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1

Systematic variation in gene expression patterns in human cancer cell lines

Ross, Douglas T., Scherf, Uwe, Eisen, Michael B., Perou, Charles M., Rees, Christian, Spellman, Paul, Iyer, Vishwanath, Jeffrey, Stefanie S., Van de Rijn, Matt, Waltham, Mark

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 1.47 MB

english, 2000

2

An Adaptive Single-step FDR Procedure with Applications to DNA Microarray Analysis

Vishwanath Iyer, Sanat Sarkar

Journal:

Biometrical Journal

Year:

2007

Language:

english

File:

PDF, 145 KB

english, 2007

3

Involvement of JNK/p73/NOXA in vitamin E analog-induced apoptosis of human breast cancer cells

Pei Wang, Weiping Yu, Zhanzhi Hu, Li Jia, Vishwanath R. Iyer, Bob G. Sanders, Kimberly Kline

Journal:

Molecular Carcinogenesis

Year:

2008

Language:

english

File:

PDF, 221 KB

english, 2008

4

Fur regulates acid resistance in Shigella flexneri via RyhB and ydeP

Amanda G. Oglesby, Erin R. Murphy, Vishwanath R. Iyer, Shelley M. Payne

Journal:

Molecular Microbiology

Year:

2005

Language:

english

File:

PDF, 237 KB

english, 2005

5

Genome-wide maps of DNA-protein interactions using a yeast ORF and intergenic microarray

Iyer, Vishwanath R., Horak, Christine, Kuras, Laurent, Kosa, Peter, Scafe, Charles, Botstein, David, Struhl, Kevin, Snyder, Michael, Brown, Patrick O.

Journal:

Nature Genetics

Year:

1999

Language:

english

File:

PDF, 91 KB

english, 1999

6

Drug target validation and identification of secondary drug target effects using DNA microarrays

Marton, Matthew J., DeRisi, Joseph L., Bennett, Holly A., Iyer, Vishwanath R., Meyer, Michael R., Roberts, Christopher J., Stoughton, Roland, Burchard, Julja, Slade, David, Dai, Hongyue

Journal:

Nature Medicine

Year:

1998

Language:

english

File:

PDF, 596 KB

english, 1998

7

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

Iyer, Vishwanath R., Horak, Christine E., Scafe, Charles S., Botstein, David, Snyder, Michael, Brown, Patrick O.

Journal:

Year:

2001

Language:

english

File:

PDF, 363 KB

english, 2001

8

Characterizing the physical genome

Pollack, Jonathan R., Iyer, Vishwanath R.

Journal:

Nature Genetics

Year:

2002

Language:

english

File:

PDF, 1.00 MB

english, 2002

9

Genetic reconstruction of a functional transcriptional regulatory network

Hu, Zhanzhi, Killion, Patrick J, Iyer, Vishwanath R

Journal:

Nature Genetics

Year:

2007

Language:

english

File:

PDF, 208 KB

english, 2007

10

Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment

Kim, Jonghwan, Bhinge, Akshay A, Morgan, Xochitl C, Iyer, Vishwanath R

Journal:

Year:

2004

Language:

english

File:

PDF, 278 KB

english, 2004

11

CARM1 promotes adipocyte differentiation by coactivating PPARγ

Yadav, Neelu, Cheng, Donghang, Richard, Stephane, Morel, Melanie, Iyer, Vishwanath R, Aldaz, C Marcelo, Bedford, Mark T

Journal:

Year:

2008

Language:

english

File:

PDF, 199 KB

english, 2008

12

The chromo domain protein Chd1p from budding yeast is an ATP-dependent chromatin-modifying factor

Tran, Hien G, Steger, David J, Iyer, Vishwanath R, Johnson, Alexander D

Journal:

The EMBO Journal

Year:

2000

Language:

english

File:

PDF, 606 KB

english, 2000

13

Nucleosome positioning: bringing order to the eukaryotic genome

Vishwanath R. Iyer

Journal:

Trends in Cell Biology

Year:

2012

Language:

english

File:

PDF, 783 KB

english, 2012

14

Exploring the post-transcriptional RNA world with DNA microarrays

Vishwanath R. Iyer

Journal:

Trends in Biotechnology

Year:

2004

Language:

english

File:

PDF, 196 KB

english, 2004

15

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

Patrick J Killion, Gavin Sherlock, Vishwanath R Iyer

Journal:

BMC Bioinformatics

Year:

2003

Language:

english

File:

PDF, 261 KB

english, 2003

16

Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

Xochitl C Morgan, Shulin Ni, Daniel P Miranker, Vishwanath R Iyer

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.16 MB

english, 2007

17

Quantitative gene expression assessment identifies appropriate cell line models for individual cervical cancer pathways

Mark W Carlson, Vishwanath R Iyer, Edward M Marcotte

Journal:

Year:

2007

Language:

english

File:

PDF, 1.35 MB

english, 2007

18

Genome-wide analysis of chromatin status using tiling microarrays

Sushma Shivaswamy, Vishwanath R. Iyer

Journal:

Year:

2007

Language:

english

File:

PDF, 528 KB

english, 2007

19

Coordinate Regulation of Yeast Ribosomal Protein Genes Is Associated with Targeted Recruitment of Esa1 Histone Acetylase

Juliet L Reid, Vishwanath R Iyer, Patrick O Brown, Kevin Struhl

Journal:

Year:

2000

Language:

english

File:

PDF, 495 KB

english, 2000

20

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

Yunyun Ni, Amelia Weber Hall, Anna Battenhouse, Vishwanath R Iyer

Journal:

Year:

2012

Language:

english

File:

PDF, 277 KB

english, 2012

21

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

Patrick J Killion, Vishwanath R Iyer

Journal:

Year:

2008

Language:

english

File:

PDF, 11.61 MB

english, 2008

22

PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli

Jian Gu, Vishwanath R Iyer

Journal:

Year:

2006

Language:

english

File:

PDF, 10.68 MB

english, 2006

23

Translating genome sequences into biological understanding

Vishwanath R Iyer

Journal:

Year:

2003

Language:

english

File:

PDF, 51 KB

english, 2003

24

Bright/Arid3A Acts as a Barrier to Somatic Cell Reprogramming through Direct Regulation of Oct4, Sox2, and Nanog

Popowski, Melissa, Templeton, Troy D., Lee, Bum-Kyu, Rhee, Catherine, Li, He, Miner, Cathrine, Dekker, Joseph D., Orlanski, Shari, Bergman, Yehudit, Iyer, Vishwanath R., Webb, Carol F., Tucker, Haley

Journal:

Stem Cell Reports

Year:

2014

Language:

english

File:

PDF, 2.39 MB

english, 2014

25

An eQTL analysis of the human glioblastoma multiforme genome

Shpak, Max, Hall, Amelia Weber, Goldberg, Marcus M., Derryberry, Dakota Z., Ni, Yunyun, Iyer, Vishwanath R., Cowperthwaite, Matthew C.

Journal:

Year:

2014

Language:

english

File:

PDF, 879 KB

english, 2014

26

Absolute mRNA Levels and Transcriptional Initiation Rates in Saccharomyces cerevisiae

Vishwanath Iyer and Kevin Struhl

Journal:

Proceedings of the National Academy of Sciences

Year:

1996

Language:

english

File:

PDF, 1.09 MB

english, 1996

27

Global Transcriptional Profiling Reveals Distinct Functions of Thymic Stromal Subsets and Age-Related Changes during Thymic Involution

Ki, Sanghee, Park, Daechan, Selden, Hilary J., Seita, Jun, Chung, Haewon, Kim, Jonghwan, Iyer, Vishwanath R., Ehrlich, Lauren I.R.

