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Oct 23, 2013 (3 years and 9 months ago)

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1


BIOGRAPHICAL SKETCH



NAME

Steve Horvath

POSITION TITLE

Professor, Human Genetics, David Geffen School of
Medicine; Biostatistics, School of Public Health,
University of California,
LA

eRA COMMONS USER NAME

Horvath2

EDUCATION/TRAINING
(Begin with baccalaureate or other initial professional education, such as nursing, and include postdoctoral training.)

INSTITUTION AND LOCATION

DEGREE

(if applicable)

YEAR(s)

FIELD OF STUDY

University of Berlin, Germany

BSc


1989

Mathematics/Physics

University of North Carolina, Chapel Hill

PhD

1995

Mathematics

Harvard School of Public Health

ScD

2000

Biostatistics


A.

Personal Statement

Dr Horvath is a Professor of Human Genetics and Biostatistics at UCLA.
His group develops and applies

biostatistical and bioinformatics methods for

genomic and medical data.
Research topics include
a) gene
networks, b) allelic association tests for
mapping complex disease genes based on genetic markers c) data
mining methods, and d) cancer genetic applications.

Dr Horvath's group has developed systems biologic and systems genetic data mining methods for studying
complex diseases and phenotypes (e.g.
weighted correlation network analysis).


B
. POSITIONS

06/1996

10/1996

Consulting statistical geneticist with Millenium Pharmaceuticals

10/1996

06/1997

Statistical Consultant at the Harvard Biostatistics Consulting Lab

07/1997

02/1998

Statistical Consultant

at the Program for Population Genetics, Harvard

04/1998

12/1998

Management consultant for McKinsey & Company, Germany

01/1999

10/2000

Visiting Scientist (Postdoc level), Inst. for Medical Statistics University of Bonn

11/2000

0
6/2006

Assistant Professor
in

Hum
an Genetics & Biostatistics
, Uni of Calif., LA

07/2007

06/2009

Tenured Associate Professor in Hum Genetics & Biostatistics, Uni of Calif., LA

07/2009



Tenured Full Professor in Hum Genetics & Biostatistics, Uni of Calif., LA


HONORS

1989

Fulbright S
cholarship

1995

Harvard Biostatistics Drolette Prize

1997

Robert Reed Prize from Harvard

2002

Membership in Delta Omega, Honorary Public Health Society

2003

A
ward from the European Society of Human Genetics: second most cited paper

of the European Journal of Human Genetics in 2001. Details: Horvath, S, Xu X, Laird NM (2001) “The
family based asso
ciation test method: strategies.
Euro J Hum Gen 9: 301
-
306

2003

Co
-
authored paper is the

2nd place essay winner at the American Urological A
ssociation National

M
eeting. Details: Bui MHT, Seligson D, Han K, Pantuck AJ, Dorey FJ, Huang Y, Horvath S, Leibovich
BC, Liao S, Stanbridge E, Lerman M, Palotie A, deKernion JB, Figlin RA and Belldegrun AS (2002)
Carbonic Anhydrase IX is an Independent
Predictor of Survival in Advanced Renal Cell Carcinoma:
Implications for Molecular Classification and Prognostication. Clin Can
cer Res. 2003 Feb;9(2):802
-
11.)

Jan 2004 Co
-
authored

paper wins the 1st prize at the annual American Urologic Association annual
meeting

(San Francisco
, 2004)/ACMi essay contest:
Han KR, Seligson DB, Liu X, Horvath S, Shintaku PI,
Thomas GV, Said JW, and Reiter RE. Prostate Stem Cell Antigen (PSCA) expression is associated
with Gleason score, seminal vesicle invasion, and capsula
r

invasion in prostate cancer.

2005

Best Paper Award from the International Genetic Epidemiology Society for the paper
:

Horvath S, Xu X, Lake SL, Silverman EK, Weiss ST, Laird NM (2004) Family based tests for
associating haplotypes with general phenotyp
e data:
asthma
. Genet Epidemiol, Vol 26, No 1, 61
-
69


2

2006

Best Paper

Award
“Critical Assessment of Microarray Data Analysis”


A Presson, E

Sobel
, JC Papp, AJ Lusis, S Horvath (2006)
Integration of Genetic and Genomic

Approaches for the Analysis of Chronic Fatigue Syndrome Implicates Forkhead Box N1
.

2006

Joint first authored paper is elected as “Nature Milestone”.
Nature Milest
ones highlights key discoveries
that have shaped different scientific fields and enables the wide
r recognition of these classic findings
.

Reference:
Seligson DB, Horvath S,
et al (
2005) Global histone modification patterns predict risk of
prostate cancer recurrence. Nature 435, 1262
-
1266

2007

The brain tumor research portal (at
www.braintumour.net
) elects

the following paper as the second
most influential brain tumor publication in the year 2006.
Horvath et al. (2006) Analysis of oncogenic
signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A
.

2007 Elected
to the top 100 author list at BioMed Central



C
. REVIEWED RESEARCH PAPERS


1.

Horvath S (2013) DNA methylation age of human tissues and cell types. Genome Biology. Accepted.

