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1

Fisher’s exact approach for post hoc analysis of a chi-squared test

Shan, Guogen, Gerstenberger, Shawn, Benos, Panayiotis V.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.56 MB

english, 2017

2

Dicoogle, a Pacs Featuring Profiled Content Based Image Retrieval

Valente, Frederico, Costa, Carlos, Silva, Augusto, Benos, Panayiotis V.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.99 MB

english, 2013

3

Is there a code for protein–DNA recognition? Probab(ilistical)ly…

Panayiotis V. Benos, Alan S. Lapedes, Gary D. Stormo

Journal:

Year:

2002

Language:

english

File:

PDF, 236 KB

english, 2002

4

Self-organizing neural networks to support the discovery of DNA-binding motifs

Shaun Mahony, Panayiotis V. Benos, Terry J. Smith, Aaron Golden

Journal:

Neural Networks

Year:

2006

Language:

english

File:

PDF, 1.07 MB

english, 2006

5

Extracting biologically significant patterns from short time series gene expression data

Alain B Tchagang, Kevin V Bui, Thomas McGinnis, Panayiotis V Benos

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 906 KB

english, 2009

6

HHMMiR: efficientde novoprediction of microRNAs using hierarchical hidden Markov models

Sabah Kadri, Veronica Hinman, Panayiotis V Benos

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.88 MB

english, 2009

7

Probabilistic Code for DNA Recognition by Proteins of the EGR Family

Panayiotis V. Benos, Alan S. Lapedes, Gary D. Stormo

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 2.51 MB

english, 2002

8

To bind or not to bind - FoxA1 determines estrogen receptor action in breast cancer progression

Rebecca J Watters, Panayiotis V Benos, Steffi Oesterreich

Journal:

Breast Cancer Research

Year:

2012

Language:

english

File:

PDF, 87 KB

english, 2012

9

Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways

Lu, Tung-Ying, Lin, Bo, Li, Yang, Arora, Arshi, Han, Lu, Cui, Cheng, Coronnello, Claudia, Sheng, Yi, Benos, Panayiotis V., Yang, Lei

Journal:

Journal of Molecular and Cellular Cardiology

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

10

Combined analysis reveals a core set of cycling genes

Yong Lu, Shaun Mahony, Panayiotis V Benos, Roni Rosenfeld, Itamar Simon…

Journal:

Year:

2007

Language:

english

File:

PDF, 454 KB

english, 2007

11

Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Shaun Mahony, David L Corcoran, Eleanor Feingold, Panayiotis V Benos

Journal:

Year:

2007

Language:

english

File:

PDF, 560 KB

english, 2007

12

Profibrotic Role of miR-154 in Pulmonary Fibrosis

Milosevic, Jadranka, Pandit, Kusum, Magister, Marcus, Rabinovich, Einat, Ellwanger, Daniel C., Yu, Guoying, Vuga, Louis J., Weksler, Benny, Benos, Panayiotis V., Gibson, Kevin F., McMillan, Michael, K

Journal:

American Journal of Respiratory Cell and Molecular Biology

Year:

2012

Language:

english

File:

PDF, 941 KB

english, 2012

13

[IEEE ICASSP 2008 - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing - Las Vegas, NV, USA (2008.03.31-2008.04.4)] 2008 IEEE International Conference on Acoustics, Speech and Signal Processing - Biological evaluation of biclustering algorithms using Gene Ontology and chIP-chip data

Tchagang, Alain B., Tewfik, Ahmed H., Benos, Panayiotis V.

Year:

2008

Language:

english

File:

PDF, 255 KB

english, 2008

14

DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies

Mahony, Shaun, Auron, Philip E., Benos, Panayiotis V.

Journal:

PLoS Computational Biology

Year:

2007

Language:

english

File:

PDF, 1.05 MB

english, 2007

15

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density

Coronnello, Claudia, Hartmaier, Ryan, Arora, Arshi, Huleihel, Luai, Pandit, Kusum V., Bais, Abha S., Butterworth, Michael, Kaminski, Naftali, Stormo, Gary D., Oesterreich, Steffi, Benos, Panayiotis V.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.02 MB

english, 2012

16

The Center for causal discovery of biomedical knowledge from Big Data

Cooper, Gregory F., Bahar, Ivet, Becich, Michael J., Benos, Panayiotis V., Berg, Jeremy, Espino, Jeremy U., Glymour, Clark, Jacobson, Rebecca Crowley, Kienholz, Michelle, Lee, Adrian V., Lu, Xinghua,

Journal:

Journal of the American Medical Informatics Association

Year:

2015

Language:

english

File:

PDF, 830 KB

english, 2015

17

Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells

Chandran, Uma R., Luthra, Soumya, Santana-Santos, Lucas, Mao, Ping, Kim, Sung-Hak, Minata, Mutsuko, Li, Jianfeng, Benos, Panayiotis V., DeWang, Mao, Hu, Bo, Cheng, Shi-Yuan, Nakano, Ichiro, Sobol, Rob

Journal:

Year:

2015

Language:

english

File:

PDF, 627 KB

english, 2015

18

Regulation of alveolar septation by microRNA-489

Olave, Nelida, Lal, Charitharth V., Halloran, Brian, Pandit, Kusum, Cuna, Alain C., Faye-Petersen, Ona M., Kelly, David R., Nicola, Teodora, Benos, Panayiotis V., Kaminski, Naftali, Ambalavanan, Namas

Journal:

AJP Lung Cellular and Molecular Physiology

Year:

2016

Language:

english

File:

PDF, 2.89 MB

english, 2016

19

MicroRNA expression profiling predicts clinical outcome of carboplatin/paclitaxel-based therapy in metastatic melanoma treated on the ECOG-ACRIN trial E2603

Villaruz, Liza C., Huang, Grace, Romkes, Marjorie, Kirkwood, John M., Buch, Shama C., Nukui, Tomoko, Flaherty, Keith T., Lee, Sandra J., Wilson, Melissa A., Nathanson, Katherine L., Benos, Panayiotis

Journal:

Clinical Epigenetics

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

20

[American Thoracic Society American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado - ()] D37. SYSTEMS BIOLOGY AND MOLECULAR PROFILING IN PULMONARY HEALTH AND DISEASE - Whole Transcriptome Study Of Mesenchymal Stem Cell Response To TGF-Beta 1

Kapetanaki, Maria, Gupta, Naveen, Chensny, Lara, Rojas, Mauricio, Benos, Panayiotis, Kaminski, Naftali

Year:

2011

Language:

english

File:

PDF, 17 KB

english, 2011

21

[American Thoracic Society American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans - ()] A97. EPIGENETIC MECHANISMS IN LUNG FIBROSIS - Regulation Telomerase and Telomere Length In IPF By MicroRNAs.

Singh, Mandal K., Tzfati, Yehuda, Chensny, Lara J., Benos, Panayiotis V., Kaminski, Naftali

Year:

2010

Language:

english

File:

PDF, 18 KB

english, 2010

22

Expression of Regulatory Platelet MicroRNAs in Patients with Sickle Cell Disease

Jain, Shilpa, Kapetanaki, Maria G., Raghavachari, Nalini, Woodhouse, Kimberly, Yu, Guoying, Barge, Suchitra, Coronnello, Claudia, Benos, Panayiotis V., Kato, Gregory J., Kaminski, Naftali, Gladwin, Ma

Journal:

Year:

2013

Language:

english

File:

PDF, 2.50 MB

english, 2013

23

Epigenetic and Transcriptomic Regulation of Lung Repair during Recovery from Influenza Infection

Pociask, Derek A., Robinson, Keven M., Chen, Kong, McHugh, Kevin J., Clay, Michelle E., Huang, Grace T., Benos, Panayiotis V., Janssen-Heininger, Yvonne M.W., Kolls, Jay K., Anathy, Vikas, Alcorn, Joh

Journal:

The American Journal of Pathology

Year:

2017

Language:

english

File:

PDF, 3.58 MB

english, 2017

24

[IEEE 2017 IEEE 33rd International Conference on Data Engineering (ICDE) - San Diego, CA, USA (2017.4.19-2017.4.22)] 2017 IEEE 33rd International Conference on Data Engineering (ICDE) - Integrated Theory-and Data-Driven Feature Selection in Gene Expression Data Analysis

Raghu, Vineet K., Ge, Xiaoyu, Chrysanthis, Panos K., Benos, Panayiotis V.

Year:

2017

Language:

english

File:

PDF, 932 KB

english, 2017

25

Non-coding single nucleotide variants affecting estrogen receptor binding and activity

Amir Bahreini,Kevin Levine,Lucas Santana-Santos,Panayiotis V. Benos…

Journal:

Genome Medicine

Year:

2016

Language:

english

File:

PDF, 1.14 MB

english, 2016

26

Learning mixed graphical models with separate sparsity parameters and stability-based model selection

Andrew J. Sedgewick,Ivy Shi,Rory M. Donovan,Panayiotis V. Benos

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 955 KB

english, 2016

27

Biomarker identification for statin sensitivity of cancer cell lines

Raghu, Vineet K., Beckwitt, Colin H., Warita, Katsuhiko, Wells, Alan, Benos, Panayiotis V., Oltvai, Zoltán N.

