Publications by Year

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A transcriptional and metabolic signature of primary aneuploidy is present in chromosomally-unstable cancer cells and informs clinical prognosis

Jason M. Sheltzer; Published Online First September 16, 2013; doi: 10.1158/0008-5472.CAN-13-0749


Nfix is a novel regulator of murine hematopoietic stem and progenitor cell survival

Per Holmfeldt, Jennifer Pardieck, Anjelica C. Saulsberry, Satish Kumar Nandakumar, David Finkelstein, John T. Gray, Derek A. Persons, and Shannon McKinney-Freeman; Blood First Edition Paper, prepublished online September 16, 2013; DOI 10.1182/blood-2013-04-493973


Evidence for differential alternative splicing in blood of young boys with autism spectrum disorders

Boryana S Stamova, Yingfang Tian, Christine W Nordahl, Mark D Shen, Sally Rogers, David G Amaral and Frank R Sharp; Stamova et al. Molecular Autism 2013, 4:30 doi:10.1186/2040-2392-4-30


A map of cell type-specific auxin responses

Bastiaan O R Bargmann, Steffen Vanneste, Gabriel Krouk, Tal Nawy, Idan Efron, Eilon Shani, Goh Choe; Molecular Systems Biology 9 Article number: 688;doi:10.1038/msb.2013.40 Published online: 10 September 2013


Chordoma Low-Template Microarray Analysis

Julia Feichtinger, Amin El-Heliebi, Thomas Kroneis, Karin Wagner, Bernadette Liegl-Atzwanger, Andreas Leithner, Gerhard G. Thallinger, and Beate Rinner; Biomedical Engineering / Biomedizinische Technik. Pages 1862-278X, ISSN (Print) 0013-5585, DOI:10.1515/bmt-2013-4310, September 2013


Downstream Signaling Pathways in Mouse Adipose Tissues Following Acute In Vivo Administration of Fibroblast Growth Factor 21

Muise ES, Souza S, Chi A, Tan Y, Zhao X, et al. PLoS ONE 8(9): e73011. doi:10.1371/journal.pone.0073011


Ubiquitin-specific protease 2-69 in macrophages potentially modulates metainflammation

Hiroshi Kitamura, Shunsuke Kimura, Yoshinori Shimamoto, Jun Okabe, Masatoshi Ito, Tomomi Miyamoto, Yoshinori Naoe, Chisato Kikuguchi, Bob Meek, Chitoku Toda, Shiki Okamoto, Katsushi Kanehira, Koji Hase, Hiroshi Watarai, Mayumi Ishizuka, Assam El-Osta, Osamu Ohara and Ichiro Miyoshi: Published online before print September 4, 2013, doi: 10.1096/fj.13-233528


Effects of Pleiotrophin Overexpression on Mouse Skeletal Muscles in Normal Loading and in Actual and Simulated Microgravity

Camerino GM, Pierno S, Liantonio A, De Bellis M, Cannone M, et al. PLoS ONE 8(8): e72028. doi:10.1371/journal.pone.0072028


Sex-specific control of CNS autoimmunity by p38 MAPK signaling in myeloid cells

Krementsov, Dimitry N., Noubade, Rajkumar, Dragon, Julie A., Otsu, Kinya, Rincon, Mercedes, Teuscher, Cory; Ann Neurol.1531-8249 10.1002/ana.24020


Whole transcriptome RNA-Seq allelic expression in human brain

Ryan M Smith, Amy Webb, Audrey C Papp, Leslie C Newman, Samuel K Handelman, Adam Suhy, Roshan Mascarenhas, John Oberdick and Wolfgang Sadee; BMC Genomics 2013, 14:571 doi:10.1186/1471-2164-14-571


Isolation and molecular characterization of Fikirini rhabdovirus, a novel virus from a Kenya bat.

Kading RC, Gilbert AT, Mossel EC, Crabtree MB, Kuzmin IV, Niezgoda M, Agwanda B, Markotter W, Weil MR, Montgomery JM, Rupprecht CE, Miller BR.J Gen Virol. 2013 Aug 12. Epub ahead of print PMID:23939976 [PubMed - as supplied by publisher]


Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways

Taylor CM, Wang Q, Rosa BA, Huang SC-C, Powell K, et al. (2013) Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways. PLoS Pathog 9(8): e1003505. doi:10.1371/journal.ppat.1003505


Increased ID2 Levels in Adult Precursor B Cells as Compared with Children Is Associated with Impaired Ig Locus Contraction and Decreased Bone Marrow Output

Kristin Jensen, Magdalena B. Rother, Berit Sletbakk Brusletto, Ole K. Olstad, Hans Christian Dalsbotten Aass, Menno C. van Zelm, Peter Kierulf and Kaare M. Gautvik, The Journal of Immunology, August 1, 2013, vol. 191 no. 3 1210-1219,nbsp; doi: 10.4049/jimmunol.1203462


Oxidative Damage to Rhesus Macaque Spermatozoa Results in Mitotic Arrest and Transcript Abundance Changes in Early Embryos

Victoria Burruel, Katie L. Klooster, James Chitwood, Pablo J. Ross and Stuart A. Meyers; Biology of Reproduction July 31, 2013 biolreprod.113.110981


Transcriptional Profiling of mRNAs and microRNAs in Human Bone Marrow Precursor B Cells Identifies Subset- and Age-Specific Variations

