE, Gatti DM, Morgan DL, Kissling GE, Shockley KR, Knudsen GA, Shepard KG, Price HC, King D, Witt KL, Pedersen LC, Munger SC, Svenson KL, Churchill GA. Diversity Outbred Mice Identify Population-Based Exposure Thresholds and Genetic Factors that Influence Benzene-Induced Genotoxicity. Environ Health Perspect. 2015 Mar;123(3):237-45.

Simecek P, Churchill GA, Yang H, Rowe LB, Herberg L, Serreze DV, Leiter EH. Genetic Analysis of Substrain Divergence in Non-Obese Diabetic (NOD) Mice. G3 (Bethesda). 2015 Mar 3;5(5):771-5.

Church RJ, Gatti DM, Urban TJ, Long N, Yang X, Shi Q, Eaddy JS, Mosedale M, Ballard S, Churchill GA, Navarro V, Watkins PB, Threadgill DW, Harrill AH. Sensitivity to hepatotoxicity due to epigallocatechin gallate is affected by genetic background in diversity outbred mice. Food Chem Toxicol. 2015 Feb;76:19-26.

Burgess RW, Cox GA, Seburn KL. 2016. Neuromuscular disease models and analysis. Methods Mol. Biol. 1438: 349-394, 2016. 

Coley WD, Bogdanik L, Vila MC, Yu Q, van der Meulen JH, Rayavarapu S, Novak JS, Nearing M, Quinn JL, Saunders A, Dolan C, Andrews W, Lammert C, Austin A, Partridge TA, Cox GA, Lutz C, Nagaraju K. 2016. Effect of genetic background on the dystrophic phenotype in mdx mice. Hum Mol Genet.  25:130-145, 2016.

Sher RB, Heiman-Patterson TD, Blankenhorn EA, Jiang J, Alexander G, Deitch JS, Cox GA. 2014. A major QTL on mouse chromosome 17 resulting in lifespan variability in SOD1-G93A transgenic mouse models of amyotrophic lateral sclerosis. Amyotroph Lateral Scler. 15(7-8):588-600, 2014. 

Mitsuhashi S, Ohkuma A, Talim B, Karahashi M, Koumura T, Aoyama C, Kurihara M, Quinlivan R, Sewry C, Mitsuhashi H, Goto K, Koksal B, Kale G, Ikeda K, Taguchi R, Noguchi S, Hayashi YK, Nonaka I, Sher RB, Sugimoto H, Nakagawa Y, Cox GA, Topaloglu H, Nishino I. 2011. A congenital muscular dystrophy with mitochondrial structural abnormalities caused by defective de novo phosphatidylcholine biosynthesis. Am. J. Hum Gen. 88:845-851, 2011.

Sher, RB, Aoyoma, C, Huebsch, KA, Ji, S, Kerner, K, Yang, Y, Frankel, WN, Hoppel, CL, Wood, PA, Vance, DE, Cox, GA. 2006. A rostrocaudal muscular dystrophy caused by a defect in choline kinase beta, the first enzyme in phosphatidylcholine biosynthesis. J. Biol. Chem.  281: 4938-4948, 2005.

Maddatu, TP, Garvey, SM, Schroeder, DG, Zhang, W, Kim, S-Y, Nicholson, AI, Davis, CJ, Cox, GA. 2005. Dilated cardiomyopathy (DCM) in the nmd mouse: Transgenic rescue and QTLs that improve cardiac function and survival. Hum. Mol. Genet. 14: 3179-3189, 2005.

Maddatu TP, Garvey SM, Shroeder DG, Hampton TG, Cox GA. 2004.  Transgenic rescue of neurogenic atrophy in the nmd mouse reveals a role for Ighmbp2 in dilated cardiomyopathy.  Hum. Mol. Genet. 13: 1105-1115,  2004.

Dumont BL. X-Chromosome control of genome-scale recombination rates in house mice. Genetics 205: 1649-1656, 2017.

Dumont BL. Variation and evolution of the meiotic requirement for crossing over in mammals. Genetics 205: 155-168, 2017. 

Dumont BL. Interlocus gene conversion explains at least. 7% of single nucleotide variants in human segmental duplications. BMC Genomics. 16:456, 2015 

Borodin PM, Basheva EA, Torgasheva AA, Dashkevich OA, Golenishchev FN, Kartavtseva IV, Mekada K, Dumont BL. Multiple independent evolutionary losses of XY pairing at meiosis in the grey voles. Chromosome Res. 20(2):259-68 ,2012

Campbell CD, Chong JX, Malig M, Ko A, Dumont BL, Han L, Vives L, O'Roak BJ, Sudmant PH, Shendure J, Abney M, Ober C, Eichler EE. Estimating the human mutation rate using autozygosity in a founder population. Nat Genet. 44(11):1277-81, 2012

Bolcun-Filas E, MAH Handel. Meiosis: The chromosomal foundation of reproduction. Biol Reprod doi:10.1093/biolre/ioy021. 2018. 