2.

Xue Z, Huang K, Cai C, Cai L, Jiang CY, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu
JY, Horvath S, Fan G. (2013)
Genetic programs in human and mouse early embryos revealed by single
-
cell RNA?sequencing. Nature. 2013 Jul 28.
doi: 10.1038/nature12364 PMID: 23892778

3.

Langfelder P, Mischel PS, Horvath S (2013) When Is Hub Gene Selection Better

than Standard Meta
-
Analysis? PLoS
ONE 8(4): e61505. doi:10.1371/journal.pone.0061505

PMID: 2361386

PMCID: PMC3629234

4.

Ranola JM, Langfelder P, Lange K, Horvath S

Cluster and propensity based approximation of a network.

BMC Syst
Biol. 2013 Mar 14;7(1):21

PM
ID: 23497424

PMCID: PMC3663730

5.

Levine AJ, Miller JA, Shapshak P, Gelman B, Singer EJ, Hinkin CH, Commins D, Morgello S, Grant I, Horvath S

(2013)
Systems analysis of human brain gene expression: mechanisms for HIV
-
associated neurocognitive impairment
and
common pathways with Alzheimer's disease.

BMC Med Genomics. 2013 Feb 13;6(1):4

PMID: 23406646

6.

Ho ME, Quek SI, True LD, Morrissey C, Corey E, Vessella RL, Dumpit R, Nelson PS, Maresh EL, Mah V, Alavi M,
Kim SR, Bagryanova L, Horvath S, Chia D, Goodglick L,
Liu AY.

Prostate cancer cell phenotypes based on AGR2 and
CD10 expression.

Mod Pathol. 2013

PMID: 23348903

7.

Song L, Langfelder P, Horvath S (2013)
Random generalized linear model: a highly accurate and interpretable
ensemble predictor
. BMC Bioinformatics. J
an 2013

PMID: 23323760

PMCID: PMC3645958

8.

Haas BE, Horvath S, Pietiläinen KH, Cantor RM, Nikkola E, Weissglas
-
Volkov D, Rissanen A, Civelek M, Cruz
-
Bautista I, Riba L, Kuusisto J, Kaprio J, Tusie
-
Luna T, Laakso M, Aguilar
-
Salinas CA, Pajukanta P.

Adipose Co
-
expression networks across Finns and Mexicans identify novel triglyceride
-
associated genes.

BMC Med Genomics.
2012 Dec 6;5(1):61

PMID: 23217153

9.

Song L, Langfelder P, Horvath S.

(2012)
Comparison of co
-
expression measures: mutual information, correlation,
and
model based indices.
BMC Bioinformatics
;13(1):328.

PMID: 23217028

10.

van Eijk KR, de Jong S, Boks MP, Langeveld T, Colas F, Veldink JH, de Kovel CG, Janson E, Strengman E,
Langfelder P, Kahn RS, van den Berg LH, Horvath S, Ophoff RA (2012) Genetic analysis

of DNA methylation and
gene expression levels in whole blood of healthy human subjects BMC Genomics. 2012 Nov 17;13(1):636 PMID:
23157493

11.

Hilliard AT, Miller JE, Horvath S, White SA. (2012) Distinct neurogenomic States in Basal Ganglia subregions relate
differently to singing behavior in songbirds. PLoS Comput Biol. 2012 Nov;8(11):e1002773. doi:
10.1371/journal.pcbi.1002773 PMID: 23144607

12.

Horvath S, Nazmul
-
Hossain AN, Pollard RP, Kroese FG, Vissink A, Kallenberg CG, Spijkervet FK, Bootsma H, Michie
SA, Go
rr SU, Peck AB, Cai C, Zhou H, Wong DT.(2012) Systems analysis of primary Sjogren's syndrome
pathogenesis in salivary glands identifies shared pathways in human and a mouse model. Arthritis Res Ther.
1;14(6):R238 PMID: 23116360

13.

Schwartz SM, Schwartz HT, Ho
rvath S, Schadt E, Lee SI.

A Systematic Approach to Multifactorial Cardiovascular
Disease: Causal Analysis.

Arterioscler Thromb Vasc Biol. 20
12 Oct 18.
PMID: 23087359

14.

Horvath S, Zhang Y, Langfelder P, Kahn RS, Boks MP, van Eijk K, van den Berg LH, Ophoff R
A.

Aging effects on
DNA methylation modules in human brain and blood tissue.

Genome Biol. 2012 Oct 3;13(10):R97. PMID: 23034122

15.