Jensen K, Brusletto BS, Aass HCD, Olstad OK, Kierulf P, et al. (2013) Transcriptional Profiling of mRNAs and microRNAs in Human Bone Marrow Precursor B Cells Identifies Subset- and Age-Specific Variations. PLoS ONE 8(7): e70721. doi:10.1371/journal.pone.0070721


Orchestrating osteogenic differentiation of mesenchymal stem cells – identification of placental growth factor as a mechanosensitive gene with a pro-osteogenic role

McCoy R.J. Eng.D, Widaa A. Ph.D, Watters K.M. Ph.D, Wuerstle M.,Stallings R. L. Ph.D, Duffy G. P. Ph.D, O'Brien F.J. Ph.D; DOI:10.1002/stem.1482


A novel method to predict regulatory regions based on histone mark landscapes in macrophages

G Nagy, B Daniel, D Jonas, L Nagy, E Barta - Immunobiology, 2013


Microarray characterization of gene expression changes in blood during acute ethanol exposure

DM Kupfer, VL White, DL Strayer, DJ Crouch, D Burian - BMC Medical Genomics, 2013


Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803

H Zhu, X Ren, J Wang, Z Song, M Shi, J Qiao, X Tian- Biotechnology for Biofuels, 2013


Transcriptional analysis through RNA sequencing of giant cells induced by Meloidogyne graminicola in rice roots

Hongli Ji, Godelieve Gheysen, Simon Denil, Keith Lindsey, Jennifer F. Topping, Kamrun Nahar, Annelies Haegeman, Winnok H. De Vos, Geert Trooskens , Wim Van Criekinge, Tim De Meyer2 and Tina Kyndt


Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation inSynechocystis sp. PCC 6803

Huang Siqiang, Lei Chen, Rigen Te, Jianjun Qiao, Jiangxin Wang  and Weiwen Zhang  Mol. BioSyst., 2013, Accepted Manuscript DOI: 10.1039/C3MB70188C


T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling

Kristine Germar, Marei Dose, Tassos Konstantinou, Jiangwen Zhang, Hongfang Wang, Camille Lobry, Kelly L. Arnett, Stephen C. Blacklow, Iannis Aifantis, Jon C. Aster, and Fotini Gounari. PNAS, December 13, 2011, 108(50): 20060-20065. doi:10.1073/pnas.1110230108


Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling

Shihong Mao, Robert J. Goodrich, Russ Hauser, Steven M. Schrader ,Zhen Chen and Stephen A. Krawetz


Electroconvulsive seizure-induced changes in gene expression in the mouse hypothalamic paraventricular nucleus

Mari Sakaida, Mamiko Sukeno, Yuhki Imoto, Soken Tsuchiya, Yukihiko Sugimoto, Yasushi Okuno, Eri Segi-Nishida


Complement anaphylatoxin C3a is a potent inducer of embryonic chick retina regeneration

Tracy Haynes, Agustin Luz-Madrigal, Edimara S. Reis, Nancy P. Echeverri Ruiz, Erika Grajales-Esquivel, Apostolia Tzekou, Panagiotis A. Tsonis, John D. Lambris and Katia Del Rio-Tsonis


Identification of Biomarkers of Response to IFNg during Endotoxin Tolerance: Application to Septic Shock

Allantaz-Frager F, Turrel-Davin F, Venet F, Monnin C, De Saint Jean A, et al. (2013) Identification of Biomarkers of Response to IFNg during Endotoxin Tolerance: Application to Septic Shock. PLoS ONE 8(7): e68218. doi:10.1371/journal.pone.0068218


A Neurodegeneration-Specific Gene-Expression Signature of Acutely Isolated Microglia from an Amyotrophic Lateral Sclerosis Mouse Model

 Isaac M. Chiu, Emiko T.A. Morimoto, Hani Goodarzi, Jennifer T. Liao, Sean O’Keeffe, Hemali P. Phatnani, Michael Muratet, Michael C. Carroll, Shawn Levy, Saeed Tavazoie, Richard M. Myers, Tom Maniatis


Molecular profiling supports the role of epithelial-to-mesenchymal transition (EMT) in ovarian cancer metastasis

Loukia N Lili, Lilya V Matyunina , L DeEtte Walker, Stephen L Wells, Benedict B Benigno , John F McDonald  Journal of Ovarian Research 2013, 6:49 doi:10.1186/1757-2215-6-49


Molecular profiling supports the role of epithelial-to-mesenchymal transition (EMT) in ovarian cancer metastasis

Lili LN, Matyunina LV, Walker LD, Wells SL, Benigno BB, McDonald JF, J Ovarian Res. 2013 Jul 10;6(1):49. doi: 10.1186/1757-2215-6-49


Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias 

Rui Chen,Silvia Giliani,  Gaetana Lanzi, George I. Mias,Silvia Lonardi, Kerry Dobbs, John Manis, Hogune Im, Jennifer E. Gallagher, Douglas H. Phanstiel, Ghia Euskirchen, Philippe Lacroute, Keith Bettinger, Daniele Moratto, Katja Weinacht, Davide Montin, Eleonora Gallo, Giovanna Mangili, Fulvio Porta,  Lucia D. Notarangelo, Stefania Pedretti, Waleed Al-Herz,Wasmi Alfahdli,Anne Marie Comeau,Russell S. Traister, Sung-Yun Pai, Graziella Carella,Fabio Facchetti, Kari C. Nadeau, Michael Snyder, Luigi D. Notarangelo


Comprehensive high-resolution genomic profiling and cytogenetics of two pediatric and one adult medulloblastoma

Heidrun Holland, Li-Xin Xu , Peter Ahnert , Holger Kirsten, Ronald Koschny, Manfred Bauer, Ralf Schober, Jürgen Meixensberger, Wolfgang Krupp


A Systems Analysis Identifies a Feedforward Inflammatory Circuit Leading to Lethal Influenza Infection

Marlène Brandes,Frederick Klauschen, Stefan Kuchen, Ronald N. Germain


The genome sequence of the colonial chordate, Botryllus schlosseri

Voskoboynik A, Neff NF, Sahoo D, Newman AM, Pushkarev D, Koh W, Passarelli B, Fan HC, Mantalas GL, Palmeri KJ, Ishizuka KJ, Gissi C, Griggio F, Ben-Shlomo R, Corey DM, Penland L, White RA, Weissman IL, Quake SR.


