Ay, Ferhat: search on Z-Library

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1

Hypergraph-based connectivity measures for signaling pathway topologies

Franzese, Nicholas, Groce, Adam, Murali, T. M., Ritz, Anna, Ay, Ferhat

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 7.02 MB

2019

2

Hypergraph-based connectivity measures for signaling pathway topologies

Franzese, Nicholas, Groce, Adam, Murali, T. M., Ritz, Anna, Ay, Ferhat

Journal:

PLoS Computational Biology

Year:

2019

Language:

english

File:

PDF, 7.02 MB

english, 2019

3

Form and function of topologically associating genomic domains in budding yeast

Eser, Umut, Chandler-Brown, Devon, Ay, Ferhat, Straight, Aaron F., Duan, Zhijun, Noble, William Stafford, Skotheim, Jan M.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 2.13 MB

english, 2017

4

The relationship between inferior vena cava diameter measured by bedside ultrasonography and central venous pressure value

Citilcioglu, Serenat, Sebe, Ahmet, Ay, Mehmet Oguzhan, Icme, Ferhat, Avci, Akkan, Gulen, Muge, Sahan, Mustafa, Satar, Salim

Journal:

Pakistan Journal of Medical Sciences

Year:

2014

Language:

english

File:

PDF, 923 KB

english, 2014

5

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

Su, Yufeng, Luo, Yunan, Zhao, Xiaoming, Liu, Yang, Peng, Jian, Ay, Ferhat

Journal:

PLoS Computational Biology

Year:

2019

File:

PDF, 1.54 MB

2019

6

SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

Ay, Ferhat, Kellis, Manolis, Kahveci, Tamer

Journal:

Journal of Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

7

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

Ay, Ferhat, Bunnik, Evelien M., Varoquaux, Nelle, Vert, Jean-Philippe, Noble, William Stafford, Le Roch, Karine G.

Journal:

Year:

2015

Language:

english

File:

PDF, 989 KB

english, 2015

8

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

Dileep, Vishnu, Ay, Ferhat, Sima, Jiao, Vera, Daniel L., Noble, William S., Gilbert, David M.

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 11.68 MB

english, 2015

9

Spontaneous Hemothorax Secondary to Oral Anticoagulation Therapy

Avci, Akkan, Kocer, Mursel, Gulen, Muge, Ay, Mehmet Oguzhan, Icme, Ferhat, Avci, Begum Seyda

Journal:

Journal of Academic Emergency Medicine Case Reports

Year:

2014

Language:

turkish

File:

PDF, 81 KB

turkish, 2014

10

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

Ma, Wenxiu, Ay, Ferhat, Lee, Choli, Gulsoy, Gunhan, Deng, Xinxian, Cook, Savannah, Hesson, Jennifer, Cavanaugh, Christopher, Ware, Carol B., Krumm, Anton, Shendure, Jay, Blau, C. Anthony, Disteche, Ch

Journal:

Year:

2018

Language:

english

File:

PDF, 1.61 MB

english, 2018

11

[ACM Press the First ACM International Conference - Niagara Falls, New York (2010.08.02-2010.08.04)] Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10 - Functional similarities of reaction sets in metabolic pathways

Ay, Ferhat, Kahveci, Tamer

Year:

2010

Language:

english

File:

PDF, 494 KB

english, 2010

12

Analysis methods for studying the 3D architecture of the genome

Ay, Ferhat, Noble, William S.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.99 MB

english, 2015

13

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control

Rivera-Mulia, Juan Carlos, Kim, Sebo, Gabr, Haitham, Chakraborty, Abhijit, Ay, Ferhat, Kahveci, Tamer, Gilbert, David M.