Hawrylycz MJ, Lein ES, Guillozet
-
Bongaarts AL, Shen EH, Ng L, Miller JA, van de Lagemaat LN, Smith KA, Ebbert A,
Riley ZL, Abaji
an C, Beckmann CF, Bernard A, Bertagnolli D, Boe AF, Cartagena PM, Chakravarty MM, Chapin M,
Chong J, Dalley RA, Daly BD, Dang C, Datta S, Dee N, Dolbeare TA, Faber V, Feng D, Fowler DR, Goldy J, Gregor
BW, Haradon Z, Haynor DR, Hohmann JG, Horvath S, Howa
rd RE, Jeromin A, Jochim JM, Kinnunen M, Lau C,
Lazarz ET, Lee C, Lemon TA, Li L, Li Y, Morris JA, Overly CC, Parker PD, Parry SE, Reding M, Royall JJ, Schulkin J,
Sequeira PA, Slaughterbeck CR, Smith SC, Sodt AJ, Sunkin SM, Swanson BE, Vawter MP, Williams

D, Wohnoutka
P, Zielke HR, Geschwind DH, Hof PR, Smith SM, Koch C, Grant SG, Jones AR (2012) An anatomically

3

comprehensive atlas of the adult human brain transcriptome. Nature. 2012 Sep 20;489(7416):391
-
9. doi:
10.1038/nature11405. PMID: 22996553.

16.

Weiss
JN, Karma A, Maclellan WR, Deng M, Rau CD, Rees CM, Wang J, Wisniewski N, Eskin E, Horvath S, Qu Z,
Wang Y, Lusis AJ. (2012) "Good enough solutions" and the genetics of complex diseases. Circ Res. 2012 Aug
3;111(4):493
-
504. PMID: 22859671

17.

Shirasaki DI, Gre
iner ER, Al
-
Ramahi I, Gray M, Boontheung P, Geschwind DH, Botas J, Coppola G, Horvath S, Loo
JA, Yang XW. (2012) Network organization of the huntingtin proteomic interactome in Mammalian brain. Neuron.
2012 Jul 12;75(1):41
-
57. PMID: 22794259

18.

de Jong S, Bo
ks MP, Fuller TF, Strengman E, Janson E, de Kovel CG, Ori AP, Vi N, Mulder F, Blom JD, Glenthøj B,
Schubart CD, Cahn W
, Kahn RS, Horvath S, Ophoff RA (2012)
A gene co
-
expression network in whole blood of
schizophrenia patients is independent of antipsychot
ic
-
use and enriched for brain
-
expressed genes.

PLoS One.
201
2;7(6):e39498.
PMID: 22761806

19.

Gorr SU, Wennblom TJ, Horvath S, Wong DT, Michie SA
(2012)
Text
-
mining applied to autoimmun
e disease
research: the Sjögren'
s syndrome knowledge base.

BMC
Musculoskelet Disord. 2012 Jul 3;
13(1):119.
PMID:
22759918

20.

Old
ham MC, Langfelder P, Horvath S (2012)
Network methods for describing sample relationships in genomic
datasets: application to Huntington's disease.

BMC Syst Biol. 2012 Jun 12;6(1):63. PMID: 226
91535

PMCID:
PMC3441531

21.

Vivanco I, Robins HI, Rohle D, Campos C, Grommes C, Nghiemphu PL, Kubek S, Oldrini B, Chheda MG, Yannuzzi
N, Tao H, Zhu S, Iwanami A, Kuga D, Dang J, Pedraza A, Brennan CW, Heguy A, Liau LM, Lieberman F, Yung WK,
Gilbert MR, Reardon

DA, Drappatz J, Wen PY, Lamborn KR, Chang SM, Prados MD, Fine HA, Horvath S, Wu N,
Lassman AB, Deangelis LM, Yong WH, Kuhn JG, Mischel PS, Mehta MP, Cloughesy TF, Mellinghoff IK. Differential
Sensitivity of Glioma
-

versus Lung Cancer
-
Specific EGFR Mutatio
ns to EGFR Kinase Inhibitors. Cancer Discov. 2012
May;2(5):458
-
471 PMID: 22588883, PMC3354723

22.

Diekstra FP, Saris CG, van Rheenen W, Franke L, Jansen RC, van Es MA, van Vught PW, Blauw HM, Groen EJ,
Horvath S, Estrada K, Rivadeneira F, Hofman A, Uitterlinde
n AG, Robberecht W, Andersen PM, Melki J, Meininger V,
Hardiman O, Landers JE, Brown RH Jr, Shatunov A, Shaw CE, Leigh PN, Al
-
Chalabi A, Ophoff
RA, van den Berg LH,
Veldink JH (2012)
Mapping of Gene Expression Reveals CYP27A1 as a Susceptibility Gene for S
poradic ALS.

PLoS
One. 2012;7(4):e35333. PMID: 22509407

23.

Leuchter AF, Cook
IA, Hunter AM, Cai C, Horvath S (2012)
Resting
-
state quantitative electroencephalography
reveals increased neurophysiologic connectivity in depression.

PLoS One. 201
2;7(2):e32508.
PM
ID: 22384265

24.

Huynh TP, Mah V, Sampson VB, Chia D, Fishbein MC, Horvath S, Alavi M, Wu DC, Harper J, Sarafian T, Dubinett
SM, Langhans SA, Goodglick L, Rajasekaran AK

(2012)
Na,K
-
ATPase is a target of cigarette smoke and reduced
expression predicts poor pat
ient outcome of smokers with lung cancer.

Am J Physiol Lung Cell Mol Physiol

PMID:
22345575

25.