The Role of Oxidative Stress in Nervous System Aging

Sims-Robinson C, Hur J, Hayes JM, Dauch JR, Keller PJ, et al. (2013) The Role of Oxidative Stress in Nervous System Aging. PLoS ONE 8(7): e68011. doi:10.1371/journal.pone.0068011


A multi-site feasibility study for personalized medicine in canines with Osteosarcoma

Noel R Monks, David M Cherba1, Steven G Kamerling, Heather Simpson, Anthony W Rusk, Derrick Carter, Emily Eugster, Marie Mooney, Robert Sigler, Matthew Steensma, Tessa Grabinski, Keith R Marotti and Craig P Webb doi:10.1186/1479-5876-11-158


Deep Sequencing of the Murine IghRepertoire Reveals Complex Regulation of Nonrandom V Gene Rearrangement Frequencies

Nancy M. Choi, Salvatore Loguercio, Jiyoti Verma-Gaur, Stephanie C. Degner,Ali Torkamani, Andrew I. Su, Eugene M. Oltz, Maxim Artyomov andAnn J. Feeney; The Journal of Immunology July 29, 2013 1301279


Cellular Metabolic Regulators: Novel Indicators of Low-Grade Inflammation in Humans

Haimovich, Beatrice PhD; Zhang, Zhiyong PhD; Calvano, Jacqueline E. MSc; Calvano, Steve E. PhD; Kumar, Ashwini BSc; Macor, Marie A. RN; Corbett, Siobhan MD; Coyle, Susette M. RN, MSN; Lowry, Stephen F. MD, MBA doi: 10.1097/SLA.0b013e31829a4352


The Time Course of Gene Expression during Reactive Gliosis in the Optic Nerve

Qu J, Jakobs TC (2013) The Time Course of Gene Expression during Reactive Gliosis in the Optic Nerve. PLoS ONE 8(6): e67094. doi:10.1371/journal.pone.0067094


Mesenchymal Stem/Progenitors and Other Endometrial Cell Types from Women with Polycystic Ovary Syndrome (PCOS) Display Inflammatory and Oncogenic Potential

TT Piltonen, J Chen, DW Erikson, TLB Spitzer, F Barragan, JT Rabban, H Huddleston,JC Irwin and LC Giudice


Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis)

Fabio A Vannucci, Douglas N Foster and Connie J Gebhart BMC Genomics 2013, 14:421 doi:10.1186/1471-2164-14-421


Progressive morphological changes and impaired retinal function associated with temporal regulation of gene expression after retinal ischemia/reperfusion injury in mice

Byung-Jin Kim, Terry A Braun, Robert J Wordinger and Abbot F Clark, Molecular Neurodegeneration 2013, 8:21 doi:10.1186/1750-1326-8-21


Lichen planopilaris is characterized by immune privilege collapse of the hair follicle's epithelial stem cell niche

Matthew J. Harries, Katja Meyer, Iskander Chaudhry, Jennifer Kloepper, Enrique Poblet, Christopher E. M. Griffiths,Ralf Paus DOI: 10.1002/path.4233


The Ubiquitin Ligase FBXW7 Modulates Leukemia-Initiating Cell Activity by Regulating MYC Stability

Bryan King,Thomas Trimarchi,Linsey Reavie,Luyao Xu,Jasper Mullenders,Panagiotis Ntziachristos,Beatriz Aranda-Orgilles,Arianne Perez-Garcia,Junwei Shi,Christopher Vakoc,Peter Sandy,Steven S. Shen,Adolfo Ferrando,Iannis Aifantis Cell, Volume 153, Issue 7, 1552-1566, 20 June 2013


Histone demethylase Lsd1 represses hematopoietic stem and progenitor cell signatures during blood cell maturation

Marc A Kerenyi, Zhen Shao, Yu-Jung Hsu, Guoji Guo, Sidinh Luc, Kassandra O'Brien, Yuko Fujiwara, Cong Peng, Minh Nguyen, Stuart H Orkin eLife 2013;2:e00633


Sexual dimorphisms in zonal gene expression in mouse liver

Kosuke Saito, Masahiko Negishi, E. James Squires


Isolation of a novel orthobunyavirus (Brazoran virus) with a 1.7 kb S segment that encodes a unique nucleocapsid protein possessing two putative functional domains

Robert S. Lanciotti, Olga I. Kosoy, Angela M. Bosco-Lauth, Jan Pohl Olga Stuchlik, Matthew Reed, Amy J. Lambert


Signal transduction involved in GnRH2-stimulation of identified LH-producing gonadotropes from lhb-GFP transgenic medaka (Oryzias latipes)

Strandabo RA, Hodne K, Ager-Wick E, Sand O, Weltzien FA, Haug TM., Mol Cell Endocrinol. 2013 Jun 15;372(1-2):128-39. doi: 10.1016/j.mce.2013.03.022. Epub 2013 Apr 3.


