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1

A call for deep-learning healthcare

Norgeot, Beau, Glicksberg, Benjamin S., Butte, Atul J.

Journal:

Nature Medicine

Year:

2019

Language:

english

File:

PDF, 836 KB

english, 2019

2

Sex Differences in Reported Pain Across 11,000 Patients Captured in Electronic Medical Records

David Ruau, Linda Y. Liu, J. David Clark, Martin S. Angst, Atul J. Butte

Journal:

The Journal of Pain

Year:

2012

Language:

english

File:

PDF, 424 KB

english, 2012

3

Deep learning for lung cancer prognostication: A retrospective multi-cohort radiomics study

Hosny, Ahmed, Parmar, Chintan, Coroller, Thibaud P., Grossmann, Patrick, Zeleznik, Roman, Kumar, Avnish, Bussink, Johan, Gillies, Robert J., Mak, Raymond H., Aerts, Hugo J. W. L., Butte, Atul J.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.46 MB

english, 2018

4

Performance comparison of whole-genome sequencing platforms

Lam, Hugo Y K, Clark, Michael J, Chen, Rui, Chen, Rong, Natsoulis, Georges, O'Huallachain, Maeve, Dewey, Frederick E, Habegger, Lukas, Ashley, Euan A, Gerstein, Mark B, Butte, Atul J, Ji, Hanlee P, Sn

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

5

Performance comparison of whole-genome sequencing platforms

Lam, Hugo Y K, Clark, Michael J, Chen, Rui, Chen, Rong, Natsoulis, Georges, O'Huallachain, Maeve, Dewey, Frederick E, Habegger, Lukas, Ashley, Euan A, Gerstein, Mark B, Butte, Atul J, Ji, Hanlee P, Sn

Journal:

Nature Biotechnology

Year:

2012

Language:

english

File:

PDF, 65 KB

english, 2012

6

The Personal Internetworked Notary and Guardian

Alberto Riva, Kenneth D Mandl, Do Hoon Oh, Daniel J Nigrin, Atul Butte, Peter Szolovits, Isaac S Kohane

Journal:

International Journal of Medical Informatics

Year:

2001

Language:

english

File:

PDF, 117 KB

english, 2001

7

Variation in the Human Immune System Is Largely Driven by Non-Heritable Influences

Brodin, Petter, Jojic, Vladimir, Gao, Tianxiang, Bhattacharya, Sanchita, Angel, Cesar J. Lopez, Furman, David, Shen-Orr, Shai, Dekker, Cornelia L., Swan, Gary E., Butte, Atul J., Maecker, Holden T., D

Journal:

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

8

RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data

Shankar, Ravi D., Bhattacharya, Sanchita, Jujjavarapu, Chethan, Andorf, Sandra, Wiser, Jeffery A., Butte, Atul J.

Journal:

Year:

2017

Language:

english

File:

PDF, 121 KB

english, 2017

9

Genetic analysis in a patient with nine primary malignant neoplasms: a rare case of Li-Fraumeni syndrome

Li, Xiaoyuan, Kang, Juan, Pan, Qi, Sikora-Wohlfeld, Weronika, Zhao, Dachun, Meng, Changting, Bai, Chunmei, Patwardhan, Anil, Chen, Richard, Ren, Hong, Butte, Atul, Ding, Keyue

Journal:

Oncology Reports

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

10

Repurpose terbutaline sulfate for amyotrophic lateral sclerosis using electronic medical records

Paik, Hyojung, Chung, Ah-Young, Park, Hae-Chul, Park, Rae Woong, Suk, Kyoungho, Kim, Jihyun, Kim, Hyosil, Lee, KiYoung, Butte, Atul J.

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 1.65 MB

english, 2015

11

Cancer Cell–Autonomous Parainflammation Mimics Immune Cell Infiltration

Lasry, Audrey, Aran, Dvir, Butte, Atul J., Ben-Neriah, Yinon

Journal:

Cancer Research

Year:

2017

Language:

english

File:

PDF, 401 KB

english, 2017

12

Big data opens a window onto wellness

Journal:

Nature Biotechnology

Year:

2017

Language:

english

File:

PDF, 199 KB

english, 2017

13

Personal Mutanomes Meet Modern Oncology Drug Discovery and Precision Health

Cheng, Feixiong, Liang, Han, Butte, Atul J., Eng, Charis, Nussinov, Ruth, Gottesman, Michael M.

Journal:

Pharmacological Reviews

Year:

2019

Language:

english

File:

PDF, 1.77 MB

english, 2019

14

Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis

Norgeot, Beau, Glicksberg, Benjamin S., Trupin, Laura, Lituiev, Dmytro, Gianfrancesco, Milena, Oskotsky, Boris, Schmajuk, Gabriela, Yazdany, Jinoos, Butte, Atul J.

Journal:

JAMA Network Open

Year:

2019

File:

PDF, 965 KB

2019

15

Characteristics and challenges of the clinical pipeline of digital therapeutics

Patel, Nisarg A., Butte, Atul J.