Journal:

Genome Research

Year:

2019

Language:

english

File:

PDF, 6.85 MB

english, 2019

14

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

Ay, Ferhat, Vu, Thanh H, Zeitz, Michael J, Varoquaux, Nelle, Carette, Jan E, Vert, Jean-Philippe, Hoffman, Andrew R, Noble, William S

Journal:

Year:

2015

Language:

english

File:

PDF, 2.66 MB

english, 2015

15

Evaluation of electrocardiographic parameters in patients with diabetes insipidus

Deniz, Ferhat, Kepez, Alper, Ay, Seyit Ahmet, Ergogan, Okan, Baskoy, Kamil, Guncıkan, Mustafa Nuri, Dogan, Zekeriya, Yonem, Arif

Journal:

Wiener klinische Wochenschrift

Year:

2015

Language:

english

File:

PDF, 344 KB

english, 2015

16

Selfish: discovery of differential chromatin interactions via a self-similarity measure

Ardakany, Abbas Roayaei, Ay, Ferhat, Lonardi, Stefano

Journal:

Year:

2019

Language:

english

File:

PDF, 845 KB

english, 2019

17

Serum SIRT1 level is higher in male patient with isolated hypogonadotropic hypogonadism: The first study in human

Başpınar, Ebubekir, Ay, Seyid Ahmet, Deniz, Ferhat, Başal, Şeref, Özsarı, Levent, Ipcioglu, Osman Metin, Cagiltay, Eylem, Baskoy, Kamil, Onem, Yalçın, Yonem, Arif

Journal:

Revista Internacional de Andrología

Year:

2016

Language:

english

File:

PDF, 562 KB

english, 2016

18

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

Kaul, Arya, Bhattacharyya, Sourya, Ay, Ferhat

Journal:

Nature Protocols

Year:

2020

File:

PDF, 1.13 MB

2020

19

Bipartite structure of the inactive mouse X chromosome

Deng, Xinxian, Ma, Wenxiu, Ramani, Vijay, Hill, Andrew, Yang, Fan, Ay, Ferhat, Berletch, Joel B., Blau, Carl Anthony, Shendure, Jay, Duan, Zhijun, Noble, William S., Disteche, Christine M.

Journal:

Year:

2015

Language:

english

File:

PDF, 7.97 MB

english, 2015

20

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

Lhoumaud, Priscillia, Badri, Sana, Rodriguez-Hernaez, Javier, Sakellaropoulos, Theodore, Sethia, Gunjan, Kloetgen, Andreas, Cornwell, MacIntosh, Bhattacharyya, Sourya, Ay, Ferhat, Bonneau, Richard, Ts

Journal:

Nature Communications

Year:

2019

File:

PDF, 4.42 MB

2019

21

Metastatic Prostate Adenocarcinoma of the Mandible Diagnosed With Oral Manifestations

Ayranci, Ferhat, Omezli, Mehmet Melih, Torul, Damla, Ay, Mustafa

Journal:

Journal of Craniofacial Surgery

Year:

2019

File:

PDF, 263 KB

2019

22

A FAST AND ACCURATE ALGORITHM FOR COMPARATIVE ANALYSIS OF METABOLIC PATHWAYS

AY, FERHAT, KAHVECI, TAMER, DE CRÉCY-LAGARD, VALÉRIE

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2009

Language:

english

File:

PDF, 1.76 MB

english, 2009

23

latrogenic Pneumothorax after Liver Biopsy

Gulen, Muge, Ay, Mehmet Oguzhan, Kaplan, Davut, Dizen, Hayrettin, Icme, Ferhat

Journal:

Journal of Academic Emergency Medicine Case Reports

Year:

2014

Language:

turkish

File:

PDF, 163 KB

turkish, 2014

24

[IEEE 2010 IEEE International Conference on BioInformatics and BioEngineering - Philadelphia, PA, USA (2010.05.31-2010.06.3)] 2010 IEEE International Conference on BioInformatics and BioEngineering - Finding Dynamic Modules of Biological Regulatory Networks

Ay, Ferhat, Dinh, Thang N., Thai, My T., Kahveci, Tamer

Year:

2010

Language:

english

File:

PDF, 295 KB

english, 2010

25

Identification of copy number variations and translocations in cancer cells from Hi-C data

