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1

Metabolite identification and quantitation in LC-MS/MS-based metabolomics

Jun Feng Xiao, Bin Zhou, Habtom W. Ressom

Journal:

TrAC Trends in Analytical Chemistry

Year:

2012

Language:

english

File:

PDF, 641 KB

english, 2012

2

LC-MS-based metabolomics

Zhou, Bin, Xiao, Jun Feng, Tuli, Leepika, Ressom, Habtom W.

Journal:

Molecular BioSystems

Year:

2012

Language:

english

File:

PDF, 2.86 MB

english, 2012

3

Adaptive double self-organizing maps for clustering gene expression profiles

H. Ressom, D. Wang, P. Natarajan

Journal:

Neural Networks

Year:

2003

Language:

english

File:

PDF, 297 KB

english, 2003

4

Gamma-tocotrienol induced apoptosis is associated with unfolded protein response in human breast cancer cells

Dorrelyn Patacsil, Anh Thu Tran, Youn Sook Cho, Simeng Suy, Francisco Saenz, Irina Malyukova, Habtom Ressom, Sean P. Collins, Robert Clarke, Deepak Kumar

Journal:

The Journal of Nutritional Biochemistry

Year:

2012

Language:

english

File:

PDF, 876 KB

english, 2012

5

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke, Habtom W Ressom

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.05 MB

english, 2008

6

Increasing the efficiency of fuzzy logic-based gene expression data analysis

Ressom, Habtom, Reynolds, Robert, Varghese, Rency S.

Journal:

Physiological Genomics

Year:

2003

Language:

english

File:

PDF, 1.45 MB

english, 2003

7

MOTA: Network-Based Multi-Omic Data Integration for Biomarker Discovery

Fan, Ziling, Zhou, Yuan, Ressom, Habtom W.

Journal:

Year:

2020

File:

PDF, 1.08 MB

2020

8

A new method for alignment of LC-MALDI-TOF data

Zhiqun Tang, Lihua Zhang, Amrita K Cheema, Habtom W Ressom

Journal:

Proteome Science

Year:

2011

Language:

english

File:

PDF, 384 KB

english, 2011

9

Enrichment of low molecular weight fraction of serum for MS analysis of peptides associated with hepatocellular carcinoma

Eduard Orvisky, Steven K. Drake, Brian M. Martin, Mohamed Abdel-Hamid, Habtom W. Ressom, Rency S. Varghese, Yanming An, Daniel Saha, Glen L. Hortin, Christopher A. Loffredo, Radoslav Goldman

Journal:

Year:

2006

Language:

english

File:

PDF, 700 KB

english, 2006

10

A ciliary neuronotrophic factor from peripheral nerve and smooth muscle which is not retrogradely transported

P. J. Smet, I. K. Abrahamson, R. E. Ressom, R. A. Rush

Journal:

Neurochemical Research

Year:

1991

Language:

english

File:

PDF, 852 KB

english, 1991

11

Learning Premises of Fuzzy Rules for Knowledge Acquisition in Classification Problems

N. Xiong, L. Litz, H. Ressom

Journal:

Knowledge and Information Systems

Year:

2002

Language:

english

File:

PDF, 129 KB

english, 2002

12

Neural network-based light attenuation model for monitoring seagrass population in the Indian river lagoon

M. T. Musavi, H. Ressom, S. Srirangam, P. Natarajan, R. W. Virnstein, L. J. Morris, W. Tweedale

Journal:

Journal of Intelligent Information Systems

Year:

2007

Language:

english

File:

PDF, 321 KB

english, 2007

13

Applications of fuzzy logic in genomics

H. Ressom, P. Natarajan, R.S. Varghese, M.T. Musavi

Journal:

Fuzzy Sets and Systems

Year:

2005

Language:

english

File:

PDF, 553 KB

english, 2005

14

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data

Clarke, Robert, Ressom, Habtom W., Wang, Antai, Xuan, Jianhua, Liu, Minetta C., Gehan, Edmund A., Wang, Yue

Journal:

Nature Reviews Cancer

Year:

2008

Language:

english

File:

PDF, 521 KB

english, 2008

15

Effect of Akt inhibition on scatter factor-regulated gene expression in DU-145 human prostate cancer cells

Xu, J, Gao, M, Fan, S, Meng, Q, Goldberg, I D, Abounader, R, Ressom, H, Laterra, J J, Rosen, E M

Journal:

Year:

2006

Language:

english

File:

PDF, 436 KB

english, 2006

16

Identification of aberrant pathways and network activities from high-throughput data

Wang, J., Zhang, Y., Marian, C., Ressom, H. W.

