Kocher, Jean Pierre A.: search on Z-Library

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1

Genetic and Physical Mapping of Sex-Linked AFLP Markers in Nile Tilapia (Oreochromis niloticus)

Bo-Young Lee, Jean-Pierre Coutanceau, Catherine Ozouf-Costaz, Helena D’Cotta, Jean-Francois Baroiller, Thomas D. Kocher

Journal:

Marine Biotechnology

Year:

2011

Language:

english

File:

PDF, 204 KB

english, 2011

2

CpGtools: A Python Package for DNA Methylation Analysis

Wei, Ting, Nie, Jinfu, Larson, Nicholas B, Ye, Zhenqing, Eckel Passow, Jeanette E, Robertson, Keith D, Kocher, Jean-Pierre A, Wang, Liguo, Valencia, Alfonso

Journal:

Year:

2019

File:

PDF, 452 KB

2019

3

Circular RNAs and their associations with breast cancer subtypes

Nair, Asha A., Niu, Nifang, Tang, Xiaojia, Thompson, Kevin J., Wang, Liewei, Kocher, Jean-Pierre, Subramanian, Subbaya, Kalari, Krishna R.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.83 MB

english, 2016

4

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files

Hart, Steven N., Duffy, Patrick, Quest, Daniel J., Hossain, Asif, Meiners, Mike A, Kocher, Jean-Pierre

Journal:

Briefings in Bioinformatics

Year:

2015

Language:

english

File:

PDF, 352 KB

english, 2015

5

Multilevel Parallelization of AutoDock 4.2

Andrew P Norgan, Paul K Coffman, Jean-Pierre A Kocher, David J Katzmann, Carlos P Sosa

Journal:

Journal of Cheminformatics

Year:

2011

Language:

english

File:

PDF, 756 KB

english, 2011

6

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

Ravikumar, Komandur Elayavilli, Wagholikar, Kavishwar B., Li, Dingcheng, Kocher, Jean-Pierre, PhD, Hongfang Liu

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 4.08 MB

english, 2015

7

Free Energy of Cavity Formation in Liquid Water and Hexane

Prévost, Martine, Oliveira, Isabel T., Kocher, Jean-Pierre, Wodak, Shoshana J.

Journal:

Journal of Physical Chemistry

Year:

1996

Language:

english

File:

PDF, 330 KB

english, 1996

8

Erratum to: Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature

Ravikumar, Komandur Elayavilli, Wagholikar, Kavishwar B., Li, Dingcheng, Kocher, Jean-Pierre, Liu, Hongfang

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 333 KB

english, 2016

9

Copy number variation and cytidine analogue cytotoxicity: A genome-wide association approach

Krishna R Kalari, Scott J Hebbring, High Seng Chai, Liang Li, Jean-Pierre A Kocher, Liewei Wang, Richard M Weinshilboum

Journal:

Year:

2010

Language:

english

File:

PDF, 1.24 MB

english, 2010

10

Calculating Sample Size Estimates for RNA Sequencing Data

Hart, Steven N., Therneau, Terry M., Zhang, Yuji, Poland, Gregory A., Kocher, Jean-Pierre

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 366 KB

english, 2013

11

Exploring genetic associations with ceRNA regulation in the human genome

Li, Mulin Jun, Zhang, Jian, Liang, Qian, Xuan, Chenghao, Wu, Jiexing, Jiang, Peng, Li, Wei, Zhu, Yun, Wang, Panwen, Fernandez, Daniel, Shen, Yujun, Chen, Yiwen, Kocher, Jean-Pierre A., Yu, Ying, Sham,

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 5.73 MB

english, 2017

12

Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation

Baheti, Saurabh, Singh, Prachi, Zhang, Yun, Evans, Jared, Jensen, Michael D, Somers, Virend K, Kocher, Jean-Pierre A, Sun, Zhifu, Chakkera, Harini A

Journal:

Year:

2017

Language:

english

File:

PDF, 693 KB

english, 2017

13

Author Correction: UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq

Sun, Zhifu, Nair, Asha, Chen, Xianfeng, Prodduturi, Naresh, Wang, Junwen, Kocher, Jean-Pierre

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 661 KB

english, 2018

14

Mass Homozygotes Accumulation in the NCI-60 Cancer Cell Lines As Compared to HapMap Trios, and Relation to Fragile Site Location

Ruan, Xiaoyang, Kocher, Jean-Pierre A., Pommier, Yves, Liu, Hongfang, Reinhold, William C., Tan, Patrick

Journal:

Year:

2012

Language:

english

File:

PDF, 512 KB

english, 2012

15

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models

Larson, Nicholas B., Wang, Chen, Na, Jie, Rowsey, Ross A., Highsmith, William Edward, Hoppman, Nicole L., Kocher, Jean-Pierre, Klee, Eric W.