Hilliard AT, Miller JE, Fraley ER, Horvath S, White SA

(2012)
Molecular microcircuitry underlies functional
specification in a Basal Ganglia circuit dedicated to vo
cal learning. Neuron

PMID: 22325205

26.

Luykx JJ, Bakker SC, Lentjes E, Boks MP, van Geloven N, Eijkemans MJ, Janson E, Strengman E, de Lepper AM,
Westenberg H, Klopper KE, Hoorn HJ, Gelissen HP, Jordan J, Tolenaar NM, van Dongen EP, Michel B, Abramovic L,
Hor
vath S, Kappen T, Bruins P, Keijzers P, Borgdorff P, Ophoff RA, Kahn RS

(2012)

Season of sampling and season
of birth influence serotonin metabolite levels in human cerebrospinal fluid.

PLoS One. 2012;7(2):e30497

PMID:
22312427

27.

Langfelder P, Horvath
(2012
) Fast R Functions For Robust Correlations And
Hierarchical Clustering. J Stat Software
(46) 11

PMID: 23050260

28.

Miller JA, Cai C, Langfelder P, Geschwind DH, Kurian SM, Salomon DR, Horvath S (2011) Strategies for aggregating
gene expression data: The collap
seRows R function. BMC Bioinformatics
.

4;12(1):322

PMID: 21816037

PMCID:
PMC3166942

29.

Langfelder P, Castellani LW, Zhou Z, Paul E, Davis R, Schadt EE, L
usis AJ, Horvath S, Mehrabian M (2011)

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

Biochim Biophys Acta.

PMID: 21807117

30.

Maresh EL, Mah V, Alavi M, Presson A, Bagryanova L, Yoon N, Chang G, Elshimali Y, Shevlin L, Zhang L, Hong L,
Schatz S, Li A, Fu M, Wadehra M, Chia D, Horvath S, and Goodgli
ck L. Development and Application of Tissue
Microarrays for Biomarker Studies. Forum on Immunopathological Diseases and Therapeutics. 2011; 2(2):145
-
159

31.

Levitsky J, Salomon DR, Abecassis M, Langfelder P, Horvath S, Friedewald J, Wang E, Kurian SM, Mondala
T, Gil S,
McDade R, Ballard K, Gallon L.
(2011)
Clinical and Plasma Proteomic Markers Correlating With Chronic Kidney
Disease After Liver Transplantation.

Am J Transplant. 2011 Jul 27. doi: 1
0.1111
PMID: 21794091

32.

Bocklandt S, Lin W, Sehl ME, Sánchez FJ, Sin
sheimer JS,
Horvath S,
Vilain E (
2011
)

Epigenetic Predictor of Age.
PLoS ONE 6(6): e14821.
doi:10.1371

PMID: 21731603


33.

Huerta
-
Yepez S, Yoon NK, Hernandez
-
Cueto A, Mah V, Rivera
-
Pazos CM, Chatterjee D, Vega MI, Maresh EL,
Horvath S, Chia D, Bonavida B,
Goodglick L.

(2011)
Expression of Phosphorylated Raf Kinase Inhibitor Protein
(pRKIP) is a Predictor of Lung Cancer Survival.

BMC Cancer. 11(1):259.

PMID: 21689459


4

34.

Presson AP, Yoon NK, Bagryanova L, Mah V, Alavi M, Maresh EL, Rajasekaran AK,

Goodglick L, C
hia D, Horvath S
(2011)
Protein expression based multimarker analysis of breast cancer samples.

BMC Cancer. 11(1):230

PMID:
21651811

35.

Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y,
Horvath S
, Mill J, Cantor R
,

Blencowe BJ,
Geschwind DH (2011)
Transcripto
mic analysis of autistic brain reveals

convergent molecular pathology
. Nature.
25;474(7351):380
-
4
PMID:
21614001

36.

Marquez
-
Garban DC, Mah V, Alavi M, Maresh EL, Chen HW, Bagryanova L,
Horvath S
, Chia D, Garon E, Goodglick
L, Pietras RJ.
(2011)
Progesterone
and estrogen receptor expression and activity in human non
-
small cell lung cancer.

Steroids.
May
.
PMID: 21600232

37.

Wang A, Huang K, Shen Y, Xue Z, Cai C,
Horvath S
, Fan G

(2011)
Functional Modules Distinguish Human Induced
Pluripotent Stem Cells from Embryon
ic Stem Cells.

Stem Cells Dev. 2011

PMID: 21542696

38.

Mah V, Marquez D, Alavi M, Maresh EL, Zhang L, Yoon N,
Horvath S
, Bagryanova L, Fishbein MC, Chia D, Pietras
R, Goodg
lick L (2011)
Expression levels of estrogen receptor beta in conjunction with aromatase
predict survival in
non
-
small cell lung cancer.

Lung Cancer. 2011

PMID: 21511357

39.

Park CC, Gale GD, Dejong S, Ghazalpour A, Bennett B, Farber CR, Langfelder P, Lin A, Khan AH, Eskin E,
Horvath

S, Lusis AJ, Ophoff RA, Smith DJ

(2011)
Gene networks associated

with conditional fear in mice identified using a
systems genetics approach
.
BMC Syst Biol.5(1):43
.
PMID: 21410935

40.

