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1

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Basenko, Evelina, Pulman, Jane, Shanmugasundram, Achchuthan, Harb, Omar, Crouch, Kathryn, Starns, David, Warrenfeltz, Susanne, Aurrecoechea, Cristina, Stoeckert, Christian, Kissinger, Jessica, Roos, D

Journal:

Journal of Fungi

Year:

2018

Language:

english

File:

PDF, 13.00 MB

english, 2018

2

The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data : Report of a workshop on integration of anatomy ontologies, held at the MRC human genetics unit, Edinburgh, 7–8 April 2004

Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B. L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert Jr, Dunc

Journal:

Comparative and Functional Genomics

Year:

2004

Language:

english

File:

PDF, 148 KB

english, 2004

3

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

Oliveira, Francislon S, Brestelli, John, Cade, Shon, Zheng, Jie, Iodice, John, Fischer, Steve, Aurrecoechea, Cristina, Kissinger, Jessica C, Brunk, Brian P, Stoeckert, Christian J, Fernandes, Gabriel

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 3.04 MB

english, 2018

4

Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis

Held, Matthew A., Greenfest-Allen, Emily, Jachimowicz, Edward, Stoeckert, Christian J., Stokes, Matthew P., Wood, Antony W., Wojchowski, Don M.

Journal:

Experimental Hematology

Year:

2020

File:

PDF, 3.36 MB

2020

5

LKB1 Regulates Pancreatic β Cell Size, Polarity, and Function

Zvi Granot, Avital Swisa, Judith Magenheim, Miri Stolovich-Rain, Wakako Fujimoto, Elisabetta Manduchi, Takashi Miki, Jochen K. Lennerz, Christian J. Stoeckert Jr., Oded Meyuhas, Susumu Seino, M. Alan

Journal:

Cell Metabolism

Year:

2009

Language:

english

File:

PDF, 3.46 MB

english, 2009

6

Functional Genomics of the β-Cell: Short-Chain 3-Hydroxyacyl-Coenzyme A Dehydrogenase Regulates Insulin Secretion Independent of K + Currents

Hardy, Olga T., Hohmeier, Hans E., Becker, Thomas C., Manduchi, Elisabetta, Doliba, Nicolai M., Gupta, Rana K., White, Peter, Stoeckert, Christian J., Matschinsky, Franz M., Newgard, Christopher B., K

Journal:

Molecular Endocrinology

Year:

2007

Language:

english

File:

PDF, 195 KB

english, 2007

7

The MGED ontology: a framework for describing functional genomics experiments

Christian J. Stoeckert Jr, Helen Parkinson

Journal:

Comparative and Functional Genomics

Year:

2003

Language:

english

File:

PDF, 122 KB

english, 2003

8

Top-down standards will not serve systems biology

Quackenbush, John, Stoeckert, Christian, Ball, Catherine, Brazma, Alvis, Gentleman, Robert, Huber, Wolfgang, Irizarry, Rafael, Salit, Marc, Sherlock, Gavin, Spellman, Paul

Journal:

Year:

2006

Language:

english

File:

PDF, 120 KB

english, 2006

9

OBIB-a novel ontology for biobanking

Brochhausen, Mathias, Zheng, Jie, Birtwell, David, Williams, Heather, Masci, Anna Maria, Ellis, Helena Judge, Stoeckert, Christian J.

Journal:

Journal of Biomedical Semantics

Year:

2016

Language:

english

File:

PDF, 1.40 MB

english, 2016

10

Clustering of genes into regulons using integrated modeling-COGRIM

Guang Chen, Shane T Jensen, Christian J Stoeckert Jr

Journal:

Year:

2007

Language:

english

File:

PDF, 946 KB

english, 2007

11

Spatial phenotyping of the endocardial endothelium as a function of intracardiac hemodynamic shear stress

McCormick, Margaret E., Manduchi, Elisabetta, Witschey, Walter R.T., Gorman, Robert C., Gorman, Joseph H., Jiang, Yi-Zhou, Stoeckert, Christian J., Barker, Alex J., Yoon, Samuel, Markl, Michael, Davie

Journal:

Journal of Biomechanics

Year:

2016

Language:

english

File:

PDF, 2.00 MB

english, 2016

12

Microarray databases: standards and ontologies

Stoeckert, Christian J., Causton, Helen C., Ball, Catherine A.

Journal:

Nature Genetics

Year:

2002

Language:

english

File:

PDF, 483 KB

english, 2002

13

Assessing the Significance of Conserved Genomic Aberrations Using High Resolution Genomic Microarrays

Guttman, Mitchell, Mies, Carolyn, Dudycz-Sulicz, Katarzyna, Diskin, Sharon J., Baldwin, Don A., Stoeckert, Christian J., Grant, Gregory R.

