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1

SWATH-MS in proteomics: current status

Wang, Jing, Sheng, Quanhu, Shyr, Yu

Journal:

International Journal of Computational Biology and Drug Design

Year:

2015

Language:

english

File:

PDF, 708 KB

english, 2015

2

p73 Is Required for Ovarian Follicle Development and Regulates a Gene Network Involved in Cell-to-Cell Adhesion

Santos Guasch, Gabriela L., Beeler, J Scott, Marshall, Clayton B., Shaver, Timothy M., Sheng, Quanhu, Johnson, Kimberly N., Boyd, Kelli L., Venters, Bryan J., Cook, Rebecca S., Pietenpol, Jennifer A.

Journal:

Year:

2018

Language:

english

File:

PDF, 14.78 MB

english, 2018

3

Inflammatory Heterogeneity in Aspirin Exacerbated Respiratory Disease

Scott, Will, Cahill, Katherine N., Milne, Ginger L., Li, Ping, Sheng, Quanhu, Huang, Li Ching, Dennis, Spencer, Snyder, Jacob, Bauer, Ashley M., Chandra, Rakesh K., Chowdhury, Naweed I., Turner, Justi

Journal:

Journal of Allergy and Clinical Immunology

Year:

2020

File:

PDF, 2.24 MB

2020

4

On the estimation of false positives in peptide identifications using decoy search strategy

Changyu Shen, Quanhu Sheng, Jie Dai, Yixue Li, Rong Zeng, Haixu Tang

Journal:

Year:

2009

Language:

english

File:

PDF, 605 KB

english, 2009

5

ProteinQuant Suite: a bundle of automated software tools for label-free quantitative proteomics

Benjamin Mann, Milan Madera, Quanhu Sheng, Haixu Tang, Yehia Mechref, Milos V. Novotny

Journal:

Rapid Communications in Mass Spectrometry

Year:

2008

Language:

english

File:

PDF, 245 KB

english, 2008

6

A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Quanhu Sheng, Yehia Mechref, Yixue Li, Milos V. Novotny, Haixu Tang

Journal:

Rapid Communications in Mass Spectrometry

Year:

2008

Language:

english

File:

PDF, 446 KB

english, 2008

7

SRMBUILDER: A USER-FRIENDLY TOOL FOR SELECTED REACTION MONITORING DATA ANALYSIS

SHENG, QUANHU, WU, CHAOCHAO, SU, ZHIDUAN, ZENG, RONG

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.51 MB

english, 2011

8

Very Low-Level Heteroplasmy mtDNA Variations Are Inherited in Humans

Guo, Yan, Li, Chung-I, Sheng, Quanhu, Winther, Jeanette F., Cai, Qiuyin, Boice, John D., Shyr, Yu

Journal:

Journal of Genetics and Genomics

Year:

2013

Language:

english

File:

PDF, 886 KB

english, 2013

9

Proteomic Changes in the Photoreceptor Outer Segment upon Intense Light Exposure

Hajkova, Dagmar, Imanishi, Yoshikazu, Palamalai, Vikram, Rao, K. C. Sekhar, Yuan, Chao, Sheng, Quanhu, Tang, Haixu, Zeng, Rong, Darrow, Ruth M., Organisciak, Daniel T., Miyagi, Masaru

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 2.16 MB

english, 2010

10

Multi-perspective quality control of Illumina exome sequencing data using QC3

Guo, Yan, Zhao, Shilin, Sheng, Quanhu, Ye, Fei, Li, Jiang, Lehmann, Brian, Pietenpol, Jennifer, Samuels, David C., Shyr, Yu

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

11

BuildSummary: Using a Group-Based Approach To Improve the Sensitivity of Peptide/Protein Identification in Shotgun Proteomics

Sheng, Quanhu, Dai, Jie, Wu, Yibo, Tang, Haixu, Zeng, Rong

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 929 KB

english, 2012

12

Illumina human exome genotyping array clustering and quality control

Guo, Yan, He, Jing, Zhao, Shilin, Wu, Hui, Zhong, Xue, Sheng, Quanhu, Samuels, David C, Shyr, Yu, Long, Jirong

Journal:

Nature Protocols

Year:

2014

Language:

english

File:

PDF, 2.82 MB

english, 2014

13

Delicate Analysis of Post-Translational Modifications on Dishevelled 3

Wu, Chaochao, Wei, Wei, Li, Chen, Li, Qingrun, Sheng, Quanhu, Zeng, Rong

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 3.83 MB

english, 2012

14

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

Tu, Chengjian, Li, Jun, Sheng, Quanhu, Zhang, Ming, Qu, Jun

Journal:

Journal of Proteome Research

Year:

2014

Language:

english

File:

PDF, 1.83 MB

english, 2014

15

[IEEE 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA) - Changsha, China (2010.09.23-2010.09.26)] 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA) - QuantWiz: A scalable parallel software package for label-free protein quantification

Wang, Jing, Zhang, Yunquan, Zhang, Xianyi, Sun, Xiangzheng, Quanhu Sheng,

Year:

2010

Language:

english

File:

PDF, 1.13 MB

english, 2010

16

ICan: An Optimized Ion-Current-Based Quantification Procedure with Enhanced Quantitative Accuracy and Sensitivity in Biomarker Discovery

Tu, Chengjian, Sheng, Quanhu, Li, Jun, Shen, Xiaomeng, Zhang, Ming, Shyr, Yu, Qu, Jun

Journal:

Journal of Proteome Research

Year:

2014

Language:

english

File:

PDF, 2.31 MB

english, 2014

17

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

Li, Yong Fuga, Arnold, Randy J., Li, Yixue, Radivojac, Predrag, Sheng, Quanhu, Tang, Haixu

Journal:

Journal of Computational Biology

Year:

2009

Language:

english

File:

PDF, 225 KB

english, 2009

18

Preprocessing Significantly Improves the Peptide/Protein Identification Sensitivity of High-resolution Isobarically Labeled Tandem Mass Spectrometry Data

Sheng, Quanhu, Li, Rongxia, Dai, Jie, Li, Qingrun, Su, Zhiduan, Guo, Yan, Li, Chen, Shyr, Yu, Zeng, Rong

Journal:

Molecular & Cellular Proteomics

Year:

2015

Language:

english

File:

PDF, 2.88 MB

english, 2015

19

Monitoring Newly Synthesized Proteins over the Adult Life Span of Caenorhabditis elegans

Vukoti, Krishna, Yu, Xiaokun, Sheng, Quanhu, Saha, Sudipto, Feng, Zhaoyang, Hsu, Ao-Lin, Miyagi, Masaru

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 783 KB

english, 2015

20

Detection of internal exon deletion with exon Del

Guo, Yan, Zhao, Shilin, Lehmann, Brian D, Sheng, Quanhu, Shaver, Timothy M, Stricker, Thomas P, Pietenpol, Jennifer A, Shyr, Yu

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 767 KB

english, 2014

21

DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis

Sheng, Quanhu, Shyr, Yu, Chen, Xi

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 220 KB

english, 2014

22

Serum Proteome Changes in Healthy Subjects with Different Genotypes of NOS1AP in the Chinese Population

Jiang, Feng, Wang, Congrong, Li, Rongxia, Sheng, Quanhu, Hu, Cheng, Zhang, Rong, Fang, Qichen, Bao, Yuqian, Xiang, Kunsan, Zeng, Rong, Jia, Weiping

Journal:

Journal of Diabetes Research

Year:

2013

Language:

english

File:

PDF, 421 KB

english, 2013

23

MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control

Guo, Yan, Zhao, Shilin, Ye, Fei, Sheng, Quanhu, Shyr, Yu

Journal:

BioMed Research International

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

24

Advanced Heat Map and Clustering Analysis Using Heatmap3

Zhao, Shilin, Guo, Yan, Sheng, Quanhu, Shyr, Yu

Journal:

BioMed Research International

Year:

2014

Language:

english

File:

PDF, 731 KB

english, 2014

25

Optimization of search engines and post-processing approaches to maximize peptide/protein identification for high-resolution mass data

Tu, Chengjian, Sheng, Quanhu, Li, Jun, Ma, Danjun, Shen, Xiaomeng, Wang, Xue, Shyr, Yu, Yi, Zhengping, Qu, Jun

Journal:

Journal of Proteome Research

Year:

2015

Language:

english

File:

PDF, 2.13 MB

english, 2015

26

Practicability of detecting somatic point mutation from RNA high throughput sequencing data

Sheng, Quanhu, Zhao, Shilin, Li, Chung-I, Shyr, Yu, Guo, Yan

Journal:

Year:

2016

Language:

english

File:

PDF, 903 KB

english, 2016

27

Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes

Guo, Yan, Bosompem, Amma, Mohan, Sanjay, Erdogan, Begum, Ye, Fei, Vickers, Kasey C., Sheng, Quanhu, Zhao, Shilin, Li, Chung-I, Su, Pei-Fang, Jagasia, Madan, Strickland, Stephen A., Griffiths, Elizabet

Journal:

Year:

2015

Language:

english

File:

PDF, 1.01 MB

english, 2015

28

Multi-perspective quality control of Illumina RNA sequencing data analysis

Sheng, Quanhu, Vickers, Kasey, Zhao, Shilin, Wang, Jing, Samuels, David C., Koues, Olivia, Shyr, Yu, Guo, Yan

Journal:

Briefings in Functional Genomics

Year:

2016

Language:

english

File:

PDF, 1.35 MB

english, 2016

29

High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML

Zhao, Yue, Liu, Qi, Acharya, Pankaj, Stengel, Kristy R., Sheng, Quanhu, Zhou, Xiaofan, Kwak, Hojoong, Fischer, Melissa A., Bradner, James E., Strickland, Stephen A., Mohan, Sanjay R., Savona, Michael

Journal:

Year:

2016

Language:

english

File:

PDF, 4.30 MB

english, 2016

30

lncRNA expression in the auditory forebrain during postnatal development

Guo, Yan, Zhang, Pan, Sheng, Quanhu, Zhao, Shilin, Hackett, Troy A.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.87 MB

english, 2016

31

Clinical and Biological Insights Into Combined Post- and Pre-Capillary Pulmonary Hypertension

Assad, Tufik R., Hemnes, Anna R., Larkin, Emma K., Glazer, Andrew M., Xu, Meng, Wells, Quinn S., Farber-Eger, Eric H., Sheng, Quanhu, Shyr, Yu, Harrell, Frank E., Newman, John H., Brittain, Evan L.

Journal:

Journal of the American College of Cardiology

Year:

2016

Language:

english

File:

PDF, 977 KB

english, 2016

32

A peptide-retrieval strategy enables significant improvement of quantitative performance without compromising confidence of identification

Tu, Chengjian, Shen, Shichen, Sheng, Quanhu, Shyr, Yu, Qu, Jun

Journal:

Journal of Proteomics

Year:

2017

Language:

english

File:

PDF, 1.61 MB

english, 2017

33

Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing

Guo, Yan, Vickers, Kasey, Xiong, Yanhua, Zhao, Shilin, Sheng, Quanhu, Zhang, Pan, Zhou, Wanding, Flynn, Charles R.

Journal:

Year:

2017

Language:

english

File:

PDF, 1.77 MB

english, 2017

34

MicroRNAs and tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute myeloid leukemia

Guo, Yan, Strickland, Stephen A., Mohan, Sanjay, Li, Shaoying, Bosompem, Amma, Vickers, Kasey C., Zhao, Shilin, Sheng, Quanhu, Kim, Annette S.

Journal:

Leukemia and Lymphoma

Year:

2017

Language:

english

File:

PDF, 1.53 MB

english, 2017

35

Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Jovanović, Bojana, Sheng, Quanhu, Seitz, Robert S., Lawrence, Kasey D., Morris, Stephan W., Thomas, Lance R., Hout, David R., Schweitzer, Brock L., Guo, Yan, Pietenpol, Jennifer A., Lehmann, Brian D.

Journal:

Year:

2017

Language:

english

File:

PDF, 2.82 MB

english, 2017

36

Heatmap3: an improved heatmap package with more powerful and convenient features

Shilin Zhao,Yan Guo,Quanhu Sheng,Yu Shyr

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.87 MB

english, 2014

37

Isolation of High-density Lipoproteins for Non-coding Small RNA Quantification

Michell, Danielle L., Allen, Ryan M., Landstreet, Stuart R., Zhao, Shilin, Toth, Cynthia L., Sheng, Quanhu, Vickers, Kasey C.