Langfelder P, Luo R, Oldham MC,
Horvath S

(2011) Is my network module preserved and reproducible? PloS Comp
Biol.

7(1): e1001057.

PMID:
21283776

41.

Zhao

W,
Langfelder

P,
Fuller

T,
Dong

J,
Li

A,
Horvath S

(2010)
Weighted gene coexpression network analysis: state
of the art.

J Biopharm Stat. 20(2):281
-
300.

PMID: 20309759

42.

Leuchter AF, Cook IA, Hamilton SP, Narr KL, Toga A, Hunter AM, Faull K, Wh
itelegge J, Andrews AM, Loo J, Way B,
Nelson SF,
Horvath S,

Lebowitz BD (2010) Biomarkers to predict antidepressant response. Curr Psychiatry Rep.
12(6):553
-
62. PMID: 20963521

43.

Tanaka H, Kono E, Tran CP, Miyazaki H, Yamashiro J, Shimomura T, Fazli L, Wada R, Huang J, Vessella RL, An J,
Horvath S
, Gleave M, Rettig MB, Wainberg ZA, Reiter RE (2010) Monoclonal antibody targeting of N
-
cadherin
inhibits prostate cancer growth, metasta
sis and castration resistance. Nat Med. 2010 Dec;16(12):1414
-
20. PMID:
21057494
.
PMCID: PMC3088104

44.

Yoon NK, Maresh EL, Shen D, Elshimali Y, Apple S,
Horvath S
, Mah V, Bose S, Chia D, Chang HR, Goodglick L
(2010) Higher levels of GATA3 predict better surviv
al in women with breast cancer. Hum Pathol. 41(12):1794
-
801.
PMID: 21078439

45.

Dewey FE, Perez MV, Wheeler MT, Watt C, Spin J, Langfelder P,
Horvath S,

Hannenhalli S, Cappola TP, Ashley EA
(2010) Gene Coexpression Network Topology of Cardiac Development, Hype
rtrophy, and Failure. Circ Cardiovasc
Genet. PMID: 21127201

PMC3324316

46.

Maresh EL, Mah V, Alavi M,
Horvath S
, Bagryanova L, Liebeskind ES, Knutzen LA, Zhou Y, Chia D, Liu AY,
Goodglick L (2010) Differential expression of anterior gradient gene AGR2 in prost
ate cancer. BMC Cancer.10:680.
PMID: 21144054

47.

Cai

C, Langfelder P, Fuller T, Oldham M, Luo R, van den Berg L,Ophoff R,
Horvath S

(2010)

Is human blood a good
surrogate for brain tissue in transcriptional studies? BMC Genomics

11:589
.
PMID: 20961428

48.

Miller JA,
Horvath S,

Geschwind DH.
(2010) Divergence of human and mouse brain transcriptome highlights
Alzheimer disease pathways.

Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12698
-
703. PMID
: 20616000

49.

Yoon NK, Maresh EL, Elshimali Y, Li A,
Horvath S
, S
e
ligson DB, Chia D, Goodglick L (2010)
Elevated MED28
expression predicts poor outcome in women with breast cancer.

BMC Cancer. 10:335.PMID: 20584319

50.

Habeeb O, Goodglick L, Soslow RA, Rao RG, Gordon LK, Schirripa O,
Horvath S
,
Braun J, Seligson DB, Wadehra
M (2010)
Epithelial membrane protein
-
2 expression is an early predictor of endometrial cancer development.

Cancer.
PMID: 20578181

51.

Mumford JA,
Horvath S
, Oldham MC, Langfeld
er P, Geschwind DH, Poldrack RA (2010)
Detecting network modules
in fMRI time series
: a weighted network analysis approach.

Neuroimage.
52(4):1465
-
76. PMID: 20553896

52.

Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R,
Horvath S
,
Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB

(2010)
Inaugural article: Global analysis of gene
activity during Arabidopsis seed development and identification of seed
-
specific transcription factors.

Proc Natl Acad
Sci U S A. 2010 Apr 12

PMID: 20385809

53.

Manuyakorn A, Paulus R, Farrell J, Dawson NA, Tze S, Che
ung
-
Lau G, Hines OJ, Reber H, Seligson DB,
Horvath S
,
Kurdistani SK, Guha C, Dawson DW

(2010)
Cellular Histone Modification Patterns Predict Prognosis and Treatment
Response in Resectable Pancreatic Adenocarcinoma: Results From RTOG 9704.

J Clin Oncol. 201
0 Mar
10;28(8):1358
-
65

J Clin Oncol.
PMID: 20385809

54.

de Jong S, Fuller TF, Janson E, Strengman E,
Horvath S
, Kas MJ, Ophoff RA

(2010)
Gene expression profiling in
C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions in
depen
dent of genetic
background.
BMC Genomics. 2010 Jan 11;11(1):20

PMID: 20064228

55.