Dystrophin-deficient pigs provide new insights into the hierarchy of physiological derangements of dystrophic muscle

Nikolai Klymiuk, Andreas Blutke , Alexander Graf , Sabine Krause, Katinka Burkhardt, Annegret Wuensch, Stefan Krebs, Barbara Kessler, Valeri Zakhartchenko, Mayuko Kurome, Elisabeth Kemter, Hiroshi Nagashima, Benedikt Schoser, Nadja Herbach, Helmut Blum, Rüdiger Wanke, Annemieke Aartsma-Rus, Christian Thirion, Hanns Lochmüller, Maggie C. Walter and Eckhard Wolf


Mutations in KARS, Encoding Lysyl-tRNA Synthetase, Cause Autosomal-Recessive Nonsyndromic Hearing Impairment DFNB89

Regie Lyn P. Santos-Cortez, Kwanghyuk Lee, Zahid Azeem, Patrick J. Antonellis, Lana M. Pollock, Saadullah Khan, Irfanullah, Paula B. Andrade-Elizondo, Ilene Chiu, Mark D. Adams,Sulman Basit, Joshua D. Smith, University of Washington Center for Mendelian Genomics Deborah A. Nickerson, Brian M. McDermott Jr., Wasim Ahmad, Suzanne M. Leal


SAL-RNAs: Senescence-associated long non-coding RNAs

Kotb Abdelmohsen, Amaresh Panda, Min-Ju Kang, Jason Xu, Roza Selimyan,Je-Hyun Yoon, Jennifer L. Martindale, Supriyo De, William H. Wood, Kevin G. Becker, Myriam Gorospe DOI: 10.1111/acel.12115


Methods and Composition for Sample Identification

Abdueva, Diana ,Kennedy, Giulia C., Walsh, Sean P.


MIR-33 Inhibitors and Uses Thereof

Fernandez-hernando, Carlos ,Moore, Kathryn J. ,Suarez, Yajaira ,Rayner, Katey J.


Gene expression in the deep biosphere

William D. Orsi, Virginia P. Edgcomb, Glenn D. Christman & Jennifer F. Biddle  doi:10.1038/nature12230


Wnt activation in nail epithelium couples nail growth to digit regeneration

Makoto Takeo, Wei Chin Chou, Qi Sun, Wendy Lee, Piul Rabbani, Cynthia Loomis, M. Mark Taketo & Mayumi Ito doi:10.1038/nature12214


The epigenetic modifier Ubiquitin Specific Protease 22 (Usp22) regulates embryonic stem cell differentiation via transcriptional repression of Sex determining region Y-box 2 (Sox2)

Robyn T. Sussman, Timothy J. Stanek, Paul Esteso, John D. Gearhart, Karen E. Knudsen and Steven B. McMahon, jbc.M113.469783 doi: 10.1074/jbc.M113.469783


Returning to overuse activity following a supraspinatus and infraspinatus tear leads to joint damage in a rat model

Katherine E. Reuther, Stephen J. Thomas, Elisabeth F. Evans, Jennica J. Tucker, Joseph J. Sarver,Sarah Ilkhani-Pour,Chancellor F. Gray, Pramod B. Voleti, David L. Glaser, Louis J. Soslowsky


A Role for Hedgehog Signaling in the Differentiation of the Insertion Site of the Patellar Tendon in the Mouse

Liu C-F, Breidenbach A, Aschbacher-Smith L, Butler D, Wylie C (2013) A Role for Hedgehog Signaling in the Differentiation of the Insertion Site of the Patellar Tendon in the Mouse. PLoS ONE 8(6): e65411. doi:10.1371/journal.pone.0065411


A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples

Batty EM, Wong THN, Trebes A, Argoud K, Attar M, et al. (2013) A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples. PLoS ONE 8(6): e66129. doi:10.1371/journal.pone.0066129


Alternatively Spliced Tissue Factor Contributes to Tumor Spread and Activation of Coagulation in Pancreatic Ductal Adenocarcinoma

Dusten Unruh, Kevin Turner,Ramprasad Srinivasan ,Begüm Kocatürk, Xiaoyang Qi, Zhengtao Chu,Bruce J. Aronow, David R. Plas, Catherine A. Gallo, Holger Kalthoff, Daniel Kirchhofer, Wolfram Ruf, Syed A. Ahmad, Fred V. Lucas, Henri H. Versteeg, Vladimir Y. Bogdanov DOI: 10.1002/ijc.28327


Utilizing transcriptomics to identify mediators of pathogenesis in Shigella flexneri: characterization of intracellular growth regulator, icgR

Carolyn R. Morris, Christen L. Grassel, Julia C. Redman, Jason W. Sahl, Eileen M. Barry and David A. Rasko doi: 10.1128/IAI.00537-13


Characterization of Intracellular Growth Regulator icgR by Utilizing Transcriptomics To Identify Mediators of Pathogenesis in Shigella flexneri

Carolyn R. Morris, Christen L. Grassel, Julia C. Redman, Jason W. Sahl, Eileen M. Barry and David A. Rasko Published ahead of print 10 June 2013, doi: 10.1128/IAI.00537-13 Infect. Immun. September 2013 vol. 81 no. 9 3068-3076


Heat stress effects on the cumulus cells surrounding the bovine oocyte during maturation: altered matrix metallopeptidase 9 and progesterone production

