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1

Computational solutions to large-scale data management and analysis

Schadt, Eric E., Linderman, Michael D., Sorenson, Jon, Lee, Lawrence, Nolan, Garry P.

Journal:

Nature Reviews Genetics

Year:

2010

Language:

english

File:

PDF, 1.61 MB

english, 2010

2

Genetics of gene expression surveyed in maize, mouse and man

Schadt, Eric E., Monks, Stephanie A., Drake, Thomas A., Lusis, Aldons J., Che, Nam, Colinayo, Veronica, Ruff, Thomas G., Milligan, Stephen B., Lamb, John R., Cavet, Guy

Journal:

Year:

2003

Language:

english

File:

PDF, 383 KB

english, 2003

3

The changing privacy landscape in the era of big data

Journal:

Molecular Systems Biology

Year:

2012

Language:

english

File:

PDF, 779 KB

english, 2012

4

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

Beaulaurier, John, Zhang, Xue-Song, Zhu, Shijia, Sebra, Robert, Rosenbluh, Chaggai, Deikus, Gintaras, Shen, Nan, Munera, Diana, Waldor, Matthew K., Chess, Andrew, Blaser, Martin J., Schadt, Eric E., F

Journal:

Nature Communications

Year:

2015

Language:

english

File:

PDF, 1008 KB

english, 2015

5

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

Eric E. Schadt, Cheng Li, Byron Ellis, Wing H. Wong

Journal:

Journal of Cellular Biochemistry

Year:

2001

Language:

english

File:

PDF, 187 KB

english, 2001

6

Glyoxalase 1 and glutathione reductase 1 regulate anxiety in mice

Hovatta, Iiris, Tennant, Richard S., Helton, Robert, Marr, Robert A., Singer, Oded, Redwine, Jeffrey M., Ellison, Julie A., Schadt, Eric E., Verma, Inder M., Lockhart, David J.

Journal:

Year:

2005

Language:

english

File:

PDF, 361 KB

english, 2005

7

Molecular networks as sensors and drivers of common human diseases

Schadt, Eric E.

Journal:

Year:

2009

Language:

english

File:

PDF, 3.46 MB

english, 2009

8

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

Zhu, Jun, Zhang, Bin, Smith, Erin N, Drees, Becky, Brem, Rachel B, Kruglyak, Leonid, Bumgarner, Roger E, Schadt, Eric E

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 519 KB

english, 2008

9

An integrative genomics approach to infer causal associations between gene expression and disease

Schadt, Eric E, Lamb, John, Yang, Xia, Zhu, Jun, Edwards, Steve, GuhaThakurta, Debraj, Sieberts, Solveig K, Monks, Stephanie, Reitman, Marc, Zhang, Chunsheng

Journal:

Nature Genetics

Year:

2005

Language:

english

File:

PDF, 280 KB

english, 2005

10

Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis

Lock, Christopher, Hermans, Guy, Pedotti, Rosetta, Brendolan, Andrea, Schadt, Eric, Garren, Hideki, Langer-Gould, Annette, Strober, Samuel, Cannella, Barbara, Allard, John

Journal:

Nature Medicine

Year:

2002

Language:

english

File:

PDF, 1.23 MB

english, 2002

11

Mapping the Genetic Architecture of Gene Expression in Human Liver

Schadt, Eric E., Molony, Cliona, Chudin, Eugene, Hao, Ke, Yang, Xia, Lum, Pek Y., Kasarskis, Andrew, Zhang, Bin, Wang, Susanna, Suver, Christine, Zhu, Jun, Millstein, Joshua, Sieberts, Solveig, Lamb,

Journal:

Year:

2008

Language:

english

File:

PDF, 746 KB

english, 2008

12

Increasing the Power to Detect Causal Associations by Combining Genotypic and Expression Data in Segregating Populations

Zhu, Jun, Wiener, Matthew C., Zhang, Chunsheng, Fridman, Arthur, Minch, Eric, Lum, Pek Y., Sachs, Jeffrey R., Schadt, Eric E.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 543 KB

english, 2007

13

Disentangling molecular relationships with a causal inference test

Millstein, Joshua, Zhang, Bin, Zhu, Jun, Schadt, Eric E

Journal:

Year:

2009

Language:

english

File:

PDF, 1.75 MB

english, 2009

14

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

Beaulaurier, John, Zhu, Shijia, Deikus, Gintaras, Mogno, Ilaria, Zhang, Xue-Song, Davis-Richardson, Austin, Canepa, Ronald, Triplett, Eric W, Faith, Jeremiah J, Sebra, Robert, Schadt, Eric E, Fang, Ga

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 1.84 MB

english, 2017

15

From smartphone to EHR: a case report on integrating patient-generated health data

Genes, Nicholas, Violante, Samantha, Cetrangol, Christine, Rogers, Linda, Schadt, Eric E., Chan, Yu-Feng Yvonne

Journal:

npj Digital Medicine

Year:

2018

Language:

english

File:

PDF, 1.46 MB

english, 2018

16

Contribution of Gene Regulatory Networks to Heritability of Coronary Artery Disease

Zeng, Lingyao, Talukdar, Husain A., Koplev, Simon, Giannarelli, Chiara, Ivert, Torbjörn, Gan, Li-Ming, Ruusalepp, Arno, Schadt, Eric E., Kovacic, Jason C., Lusis, Aldons J., Michoel, Tom, Schunkert, H

Journal:

Journal of the American College of Cardiology

Year:

2019

Language:

english

File:

PDF, 1.92 MB

english, 2019

17

Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases

Yang, Jialiang, Peng, Shouneng, Zhang, Bin, Houten, Sander, Schadt, Eric, Zhu, Jun, Suh, Yousin, Tu, Zhidong

Journal:

Year:

2019

Language:

english

File:

PDF, 1.93 MB

english, 2019

18

Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases

Yang, Jialiang, Peng, Shouneng, Zhang, Bin, Houten, Sander, Schadt, Eric, Zhu, Jun, Suh, Yousin, Tu, Zhidong

Journal:

Year:

2019

File:

PDF, 1.93 MB

2019

19

Comparison of brain connectomes by MRI and genomics and its implication in Alzheimerâs disease

Woo, Young Jae, Roussos, Panos, Haroutunian, Vahram, Katsel, Pavel, Gandy, Samuel, Schadt, Eric E., Zhu, Jun

Journal:

Year:

2020

Language:

english

File:

PDF, 2.38 MB

english, 2020

20

Analyzing high-density oligonucleotide gene expression array data

Eric E. Schadt, Cheng Li, Cheng Su, Wing H. Wong

Journal:

Journal of Cellular Biochemistry

Year:

2001

Language:

english

File:

PDF, 289 KB

english, 2001

21

The making of a bioinformatician

Journal:

Journal of Cellular Biochemistry

Year:

2001

Language:

english

File:

PDF, 67 KB

english, 2001

22

On the adjustment for covariates in genetic association analysis: a novel, simple principle to infer direct causal effects

Stijn Vansteelandt, Sylvie Goetgeluk, Sharon Lutz, Irwin Waldman, Helen Lyon, Eric E. Schadt, Scott T. Weiss, Christoph Lange

Journal:

Genetic Epidemiology

Year:

2009

Language:

english

File:

PDF, 182 KB

english, 2009

23

Exploiting naturally occurring DNA variation and molecular profiling data to dissect disease and drug response traits

Journal:

Current Opinion in Biotechnology

Year:

2005

Language:

english

File:

PDF, 437 KB

english, 2005

24

Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies

Ke Hao, Eugene Chudin, Joshua McElwee, Eric E Schadt

Journal:

Year:

2009

Language:

english

File:

PDF, 843 KB

english, 2009

25

Inferring causal genomic alterations in breast cancer using gene expression data

Linh M Tran, Bin Zhang, Zhan Zhang, Chunsheng Zhang, Tao Xie, John R Lamb, Hongyue Dai, Eric E Schadt, Jun Zhu