Journal:

Year:

2014

Language:

english

File:

PDF, 5.07 MB

english, 2014

28

[IEEE 2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI) - Delhi, India (2014.9.24-2014.9.27)] 2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI) - A novel technique of Iris Identification for biometric systems

Garagad, Vishwanath G., Iyer, Nalini C.

Year:

2014

Language:

english

File:

PDF, 1.77 MB

english, 2014

29

Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns

Park, Daechan, Shivram, Haridha, Iyer, Vishwanath R

Journal:

Epigenetics & Chromatin

Year:

2014

Language:

english

File:

PDF, 1.19 MB

english, 2014

30

miR-503 represses human cell proliferation and directly targets the oncogene DDHD2 by non-canonical target pairing

Polioudakis, Damon, Abell, Nathan S, Iyer, Vishwanath R

Journal:

Year:

2015

Language:

english

File:

PDF, 1.23 MB

english, 2015

31

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Shibata, Yoichiro, Sheffield, Nathan C., Fedrigo, Olivier, Babbitt, Courtney C., Wortham, Matthew, Tewari, Alok K., London, Darin, Song, Lingyun, Lee, Bum-Kyu, Iyer, Vishwanath R., Parker, Stephen C.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.56 MB

english, 2012

32

Mechanisms of Cell Cycle Control Revealed by a Systematic and Quantitative Overexpression Screen in S. cerevisiae

Niu, Wei, Li, Zhihua, Zhan, Wenjing, Iyer, Vishwanath R., Marcotte, Edward M., Snyder, Michael

Journal:

Year:

2008

Language:

english

File:

PDF, 1.26 MB

english, 2008

33

Correction: Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Ding, Zhihao, Ni, Yunyun, Timmer, Sander W., Lee, Bum-Kyu, Battenhouse, Anna, Louzada, Sandra, Yang, Fengtang, Dunham, Ian, Crawford, Gregory E., Lieb, Jason D., Durbin, Richard, Iyer, Vishwanath R.,

Journal:

Year:

2015

Language:

english

File:

PDF, 53 KB

english, 2015

34

Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association

Ding, Zhihao, Ni, Yunyun, Timmer, Sander W., Lee, Bum-Kyu, Battenhouse, Anna, Louzada, Sandra, Yang, Fengtang, Dunham, Ian, Crawford, Gregory E., Lieb, Jason D., Durbin, Richard, Iyer, Vishwanath R.,

Journal:

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

35

Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation

Shivaswamy, Sushma, Bhinge, Akshay, Zhao, Yongjun, Jones, Steven, Hirst, Martin, Iyer, Vishwanath R.

Journal:

Year:

2008

Language:

english

File:

PDF, 956 KB

english, 2008

36

Patterns of Gene Expression in the Frontal Cortex Discriminate Alcoholic from Nonalcoholic Individuals

Liu, Jianwen, Lewohl, Joanne M, Harris, R Adron, Iyer, Vishwanath R, Dodd, Peter R, Randall, Patrick K, Mayfield, R Dayne

Journal:

Neuropsychopharmacology

Year:

2006

Language:

english

File:

PDF, 232 KB

english, 2006

37

Low-Frequency Electromagnetic Modeling for Electrical and Biological Systems Using MATLAB [Book Reviews]

King, Paul, Iyer, Vishwanath

Journal:

Year:

2016

Language:

english

File:

PDF, 324 KB

english, 2016

38

The Determinants of Directionality in Transcriptional Initiation

Bagchi, Dia N., Iyer, Vishwanath R.

Journal:

Trends in Genetics

Year:

2016

Language:

english

File:

PDF, 1.65 MB

english, 2016

39

TEMPORARY REMOVAL: Deep RNA-Seq analysis reveals unexpected features of human prostate basal epithelial cells

Zhang, Dingxiao, Park, Daechan, Lu, Yue, Shen, Jianjun, Iyer, Vishwanath R., Tang, Dean G.