Journal:

Biochemical and Biophysical Research Communications

Year:

2017

Language:

english

File:

PDF, 1.04 MB

english, 2017

28

Comparison of strategies for scalable causal discovery of latent variable models from mixed data

Raghu, Vineet K., Ramsey, Joseph D., Morris, Alison, Manatakis, Dimitrios V., Sprites, Peter, Chrysanthis, Panos K., Glymour, Clark, Benos, Panayiotis V.

Journal:

International Journal of Data Science and Analytics

Year:

2018

Language:

english

File:

PDF, 693 KB

english, 2018

29

High Throughput Determination of TGFβ1/SMAD3 Targets in A549 Lung Epithelial Cells

Zhang, Yingze, Handley, Daniel, Kaplan, Tommy, Yu, Haiying, Bais, Abha S., Richards, Thomas, Pandit, Kusum V., Zeng, Qilu, Benos, Panayiotis V., Friedman, Nir, Eickelberg, Oliver, Kaminski, Naftali, R

Journal:

Year:

2011

Language:

english

File:

PDF, 770 KB

english, 2011

30

RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star

Kadri, Sabah, Hinman, Veronica F., Benos, Panayiotis V., Dupuy, Denis

Journal:

Year:

2011

Language:

english

File:

PDF, 576 KB

english, 2011

31

Transcriptional Program of Ciliated Epithelial Cells Reveals New Cilium and Centrosome Components and Links to Human Disease

Hoh, Ramona A., Stowe, Timothy R., Turk, Erin, Stearns, Tim, Benos, Panayiotis V.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.78 MB

english, 2012

32

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

Mostafavi, Sara, Battle, Alexis, Zhu, Xiaowei, Urban, Alexander E., Levinson, Douglas, Montgomery, Stephen B., Koller, Daphne, Benos, Panayiotis V.

Journal:

Year:

2013

Language:

english

File:

PDF, 752 KB

english, 2013

33

Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression

Garcia-Vedrenne, Ana Elisa, Groner, Maya, Page-Karjian, Annie, Siegmund, Gregor-Fausto, Singhal, Sonia, Sziklay, Jamie, Roberts, Steven, Benos, Panayiotis V.

Journal:

Year:

2013

Language:

english

File:

PDF, 1004 KB

english, 2013

34

SOP 3 : a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing®

Alexander, Angela M., Pecoraro, Christopher, Styche, Alexis, Rudert, William A., Benos, Panayiotis V., Ringquist, Steven, Trucco, Massimo

Journal:

Year:

2005

Language:

english

File:

PDF, 478 KB

english, 2005

35

ECCB 2018: The 17th European Conference on Computational Biology

Hatzigeorgiou, Artemis G, Bagos, Pantelis, Benos, Panayiotis V, Nikolaou, Christoforos, Moreau, Yves, Kavakiotis, Ioannis

Journal:

Year:

2018

Language:

english

File:

PDF, 119 KB

english, 2018

36

An Insulin-Responsive Sensor in the SIRT1 Disordered Region Binds DBC1 and PACS-2 to Control Enzyme Activity

Krzysiak, Troy C., Thomas, Laurel, Choi, You-Jin, Auclair, Sylvain, Qian, Yiqi, Luan, Shan, Krasnow, Stephanie M., Thomas, Laura L., Koharudin, Leonardus M.I., Benos, Panayiotis V., Marks, Daniel L.,

Journal:

Year:

2018

Language:

english

File:

PDF, 4.67 MB

english, 2018

37

piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks

Manatakis, Dimitris V, Raghu, Vineet K, Benos, Panayiotis V

Journal:

Year:

2018

Language:

english

File:

PDF, 522 KB

english, 2018

38

Mitochondria are a Substrate of Cellular Memory

Cheikhi, Amin, Wallace, Callen, Croix, Claudette St, Cohen, Charles, Tang, Wan-Yee, Wipf, Peter, Benos, Panayiotis V., Ambrosio, Fabrisia, Barchowsky, Aaron

Journal:

Free Radical Biology and Medicine

Year:

2018

Language:

english

File:

PDF, 1.47 MB

english, 2018

39

PARP1 rs1805407 Increases Sensitivity to PARP1 Inhibitors in Cancer Cells Suggesting an Improved Therapeutic Strategy

Abecassis, Irina, Sedgewick, Andrew J., Romkes, Marjorie, Buch, Shama, Nukui, Tomoko, Kapetanaki, Maria G., Vogt, Andreas, Kirkwood, John M., Benos, Panayiotis V., Tawbi, Hussein

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 1.96 MB

english, 2019

40

NanoR: A user-friendly R package to analyze and compare nanopore sequencing data

Bolognini, Davide, Bartalucci, Niccolò, Mingrino, Alessandra, Vannucchi, Alessandro Maria, Magi, Alberto, Benos, Panayiotis V.