Louisa A Rispoli, Rebecca R Payton, Cedric Gondro,Arnold M Saxton, Kimberly A Nagle, Brooke W Jenkins,F Neal Schrick and J Lannett Edwards


De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability

Anne Gregor, Martin Oti, Evelyn N. Kouwenhoven, Juliane Hoyer, Heinrich Sticht, Arif B. Ekici,Susanne Kjaergaard, Anita Rauch, Hendrik G. Stunnenberg,Steffen Uebe, Georgia Vasileiou, Andrea cute; Reis, Huiqing Zhou, Christiane Zweier


Selective suppression of endothelial cytokine production by progesterone receptor

Lauren M. Goddard, Amy N. Ton,Totilde Org, Hanna K.A. Mikkola, M. Luisa Iruela-Arispe; Vascular Pharmacology Vol. 59, Issues 1-2, July-August 2013, pg 36-43

 

Exon-level Expression Profiling of Ocular Tissues

Alex H. Wagner, V. Nikhil Anand, Wan-Heng Wang, Jon E. Chatterton, Duo Sun, Allan R. Shepard, Nasreen Jacobson, Iok-Hou Pang, Adam P. DeLuca, Thomas L. Casavant, Todd E. Scheetz, Robert F. Mullins, Terry A. Braun, Abbot F. Clark, Experimental Eye Research, Volume 111, June 2013, Pages 105-111, http://dx.doi.org/10.1016/j.exer.2013.03.004


The Absence of ER-β Results in Altered Gene Expression in Ovarian Granulosa Cells Isolated From In Vivo Preovulatory Follicles

April K. Binder, Karina F. Rodriguez, Katherine J. Hamilton, Patricia S. Stockton, Casey E. Reed and Kenneth S. Korach, Endocrinology June 1, 2013 vol. 154 no. 6 2174-2187


Genomic Signatures of Pregnancy-Associated Breast Cancer Epithelia and Stroma and their Regulation by Estrogens and Progesterone

Djuana M. E. Harvell, Jihye Kim, Jenean Orsquo Brien, Aik-Choon Tan, Virginia F. Borges, Pepper Schedin, Britta M. Jacobsen, Kathryn B. Horwitz, Hormones and Cancer June 2013, Volume 4, Issue 3, pp 140-153


Brain Region-Specific Transcriptomic Markers of Serotonin-1A Receptor Agonist Action Mediating Sexual Rejection and Aggression in Female Marmoset Monkeys

Aubert, Y., Allers, K. A., Sommer, B., de Kloet, E. R., Abbott, D. H. and Datson, N. A. (2013), Journal of Sexual Medicine, 10: 1461-1475. doi: 10.1111/jsm.12131


BreastPRS is a gene expression assay that stratifies intermediate-risk Oncotype DX patients into high-or low-risk for disease recurrence

D'Alfonso TM, van Laar RK, Vahdat LT, Hussain W, Flinchum R, Brown N, John LS, Shin SJ, Breast Cancer Res Treat. 2013 Jun;139(3):705-15. doi: 10.1007/s10549-013-2604-0


Increased ID2 Levels in Adult Precursor B Cells as Compared with Children Is Associated with Impaired Ig Locus Contraction and Decreased Bone Marrow Output

Kristin Jensen, Magdalena B. Rother, Berit Sletbakk Brusletto,Ole K. Olstad, Hans Christian Dalsbotten Aass, Menno C. van Zelm,Peter Kierulf and Kaare M. Gautvik


Fibroblast Growth Factor-1 is a mesenchymal stromal cell secreted factor stimulating proliferation of osteoarthritic chondrocytes in co-culture

Ling Wu, Jeroen Leijten, Clemens A. van Blitterswijk, and Marcel Karperien, Stem Cells and Development. -Not available-, ahead of print. doi:10.1089/scd.2013.0118.


The presence, role and clinical use of spermatozoal RNAs

Meritxell Jodar, Sellappan Selvaraju, Edward Sendler, Michael P. Diamond, Stephen A. Krawetz


Transcriptional Dissection of Human Limbal Niche Compartments by Massive Parallel Sequencing

Bath C, Muttuvelu D, Emmersen J, Vorum H, Hjortdal J, et al. (2013) Transcriptional Dissection of Human Limbal Niche Compartments by Massive Parallel Sequencing. PLoS ONE 8(5): e64244. doi:10.1371/journal.pone.0064244


In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue

Hjelm BE, Salhia B, Kurdoglu A, Szelinger S, Reiman RA, Sue LI, Beach TG, Huentelman MJ, Craig DW,Hum Mol Genet. 2013 May 21.


Comparative analysis of RNA sequencing methods for degraded or low-input samples

Adiconis X, Borges-Rivera D, Satija R, Deluca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ, Nat Methods. 2013 May 19. doi: 10.1038/nmeth.2483


Hoxa9 and Flt3 Signaling Synergistically Regulate an Early Checkpoint in Lymphopoiesis

Kimberly A. Gwin, Mariya B. Shapiro, Joseph J. Dolence, Zhixin L. Huang and Kay L. Medina


Fibrocytes represent a novel MDSC subset circulating in patients with metastatic cancer

Hua Zhang, Irena Maric, Michael J. DiPrima, Javed KhanRimas, J. OrentasRosandra, N. Kaplan and Crystal L. Mackall


Deletion of the NF-κB subunit p65/RelA in the hematopoietic compartment leads to defects in hematopoietic stem cell function

Sarah J. Stein and Albert S. Baldwin, Blood. 2013 Jun 20;121(25):5015-5024. Epub 2013 May 13.


Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

Juliana Marcolino-Gomes, Fabiana Aparecida Rodrigues, Maria Cristina Neves Oliveira, Jose Renato Boucas Farias, Norman Neumaier, Ricardo Vilela Abdelnoor, Francismar Corrêa Marcelino-Guimaraes, Alexandre Lima Nepomuceno, PLoS One. 2013 May 7;8(5):e62294. doi: 10.1371/journal.pone.0062294. Print 2013.


An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples

Marlene Thomas, Manuela Poignée-Heger, Martin Weisser, Stephanie Wessner and Anton Belousov, Journal of Clinical Bioinformatics 2013, 3:10


Reproducibility, fidelity, and discriminant validity of linear RNA amplification for microarray-based identification of major human enteric viruses

Haifeng Chen, Xuemei Chen, Yuan Hu, Huijun Yan, Applied Microbiology and Biotechnology, May 2013, Volume 97, Issue 9, pp 4129-4139


Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse Large B-Cell Lymphoma

Kim Linton, Christopher Howarth, Mark Wappett, Gillian Newton, Cynthia Lachel, Javeed Iqbal, Stuart Pepper, Richard Byers, Wing (John) Chan, John Radford, The Journal of Molecular Diagnostics, Volume 14, Issue 3, May-June 2012, Pages 223-232


Evaluation of Whole Transcriptome Amplification Methods by RNA-Seq

Karin Zueckert-Gaudenz, Jim Vallandingham, Brian Fleharty, Allison Peak,  Karen Staehling,  Anoja Perera and Hua Li; J Biomol Tech. 2013 May; 24(Suppl): S57–S58.


Effect of the Leptin Receptor Q223R Polymorphism on the Host Transcriptome following Infection with Entamoeba histolytica

Nicole M. Mackey-Lawrence, Xiaoti Guo, Daniel E. Sturdevant, Kimmo Virtaneva, Matthew M. Hernandez, Eric Houpt, Alan Sher, Stephen F. Porcella and William A. Petri Jr., Infect. Immun. May 2013 vol. 81 no. 5 1460-1470,  doi: 10.1128/IAI.01383-12


Visualizing the Transcriptome: A Comparison of Different RNA Library Preparation Methods

Xiaoping Su, Louis Ramagli, Hongli Tang, Erika Thompson, Kanhav Khanna; J Biomol Tech. 2013 May; 24(Suppl): S39-S40.


Patients with activated B-cell like diffuse large B-cell lymphoma in high and low infectious disease areas have different inflammatory gene signatures

Hogfeldt T, Bahnassy AA, Kwiecinska A, Osterborg A, Tamm KP, Porwit A, Zekri AR, Lundahl J, Khaled HM, Mellstedt H, Moshfegh A., Leuk Lymphoma. 2013 May;54(5):996-1003. doi: 10.3109/10428194.2012.738365. Epub 2012 Nov 8


Factors Expressed by Murine Embryonic Pancreatic Mesenchyme Enhance Generation of Insulin-Producing Cells From hESCs

Tingxia Guo, Limor Landsman, Na Li and Matthias Hebrok, Diabetes May 2013 vol. 62 no. 5 1581-1592, doi: 10.2337/db12-0167


Comparative effects of statins on murine cardiac gene expression profiles in normal mice

Kumazaki M, Ando H, Ushijima K, Fujimura A, Eur J Pharmacol. 2013 May 5;707(1-3):71-7. doi: 10.1016/j.ejphar.2013.03.022


Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium

Fabienne Meier-Abt, Emanuela Milani, Tim Roloff, Heike Brinkhaus, Stephan Duss, Dominique S Meyer, Ina Klebba, Piotr J Balwierz, Erik van Nimwegen and Mohamed Bentires-Alj, Breast Cancer Research 2013, 15:R36 doi:10.1186/bcr3419


Genome wide differences of gene expression associated with HLA-DRB1 genotype in multiple sclerosis: A pilot study

Apperson ML, Tian Y, Stamova B, Ander BP, Jickling GC, Agius MA, Sharp FR, J Neuroimmunol. 2013 Apr 15;257(1-2):90-6. doi: 10.1016/j.jneuroim.2013.02.004


Bleomycin Induces Molecular Changes Directly Relevant to Idiopathic Pulmonary Fibrosis: A Model for “Active” Disease

Ruoqi Peng, Sriram Sridhar, Gaurav Tyagi, Jonathan E. Phillips, Rosario Garrido, Paul Harris, Lisa Burns, Lorena Renteria, John Woods, Leena Chen, John Allard, Palanikumar Ravindran, Hans Bitter, Zhenmin Liang, Cory M. Hogaboam, Chris Kitson, David C. Budd, Jay S. Fine, Carla MT. Bauer, Christopher S. Stevenson, PLoS One. 2013;8(4):e59348. doi: 10.1371/journal.pone.0059348. Epub 2013 Apr 2.