Chakraborty, Abhijit, Ay, Ferhat

Journal:

Year:

2017

Language:

english

File:

PDF, 893 KB

english, 2017

26

Genomic Interaction Profiles in Breast Cancer Reveal Altered Chromatin Architecture

Zeitz, Michael J., Ay, Ferhat, Heidmann, Julia D., Lerner, Paula L., Noble, William S., Steelman, Brandon N., Hoffman, Andrew R., Deb, Sumitra

Journal:

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

27

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome

Zeitz, Michael J, Lerner, Paula P, Ay, Ferhat, Van Nostrand, Eric, Heidmann, Julia D, Noble, William S, Hoffman, Andrew R

Journal:

Nucleus (Landes Bioscience)

Year:

2013

Language:

english

File:

PDF, 2.06 MB

english, 2013

28

A predictive modeling approach for cell line-specific long-range regulatory interactions

Roy, Sushmita, Siahpirani, Alireza Fotuhi, Chasman, Deborah, Knaack, Sara, Ay, Ferhat, Stewart, Ron, Wilson, Michael, Sridharan, Rupa

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 8.25 MB

english, 2015

29

The relationship between neutrophil to lymphocyte ratio, platelet to lymphocyte ratio and thrombolysis in myocardial infarction risk score in patients with ST elevation acute myocardial infarction before primary coronary intervention

Acet, Halit, Ertaş, Faruk, Bilik, Mehmet Zihni, Akıl, Mehmet Ata, Özyurtlu, Ferhat, Aydın, Mesut, Oylumlu, Mustafa, Polat, Nihat, Yüksel, Murat, Yildiz, Abdulkadir, Kaya, Hasan, Akyüz, Abdurrahman, Ay

Journal:

Advances in Interventional Cardiology

Year:

2015

Language:

english

File:

PDF, 126 KB

english, 2015

30

Levofloxacin-Induced Hepatotoxicity and Death

Gulen, Muge, Ay, Mehmet Oguzhan, Avci, Akkan, Acikalin, Ayca, Icme, Ferhat

Journal:

American Journal of Therapeutics

Year:

2015

Language:

english

File:

PDF, 249 KB

english, 2015

31

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

Ay, Ferhat, Xu, Fei, Kahveci, Tamer, Isalan, Mark

Journal:

Year:

2009

Language:

english

File:

PDF, 357 KB

english, 2009

32

Effectiveness of therapeutic plasma exchange in patients with intermediate syndrome due to organophosphate intoxication

Yilmaz, Mustafa, Sebe, Ahmet, Ay, Mehmet Oguzhan, Gumusay, Umut, Topal, Metin, Atli, Mesude, Icme, Ferhat, Satar, Salim

Journal:

The American Journal of Emergency Medicine

Year:

2013

Language:

english

File:

PDF, 463 KB

english, 2013

33

[ACM Press the 2nd ACM Conference - Chicago, Illinois (2011.08.01-2011.08.03)] Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11 - A novel framework for large scale metabolic network alignments by compression

Dang, Michael, Ay, Ferhat, Kahveci, Tamer

Year:

2011

Language:

english

File:

PDF, 250 KB

english, 2011

34

The role of 3D genome organization in disease: From compartments to single nucleotides

Chakraborty, Abhijit, Ay, Ferhat

Journal:

Seminars in Cell & Developmental Biology

Year:

2018

Language:

english

File:

PDF, 2.07 MB

english, 2018

35

Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq

Sun, Xiangying, Wang, Zhezhen, Hall, Johnathon M., Perez-Cervantes, Carlos, Ruthenburg, Alexander J., Moskowitz, Ivan P., Gribskov, Michael, Yang, Xinan H., Ay, Ferhat

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 3.88 MB

2020

36

S-100B Levels in Stroke Patients

Satar, Salim, Açikalin, Ayça, Akpinar, Onur, Koc, Filiz, Sahan, Mustafa, Gulen, Muge, Icme, Ferhat, Topal, Metin, Ay, Mehmet O.