Journal:

Briefings in Bioinformatics

Year:

2012

Language:

english

File:

PDF, 530 KB

english, 2012

17

Metabolomic profiling for biomarker discovery in pancreatic cancer

Prabhjit Kaur, Kathryn Sheikh, Alexander Kirilyuk, Ksenia Kirilyuk, Rajbir Singh, Habtom W. Ressom, Amrita K. Cheema

Journal:

International Journal of Mass Spectrometry

Year:

2012

Language:

english

File:

PDF, 1.17 MB

english, 2012

18

Reverse engineering module networks by PSO-RNN hybrid modeling

Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke, Habtom W Ressom

Journal:

Year:

2009

Language:

english

File:

PDF, 517 KB

english, 2009

19

An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice

Chen Cheng, Kil-Young Yun, Habtom W Ressom, Bijayalaxmi Mohanty, Vladimir B Bajic, Yulin Jia, Song Joong Yun, Benildo G de los Reyes

Journal:

Year:

2007

Language:

english

File:

PDF, 651 KB

english, 2007

20

Using a spike-in experiment to evaluate analysis of LC-MS data

Leepika Tuli, Tsung-Heng Tsai, Rency S Varghese, Jun Feng Xiao, Amrita Cheema, Habtom W Ressom

Journal:

Proteome Science

Year:

2012

Language:

english

File:

PDF, 351 KB

english, 2012

21

Ion annotation-assisted analysis of LC-MS based metabolomic experiment

Varghese, Rency S, Zhou, Bin, Ranjbar, Mohammad, Zhao, Yi, Ressom, Habtom W

Journal:

Proteome Science

Year:

2012

Language:

english

File:

PDF, 640 KB

english, 2012

22

Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis

Habtom W. Ressom, Jun Feng Xiao, Leepika Tuli, Rency S. Varghese, Bin Zhou, Tsung-Heng Tsai, Mohammad R. Nezami Ranjbar, Yi Zhao, Jinlian Wang, Cristina Di Poto, Amrita K. Cheema, Mahlet G. Tadesse, R

Journal:

Analytica Chimica Acta

Year:

2012

Language:

english

File:

PDF, 1.02 MB

english, 2012

23

Inversion of ocean color observations using particle swarm optimization

Slade, W.H., Ressom, H.W., Musavi, M.T., Miller, R.L.

Journal:

IEEE Transactions on Geoscience and Remote Sensing

Year:

2004

Language:

english

File:

PDF, 942 KB

english, 2004

24

Prioritization of putative metabolite identifications in LC-MS/MS experiments using a computational pipeline

Zhou, Bin, Xiao, Jun Feng, Ressom, Habtom W.

Journal:

Year:

2013

Language:

english

File:

PDF, 828 KB

english, 2013

25

Focus on Bioinformatics in Proteomics

Wu, Fang-Xiang, Ressom, Habtom, Dunn, Michael J.

Journal:

Year:

2013

Language:

english

File:

PDF, 556 KB

english, 2013

26

Feasibility of Identifying the Tobacco-related Global Metabolome in Blood by UPLC–QTOF-MS

Hsu, Ping-Ching, Zhou, Bin, Zhao, Yi, Ressom, Habtom W., Cheema, Amrita K., Pickworth, Wallace, Shields, Peter G.

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 1.51 MB

english, 2013

27

Analysis of LC−MS Data for Characterizing the Metabolic Changes in Response to Radiation

Varghese, Rency S., Cheema, Amrita, Cheema, Prabhdeep, Bourbeau, Marc, Tuli, Leepika, Zhou, Bin, Jung, Mira, Dritschilo, Anatoly, Ressom, Habtom W.