Hu J, F Sun, MA Handel. Nuclear localization of EIF4G3 suggests a role for the XY body in translational regulation during spermatogenesis in mice. Biol Reprod 98:102-114. doi/10.1093/biolre/iox150. 2017. 

Ball RL, Y Fujiwara, F Sun, J Hu, M Hibbs, MA Handel, GW Carter. Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes. BMC Genomics 17:628. 2016. 

Sun F, Fujiwara Y, Reinholdt LG, Hu J, Saxl RL, Baker CL, Petkov PM, Paigen K, Handel MA. Nuclear localization of PRDM9 and its role in meiotic chromatin modifications and homologous synapsis. Chromosoma. 124(3):397-415, 2015.

Reifsnyder PC, Flurkey K, Te A, Harrison DE, 2016. Rapamycin treatment benefits glucose metabolism in mouse models of type 2 diabetes. Aging 8(11):3120-3130. 2016.

Strong R, Miller RA, Antebi A, Astle CM, Bogue M, Denzel MS, Fernandez E, Flurkey K, Hamilton KL, Lamming DW, Javors M, de Magalhães JP, Marinez PA, McCord JM, Miller JM, Muller M, Nelson JF, Ndukum J, Rainger GE, Richardson A, Sabatini DM, Salmon AB, Simpkins JW, Steegenga WT, Nadon NL, Harrison DE. 2016. Longer lifespan in male mice treated with a weakly-estrogenic agonist, an antioxidant, an α-glucosidase inhibitor or a Nrf2-inducer. Aging Cell. 15: 872–884. 2016.

Lee B, Buric I, Anupriuya G-P, Flurkey K, Harrison DE, Yuan R, Peters L, Kuchel G, Melzer D, Harries L. 2017. MicroRNAs miR-203-3p, miR-664-3p and miR-708-5p are associated with median strain lifespan in mice. Scientific Reports, Nature. in press 2-10-17; Ms SREP-16-47467A. 2017.

Jiang Z, Harrison DE, Parsons ME, McClatchy S, Jacobs L, Pazdro R. 2016. Heritability of in vitro phenotypes exhibited by murine adipose-derived stromal cells. Mamm Genome 27: 460-468. 2016.

Nadon NL, Strong R, Miller RA, Harrison DE. 2016. NIA Interventions Testing Program: Investigating Putative Aging Intervention Agents in a Genetically Heterogeneous Mouse Model. eBioMedicine pii: S2352-3964(16)30554-0. 2016.

Lee BP, Pilling LC, Emond F, Flurkey K, Harrison DE, Yuan R, Peters LL, Kuchel GA, Ferrucci L, Melzer D, Harries LW. 2016. Changes in the expression of splicing factor transcripts and variations in alternative splicing are associated with lifespan in mice and humans. Aging Cell. 15(5):903-13. 2016

DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell. pii: S1534-5807(16)30682-7. 2016.

Hinson JT, Chopra A, Nafissi N, Polacheck WJ, Benson CC, Swist S, Gorham J, Yang L, Schafer S, Sheng CC, Haghighi A, Homsy J, Hubner N, Church G, Cook SA, Linke WA, Chen CS, Seidman JG, Seidman CE. Titin mutations in iPS cells define sarcomere insufficiency as a cause of dilated cardiomyopathy. Science.  349(6251):982-6. 2015.

Hinson JT, Nakamura K, Wu SM. Induced pluripotent stem cell modeling of complex genetic diseases. Drug Discov Today Dis Models. 9(4):e147-e152. 2012.

Palmer BM, Wang Y, Teekakirikul P, Hinson JT, Fatkin D, Strouse S, Vanburen P, Seidman CE, Seidman JG, Maughan DW. Myofilament mechanical performance is enhanced by R403Q myosin in mouse myocardium independent of sex. Am J Physiol Heart Circ Physiol. 294(4):H1939-47.  2008.

Hinson JT, Fantin VR, Schönberger J, Breivik N, Siem G, McDonough B, Sharma P, Keogh I, Godinho R, Santos F, Esparza A, Nicolau Y, Selvaag E, Cohen BH, Hoppel CL, Tranebjaerg L, Eavey RD, Seidman JG, Seidman CE. Missense mutations in the BCS1L gene as a cause of the Björnstad syndrome. N Engl J Med. 356(8):809-19. 2007.

Klugherz BD, Song C, DeFelice S, Cui X, Lu Z, Connolly J, Hinson JT, Wilensky RL, Levy RJ. Gene delivery to pig coronary arteries from stents carrying antibody-tethered adenovirus. Hum Gene Ther. 13(3):443-54. 2002.