Guo D, Prins RM, Dang J, Kuga D, Iwanami A, Soto H, Lin KY, Huang TT, Akhavan D, Hock MB, Zhu S, Kofman AA,
Bensinger SJ, Yong WH, Vinters HV, Horvath S, Watson AD, Kuhn JG, Robi
ns HI, Mehta MP, Wen PY, DeAngelis

5

LM, Prados MD, Mellinghoff IK, Cloughesy TF, Mischel PS

(2010)
EGFR signaling through an Akt
-
SREBP
-
1
-
dependent, rapamycin
-
resistant pathway sensitizes glioblastomas to antilipogenic therapy.

Sci Signal. ;2(101):ra82

PMID:

20009104

56.

Plaisier

CL,
Horvath S
,
Huertas
-
Vazquez

A, Cruz
-
Bautista I, Herrera MF, Tusie
-
Luna T, Aguilar
-
Salinas C, Pajukanta
P (2009)
A systems genetics approach implicates USF1, FADS3 and other causal candidate genes for familial
combined hyperlipidemia
.
PloS Genetics
;5(9):e1000642

PMID: 19750004

57.

Yoon NK, Seligson DB, Chia D, Elshimali Y, Sulur G, Li A,
Horvath S
, Maresh E, Mah V,
Bose S, Bonavida B,
Goodglick L(2009)
Higher expression levels of 14
-
3
-
3sigma in ductal carcinoma in situ of the breast predict

poorer
outcome
.
Cancer Biomark. 2009;5(4):215
-
24.

PMID: 19729831

58.

Saris

CG,
Horvath S

(Joint First Author),
van Vught

PW,
van Es

MA,
Blauw

HM,
Fuller

TF,
Langfelder

P,

DeYoung

J,
Wokke

JH,
Veldink

JH,
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68

137.

Mischel PS, Shai R, Shi T, Choe GY,
Horvath S
, Seligson D, Kremen TJ, Palotie A
, Liau LM, Cloughesy TF, Nelson
S (2003) Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene 22(15):2361
-
73

138.

Freedland S, Seligson DB, Liu AY, Pantuck AJ,
Horvath S
, Wieder JA, Zisman A, Nguyen D, Tso CL, Palotie A,
B
elldegrun AS (2003) Loss of CD10 (neutral endopeptidase) is a frequent and early event in prostate cancer. Prostate
55(1):71
-
80

139.

Tilgen N, Rebstock J,
Horvath S
, Propping P, Elger CE, Heils A (2003) Prodynorphin gene promotor polymorphism
and temporal lobe
epilepsy (Comment/Letter). Ann Neurol 53(2):280
-
1

140.

Tilgen N, Pfeiffer H, Rau B,
Horvath S
, Elger CE, Propping P, Heils A (2002) Association analysis between the
interleukin 1ß (
-
511) gene polymorphism and susceptibility to febrile convulsions. Neurosci Let
t. 334(1):68
-
70

141.

Visapaa H, Seligson DB, Huang Y, Rao JY, Belldegrun A,
Horvath S
, Palotie A (2003) Ki
-
67, Gelsolin and PTEN
expression in sarcomatoid renal tumors. Urol Res 30(6):387
-
9

142.

Visapaa H, Bui M, Huang Y, Seligson D, Tsai H, Pantuck A, Figlin R, Rao JY, Belldegrun A,
Horvath S

and Palotie
A (2003) Correlation of Ki67 and gelsolin expression to clinical outcome in renal clear
-
cell carcinoma. Urology 61(4)
845
-
850

143.

Ide H, Seligson DB
, Memarzadeh S,
Horvath S
, Xin L, Raffii B, Kacinski B, Palotie A, Witte ON, (2002) Expression
of colony stimulating factor 1 receptor (CSF
-
1R) in prostate development and prostate cancer progression. PNAS
99(22): 14404
-
14409

144.

Bui MHT, Seligson D, Han K, Pa
ntuck AJ, Dorey FJ, Huang Y,
Horvath S
, Leibovich BC, Liao S, Stanbridge E,
Lerman M, Palotie A, deKernion JB, Figlin RA and Belldegrun AS (2003)

Carbonic anhydrase IX is an independent
predictor of survival in advanced renal cell carcinoma: implications f
or prognosis and therapy. Clin Cancer Res
9(2):802
-
11

145.

Chiang S, Vu MC, Nguyen M, Strocker A,
Horvath S
, Shapiro N (2002) Adenotonsillar hypertrophy in pediatric
organ transplant recipients: A Cross
-
sectional Analysis. Otolaryngol Head Neck Surg 127(1):109
-
14

146.

Rao JY, Seligson DB, Visapaa H,
Horvath S
, Eeva M, Michel K, Pantuck A, Belldegrun A, Palotie A (2002) Tis
sue
microarray analysis

of cytoskeletal actin associated biomarkers gelsolin and E
-
cadherin in urothelial carcinoma.
Cancer 95(6):1247
-
57


9

147.

Azizzade
h B, Yip HT, Blackwell KE,
Horvath S
, Calcaterra TC, Buga GM, Ignarro LJ, Wang MB (2001) Nitric oxide
improves cisplatin cytotoxicity in head and neck squamous cell carcinoma. Laryngoscope 111:1896
-
1900

148.