Journal:

Year:

2007

Language:

english

File:

PDF, 5.19 MB

english, 2007

14

Differential DNA methylation patterns of athero-susceptible and protected endothelial phenotypes in vivo: epigenomic code in arterial endothelial methylome

Jiang, Yi-Zhou, Manduchi, Elisabetta, Stoeckert, Christian J., Davies, Peter F.

Journal:

Atherosclerosis

Year:

2014

Language:

english

File:

PDF, 53 KB

english, 2014

15

Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming

Clayton, Hannah W., Osipovich, Anna B., Stancill, Jennifer S., Schneider, Judsen D., Vianna, Pedro G., Shanks, Carolyn M., Yuan, Weiping, Gu, Guoqiang, Manduchi, Elisabetta, Stoeckert, Christian J., M

Journal:

Year:

2016

Language:

english

File:

PDF, 6.06 MB

english, 2016

16

Plasmodium research in the postgenomic era

Manoj Duraisingh, Michael T. Ferdig, Christian J. Stoeckert, Sarah K. Volkman, Victoria P. McGovern

Journal:

Trends in Parasitology

Year:

2006

Language:

english

File:

PDF, 89 KB

english, 2006

17

Histone positions within the nucleosome using platinum labeling and the scanning transmission electron microscope

Christian J. Stoeckert Jr, Michael Beer, J.Wendell Wiggins, John C. Wierman

Journal:

Journal of Molecular Biology

Year:

1984

Language:

english

File:

PDF, 5.91 MB

english, 1984

18

NIA GENETICS OF ALZHEIMER’S DISEASE DATA STORAGE SITE (NIAGADS): ALZHEIMER’S GENOMICS DATABASE

Greenfest-Allen, Emily, Gangadharan, Prabhakaran, Kuzma, Amanda B., Leung, Yuk Yee, Qu, Liming, Valladares, Otto, Stoeckert, Christian J., Wang, Li-San

Journal:

Alzheimer's & Dementia

Year:

2018

File:

PDF, 123 KB

2018

19

A novel tool for standardizing clinical data in a semantically rich model

Freedman, Hayden G., Williams, Heather, Miller, Mark A., Birtwell, David, Mowery, Danielle L., Stoeckert, Christian J.

Journal:

Journal of Biomedical Informatics: X

Year:

2020

File:

PDF, 3.11 MB

2020

20

Wrestling with SUMO and bio-ontologies

Stoeckert, Christian, Ball, Catherine, Brazma, Alvis, Brinkman, Ryan, Causton, Helen, Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Heiskanen, Mervi, Holstege, Frank

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 146 KB

english, 2006

21

Common Objects: Think Global, Act Local

Stoeckert, Christian J.

Journal:

Omics A Journal of Integrative Biology

Year:

2003

Language:

english

File:

PDF, 43 KB

english, 2003

22

SY 15-2 ENDOTHELIAL EPIGENETICS AND ITS ROLE IN MEDIATING BIOMECHANICAL STRESS OF HYPERTENSION

Davies, Peter F., Manduchi, Elisabetta, Stoeckert, Christian J., Jiang, Yi-Zhou

Journal:

Journal of Hypertension

Year:

2016

Language:

english

File:

PDF, 49 KB

english, 2016

23

Annotation-based meta-analysis of microarray experiments

Zheng, Jie, Liu, Junmin, Manduchi, Elisabetta, Stoeckert,, Christian

Journal:

Bioentrepreneur

Year:

2009

Language:

english

File:

PDF, 66 KB

english, 2009

24

Minimum information about a functional genomics experiment: the state of microarray standards and their extension to other technologies

Christian J Stoeckert Jr., John Quackenbush, Alvis Brazma, Catherine A Ball

Journal:

Drug Discovery Today: TARGETS

Year:

2004

Language:

english

File:

PDF, 418 KB

english, 2004

25

Osmium-labeled polysaccharides for atomic microscopy

James Resch, David Tunkel, Christian Stoeckert, Michael Beer

Journal:

Journal of Molecular Biology

Year:

1980

Language:

english

File:

PDF, 3.99 MB

english, 1980

26

IMMUNOMODULATION OF PANCREATIC ISLET ALLOGRAFTS IN MICE WITH CTLA4Ig SECRETING MUSCLE CELLS

CHAHINE, A. ALFRED, YU, MING, MCKERNAN, MELISSA M., STOECKERT, CHRISTIAN, LAU, HENRY T.