Williams PA, Tribble JR, Pepper KW, Cross SD, Morgan BP, Morgan JE, John SW, Howell GR (2016). Inhibition of the classical pathway of the complement cascade prevents early dendritic and synaptic degeneration in glaucoma. Mol Neurodegener. Apr 6;11:26.

Soto I, Grabowska WA, Onos KD, Graham LC, Jackson HM, Simeone SN, Howell GR (2016). Meox2 haploinsufficiency increases neuronal cell loss in a mouse model of Alzheimer's disease. Neurobiol Aging. Jun;42:50-60.

Williams PA, Harder JM, Foxworth NE, Cochran KE, Philip VM, Porciatti V, Smithies O,  John SWM.  Vitamin B3 modulates mitochondrial vulnerability and prevents glaucoma in aged mice. Science. 355(6326):756-760. 2017.

Harder JM, Braine CE, Williams PA, Zhu X, MacNicoll KH, Sousa GL, Buchanan RA, Smith RS, Libby RT, Howell GR*, John SWM. Early immune responses are independent of RGC dysfunction in glaucoma with complement component C3 being protective. Proc Natl Acad Sci U S A  114(19):E3839-E3848. 2017.   

Williams PA, Harder JM, Foxworth NE, Cardoza BH, Cochran KE, John SWM. Nicotinamide and WLDS act together to prevent neurodegeneration in glaucoma. Front Neurosci  11:232. 2017. 

Kizhatil K, Ryan M, Marchant J, Henrich S, John SWM. Schlemm’s canal is a unique vessel with a combination of blood vascular and lymphatic phenotypes that forms by a novel developmental process. PloS Biol 12(7):e1001912. 2014. 

Kizhatil K, Chlebowski A, Tolman N, Freeburg N, Shaw N, Ryan M, Marchant J, John SWM.  An in vitro perfusion system to enhance outflow studies in mouse eyes. Invest Ophthalmol Vis Sci 1;57(13):5207-5215. 2016. 

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Kotzin JJ, Spencer SP, McCright SJ, Kumar DB, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CC, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J., The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan, Nature. 537(7619):239-243, 2016.

Calabro S, Liu D, Gallman A, Nascimento MS, Yu Z, Zhang TT, Chen P, Zhang B, Xu L, Gowthaman U, Krishnaswamy JK, Haberman AM, Williams A, Eisenbarth SC., Differential Intrasplenic Migration of Dendritic Cell Subsets Tailors Adaptive Immunity., Cell reports. 16(9):2472-85, 2016.

Williams A, Henao-Mejia J, Flavell RA. Editing the Mouse Genome Using the CRISPR-Cas9 System. Cold Spring Harb Protoc. 2016(2):pdb.top087536, 2016.

Krishnaswamy JK, Singh A, Gowthaman U, Wu R, Gorrepati P, Sales Nascimento M, Gallman A, Liu D, Rhebergen AM, Calabro S, Xu L, Ranney P, Srivastava A, Ranson M, Gorham JD, McCaw Z, Kleeberger SR, Heinz LX, Müller AC, Bennett KL, Superti-Furga G, Henao-Mejia J, Sutterwala FS, Williams A, Flavell RA, Eisenbarth SC. Coincidental loss of DOCK8 function in NLRP10-deficient and C3H/HeJ mice results in defective dendritic cell migration. Prov Natl Acad Sci USA. 112(10):3056-61, 2015.

Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L5, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 21(2):198-206, 2014.

Williams A, Lee GR, Spilianakis CG, Hwang SS, Eisenbarth SC, Flavell RA. Hypersensitive site 6 of the Th2 locus control region is essential for Th2 cytokine expression. Proc Natl Acad Sci USA. 10(17):6955-60, 2013.

Williams A, Henao-Mejia J, Harman CC, Flavell RA. miR-181 and metabolic regulation in the immune system. Cold Spring Harb Symp Quant Biol. 78:223-30, 2013.

Henao-Mejia J, Williams A, Goff LA, Staron M, Licona-Limón P, Kaech SM, Nakayama M, Rinn JL, Flavell RA. The microRNA miR-181 is a critical cellular metabolic rheostat essential for NKT cell ontogenesis and lymphocyte development and homeostasis. Immunity. 38(5):984-97, 2013.

Hou G, Smith AG, Zhang ZW.   Lack of intrinsic GABAergic connections in the thalamic reticular nucleus of the mouse.  J. Neurosci.  36(27): 7246-52, 2016.

Zhang W, Peterson M, Beyer B, Frankel W, Zhang ZW.  Loss of MeCP2 from the forebrain excitatory neurons leads to cortical hyperexcitation and seizures.  J. Neurosci. 34(7): 2754-63, 2014.