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Integrating transcriptome and proteome profiling: Strategies and applications

author

Dhirendra Kumar

2000 -

Ankita Narang

published in: Proteomics

date of publication: 2016-06-25

main subject: RNA sequencing, transcriptome

Cites articles 92

Date

Title

Authors

2016-02-22

Tissue-specific Proteogenomic Analysis of Plutella xylostella Larval Midgut Using a Multialgorithm Pipeline

Jean Armengaud, Zhaojiang Guo
2016-02-26

An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer

Aleksandra K. Olow
2016-02-26

Targeting irradiation-induced mitogen-activated protein kinase activation in vitro and in an ex vivo model for human head and neck cancer.

Wilko Weichert
2016-03-08

ZLM-7 exhibits anti-angiogenic effects via impaired endothelial cell function and blockade of VEGF/VEGFR-2 signaling
2016-03-01

An update on transcriptional and post-translational regulation of brain voltage-gated sodium channels

Pedro Beltran-Alvarez
2015-04-24

DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis

Vadivel Ganapathy, Rajalakshmi Veeranan-Karmegam
2015-09-25

Probing the Missing Human Proteome: A Computational Perspective

Dhirendra Kumar
2015-11-23

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes

Dhirendra Kumar, Rintu Kutum
2015-11-11

Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation

Dhirendra Kumar, Amit Kumar Yadav, Xinying Jia
2015-04-17

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

Sean Grimmond, Nicola J Waddell, Anil K Madugundu
2015-05-27

Transcriptome and venom proteome of the box jellyfish Chironex fleckeri

Diane L. Brinkman, Xinying Jia, Dhirendra Kumar, David Kvaskoff
2015-08-10

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

Lukas Käll
2015-12-02

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

Charles M. Perou, Kelly V. Ruggles, Manor Askenazi, Karl R. Clauser, David Tabb, Katherine A. Hoadley, Sherri R Davies, Daniel C. Liebler, Samuel H Payne, David Fenyo, Robbert J C Slebos, Shunqiang Li
2015-06-01

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms

Bernhard Y Renard
2015-07-06

PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics

Alexei Dmitriev, Anna Kudryavtseva, Dmitry Karpov, Nataliya Melnikova
2015-12-09

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

David Tabb, Billy G. Hudson
2015-12-25

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

Anthony J Cesnik
2015-04-30

Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes

Leif Väremo, Bente Klarlund Pedersen, Jens Nielsen, Mathias Uhlén, Camilla Scheele, Intawat Nookaew, Adil Mardinoglu, Caroline Kampf, Anna Asplund, Christa Broholm
2015-01-29

Integrative proteomics and targeted transcriptomics analyses in cardiac endothelial cells unravel mechanisms of long-term radiation-induced vascular dysfunction

Omid Azimzadeh, Juliane Merl-Pham, Ramesh Yentrapalli, Michael J Atkinson, Gabriele Multhoff, Soile Tapio, Marius Ueffing
2015-10-15

Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

Richa Misra, Dhirendra Kumar, Andaleeb Sajid, Sugandha Bhatia, Yogendra Singh, Joy Sarojini Michael
2015-09-30

Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected by Anaplasma phagocytophilum Infection in Tick Cells

Pilar Alberdi, Lourdes Mateos-Hernández, José de la Fuente, Margarita Villar, Nieves Ayllón
2015-09-17

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Peer Bork, Alessandro Ori, Thomas Bock, Murat Iskar, Martin Beck
2015-01-15

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

Anna Swan, Dov J Stekel, Charlie Hodgman, David Allaway
2014-11

Proteogenomics: concepts, applications and computational strategies

Alexey I. Nesvizhskii
2014-07-24

Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis

Sutopa B Dwivedi, Tai-Chung Huang, Min-Sik Kim, Sneha M Pinto, Anil K Madugundu, Nazia Syed, T S Keshava Prasad, Vineet Bafna, Tejaswini Subbannayya, Renu Goel, Dhanashree S Kelkar, Raghothama Chaerkady, Babylakshmi Muthusamy, Srikanth S Manda, Lakshmi Dhevi N Selvan, Keshava K Datta, Santosh Renuse, Derese Getnet, Jayshree Advani, Gourav Dey, Lavanya Balakrishnan, Vishalakshi Nanjappa, Ravi Sirdeshmukh, Harsha Gowda, Steven Leach, Yashwanth Subbannayya
2014-10-02

Discovery of rare protein-coding genes in model methylotroph Methylobacterium extorquens AM1.

Dhirendra Kumar, Amit Kumar Yadav
2014-09-18

Proteogenomic characterization of human colon and rectal cancer

David Tabb, Sherri R Davies, Daniel C. Liebler, Robbert J C Slebos, Bing Zhang
2014-05-29

A draft map of the human proteome

Min-Sik Kim, Sneha M Pinto, Raja Sekhar Nirujogi, Anil K Madugundu, Arun H Patil, Sreelakshmi K Sreenivasamurthy, Gajanan Sathe, Sandip Chavan, Nazia Syed, Aafaque Ahmad Khan, Tai-Chung Huang, Jun Zhong, Kanchan K. Mukherjee, Henry Lam, Marc K. Halushka, Gary D. Bader, Ruth Isserlin, Charles G. Drake, Ralph H. Hruban, Anirban Maitra, Tejaswini Subbannayya, Renu Goel, Dhanashree S Kelkar, Raghothama Chaerkady, Babylakshmi Muthusamy, Srikanth S Manda, Lakshmi Dhevi N Selvan, Keshava K Datta, Santosh Renuse, Derese Getnet, Jayshree Advani, Gourav Dey, Lavanya Balakrishnan, Vishalakshi Nanjappa, Ravi Sirdeshmukh, Harsha Gowda, Steven Leach, Yashwanth Subbannayya, Aneesha Radhakrishnan, Susarla Krishna Shankar, T S Keshava Prasad, Arivusudar Marimuthu, Joji K Thomas, Nandini A Sahasrabuddhe, Apeksha Sahu, Soujanya D Yelamanchi, Savita Jayaram, Pavithra Rajagopalan, Subramanian Shankar, Parthasarathy Satishchandra, Candace L. Kerr, Christine A Iacobuzio-Donahue, Keshav Mudgal
2014-05-29

Mass-spectrometry-based draft of the human proteome

Mathias Wilhelm, Emanuel Ziegler, Siegfried Gessulat, Toby Mathieson, Bernhard Kuster, Karsten Schnatbaum, Ulf Reimer, Marcus Bantscheff, Mikhail M Savitski, Judith Schlegl, Simone Lemeer
2014-07-16

Analyzing the first drafts of the human proteome

Alfonso Valencia, Jesús Vázquez, Michael L Tress
2014-08-22

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

Pratik D. Jagtap, Timothy Griffin
2014-01-28

Ribosome profiling: new views of translation, from single codons to genome scale

Article - wd:Q38876517

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