Journal:

Transplantation Journal

Year:

1995

File:

PDF, 2.00 MB

1995

27

Emerging topic: Flow-related epigenetic regulation of endothelial phenotype through DNA methylation

Davies, Peter F., Manduchi, Elisabetta, Stoeckert, Christian J., Jiménez, Juan M., Jiang, Yi-Zhou

Journal:

Vascular Pharmacology

Year:

2014

Language:

english

File:

PDF, 764 KB

english, 2014

28

Molecular Analysis of Deletion and Nondeletion Hereditary Persistence of Fetal Hemoglobin and Identification of a New Mutation Causing β-Thalassemia

ELISE A. FEINGOLD, FRANCIS S. COLLINS, JAMES E. METHERALL, CHRISTIAN J. STOECKERT JR., SHERMAN M. WEISSMAN, BERNARD G. FORGET

Journal:

Annals of the New York Academy of Sciences

Year:

1985

Language:

english

File:

PDF, 587 KB

english, 1985

29

Integrated Regional Cardiac Hemodynamic Imaging and RNA Sequencing Reveal Corresponding Heterogeneity of Ventricular Wall Shear Stress and Endocardial Transcriptome

McCormick, Margaret E., Manduchi, Elisabetta, Witschey, Walter R. T., Gorman, Robert C., Gorman, Joseph H., Jiang, Yi‐Zhou, Stoeckert, Christian J., Barker, Alex J., Markl, Michael, Davies, Peter F.

Journal:

Journal of the American Heart Association

Year:

2016

Language:

english

File:

PDF, 4.56 MB

english, 2016

30

Renal Gene and Protein Expression Signatures for Prediction of Kidney Disease Progression

Wenjun Ju, Felix Eichinger, Markus Bitzer, Jun Oh, Shannon McWeeney, Celine C. Berthier, Kerby Shedden, Clemens D. Cohen, Anna Henger, Stefanie Krick, Jeffrey B. Kopp, Christian J. Stoeckert Jr., Stev

Journal:

The American Journal of Pathology

Year:

2009

Language:

english

File:

PDF, 2.86 MB

english, 2009

31

Annotation-based meta-analysis of microarray experiments

Zheng, Jie, Liu, Junmin, Manduchi, Elisabetta, Stoeckert,, Christian

Journal:

Bioentrepreneur

Year:

2009

File:

PDF, 66 KB

2009

32

PlasmoDB v5: new looks, new genomes

Christian J. Stoeckert Jr, Steve Fischer, Jessica C. Kissinger, Mark Heiges, Cristina Aurrecoechea, Bindu Gajria, David S. Roos

Journal:

Trends in Parasitology

Year:

2006

Language:

english

File:

PDF, 1.17 MB

english, 2006

33

Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet

Anthony G. Passerini, Congzhu Shi, Nadeene M. Francesco, Peiying Chuan, Elisabetta Manduchi, Gregory R. Grant, Christian J. Stoeckert Jr., John W. Karanian, Diane Wray-Cahen, William F. Pritchard, Pet

Journal:

Biochemical and Biophysical Research Communications

Year:

2005

Language:

english

File:

PDF, 539 KB

english, 2005

34

Desmin/Vimentin Intermediate Filaments Are Dispensable for Many Aspects of Myogenesis

Thomas Schultheiss, Zhongxiang Lin, Harunori Ishikawa, Iris Zamir, Christian J. Stoeckert and Howard Holtzer

Journal:

The Journal of Cell Biology

Year:

1991

Language:

english

File:

PDF, 6.83 MB

english, 1991

35

Bayesian Variable Selection and Data Integration for Biological Regulatory Networks

Shane T. Jensen, Guang Chen and Christian J. Stoeckert, Jr.

Journal:

The Annals of Applied Statistics

Year:

2007

Language:

english

File:

PDF, 1.98 MB

english, 2007

36

Computational Analysis of Constraints on Noncoding Regions, Coding Regions and Gene Expression in Relation to Plasmodium Phenotypic Diversity

Essien, Kobby, Hannenhalli, Sridhar, Stoeckert, Christian J., Hide, Winston

Journal:

Year:

2008

Language:

english

File:

PDF, 572 KB

english, 2008

37

Partial repression of human γ-globin genes by LCR element HS3 when linked to β-globin genes and LCR element HS2 in MEL cells

Stoeckert, Christian J., Cheng, Hui

Journal:

American Journal of Hematology

Year:

1996

Language:

english

File:

PDF, 855 KB

english, 1996

38

FasL — Too much of a good thing?