Journal:

Journal of Computational Biology

Year:

2018

Language:

english

File:

PDF, 504 KB

english, 2018

16

Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine

Prodduturi, Naresh, Bhagwate, Aditya, Kocher, Jean-Pierre A., Sun, Zhifu

Journal:

BMC Medical Genomics

Year:

2018

Language:

english

File:

PDF, 1.73 MB

english, 2018

17

Identifying New Therapeutic Targets via Modulation of Protein Corona Formation by Engineered Nanoparticles

Arvizo, Rochelle R., Giri, Karuna, Moyano, Daniel, Miranda, Oscar R., Madden, Benjamin, McCormick, Daniel J., Bhattacharya, Resham, Rotello, Vincent M., Kocher, Jean-Pierre, Mukherjee, Priyabrata

Journal:

Year:

2012

Language:

english

File:

PDF, 557 KB

english, 2012

18

Linnorm: improved statistical analysis for single cell RNA-seq expression data

Yip, Shun H., Wang, Panwen, Kocher, Jean-Pierre A., Sham, Pak Chung, Wang, Junwen

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 2.15 MB

english, 2017

19

[WORLD SCIENTIFIC Pacific Symposium on Biocomputing 2020 - Kohala Coast, Hawaii, USA (3 â 7 January 2020)] Biocomputing 2020 - Coverage profile correction of shallow-depth circulating cell-free DNA sequencing via multidistance learning

Larson, Nicholas B., Larson, Melissa C., Na, Jie, Sosa, Carlos P., Wang, Chen, Kocher, Jean-Pierre, Rowsey, Ross

File:

PDF, 1.54 MB

20

SNPPicker: High quality tag SNP selection across multiple populations

Hugues Sicotte, David N Rider, Gregory A Poland, Neelam Dhiman, Jean-Pierre A Kocher

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 290 KB

english, 2011

21

Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions

Rooman, Marianne J., Kocher, Jean Pierre A., Wodak, Shoshana J.

Journal:

Year:

1992

Language:

english

File:

PDF, 2.24 MB

english, 1992

22

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers

Li, Mulin Jun, Yao, Hongcheng, Huang, Dandan, Liu, Huanhuan, Liu, Zipeng, Xu, Hang, Qin, Yiming, Prinz, Jeanette, Xia, Weiyi, Wang, Panwen, Yan, Bin, Tran, Nhan L., Kocher, Jean-Pierre, Sham, Pak C.,

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

23

Factors Influencing the Ability of Knowledge-based Potentials to Identify Native Sequence-Structure Matches

Jean-Pierre A. Kocher, Marianne J. Rooman, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1994

File:

PDF, 1.01 MB

1994

24

Properties of the protein matrix revealed by the free energy of cavity formation

Jean-Pierre Kocher, Martine Prévost, Shoshana J Wodak, Byungkook Lee

Journal:

Year:

1996

Language:

english

File:

PDF, 971 KB

english, 1996

25

Novel Neural Network Approach to Predict Drug-Target Interactions Based on Drug Side Effects and Genome-Wide Association Studies

Prinz, Jeanette, Koohi-Moghadam, Mohamad, Sun, Hongzhe, Kocher, Jean-Pierre A., Wang, Junwen

Journal:

Year:

2018

Language:

english

File:

PDF, 978 KB

english, 2018

26

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays

High Seng Chai, Terry M Therneau, Kent R Bailey, Jean-Pierre A Kocher

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.24 MB

english, 2010

27

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

Sun, Zhifu, Evans, Jared, Bhagwate, Aditya, Middha, Sumit, Bockol, Matthew, Yan, Huihuang, Kocher, Jean-Pierre

Journal:

Year:

2014

Language:

english

File:

PDF, 1013 KB

english, 2014

28

cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes

Li, Mulin Jun, Li, Miaoxin, Liu, Zipeng, Yan, Bin, Pan, Zhicheng, Huang, Dandan, Liang, Qian, Ying, Dingge, Xu, Feng, Yao, Hongcheng, Wang, Panwen, Kocher, Jean-Pierre A., Xia, Zhengyuan, Sham, Pak Ch

Journal:

Year:

2017

Language:

english

File:

PDF, 5.42 MB

english, 2017

29

Understanding Protein–Nanoparticle Interaction: A New Gateway to Disease Therapeutics

Giri, Karuna, Shameer, Khader, Zimmermann, Michael T., Saha, Sounik, Chakraborty, Prabir K., Sharma, Anirudh, Arvizo, Rochelle R., Madden, Benjamin J., Mccormick, Daniel J., Kocher, Jean-Pierre A., Bh

Journal:

Bioconjugate Chemistry

Year:

2014

Language:

english

File:

PDF, 728 KB

english, 2014

30

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

Sun, Zhifu, Cunningham, Julie, Slager, Susan, Kocher, Jean-Pierre

Journal:

Year:

2015

Language:

english

File:

PDF, 929 KB

english, 2015

31

Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags

Chen, Xianfeng, Johnson, Stephen, Jeraldo, Patricio, Wang, Junwen, Chia, Nicholas, Kocher, Jean-Pierre A, Chen, Jun

Journal:

Year:

2017

Language:

english

File:

PDF, 1.56 MB

english, 2017

32

Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data

Baheti, Saurabh, Kanwar, Rahul, Goelzenleuchter, Meike, Kocher, Jean-Pierre A., Beutler, Andreas S., Sun, Zhifu

Journal:

Year:

2016

Language:

english

File:

PDF, 772 KB

english, 2016

33

Prognostic subclass of intrahepatic cholangiocarcinoma by integrative molecular–clinical analysis and potential targeted approach

Ahn, Keun Soo, O’Brien, Daniel, Kang, Yu Na, Mounajjed, Taofic, Kim, Yong Hoon, Kim, Tae-Seok, Kocher, Jean-Pierre A., Allotey, Loretta K., Borad, Mitesh J., Roberts, Lewis R., Kang, Koo Jeong

Journal:

Hepatology International

Year:

2019

Language:

english

File:

PDF, 4.51 MB

english, 2019

34

A Sequence-Based Variation Map of Zebrafish

Patowary, Ashok, Purkanti, Ramya, Singh, Meghna, Chauhan, Rajendra, Singh, Angom Ramcharan, Swarnkar, Mohit, Singh, Naresh, Pandey, Vikas, Torroja, Carlos, Clark, Matthew D., Kocher, Jean-Pierre, Clar

Journal:

Year:

2013

Language:

english

File:

PDF, 278 KB

english, 2013

35

[IEEE 2008 Eighth IEEE International Conference on Data Mining (ICDM) - Pisa, Italy (2008.12.15-2008.12.19)] 2008 Eighth IEEE International Conference on Data Mining - Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction

Hwang, TaeHyun, Tian, Ze, Kuangy, Rui, Kocher, Jean-Pierre

Year:

2008

Language:

english

File:

PDF, 672 KB

english, 2008

36

Comprehensive Assessment of Genetic Variants Within TCF4 in Fuchs' Endothelial Corneal Dystrophy

Wieben, Eric D., Aleff, Ross A., Eckloff, Bruce W., Atkinson, Elizabeth J., Baheti, Saurabh, Middha, Sumit, Brown, William L., Patel, Sanjay V., Kocher, Jean-Pierre A., Baratz, Keith H.

Journal:

Investigative Opthalmology & Visual Science

Year:

2014

Language:

english

File:

PDF, 658 KB

english, 2014

37

RNA Toxicity and Missplicing in the Common Eye Disease Fuchs Endothelial Corneal Dystrophy

Du, Jintang, Aleff, Ross A., Soragni, Elisabetta, Kalari, Krishna, Nie, Jinfu, Tang, Xiaojia, Davila, Jaime, Kocher, Jean-Pierre, Patel, Sanjay V., Gottesfeld, Joel M., Baratz, Keith H., Wieben, Eric

Journal:

Journal of Biological Chemistry

Year:

2015

Language:

english

File:

PDF, 2.96 MB

english, 2015

38

CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies

Chen, Jun, Just, Allan C., Schwartz, Joel, Hou, Lifang, Jafari, Nadereh, Sun, Zhifu, Kocher, Jean-Pierre A., Baccarelli, Andrea, Lin, Xihong

Journal:

Year:

2016

Language:

english

File:

PDF, 122 KB

english, 2016

39

The impact of pharmacokinetic gene profiles across human cancers

Zimmermann, Michael T., Therneau, Terry M., Kocher, Jean-Pierre A.