Horvath S
, Wei E, Xu X, Palmer LJ, Baur M (2001): Fa
mily
-
based association test method: age of onset traits and
covariates. Genet Epidemiol 21 Suppl 1:S403
-
8

149.

Palmer LJ, Jacobs KB, Scurrah KJ, Xu X,
Horvath S
, Weiss ST (2001) Phenotypic definition and genome wide
linkage analysis using genetic variance compo
nents in a general population sample. Genet Epidemiol21 Suppl
1:S674
-
9

150.

Xu X, Palmer LJ,
Horvath S
, Wei LJ (2001) Combining multiple phenotypic traits optimally for detecting linkage with
sibpair observations. Genet Epidemiol 21 Suppl 1:S479
-
83

151.

Horvath

S
, X
u X, Laird NM (2001) The family based association test method: strategies for studying general
genotype
-
phenotype associations. Euro J Hum Gen 9:301
-
306

152.

Horvath S

and Baur M (2000) Future directions of research in statistical genetics. Statistics in Medic
ine 19:3337
-
3343

153.

Horvath S
, Windemuth C, Knapp M (2000) The discordant maximum likelihood binomial test does not replace the
transmission disequilibrium test (Letter) Am J of Hum Genet 67(2):531
-
4

154.

Heils A, Haug K, Kunz WS, Fernandez G,
Horvath S
, Rebstoc
k J, Propping P, Elger CE (2000) Interleukin
-
1beta
gene polymorphism and susceptibility to temporal lobe epilepsy with hippocampal sclerosis (Letter). Ann Neurol
48(6):948
-
50

155.

Haug K, Hallmann K,
Horvath S
, Sander T, Kubisch C, Rau B, Dullinger J, Beyenburg

S, Bongartz U, Elger CE,
Propping P, Heils A (2000) No evidence for association between the KCNQ3 gene and susceptibility to idiopathic
generalized epilepsy. Epilepsy Res 42(1):57
-
62

156.

Laird NM,
Horvath S
, Xu X (2000) Implementing a unified approach to fam
ily based tests of association. Genetic
Epidemiology (Suppl 1) 19:36
-
42

157.

Horvath S
, Laird NM, Knapp M (2000) The transmission/desequilibrium test (TDT) and parental genotype
reconstruction for X
-
chromosomal markers. American Journal of Human Genetics 66:1
161
-
1167

158.

Horvath S

and Laird NM (1998) A discordant
-
sibship test for disequilibrium and linkage: no need for parental data.
American Journal of Human Genetics, 63:1886
-
1897

159.

Blacker D, Wilcox MA, Laird NM, Rodes L,
Horvath S
, Go RC, Perry R, Watson B Jr, B
assett SS, McInnis MG,
Albert MS, Hyman BT, Tanzi R (1998) Alpha
-
2 macroglobulin is genetically associated with alzheimer disease. Nat
Genet 19(40):357
-
60

160.

Dolan L and
Horvath S

(1995) BRST properties of spin fields. Nucl
ear Physics B448: (1
-
2) 220
-
244

161.

Dolan L and
Horvath S

(1994) Gauge bosons in superstring theory. Nuclear Physics B416: 87
-
118


Peer Reviewed Conference Papers

162.

Latecki LJ, Venugopal R, Sobel M,
Horvath S

(2003) Tree
-
structured Partitioning Based on Splitting Histograms of
Distances. Proceedings Volume. Third IEEE Int. Conf. Data Mining (ICDM'0) Melbourne, FL

Books

163.

Horvath S

(2011) Weighted Network Analysis. Applications in Genomics and Systems Biology. Sp
ringer Book.
ISBN: 978
-
1
-
4419
-
8818
-
8

164.

Horvath S
, Laird NM (2002) Review of quantitative trait transmission disequilibrium tests.
Chapter in
Book:
"Biostatistical Genetics and Genetic Epidemiology", ISBN 0471486310 Ed
itors Elston, Olson and Palmer.


Selected Research Projects


5R01AG042511
-
02

(Horvath)






07/01/2013


06/30/2017

RO1
Systems genetic and reverse phenotypic

analysis of age and retirement

Role: PI.
In this application, we propose to apply/develop state of the art computational, statis
tical, and bioinformatic
approaches with which to investigate the association between genetic data and aging
-

related phenotypes. Specifically,
the study uses data from the Health and Retirement Study (HRS) and a systems biology approach to identifying rel
evant
SNPs and genetic pathways and machine learning techniques and reverse phenotyping methods to better understand the
complex relationship between genetics and aging outcomes including cognition and wealth.


1R25GM103774
-
01 (Papp, co
-
PI Horvath)




01
/01/2013
-
12/31/2017

R25: "Statistical Genomics and Systems Biology Workshop"

National Institute of General Medical Sciences



Role: As co
-
PI, I am in charge of organizing several week
-
long network analysis workshops to be held at UCLA.