Lau, Henry T., Stoeckert, Christian J.

Journal:

Nature Medicine

Year:

1997

File:

PDF, 279 KB

1997

39

Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo

Jiang, Yi-Zhou, Manduchi, Elisabetta, Stoeckert, Christian J., Davies, Peter F.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.78 MB

english, 2015

40

SPIE Proceedings [SPIE BiOS 2001 The International Symposium on Biomedical Optics - San Jose, CA (Saturday 20 January 2001)] Microarrays: Optical Technologies and Informatics - RAD (RNA abundance database): an infrastructure for array data analysis

Manduchi, Elisabetta, Pizarro, Angel, Stoeckert, Jr., Christian, Bittner, Michael L., Chen, Yidong, Dorsel, Andreas N., Dougherty, Edward R.

Year:

2001

Language:

english

File:

PDF, 256 KB

english, 2001

41

Molecular Diagnosis of Kidney Transplant Failure by the Urine

Wiesener, Antje, Knaup, Karl X., Büttner‐Herold, Maike, Dieterle, Anne, Stoeckert, Johanna, Riedl, Bernhard, Morath, Christian, Wald, Alexandra, Vondran, Florian, Braun, Felix, Schödel, Johannes, Schu

Journal:

American Journal of Transplantation

Year:

2019

File:

PDF, 13.88 MB

2019

42

Much room for improvement in deposition rates of expression microarray datasets

Steffen, David L, Ochsner, Scott A, Stoeckert, Christian J, McKenna, Neil J

Journal:

Year:

2008

Language:

english

File:

PDF, 111 KB

english, 2008

43

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

Dugan, Vivien G., Emrich, Scott J., Giraldo-Calderón, Gloria I., Harb, Omar S., Newman, Ruchi M., Pickett, Brett E., Schriml, Lynn M., Stockwell, Timothy B., Stoeckert, Christian J., Sullivan, Dan E.,

Journal:

Year:

2014

Language:

english

File:

PDF, 868 KB

english, 2014

44

Erratum: Much room for improvement in deposition rates of expression microarray datasets

Ochsner, Scott A, Steffen, David L, Stoeckert Jr, Christian J, McKenna, Neil J

Journal:

Year:

2009

Language:

english

File:

PDF, 67 KB

english, 2009

45

Maturation and developmental stage-related changes in fetal globin gene expression are reproduced in transiently transfected primary adult human erythroblasts

Hong Ni, Xu-Dong Yang, Christian J Stoeckert Jr.

Journal:

Experimental Hematology

Year:

1999

Language:

english

File:

PDF, 436 KB

english, 1999

46

Dual Lineage-Specific Expression of Sox17 During Mouse Embryogenesis

Eunyoung Choi, Marine R-C. Kraus, Laurence A. Lemaire, Momoko Yoshimoto, Sasidhar Vemula, Leah A. Potter, Elisabetta Manduchi, Christian J. Stoeckert Jr., Anne Grapin-Botton, Mark A. Magnuson

Journal:

Year:

2012

Language:

english

File:

PDF, 1.35 MB

english, 2012

47

The myosin filament XV assembly: contributions of 195 residue segments of the myosin rod and the eight C-terminal residues

Prokash K. Chowrashi, Suzanne M. Pemrick, Shuixing Li, Peng Yi, Tom Clarke, Beth Maguire, Gereon Ader, Pierre Saintigny, Balraj Mittal, Manu Tewari, Christian Stoeckert, Hansell H. Stedman, James E. S

Journal:

Journal of Muscle Research and Cell Motility

Year:

1996

Language:

english

File:

PDF, 2.02 MB

english, 1996

48

Nia genetics of Alzheimer’s disease data storage site (NIAGADS): 2015 update

Partch, Amanda B., Laufer, Daniel, Valladares, Otto, Iodice, John, Greenfest-Allen, Emily, Childress, Daniel Micah, Malamon, John, Gangadharan, Prabhakaran, Arnold, Steven E., Stoeckert, Christian J.,

Journal:

Alzheimer's & Dementia

Year:

2015

Language:

english

File:

PDF, 50 KB

english, 2015

49

Functional genomics databases on the web

Christian J. Stoeckert Jr

Journal:

Cellular Microbiology

Year:

2005

Language:

english

File:

PDF, 249 KB

english, 2005

50

Conservation and divergence of known apicomplexan transcriptional regulons

Kobby Essien, Christian J Stoeckert

Journal:

Year:

2010

Language:

english

File:

PDF, 1.89 MB

english, 2010

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