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

26

Dosage compensation is less effective in birds than in mammals

Yuichiro Itoh, Esther Melamed, Xia Yang, Kathy Kampf, Susanna Wang, Nadir Yehya, Atila Van Nas, Kirstin Replogle, Mark R Band, David F Clayton, Eric E Schadt, Aldons J Lusis, Arthur P Arnold

Journal:

Journal of Biology

Year:

2007

Language:

english

File:

PDF, 219 KB

english, 2007

27

Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice

Veronica V. Colinayo, Jian-Hua Qiao, Xuping Wang, Kelly L. Krass, Eric Schadt, Aldons J. Lusis, Thomas A. Drake

Journal:

Mammalian Genome

Year:

2003

Language:

english

File:

PDF, 226 KB

english, 2003

28

Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice

Thomas A. Drake, Eric E. Schadt, Aldons J. Lusis

Journal:

Mammalian Genome

Year:

2006

Language:

english

File:

PDF, 642 KB

english, 2006

29

Moving toward a system genetics view of disease

Solveig K. Sieberts, Eric E. Schadt

Journal:

Mammalian Genome

Year:

2007

Language:

english

File:

PDF, 511 KB

english, 2007

30

Assessing the prospects of genome-wide association studies performed in inbred mice

Wan-Lin Su, Solveig K. Sieberts, Robert R. Kleinhanz, Karine Lux, Joshua Millstein, Cliona Molony, Eric E. Schadt

Journal:

Mammalian Genome

Year:

2010

Language:

english

File:

PDF, 281 KB

english, 2010

31

Systems biology and its potential role in radiobiology

Ludwig Feinendegen, Philip Hahnfeldt, Eric E. Schadt, Michael Stumpf, Eberhard O. Voit

Journal:

Radiation and Environmental Biophysics

Year:

2008

Language:

english

File:

PDF, 487 KB

english, 2008

32

Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments

Eric E. Schadt, Bin Zhang, Jun Zhu

Journal:

Year:

2009

Language:

english

File:

PDF, 520 KB

english, 2009

33

Drug Discovery in a Multidimensional World: Systems, Patterns, and Networks

Joel T. Dudley, Eric Schadt, Marina Sirota, Atul J. Butte, Euan Ashley

Journal:

Journal of Cardiovascular Translational Research

Year:

2010

Language:

english

File:

PDF, 266 KB

english, 2010

34

Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes

Pek Yee Lum, Yanqing Chen, Jun Zhu, John Lamb, Shlomo Melmed, Susanna Wang, Tom A. Drake, Aldons J. Lusis, Eric E. Schadt

Journal:

Journal of Neurochemistry

Year:

2006

Language:

english

File:

PDF, 589 KB

english, 2006

35

10.1038/79759

Karp, Christopher L., Grupe, Andrew, Schadt, Eric, Ewart, Susan L., Keane-Moore, Michelle, Cuomo, Peter J., Köhl, Jörg, Wahl, Larry, Kuperman, Douglas, Germer, Soren, Aud, Dee, Peltz, Gary, Wills-Karp

Journal:

Nature Immunology

Year:

2000

Language:

english

File:

PDF, 139 KB

english, 2000

36

Common variants at 30 loci contribute to polygenic dyslipidemia

Kathiresan, Sekar, Willer, Cristen J, Peloso, Gina M, Demissie, Serkalem, Musunuru, Kiran, Schadt, Eric E, Kaplan, Lee, Bennett, Derrick, Li, Yun, Tanaka, Toshiko

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 787 KB

english, 2008

37

A timely guide to the genome

Journal:

Nature Genetics

Year:

2008

Language:

english

File:

PDF, 146 KB

english, 2008

38

A network view of disease and compound screening

Schadt, Eric E., Friend, Stephen H., Shaywitz, David A.

Journal:

Nature Reviews Drug Discovery

Year:

2009

Language:

english

File:

PDF, 992 KB

english, 2009

39

Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology

Schadt, Eric E., Linderman, Michael D., Sorenson, Jon, Lee, Lawrence, Nolan, Garry P.