Vascular disrupting activity and the mechanism of action of EHT 6706, a novel anticancer tubulin polymerization inhibitor

Anne-Sophie Belzacq-Casagrande, Florence Bachelot, Catherine De Oliveira, Severine Coutadeur, Florence Maurier-Mahe, Emeline Throo, Cedric Chauvignac, Laure Pognante, Angelique Petibon, Thierry Taverne, Investigational New Drugs April 2013, Volume 31, Issue 2, pp 304-319


Chronic rhinosinusitis with nasal polyps is characterized by B-cell inflammation and EBV-induced protein 2 expression

Kathryn E. Hulse, James E. Norton, Lydia Suh, Qiu Zhong, Mahboobeh Mahdavinia, Patrick Simon, Robert C. Kern, David B. Conley, Rakesh K. Chandra, Bruce K. Tan, Anju T. Peters, Leslie C. Grammer III, Kathleen E. Harris, Roderick G. Carter, Atsushi Kato, Robert P. Schleimer, Journal of Allergy and Clinical Immunology, Volume 131, Issue 4, April 2013, Pages 1075-1083.e7


In vitro culture of mouse embryos reduces differential gene expression between inner cell mass and trophectoderm

G. Giritharan, L. Delle Piane, A. Donjacour, F. J. Esteban, J. A. Horcajadas, E. Maltepe, P. Rinaudo, Reproductive Sciences March 2012 vol. 19 no. 3 243-252


MS risk genes are transcriptionally regulated in CSF leukocytes at relapse

Jernas M, Malmestrom C, Axelsson M, Olsson C, Nookaew I, Wadenvik H, Zetterberg H, Blennow K, Lycke J, Rudemo M, Olsson B, Mult Scler. 2013 Apr;19(4):403-10. Doi: 10.1177/1352458512455466


The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression

Kui-Ming Chan, Dong Fang, Haiyun Gan, Rintaro Hashizume,Chuanhe Yu, Mark Schroeder, Nalin Gupta, Sabine Mueller, C. David James, Robert Jenkins, Jann Sarkaria and Zhiguo Zhang; Genes & Development, 2013


The human placenta methylome

Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM, Proc Natl Acad Sci U S A. 2013 Apr 9;110(15):6037-42. doi: 10.1073/pnas.1215145110. Epub 2013 Mar 25.


Endothelial Cell Whole Genome Expression Analysis in a Mouse Model of Early-Onset Fuchs' Endothelial Corneal Dystrophy

Mario Matthaei, Jianfei Hu, Huan Meng, Eva-Maria Lackner, Charles G. Eberhart, Jiang Qian, Haiping Hao and Albert S. Jun, Invest. Ophthalmol. Vis. Sci. March 15, 2013 vol. 54 no. 3 1931-1940, doi: 10.1167/iovs.12-10898


Changes in Gene Expression of Pial Vessels of the Blood Brain Barrier during Murine Neurocysticercosis

Pramod Kumar Mishra, Judy M. Teale, PLoS Negl Trop Dis. 2013 Mar;7(3):e2099. doi: 10.1371/journal.pntd.0002099. Epub 2013 Mar 14.


MicroRNA regulate immunological pathways in T-cells in immune thrombocytopenia (ITP)

Margareta Jernas, Intawat Nookaew, Hans Wadenvik, and Bob Olsson, Blood March 14, 2013 vol. 121 no. 11 2095-2098, doi: 10.1182/blood-2012-12-471250


Differential regulatory T cell activity in HIV-1-exposed seronegative individuals

Dr. Laura Pattacini, Ms. Pamela M. Murnane, Dr. Erin M. Kahle, Dr. Michael J. Bolton, Dr. Jeffrey J. Delrow, Dr. Jairam Lingappa, Dr. Elly Katabira, Dr. Deborah Donnell, Dr. Julie McElrath, Dr. Jared M. Baeten, and Dr. Jennifer M. Lund. AIDS Research and Human Retroviruses. -Not available-, ahead of print. doi:10.1089/AID.2013.0075.


Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

Irene Aksoy, Ralf Jauch, Jiaxuan Chen, Mateusz Dyla, Ushashree Divakar, Gireesh K Bogu, Roy Teo, Calista Keow Leng Ng, Wishva Herath, Sun Lili, Andrew P Hutchins, Paul Robson, Prasanna R Kolatkar and Lawrence W Stanton, The EMBO Journal 32, 938 – 953, 8 March 2013, doi:10.1038, emboj.2013.31


Stability, delivery and functions of human sperm RNAs at fertilization

Edward Sendler, Graham D. Johnson, Shihong Mao, Robert J. Goodrich, Michael P. Diamond, Russ Hauser and Stephen A. Krawetz, Nucl. Acids Res. (2013) doi: 10.1093/nar/gkt132


Protection Afforded by an HIV Vaccine Candidate in Macaques Depends on the Dose of SIVmac251 at Challenge Exposure

Monica Vaccari, Brandon F. Keele, Steven E. Bosinger, Melvin N. Doster, Zhong-Min Ma, Justin Pollara, Anna Hryniewicz, Guido Ferrari, Yongjun Guan, Donald N. Forthal, David Venzon, Claudio Fenizia, Tia Morgan, David Montefiori, Jeffrey D. Lifson, Chris J. Miller, Guido Silvestri, Margherita Rosati, Barbara K. Felber, George N. Pavlakis, James Tartaglia and Genoveffa Franchini, J. Virol. March 2013 vol. 87 no. 6 3538-3548


Molecularly Enriched Pathways and Differentially Expressed Genes Distinguishing Cutaneous Squamous Cell Carcinoma From Pseudoepitheliomatous Hyperplasia

Ra, Seong H.; Su, Albert; Li, Xinmin; Binder, Scott, Diagnostic Molecular Pathology: March 2013 - Volume 22 - Issue 1 - p 41-47 doi: 10.1097/PDM.0b013e3182707894


Butyrophilin-like 2 Modulates B7 Costimulation To Induce Foxp3 Expression and Regulatory T Cell Development in Mature T Cells