Journal:

npj Digital Medicine

Year:

2020

File:

PDF, 527 KB

2020

16

Transmission distortion in Crohn's disease risk gene ATG16L1 leads to sex difference in disease association

Linda Y. Liu, Marc A. Schaub, Marina Sirota, Atul J. Butte

Journal:

Inflammatory Bowel Diseases

Year:

2012

Language:

english

File:

PDF, 516 KB

english, 2012

17

Derivation of a Scale-Independent Parameter Which Characterizes Genetic Sequence Comparisons

Paolo B. DePetrillo, Atul J. Butte

Journal:

Computers and Biomedical Research

Year:

1993

File:

PDF, 700 KB

1993

18

A computer-simulated “wet” laboratory

Boris Rotman, Atul Butte

Journal:

Biochemical Education

Year:

1992

Language:

english

File:

PDF, 217 KB

english, 1992

19

In reply

Debra L. Weiner, Atul J. Butte, Patricia L. Hibberd, Gary R. Fleisher

Journal:

Annals of Emergency Medicine

Year:

2003

Language:

english

File:

PDF, 28 KB

english, 2003

20

Computational prediction and experimental validation associating FABP-1 and pancreatic adenocarcinoma with diabetes

Ravi N Sharaf, Atul J Butte, Kelli D Montgomery, Reetesh Pai, Joel T Dudley, Pankaj J Pasricha

Journal:

BMC Gastroenterology

Year:

2011

Language:

english

File:

PDF, 947 KB

english, 2011

21

Expression-based Pathway Signature Analysis (EPSA): Mining publicly available microarray data for insight into human disease

Jessica D Tenenbaum, Michael G Walker, Paul J Utz, Atul J Butte

Journal:

BMC Medical Genomics

Year:

2008

Language:

english

File:

PDF, 1.37 MB

english, 2008

22

Predicting environmental chemical factors associated with disease-related gene expression data

Chirag J Patel, Atul J Butte

Journal:

BMC Medical Genomics

Year:

2010

Language:

english

File:

PDF, 944 KB

english, 2010

23

Sex differences in disease risk from reported genome-wide association study findings

Linda Y. Liu, Marc A. Schaub, Marina Sirota, Atul J. Butte

Journal:

Year:

2012

Language:

english

File:

PDF, 654 KB

english, 2012

24

Personalized Medicine and Cardiovascular Disease: From Genome to Bedside

Stephen Pan, Frederick E. Dewey, Marco V. Perez, Joshua W. Knowles, Rong Chen, Atul J. Butte, Euan A. Ashley

Journal:

Current Cardiovascular Risk Reports

Year:

2011

Language:

english

File:

PDF, 233 KB

english, 2011

25

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

26

Genome-wide analysis of host responses to the Pseudomonas aeruginosa type III secretion system yields synergistic effects

Jeffrey K. Ichikawa, Sangeeta B. English, Matthew C. Wolfgang, Rebekah Jackson, Atul J. Butte, Stephen Lory

Journal:

Cellular Microbiology

Year:

2005

Language:

english

File:

PDF, 224 KB

english, 2005

27

Genome-scale expression profiling of Hutchinson–Gilford progeria syndrome reveals widespread transcriptional misregulation leading to mesodermal/mesenchymal defects and accelerated atherosclerosis

Antonei B. Csoka, Sangeeta B. English, Carl P. Simkevich, David G. Ginzinger, Atul J. Butte, Gerald P. Schatten, Frank G. Rothman, John M. Sedivy

Journal:

Year:

2004

Language:

english

File:

PDF, 180 KB

english, 2004

28

Analyzing functional genomic differences yields oncogenes and chromosomal breakpoints in ALL and AML

Butte, Atul J., Reis, Ben, Kho, Alvin, Sun, Yao, Kohane, Isaac S.

Journal:

Nature Genetics

Year:

2001

Language:

english

File:

PDF, 28 KB

english, 2001

29

In silico research in the era of cloud computing

Dudley, Joel T, Butte, Atul J

Journal:

Nature Biotechnology

Year:

2010

Language:

english

File:

PDF, 282 KB

english, 2010

30

Creation and implications of a phenome-genome network

Butte, Atul J, Kohane, Isaac S

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 1.64 MB

english, 2006

31

Prediction of preadipocyte differentiation by gene expression reveals role of insulin receptor substrates and necdin

Tseng, Yu-Hua, Butte, Atul J., Kokkotou, Efi, Yechoor, Vijay K., Taniguchi, Cullen M., Kriauciunas, Kristina M., Cypess, Aaron M., Niinobe, Michio, Yoshikawa, Kazuaki, Patti, Mary Elizabeth

Journal:

Nature Cell Biology

Year:

2005

Language:

english

File:

PDF, 858 KB

english, 2005

32

Cell type–specific gene expression differences in complex tissues

Shen-Orr, Shai S, Tibshirani, Robert, Khatri, Purvesh, Bodian, Dale L, Staedtler, Frank, Perry, Nicholas M, Hastie, Trevor, Sarwal, Minnie M, Davis, Mark M, Butte, Atul J

Journal:

Year:

2010

Language:

english

File:

PDF, 659 KB

english, 2010

33

AILUN: reannotating gene expression data automatically

Chen, Rong, Li, Li, Butte, Atul J

Journal:

Year:

2007

Language:

english

File:

PDF, 66 KB

english, 2007

34

The use and analysis of microarray data

Journal:

Nature Reviews Drug Discovery

Year:

2002

Language:

english

File:

PDF, 629 KB

english, 2002

35

Computerized recruiting for clinical trials in real time

Debra L. Weiner, Atul J. Butte, Patricia L. Hibberd, Gary R. Fleisher

Journal:

Annals of Emergency Medicine

Year:

2003

Language:

english

File:

PDF, 63 KB

english, 2003

36

Performance comparison of exome DNA sequencing technologies

Clark, Michael J, Chen, Rui, Lam, Hugo Y K, Karczewski, Konrad J, Chen, Rong, Euskirchen, Ghia, Butte, Atul J, Snyder, Michael

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 1.07 MB

english, 2011

37

Comparing the Similarity of Time-Series Gene Expression Using Signal Processing Metrics

Atul J. Butte, Ling Bao, Ben Y. Reis, Timothy W. Watkins, Isaac S. Kohane

Journal:

Journal of Biomedical Informatics

Year:

2001

Language:

english

File:

PDF, 347 KB

english, 2001

38

Extracting Knowledge from Dynamics in Gene Expression

Ben Y Reis, Atul S Butte, Isaac S Kohane

Journal:

Journal of Biomedical Informatics

Year:

2001

Language:

english

File:

PDF, 562 KB

english, 2001

39

Reply

Ben Y. Reis, Atul S. Butte, Isaac S. Kohane

Journal:

Journal of Biomedical Informatics

Year:

2001

Language:

english

File:

PDF, 45 KB

english, 2001

40

Identification of Candidate IDDM Disease Susceptibility Genes in the Idd Regions of NOD Mice by Temporal Microarray Gene Expression Data Analysis

Keiichi Kodama, Demi Dang, Claire Holness, Hideyuki Iwai, Mark Hartnett, Atul Butte, C. Garrison Fathman

Journal:

Clinical Immunology

Year:

2007

Language:

english

File:

PDF, 43 KB

english, 2007

41

Global Assessment of B Cell Alloimmunity Using Human Protein Microarrays

Persis P. Wadia, Marc Coram, Marina Sirota, David B. Miklos, Atul Butte

Journal:

Clinical Immunology

Year:

2007

Language:

english

File:

PDF, 41 KB

english, 2007

42

OR.101. Time-dependent and Tissue-specific Changes in Gene Expression During Disease Induction and Progression in NOD Mice

Linda Yip, Keiichi Kodama, Atul Butte, Remi Creusot, Leon Su, Charles Fathman

Journal:

Clinical Immunology

Year:

2008

Language:

english

File:

PDF, 46 KB

english, 2008

43

Tissue- and age-specific changes in gene expression during disease induction and progression in NOD mice

Keiichi Kodama, Atul J. Butte, Remi J. Creusot, Leon Su, Deqiao Sheng, Mark Hartnett, Hideyuki Iwai, Luis R. Soares, C. Garrison Fathman

Journal:

Clinical Immunology

Year:

2008

Language:

english

File:

PDF, 637 KB

english, 2008

44

F.40. Quantitative Assessment of the Goodness-of-fit of Mouse Models to Human Diseases

Shai Shen-Orr, Atul Butte, Mark Davis

Journal:

Clinical Immunology

Year:

2009

Language:

english

File:

PDF, 37 KB

english, 2009

45

Extracting Cell-type-specific Gene Expression Differences from Complex Tissues

Shai Shen-Orr, Alexander Gaidarski, Robert Tibshirani, Purvesh Khatri, Mark Davis, Atul Butte

Journal:

Clinical Immunology

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

46

A Systemic Age Dependent Defect in Immune-cell Signaling Response is Associated with Longevity Biomarkers

Shai Shen-Orr, David Furman, Brian Kidd, Holden Maecker, Cornelia Dekker, Atul Butte, Mark Davis

Journal:

Clinical Immunology

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

47

Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR

Sangeeta B. English, Shou-Ching Shih, Marco F. Ramoni, Lois E. Smith, Atul J. Butte

Journal:

Journal of Biomedical Informatics

Year:

2009

Language:

english

File:

PDF, 787 KB

english, 2009

48

Current methodologies for translational bioinformatics

Yves A. Lussier, Atul J. Butte, Lawrence Hunter

Journal:

Journal of Biomedical Informatics

Year:

2010

Language:

english

File:

PDF, 125 KB

english, 2010

49

Validating pathophysiological models of aging using clinical electronic medical records

David P. Chen, Alexander A. Morgan, Atul J. Butte

Journal:

Journal of Biomedical Informatics

Year:

2010

Language:

english

File:

PDF, 832 KB

english, 2010

50

Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets

David Ruau, Michael Mbagwu, Joel T. Dudley, Vijay Krishnan, Atul J. Butte

Journal:

Journal of Biomedical Informatics

Year:

2011

Language:

english

File:

PDF, 367 KB

english, 2011