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 468 KB

english, 2010

28

Analysis of MALDI-TOF Mass Spectrometry Data for Discovery of Peptide and Glycan Biomarkers of Hepatocellular Carcinoma †

Ressom, Habtom W., Varghese, Rency S., Goldman, Lenka, An, Yanming, Loffredo, Christopher A., Abdel-Hamid, Mohamed, Kyselova, Zuzana, Mechref, Yehia, Novotny, Milos, Drake, Steven K, Goldman, Radoslav

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 2.17 MB

english, 2008

29

iTRAQ-Based Quantitative Protein Expression Profiling and MRM Verification of Markers in Type 2 Diabetes

Kaur, Prabhjit, Rizk, Nasser M., Ibrahim, Sereen, Younes, Noura, Uppal, Arushi, Dennis, Kevin, Karve, Tejaswita, Blakeslee, Kenneth, Kwagyan, John, Zirie, Mahmoud, Ressom, Habtom W., Cheema, Amrita K.

Journal:

Journal of Proteome Research

Year:

2012

Language:

english

File:

PDF, 2.71 MB

english, 2012

30

Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards

Tsai, T.-H., Tadesse, M. G., Di Poto, C., Pannell, L. K., Mechref, Y., Wang, Y., Ressom, H. W.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.43 MB

english, 2013

31

509 Transcriptome Analysis Reveals Candidate Genes and Pathways Regulated by TNFAIP8, A NF-kB-inducible Oncogenic Molecule, in Androgen-refractory Metastatic Prostate Cancer Cells

Day, T., Li, X., Zou, X., Ressom, H., Kasid, U.

Journal:

European Journal of Cancer

Year:

2012

Language:

english

File:

PDF, 57 KB

english, 2012

32

[IEEE 2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Vancouver, BC (2008.08.20-2008.08.25)] 2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Network motif-based identification of breast cancer susceptibility genes

Zhang, Yuji, Xuan, Jianhua, de los Reyes, Benilo G., Clarke, Robert, Ressom, Habtom W.

Year:

2008

Language:

english

File:

PDF, 460 KB

english, 2008

33

Correction to iTRAQ-based Quantitative Protein Expression Profiling and MRM Verification of Markers in Type 2 Diabetes

Kaur, Prabhjit, Rizk, Nasser M., Ibrahim, Sereen, Younes, Noura, Uppal, Arushi, Dennis, Kevin, Karve, Tejaswita, Blakeslee, Kenneth, Kwagyan, John, Zirie, Mahmoud, Ressom, Habtom W., Cheema, Amrita K.

Journal:

Journal of Proteome Research

Year:

2013

Language:

english

File:

PDF, 117 KB

english, 2013

34

Identification of Functional Modules by Integration of Multiple Data Sources Using a Bayesian Network Classifier

Wang, J., Zuo, Y., Liu, L., Man, Y., Tadesse, M. G., Ressom, H. W.

Journal:

Circulation Cardiovascular Genetics

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

35

[IEEE 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - HongKong, China (2010.12.18-2010.12.18)] 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Using a spike-in experiment to evaluate analysis of LC-MS data

Tuli, Leepika, Tsai, Tsung-Heng, Varghese, Rency S., Cheema, Amrita, Ressom, Habtom W.

Year:

2010

Language:

english

File:

PDF, 676 KB

english, 2010

36

Network modeling to identify new mechanisms and therapeutic targets for Parkinson’s disease

MacArthur, Linda, Ressom, Habtom, Shah, Salim, Federoff, Howard J

Journal:

Expert Review of Neurotherapeutics

Year:

2013

Language:

english

File:

PDF, 1.13 MB

english, 2013

37

Integrated Analysis of ATM Mediated Gene and Protein Expression Impacting Cellular Metabolism

Cheema, Amrita K., Timofeeva, Olga, Varghese, Rency, Dimtchev, Alexandre, Shiekh, Kathryn, Shulaev, Vladimir, Suy, Simeng, Collins, Sean, Ressom, Habtom, Jung, Mira, Dritschilo, Anatoly

Journal:

Journal of Proteome Research

Year:

2011

Language:

english

File:

PDF, 3.53 MB

english, 2011

38

Identification of N -Glycan Serum Markers Associated with Hepatocellular Carcinoma from Mass Spectrometry Data

Tang, Zhiqun, Varghese, Rency S., Bekesova, Slavka, Loffredo, Christopher A., Hamid, Mohamed Abdul, Kyselova, Zuzana, Mechref, Yehia, Novotny, Milos V., Goldman, Radoslav, Ressom, Habtom W.