Journal:

Year:

2019

Language:

english

File:

PDF, 3.66 MB

english, 2019

41

Proliferating SPP1/MERTK-expressing macrophages in idiopathic pulmonary fibrosis

Morse, Christina, Tabib, Tracy, Sembrat, John, Buschur, Kristina, Bittar, Humberto Trejo, Valenzi, Eleanor, Jiang, Yale, Kass, Daniel J., Gibson, Kevin, Chen, Wei, Mora, Ana, Benos, Panayiotis V., Roj

Journal:

European Respiratory Journal

Year:

2019

Language:

english

File:

PDF, 10.65 MB

english, 2019

42

Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers

Mandel, Jordan, Wang, Huabo, Normolle, Daniel P., Chen, Wei, Yan, Qi, Lucas, Peter C., Benos, Panayiotis V., Prochownik, Edward V.

Journal:

Year:

2019

Language:

english

File:

PDF, 14.88 MB

english, 2019

43

Expression patterns of small numbers of transcripts from functionally-related pathways predict survival in multiple cancers

Mandel, Jordan, Wang, Huabo, Normolle, Daniel P., Chen, Wei, Yan, Qi, Lucas, Peter C., Benos, Panayiotis V., Prochownik, Edward V.

Journal:

Year:

2019

File:

PDF, 14.88 MB

2019

44

Causal network perturbations for instance-specific analysis of single cell and disease samples

Buschur, Kristina L, Chikina, Maria, Benos, Panayiotis V, Birol, Inanc

Journal:

Year:

2019

File:

PDF, 514 KB

2019

45

The evolution of radiographic edema in ARDS and its association with clinical outcomes: A prospective cohort study in adult patients

Kotok, Daniel, Yang, Libing, Evankovich, John W., Bain, William, Dunlap, Daniel G., Shah, Faraaz, Zhang, Yingze, Manatakis, Dimitris V., Benos, Panayiotis V., Barbash, Ian J., Rapport, Sarah F., Lee,

Journal:

Journal of Critical Care

Year:

2020

Language:

english

File:

PDF, 641 KB

english, 2020

46

Respiratory Tract Dysbiosis is Associated With Worse Outcomes in Mechanically-Ventilated Patients

Kitsios, Georgios D, Yang, Haopu, Yang, Libing, Qin, Shulin, Fitch, Adam, Wang, Xiao-Hong, Fair, Katherine, Evankovich, John, Bain, William, Shah, Faraaz, Li, Kelvin, MethÃ©, Barbara, Benos, Panayioti

Journal:

American Journal of Respiratory and Critical Care Medicine

Year:

2020

File:

PDF, 4.11 MB

2020

47

An improvement of ComiR algorithm for microRNA target prediction by exploiting coding region sequences of mRNAs

Bertolazzi, Giorgio, Benos, Panayiotis V., Tumminello, Michele, Coronnello, Claudia

Journal:

BMC Bioinformatics

Year:

2020

File:

PDF, 1.25 MB

2020

48

[American Thoracic Society American Thoracic Society 2011 International Conference, May 13-18, 2011 â¢ Denver Colorado - ()] C109. 'OMICS APPROACHES TO LUNG DISEASES - Global Microrna Profiles Of Idiopathic Pulmonary Fibrosis Lungs Indicate Reversal Of Lung Differentiation

Pandit, Kusum, Milosevic, Jadranka, Benos, Panayiotis, Coronello, Claudia, Ben-Yehudah, Ahmi, Hagood, James, Ambalavanan, Namasivayam, Kaminski, Naftali

Year:

2011

File:

PDF, 18 KB

2011

49

[American Thoracic Society American Thoracic Society 2011 International Conference, May 13-18, 2011 â¢ Denver Colorado - ()] D37. SYSTEMS BIOLOGY AND MOLECULAR PROFILING IN PULMONARY HEALTH AND DISEASE - MRNA And MicroRNA Expression Profiles Indicate Disease Severity In Patients With Idiopathic Pulmonary Fibrosis

Juan-Guardela, Brenda, Tedrow, John, Herazo, Jose D., Aboud, Caroline, Pandit, Kusum, Chensny, Lara, Gur, David, Leader, Joseph K., Benos, Panayiotis, Richards, Thomas, Correll, Mick, Quackenbush, Joh

Year:

2011

File:

PDF, 20 KB

2011

50

[American Thoracic Society American Thoracic Society 2011 International Conference, May 13-18, 2011 â¢ Denver Colorado - ()] B66. REGULATING GENE EXPRESSION: MI-RNA, GROWTH FACTORS, ETC. - Mir 30b As A Potential Modifier Of Fibroblasts Phenotypes In Lung Fibrosis

Huleihel, Luai, Ben-Yehudah, Ahmi, Manor, Esther, Milosevic, Jadranka, Benos, Panayiotis, Chensny, Lara, Kaminski, Naftali

Year:

2011

File:

PDF, 19 KB

2011