Swanson RM, Gavin MA, Escobar SS, Rottman JB, Lipsky BP, Dube S, Li L, Bigler J, Wolfson M, Arnett HA, Viney JL, J Immunol. 2013 Mar 1;190(5):2027-35. doi: 10.4049/jimmunol.1201760


Zone-specific gene expression patterns in articular cartilage

Grogan, S. P., Duffy, S. F., Pauli, C., Koziol, J. A., Su, A. I., D'Lima, D. D. and Lotz, M. K. (2013), Zone-specific gene expression patterns in articular cartilage. Arthritis & Rheumatism, 65: 418 428. doi: 10.1002/art.37760


BMS-345541 Sensitizes MCF-7 Breast Cancer Cells to Ionizing Radiation by Selective Inhibition of Homologous Recombinational Repair of DNA Double-Strand Breaks

Lixian Wu, Lijian Shao, Manna Li, Junying Zheng, Junru Wang, Wei Feng, Jianhui Chang, Yan Wang, Martin Hauer-Jensen and Daohong Zhou, Radiat Res. 2013 Feb;179(2):160-70. doi: 10.1667/RR3034.1. Epub 2012 Dec 21.


Clonal progression of prostate cancers from Gleason grade 3 to grade 4

Adam G. Sowalsky, Huihui Ye, Glenn J. Bubley, and Steven P. Balk, Cancer Res February 1, 2013 73; 1050, doi: 10.1158/0008-5472.CAN-12-2799


Intrinsic Molecular Subtypes of Glioma Are Prognostic and Predict Benefit From Adjuvant Procarbazine, Lomustine, and Vincristine Chemotherapy in Combination With Other Prognostic Factors in Anaplastic Oligodendroglial Brain Tumors

Lale Erdem-Eraslan, Lonneke A. Gravendeel, Johan de Rooi, Paul H.C. Eilers, Ahmed Idbaih, Wim G.M. Spliet, Wilfred F.A. den Dunnen, Johannes L. Teepen, Pieter Wesseling, Peter A.E. Sillevis Smitt, Johan M. Kros, Thierry Gorlia, Martin J. van den Bent and Pim J. French, JCO January 20, 2013 vol. 31 no. 3 328-336


Allelic mRNA expression imbalance in C-type lectins reveals a frequent regulatory SNP in the human surfactant protein A (SP-A) gene

A K Azad, A Curtis, A Papp, A Webb, D Knoell, W Sadee and L S Schlesinger, Genes and Immunity (2013) 14, 99–106; doi:10.1038/gene.2012.61; published online 17 January 2013


Roles of Bmp4 during tooth morphogenesis and sequential tooth formation

Shihai Jia, Jing Zhou, Yang Gao, Jin-A Baek, James F. Martin, Yu Lan and Rulang Jiang, Development140, 423-432.


Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls

Ching Yong Yick, Aeilko H Zwinderman, Peter W Kunst, Katrien Grunberg, Thais Mauad, Annemiek Dijkhuisf, Elisabeth H Bel, Frank Baas, Rene Lutter and Peter J Sterk; Published online before print January 11, 2013 doi:10.1183/09031936.00115412 Published January 11, 2013


An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo

Meng How Tan, Kin Fai Au, Denise E Leong, Kira Foygel, Wing H Wong, and Mylene WM Yaob, Mol Syst Biol. 2013; 9: 632.Published online 2013 January 8. doi: 10.1038, msb.2012.65


Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification

Christine M. Malboeuf, Xiao Yang, Patrick Charlebois, James Qu, Aaron M. Berlin, Monica Casali, Kendra N. Pesko, Christian L. Boutwell, John P. DeVincenzo, Gregory D. Ebel, Todd M. Allen, Michael C. Zody, Matthew R. Henn and Joshua Z. Levin, Nucl. Acids Res. (7 January 2013) 41 (1): e13. doi: 10.1093/nar/gks794


An efficient rRNA removal method for RNA sequencing in GC-rich bacteria

Clelia Peano, Alessandro Pietrelli, Clarissa Consolandi, Elio Rossi, Luca Petiti, Letizia Tagliabue,Gianluca De Bellis and Paolo Landini Peano et al.: An efficient rRNA removal method for RNA sequencing in GC-rich bacteria. Microbial Informatics and Experimentation 2013


Genomic Signatures of a Global Fitness Index in a Multi-Ethnic Cohort of Women

Rampersaud E, Nathanson L, Farmer J, Meshbane K, Belton RL, Dressen A, Cuccaro M, Musto A, Daunert S, Deo S, Hudson N, Vance JM, Seo D, Mendez A, Dykxhoorn DM, Pericak-Vance MA, Goldschmidt-Clermont PJ, Ann Hum Genet. 2013 Mar;77(2):147-57. doi: 10.1111/ahg.12006


Characterizing the Molecular Spatial and Temporal Field of Injury in Early-Stage Smoker Non–Small Cell Lung Cancer Patients after Definitive Surgery by Expression Profiling

Humam Kadara, Li Shen, Junya Fujimoto, Pierre Saintigny, Chi-Wan Chow, Wenhua Lang, Zuoming Chu, Melinda Garcia, Mohamed Kabbout, You-Hong Fan, Carmen Behrens, Diane A. Liu, Li Mao, J. Jack Lee, Kathryn A. Gold, Jing Wang, Kevin R. Coombes, Edward S. Kim, Waun Ki Hong, and Ignacio I. Wistuba, Cancer Prev Res January 2013 6; 8, doi: 10.1158/1940-6207.CAPR-12-0290




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