Journal:

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

40

[IEEE 2016 10th European Conference on Antennas and Propagation (EuCAP) - Davos, Switzerland (2016.4.10-2016.4.15)] 2016 10th European Conference on Antennas and Propagation (EuCAP) - Increasing the impedance bandwidth of dipole and monopole antennas with parasitic elements

Iyer, Vishwanath, Kulkarni, Shashank, Zucchelli, Giorgia, Makarov, Sergey N.

Year:

2016

Language:

english

File:

PDF, 660 KB

english, 2016

41

[IEEE 2016 IEEE International Symposium on Antennas and Propagation & USNC/URSI National Radio Science Meeting - Fajardo, PR, USA (2016.6.26-2016.7.1)] 2016 IEEE International Symposium on Antennas and Propagation (APSURSI) - Using embedded element patterns for the analysis of small arrays

Iyer, Vishwanath, Kulkarni, Shashank, Steyskal, Hans, Makarov, Sergey N.

Year:

2016

Language:

english

File:

PDF, 375 KB

english, 2016

42

The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes

Lee, Yaelim, Park, Daechan, Iyer, Vishwanath R.

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 4.45 MB

english, 2017

43

The ATP-dependent chromatin remodeler Chd1 is recruited by transcription elongation factors and maintains H3K4me3/H3K36me3 domains at actively transcribed and spliced genes

Lee, Yaelim, Park, Daechan, Iyer, Vishwanath R.

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 34 KB

english, 2017

44

BCL11A is a critical component of a transcriptional network that activates RAG expression and VDJ recombination

Lee, Baeck-Seung, Lee, Bum-Kyu, Iyer, Vishwanath R., Sleckman, Barry P., Shaffer, Arthur L., Ippolito, Gregory C., Tucker, Haley O., Dekker, Joseph D.

Journal:

Molecular and Cellular Biology

Year:

2017

Language:

english

File:

PDF, 2.41 MB

english, 2017

45

Retraction for Lee et al., “The BCL11A Transcription Factor Directly Activates RAG Gene Expression and V(D)J Recombination”

Lee, Baeck-seung, Dekker, Joseph D., Lee, Bum-kyu, Iyer, Vishwanath R., Sleckman, Barry P., Shaffer, Arthur L., Ippolito, Gregory C., Tucker, Philip W.

Journal:

Molecular and Cellular Biology

Year:

2017

Language:

english

File:

PDF, 94 KB

english, 2017

46

Bivalent chromatin domains in glioblastoma reveal a subtype-specific signature of glioma stem cells

Hall, Amelia Weber, Battenhouse, Anna M, Shivram, Haridha, Morris, Adam R, Cowperthwaite, Matthew C, Shpak, Max, Iyer, Vishwanath R

Journal:

Cancer Research

Year:

2018

Language:

english

File:

PDF, 14.22 MB

english, 2018

47

Chromatin Accessibility Mapping Identifies Mediators of Basal Transcription and Retinoid-Induced Repression of OTX2 in Medulloblastoma

Wortham, Matthew, Guo, Changcun, Zhang, Monica, Song, Lingyun, Lee, Bum-Kyu, Iyer, Vishwanath R., Furey, Terrence S., Crawford, Gregory E., Yan, Hai, He, Yiping, Zheng, Deyou

Journal:

Year:

2014

Language:

english

File:

PDF, 1.84 MB

english, 2014

48

MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes

Polioudakis, Damon, Abell, Nathan S., Iyer, Vishwanath R., Navarro, Alfons

Journal:

Year:

2015

Language:

english

File:

PDF, 2.24 MB

english, 2015

49

Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies

Shivram, Haridha, Iyer, Vishwanath R

Journal:

Year:

2018

Language:

english

File:

PDF, 3.28 MB

english, 2018

50

Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis

Wang, Likai, Zhang, Fan, Rode, Siddharth, Chin, Kevin K., Ko, Eun Esther, Kim, Jonghwan, Iyer, Vishwanath R., Qiao, Hong

Journal:

Year:

2017

Language:

english

File:

PDF, 3.68 MB

english, 2017