Journal:

Journal of Proteome Research

Year:

2010

Language:

english

File:

PDF, 1.34 MB

english, 2010

39

Biological network inference using low order partial correlation

Zuo, Yiming, Yu, Guoqiang, Tadesse, Mahlet G., Ressom, Habtom W.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

40

[IEEE 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology - Toronto, ON, Canada (2006.09.28-2006.09.29)] 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology - Biomarker Identification and Rule Extraction from Mass Spectral Serum Profiles

Ressom, H. W., Varghese, R. S., Orvisky, E., Drake, S. K., Hortin, G. L., Abdel-Hamid, M., Loffredo, C. A., Goldman, R.

Year:

2006

Language:

english

File:

PDF, 763 KB

english, 2006

41

[IEEE 2010 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2010) - Buenos Aires (2010.08.31-2010.09.4)] 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology - SVM-based spectral matching for metabolite identification

Bin Zhou,, Cheema, A K, Ressom, H W

Year:

2010

Language:

english

File:

PDF, 543 KB

english, 2010

42

[IEEE 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Shanghai, China (2013.12.18-2013.12.21)] 2013 IEEE International Conference on Bioinformatics and Biomedicine - Reconstructing biological networks using low order partial correlation

Zuo, Yiming, Yu, Guoqiang, Tadesse, Mahlet G., Ressom, Habtom W

Year:

2013

Language:

english

File:

PDF, 323 KB

english, 2013

43

[IEEE 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Atlanta, GA, USA (2011.11.12-2011.11.15)] 2011 IEEE International Conference on Bioinformatics and Biomedicine - Bayesian Alignment Model for LC-MS Data

Tsai, Tsung-Heng, Tadesse, Mahlet G., Wang, Yue, Ressom, Habtom W.

Year:

2011

Language:

english

File:

PDF, 233 KB

english, 2011

44

[IEEE 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Atlanta, GA (2011.11.12-2011.11.15)] 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Meta-analysis of LC-MS based metabolomic experiments

Varghese, R. S., Bin Zhou,, Ressom, H.

Year:

2011

Language:

english

File:

PDF, 773 KB

english, 2011

45

[IEEE 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) - Washington, DC, USA (2012.12.2-2012.12.4)] Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS) - Variability assessment of LC-MS experiments and its application to experimental design and difference detection

Zhao, Yi, Tsai, Tsung-Heng, Di Poto, Cristina, Pannell, Lewis K., Tadesse, Mahlet G., Ressom, Habtom W.

Year:

2012

Language:

english

File:

PDF, 161 KB

english, 2012

46

[IEEE 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Hong Kong, China (2010.12.18-2010.12.21)] 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Metabolomic profiling for biomarker discovery in pancreatic cancer

Kaur, Prabhjit, Sheikh, Kathryn, Kirilyuk, Alexander, Kirilyuk, Ksenia, Ressom, Habtom W., Cheema, Amrita K, Kallakury, Bhaskar

Year:

2010

Language:

english

File:

PDF, 569 KB

english, 2010

47

[IEEE 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Atlanta, GA (2011.11.12-2011.11.15)] 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Quality assessment of LC-MS metabolomic data

Ranjbar, M. R. N., Yue Wang,, Ressom, H. W.

Year:

2011

Language:

english

File:

PDF, 659 KB

english, 2011

48

[IEEE 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Atlanta, GA (2011.11.12-2011.11.15)] 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Analysis of aberrant pathways using HCC candidate biomarkers identified from high-throuput omics studies

Jinlian Wang,, Ressom, H. W.

Year:

2011

Language:

english

File:

PDF, 616 KB

english, 2011

49

[IEEE 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - La Jolla, CA, USA (2005.11.15-2005.11.15)] 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology - Analysis of MALDI-TOF Serum Profiles for Biomarker Selection and Sample Classification

Ressom, H.W., Varghese, R.S., Orvisky, E., Drake, S.K., Hortin, G.L., Abdel-Hamid, M., Loffredo, C.A., Goldman, R.

Year:

2005

Language:

english

File:

PDF, 906 KB

english, 2005

50

[IEEE 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Hong Kong, China (2010.12.18-2010.12.21)] 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - A new method for alignment of LC-MALDI-TOF data

Tang, Zhiqun, Zhang, Lihua, Amrita, K. Cheema, Habtom, W. Ressom

Year:

2010

Language:

english

File:

PDF, 460 KB

english, 2010

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