Journal:

Journal of Visualized Experiments

Year:

2016

Language:

english

File:

PDF, 483 KB

english, 2016

38

Dynamics of zebrafish heart regeneration using an HPLC-ESI-MS/MS approach

Ma, Danjun, Tu, Chengjian, Sheng, Quanhu, Yang, Yuxi, Kan, Zhisheng, Guo, Yan, Shyr, Yu, Scott, Ian C., Lou, Xin

Journal:

Journal of Proteome Research

Year:

2018

Language:

english

File:

PDF, 2.02 MB

english, 2018

39

RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment

Guo, Yan, Zhao, Shilin, Li, Chung-I, Sheng, Quanhu, Shyr, Yu

Journal:

Cancer Informatics

Year:

2014

Language:

english

File:

PDF, 918 KB

english, 2014

40

BET bromodomain proteins regulate enhancer function during adipogenesis

Brown, Jonathan D., Feldman, Zachary B., Doherty, Sean P., Reyes, Jaime M., Rahl, Peter B., Lin, Charles Y., Sheng, Quanhu, Duan, Qiong, Federation, Alexander J., Kung, Andrew L., Haldar, Saptarsi M.,

Journal:

Proceedings of the National Academy of Sciences

Year:

2018

Language:

english

File:

PDF, 12.02 MB

english, 2018

41

Directed Solutions to Address Differences in Access to Liver Transplantation

Ye, Fei, Sheng, Quanhu, Feurer, Irene D., Zhao, Zhiguo, Fan, Run, Teng, Jing, Ping, Jie, Rega, Scott A., Hanto, Douglas W., Shyr, Yu, Karp, Seth J.

Journal:

American Journal of Transplantation

Year:

2018

Language:

english

File:

PDF, 657 KB

english, 2018

42

Performance Investigation of Proteomic Identification by HCD/CID Fragmentations in Combination with High/Low-Resolution Detectors on a Tribrid, High-Field Orbitrap Instrument

Tu, Chengjian, Li, Jun, Shen, Shichen, Sheng, Quanhu, Shyr, Yu, Qu, Jun, Tang, Haixu

Journal:

Year:

2016

Language:

english

File:

PDF, 3.46 MB

english, 2016

43

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

Guo, Yan, Zhao, Shilin, Sheng, Quanhu, Guo, Mingsheng, Lehmann, Brian, Pietenpol, Jennifer, Samuels, David C., Shyr, Yu

Journal:

BioMed Research International

Year:

2015

Language:

english

File:

PDF, 2.15 MB

english, 2015

44

O18Quant: A Semiautomatic Strategy for Quantitative Analysis of High-Resolution 16 O/ 18 O Labeled Data

Guo, Yan, Miyagi, Masaru, Zeng, Rong, Sheng, Quanhu

Journal:

BioMed Research International

Year:

2014

Language:

english

File:

PDF, 1.94 MB

english, 2014

45

Corrigendum to “Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control”

Guo, Yan, Sheng, Quanhu, Samuels, David C., Lehmann, Brian, Bauer, Joshua A., Pietenpol, Jennifer, Shyr, Yu

Journal:

BioMed Research International

Year:

2017

Language:

english

File:

PDF, 1.04 MB

english, 2017

46

Recent Advances in High Throughput Sequencing Analysis

Guo, Yan, Han, Leng, Sheng, Quanhu

Journal:

International Journal of Genomics

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

47

The Landscape of Small Non-Coding RNAs in Triple-Negative Breast Cancer

Guo, Yan, Yu, Hui, Wang, Jing, Sheng, Quanhu, Zhao, Shilin, Zhao, Ying-Yong, Lehmann, Brian

Journal:

Year:

2018

Language:

english

File:

PDF, 9.28 MB

english, 2018

48

RnaSeqSampleSize: real data based sample size estimation for RNA sequencing

Zhao, Shilin, Li, Chung-I, Guo, Yan, Sheng, Quanhu, Shyr, Yu

Journal:

BMC Bioinformatics

Year:

2018

Language:

english

File:

PDF, 1.19 MB

english, 2018

49

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data

Guo, Yan, Zhao, Shilin, Sheng, Quanhu, Samuels, David C, Shyr, Yu

Journal:

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

50

Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins

Allen, Ryan M., Zhao, Shilin, Ramirez Solano, Marisol A., Zhu, Wanying, Michell, Danielle L., Wang, Yuhuan, Shyr, Yu, Sethupathy, Praveen, Linton, MacRae F., Graf, Gregory A., Sheng, Quanhu, Vickers,

Journal:

Journal of Extracellular Vesicles

Year:

2018

Language:

english

File:

PDF, 5.16 MB

english, 2018

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