CHDI (PI
William Yang, UCLA)

Collaborative Research on Huntington’s Disease Systems Biology

Role: I am one of 4 investigators who have entered into a collaborative arrangement with CHDI, which is a private, not
-
for
-
profit research organization that works with an i
nternational network of scientists to discover drugs that slow the

10

progression of Huntington’s disease. My group is in charge of collecting, pre
-
processing HD related data and to carry out
a systems biologic analysis with our method (weighted network analy
sis).


UCLA CFAR/AIDS Institute /CTSI seed grant (PI Horvath)

09/01/2012
-
01/08/2014

Diagnostic and prognostic biomarkers for HIV
-
Associated Non
-
AIDS (HANA) conditions

Role: As PI, I will direct the generation of DNA methylation data and the analysis of th
ese data.


Biostatistics Core Director
: Steve Horvath

Prostate
SPORE Director: Robert Reiter

Grant Duration: 2007
-
2012

Project Title:

UCLA Specialized Program of Research Excellence (SPORE) in Prostate Cancer.


1R01DA030913
-
01 (Levine, co
-
PI Horvath)



09/17/10
-
07/31/15

National Institute on Drug Abuse (NIDA)

Title: Pathways to HIV
-
associated neuorcognitive disorders: a systems biology approach.

In the proposed study, we will apply innovative systems biology approaches to the investigation o
f mild HIV
-
associated
neurocognitive disorders (HAND) pathogenesis. We focus our investigation on circulating blood monocytes, as these cells
are an early and key component of this pathogenesis. We will use integrated weighted gene co
-
expression network
an
alysis (IWGCNA), developed by the co
-
PI (Horvath), to develop meaningful biological pathways derived from monocyte
-
specific gene expression microarrays, HAND
-
associated genetic markers, and clinical diagnosis of HAND.


P01ES0167032 (Chesselet)





09/15/08



06/30/13

NIH/NIEHS




Center for Gene Environment in Parkinson's Disease

The UCLA
-
CGEP will explore mechanisms by which genetic and environmental influences combine to increase the risk
for Parkinson's disease in susceptible individuals through interpla
y between neurotoxic pesticides and biologic
mechanisms regulating the neurotransmitter dopamine in brain cells.



S058980 (Ophoff)






09/15/2008


06/30/2013



NIH/NATIONAL INSTITUTE OF NEUROLOGICAL


DISORDERS & STROKE

Title:
Genetics of gene expression

and gene mapping for amyotrophical lateral sclerosis

The main goal of this project is to perform a genome
-
wide gene expression profiling in peripheral blood in a sample of
Amyotrophic Lateral Sclerosis (ALS) patients and matched controls, all from a relat
ively homogeneous population in The
Netherlands. Next the expression data are used to find genetic sequence variations the expression data (eQTLs) and to
find SNPs for subtypes of the disease.



DE019255
-
01 (Wong)






05/01/2009


04/30/2011


NIH/NIDCR

Ti
tle:
Systems approach to Sjogren's syndrome pathogenesis

Identification of key molecular targets (key drivers) using weighted gene co
-
expression network analysis (WGCNA) for
both primary Sjogren's Syndrome pathogenesis and malignant lymphoma conversion. Bo
th gene expression and
proteomics data are integrated with gene ontology information to find pathways and key genes underlying the disease
phenotypes.



1 RC1 AG035610
-
01 (Coppola)

09/30/2009


07/31/2011




NIH/NIA




Title:
Genetic, genomic, and imaging

biomarkers in degenerative dementia

The major goals of this project are to integrate gene expression data and neuroimaging data to find biomarkers for
degenerative demential. Systems biologic methods will be used.



2 P01 HL030568 (Fogelman)





04/01/200
9


03/31/2014



NIH/NHLBI








Title:
Lipid and lipoprotein metabolism in atherosclerosis

The major goals of this project are to use gene expression data to find genes and pathways underlying atherosclerosis.



5 R01 DK072206 (Drake)

04/15/2009


04/14/2011




11

NIH/NIDDKD


Gene expression networks for metabolic syndrome traits in mice

The major goals of this project are to use systems biologic and systems genetic approaches for elucidating causal
networks underlying metabolic syndrome.



Consortium P
I: Steve Horvath

Core Director of Bioinformatics and Statistics

Program

Project

Director: Daniel R Salomon

Grant Number:

1U19AI063603
-
01

09/01/04
-
08/31/09

Project Title:

Genomics for Kidney Transplantation



Support Role: Co
-
Investigator

Grant Number: 1
R01 NS050151
-
01

12/01/2004
-

11/30/2009

Principal Investigator: MISCHEL, PAUL S MD

Project Title: Glioblastoma
-

Molecula
r Analysis for Clinical Trials


Grant Number: NCI CA16042

12/1/2001
-
11/20/2007

Funding agency: National Cancer Institute

Jonsson Co
mprehensive Cancer Center, UCLA

PI: Judith Gasson

Cancer Center Core grant, Base Unit Core Program


Grant number: 5 R01 HL072367
-
02

9/30/2002
-

7/31/2006

Funding agency: NIH, National Heart, Lung, and Blood Institute

PI: Stanley F Nelson

UCLA NHLBI
Shared Microarray Facility