Journal:

Nature Reviews Genetics

Year:

2011

Language:

english

File:

PDF, 247 KB

english, 2011

40

Association Studies: A genome-wide association approach to mapping the genetic determinants of the transcriptome in human populations

Journal:

European Journal of Human Genetics

Year:

2006

Language:

english

File:

PDF, 57 KB

english, 2006

41

An Integrative Genetics Approach to Identify Candidate Genes Regulating BMD: Combining Linkage, Gene Expression, and Association

Charles R Farber, Atila van Nas, Anatole Ghazalpour, Jason E Aten, Sudheer Doss, Brandon Sos, Eric E Schadt, Leslie Ingram-Drake, Richard C Davis, Steve Horvath, Desmond J Smith, Thomas A Drake, Aldon

Journal:

Journal of Bone and Mineral Research

Year:

2009

Language:

english

File:

PDF, 2.75 MB

english, 2009

42

Clustering of Hepatotoxins Based on Mechanism of Toxicity Using Gene Expression Profiles

Jeffrey F. Waring, Robert A. Jolly, Rita Ciurlionis, Pek Yee Lum, Jens T. Praestgaard, David C. Morfitt, Bruno Buratto, Chris Roberts, Eric Schadt, Roger G. Ulrich

Journal:

Toxicology and Applied Pharmacology

Year:

2001

Language:

english

File:

PDF, 1.35 MB

english, 2001

43

Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies

Hua Zhong, Xia Yang, Lee M. Kaplan, Cliona Molony, Eric E. Schadt

Journal:

The American Journal of Human Genetics

Year:

2010

Language:

english

File:

PDF, 388 KB

english, 2010

44

Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments

Jason M. Johnson, Stephen Edwards, Daniel Shoemaker, Eric E. Schadt

Journal:

Trends in Genetics

Year:

2005

Language:

english

File:

PDF, 243 KB

english, 2005

45

Statistical power of phylo-HMM for evolutionarily conserved element detection

Xiaodan Fan, Jun Zhu, Eric E Schadt, Jun S Liu

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 391 KB

english, 2007

46

Genetic validation of whole-transcriptome sequencing for mapping expression affected bycis-regulatory variation

Tomas Babak, Philip Garrett-Engele, Christopher D Armour, Christopher K Raymond, Mark P Keller, Ronghua Chen, Carol A Rohl, Jason M Johnson, Alan D Attie, Hunter B Fraser, Eric E Schadt

Journal:

Year:

2010

Language:

english

File:

PDF, 630 KB

english, 2010

47

Cis-regulatory variations: A study of SNPs around genes showingcis-linkage in segregating mouse populations

Debraj GuhaThakurta, Tao Xie, Manish Anand, Stephen W Edwards, Guoya Li, Susanna S Wang, Eric E Schadt

Journal:

Year:

2006

Language:

english

File:

PDF, 798 KB

english, 2006

48

Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Wan-Lin Su, Barmak Modrek, Debraj GuhaThakurta, Stephen Edwards, Jyoti K Shah, Amit V Kulkarni, Archie Russell, Eric E Schadt, Jason M Johnson, John C Castle

Journal:

Year:

2008

Language:

english

File:

PDF, 561 KB

english, 2008

49

A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models

Peter Langfelder, Lawrence W. Castellani, Zhiqiang Zhou, Eric Paul, Richard Davis, Eric E. Schadt, Aldons J. Lusis, Steve Horvath, Margarete Mehrabian

Journal:

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids

Year:

2012

Language:

english

File:

PDF, 2.82 MB

english, 2012

50

The Pro12Ala PPARγ2 Variant Determines Metabolism at the Gene-Environment Interface

Sami Heikkinen, Carmen Argmann, Jérôme N. Feige, Hana Koutnikova, Marie-France Champy, Nassim Dali-Youcef, Eric E. Schadt, Markku Laakso, Johan Auwerx

Journal:

Cell Metabolism

Year:

2009

Language:

english

File:

PDF, 1.60 MB

english, 2009

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