Journal:

Year:

2018

Language:

english

File:

PDF, 1.81 MB

english, 2018

40

Batch effect correction for genome-wide methylation data with Illumina Infinium platform

Zhifu Sun, High Seng Chai, Yanhong Wu, Wendy M White, Krishna V Donkena, Christopher J Klein, Vesna D Garovic, Terry M Therneau, Jean-Pierre A Kocher

Journal:

BMC Medical Genomics

Year:

2011

Language:

english

File:

PDF, 646 KB

english, 2011

41

HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data

Baheti, Saurabh, Tang, Xiaojia, O’Brien, Daniel R., Chia, Nicholas, Roberts, Lewis R., Nelson, Heidi, Boughey, Judy C., Wang, Liewei, Goetz, Matthew P., Kocher, Jean-Pierre A., Kalari, Krishna R.

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1007 KB

english, 2018

42

Prediction of protein backbone conformation based on seven structure assignments: Influence of local interactions

Marianne J. Rooman, Jean-Pierre A. Kocher, Shoshana J. Wodak

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 2.53 MB

english, 1991

43

Linnorm: improved statistical analysis for single cell RNA-seq expression data

Yip, Shun H., Wang, Panwen, Kocher, Jean-Pierre A., Sham, Pak Chung, Wang, Junwen

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 40 KB

english, 2017

44

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries

Jeraldo, Patricio, Kalari, Krishna, Chen, Xianfeng, Bhavsar, Jaysheel, Mangalam, Ashutosh, White, Bryan, Nelson, Heidi, Kocher, Jean-Pierre, Chia, Nicholas, Janssen, Paul Jaak

Journal:

Year:

2014

Language:

english

File:

PDF, 845 KB

english, 2014

45

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

Yan W Asmann, Eric W Klee, E Aubrey Thompson, Edith A Perez, Sumit Middha, Ann L Oberg, Terry M Therneau, David I Smith, Gregory A Poland, Eric D Wieben, Jean-Pierre A Kocher

Journal:

Year:

2009

Language:

english

File:

PDF, 429 KB

english, 2009

46

Predicting regulatory variants with composite statistic

Li, Mulin Jun, Pan, Zhicheng, Liu, Zipeng, Wu, Jiexing, Wang, Panwen, Zhu, Yun, Xu, Feng, Xia, Zhengyuan, Sham, Pak Chung, Kocher, Jean-Pierre A., Li, Miaoxin, Liu, Jun S., Wang, Junwen

Journal:

Year:

2016

Language:

english

File:

PDF, 916 KB

english, 2016

47

Time course transcriptome data analysis for in vitro modeling of dilated cardiomyopathy using patient-derived induced pluripotent stem cells

Xing Li,Saranya Wyles,Sybil C Hrstka,Jean-Pierre A Kocher…

Journal:

BMC Bioinformatics

Year:

2015

Language:

english

File:

PDF, 225 KB

english, 2015

48

[IEEE 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Kansas City, MO (2017.11.13-2017.11.16)] 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Unraveling complex local genomic rearrangements from long-read data

Stephens, Zachary D., Iyer, Ravishankar K., Wang, Chen, Kocher, Jean-Pierre A.

Year:

2017

Language:

english

File:

PDF, 994 KB

english, 2017

49

Correction to: the impact of pharmacokinetic gene profiles across human cancers

Zimmermann, Michael T., Therneau, Terry M., Kocher, Jean-Pierre A.

Journal:

Year:

2018

Language:

english

File:

PDF, 240 KB

english, 2018

50

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

Li, Mulin Jun, Liu, Zipeng, Wang, Panwen, Wong, Maria P., Nelson, Matthew R., Kocher, Jean-Pierre A., Yeager, Meredith, Sham, Pak Chung, Chanock, Stephen J., Xia, Zhengyuan, Wang, Junwen

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.70 MB

english, 2015

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