Journal:

Neurosurgery Quarterly

Year:

2014

Language:

english

File:

PDF, 144 KB

english, 2014

37

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

Schmiedel, Benjamin Joachim, Seumois, Grégory, Samaniego-Castruita, Daniela, Cayford, Justin, Schulten, Veronique, Chavez, Lukas, Ay, Ferhat, Sette, Alessandro, Peters, Bjoern, Vijayanand, Pandurangan

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 1.14 MB

english, 2016

38

Olfactory and gustatory functions in patients with non-complicated type 1 diabetes mellitus

Altundag, Aytug, Ay, Seyid Ahmet, Hira, Serdar, Salıhoglu, Murat, Baskoy, Kamil, Denız, Ferhat, Tekelı, Hakan, Kurt, Onuralp, Yonem, Arif, Hummel, Thomas

Journal:

European Archives of Oto-Rhino-Laryngology

Year:

2017

Language:

english

File:

PDF, 672 KB

english, 2017

39

A predictive modeling approach for cell line-specific long-range regulatory interactions

Roy, Sushmita, Siahpirani, Alireza Fotuhi, Chasman, Deborah, Knaack, Sara, Ay, Ferhat, Stewart, Ron, Wilson, Michael, Sridharan, Rupa

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 126 KB

english, 2016

40

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

Fotuhi Siahpirani, Alireza, Ay, Ferhat, Roy, Sushmita

Journal:

Year:

2016

Language:

english

File:

PDF, 3.88 MB

english, 2016

41

Retro- and orthonasal olfactory function in relation to olfactory bulb volume in patients with hypogonadotrophic hypogonadism

Salihoglu, Murat, Kurt, Onuralp, Ay, Seyid Ahmet, Baskoy, Kamil, Altundag, Aytug, Saglam, Muzaffer, Deniz, Ferhat, Tekeli, Hakan, Yonem, Arif, Hummel, Thomas

Journal:

Brazilian Journal of Otorhinolaryngology

Year:

2017

Language:

english

File:

PDF, 723 KB

english, 2017

42

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

Roayaei Ardakany, Abbas, Gezer, Halil Tuvan, Lonardi, Stefano, Ay, Ferhat

Journal:

Year:

2020

File:

PDF, 8.65 MB

2020

43

Metabolic network alignment in large scale by network compression

Ferhat Ay, Michael Dang, Tamer Kahveci

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 950 KB

english, 2012

44

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Libbrecht, Maxwell W., Ay, Ferhat, Hoffman, Michael M., Gilbert, David M., Bilmes, Jeffrey A., Noble, William Stafford

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 1.62 MB

english, 2015

45

TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer

Lio, Chan-Wang J., Shukla, Vipul, Samaniego-Castruita, Daniela, González-Avalos, Edahi, Chakraborty, Abhijit, Yue, Xiaojing, Schatz, David G., Ay, Ferhat, Rao, Anjana

Journal:

Science Immunology

Year:

2019

Language:

english

File:

PDF, 5.82 MB

english, 2019

46

Comprehensive identification and analysis of human accelerated regulatory DNA

Gittelman, Rachel M., Hun, Enna, Ay, Ferhat, Madeoy, Jennifer, Pennacchio, Len, Noble, William S., Hawkins, R. David, Akey, Joshua M.

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 1.53 MB

english, 2015

47

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

Ma, Wenxiu, Ay, Ferhat, Lee, Choli, Gulsoy, Gunhan, Deng, Xinxian, Cook, Savannah, Hesson, Jennifer, Cavanaugh, Christopher, Ware, Carol B, Krumm, Anton, Shendure, Jay, Blau, Carl Anthony, Disteche, C

Journal:

Year:

2014

Language:

english

File:

PDF, 1.47 MB

english, 2014

48

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Bhattacharyya, Sourya, Chandra, Vivek, Vijayanand, Pandurangan, Ay, Ferhat

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 2.10 MB

english, 2019

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