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Regional autozygosity association with albumin-to-creatinine ratio reveals a novel FTO region in an Indigenous Australian population

European Journal of Human Genetics
2025-02-24 | Journal article
DOI: 10.1038/s41431-025-01799-9
Contributors: Vignesh Arunachalam; Kim N. Tran; Wendy Hoy; Rodney A. Lea; Shivashankar H. Nagaraj
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Identification of Small Open Reading Frame Encoded Proteins from the Human Genome

Genomics, Proteomics & Bioinformatics
2025-02-07 | Journal article
DOI: 10.1093/gpbjnl/qzaf004
Contributors: Hitesh Kore; Satomi Okano; Keshava K Datta; Jackson Thorp; Parthiban Periasamy; Mayur Divate; Upekha Liyanage; Gunter Hartel; Shivashankar H Nagaraj; Harsha Gowda
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A Systematic Review Exploring Empirical Pharmacogenomics Research Within Global Indigenous Populations

Molecular genetics & genomic medicine
2024 | Journal article
DOI: 10.1002/mgg3.70018
Part of ISSN: 2324-9269
Contributors: Nasir, Bushra Farah; Vinayagam, Ritwika; Massi, Luciana; Nagaraj, Shivashankar H; Toombs, Maree; Rae, Kym M
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Shivashankar Hiriyur Nagaraj
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Genomic characterization of clinically significant blood group variants in Aboriginal Australians

Blood transfusion = Trasfusione del sangue
2024 | Journal article
DOI: 10.2450/bloodtransfus.664
Part of ISSN: 1723-2007
Contributors: Jadhao, Sudhir; Davison, Candice; Roulis, Eileen; Lee, Simon; Campbell, Tamika; Griffin, Reece; Toombs, Maree; Brown, Alex; Perry, Maree; Nasir, Bushra et al.
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Shivashankar Hiriyur Nagaraj
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Pharmacological induction of chromatin remodeling drives chemosensitization in triple-negative breast cancer

Cell reports. Medicine
2024 | Journal article
DOI: 10.1016/j.xcrm.2024.101504
Part of ISSN: 2666-3791
Contributors: Bagheri, Meisam; Mohamed, Gadisti Aisha; Mohamed Saleem, Mohammed Ashick; Ognjenovic, Nevena B; Lu, Hanxu; Kolling, Fred W; Wilkins, Owen M; Das, Subhadeep; LaCroix, Ian S; Nagaraj, Shivashankar H et al.
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Shivashankar Hiriyur Nagaraj
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VPBrowse: Genome-based representation of MS/MS spectra to quantify 10,000 bovine proteins

Proteomics
2024 | Journal article
DOI: 10.1002/pmic.202300431
Part of ISSN: 1615-9853
Contributors: Paramasivan, Selvam; Ashick, Mohamed; Dudley, Kevin J; Satake, Nana; Mills, Paul C; Sadowski, Pawel; Nagaraj, Shivashankar H
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Shivashankar Hiriyur Nagaraj
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Machine Learning Enabled Prediction of Biologically Relevant Gene Expression Using CT‐Based Radiomic Features in Non‐Small Cell Lung Cancer

Cancer Medicine
2024-12 | Journal article
DOI: 10.1002/cam4.70509
Contributors: Shrey S. Sukhadia; Christoph Sadée; Olivier Gevaert; Shivashankar H. Nagaraj
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Mapping the Pharmacogenetic Landscape in a Ugandan Population: Implications for Personalized Medicine in an Underrepresented Population

Clinical Pharmacology & Therapeutics
2024-10 | Journal article
DOI: 10.1002/cpt.3309
Contributors: Sumudu Rangika Samarasinghe; Seung‐been Lee; Manuel Corpas; Segun Fatumo; Henk‐Jan Guchelaar; Shivashankar H. Nagaraj
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A cold case of hemolytic disease of the fetus and newborn resolved by genomic sequencing and population studies to define a new antigen in the Rh system

Transfusion
2024-06 | Journal article
DOI: 10.1111/trf.17205
Contributors: Brett Wilson; Candice L. Davison; Genghis H. Lopez; Glenda M. Millard; Yew‐Wah Liew; Tanya Powley; Tamika Campbell; Sudhir S. Jadhao; Shivashankar H. Nagaraj; Maree Perry et al.
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Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study

Genome Medicine
2024-02-12 | Journal article
DOI: 10.1186/s13073-024-01299-3
Contributors: Vignesh Arunachalam; Rodney Lea; Wendy Hoy; Simon Lee; Susan Mott; Judith Savige; John D. Mathews; Brendan J. McMorran; Shivashankar H. Nagaraj
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Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression

bioRxiv
2023 | Journal article
DOI: 10.1101/2023.04.19.537586
Contributors: Bagheri, Meisam; Mohamed, Gadisti Aisha; Ashick, Mohammed; Saleem, Mohamed; Ognjenovic, Nevena; Lu, Hanxu; Kolling, Fred; Wilkins, Owen; Das, Subhadeep; Croix, Ian La et al.
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Shivashankar Hiriyur Nagaraj
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Predicting Distant Recurrences in Invasive Breast Carcinoma Patients Using Clinicopathological Data: A cross-institutional and AI-based study

bioRxiv
2023 | Journal article
DOI: 10.1101/2023.04.16.537076
Contributors: Sukhadia, Shrey; Muller, Kristen; Workman, Adrienne; Nagaraj, Shivashankar
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Shivashankar Hiriyur Nagaraj
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Protein-coding potential of non-canonical open reading frames in human transcriptome

Biochemical and biophysical research communications
2023 | Journal article
DOI: 10.1016/j.bbrc.2023.09.068
Part of ISSN: 0006-291X
Contributors: Kore, Hitesh; Datta, Keshava K; Nagaraj, Shivashankar H; Gowda, Harsha
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Shivashankar Hiriyur Nagaraj
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The pharmacogenomic landscape of an Indigenous Australian population

Frontiers in pharmacology
2023 | Journal article
DOI: 10.3389/fphar.2023.1180640
Part of ISSN: 1663-9812
Contributors: Samarasinghe, Sumudu Rangika; Hoy, Wendy; Jadhao, Sudhir; McMorran, Brendan J; Guchelaar, Henk-Jan; Nagaraj, Shivashankar H
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Shivashankar Hiriyur Nagaraj
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Genetic Characterization of Blood Group Antigens for Polynesian Heritage Norfolk Island Residents

Genes
2023-08-30 | Journal article
DOI: 10.3390/genes14091740
Contributors: Stacie O’Brien; Rodney Lea; Sudhir Jadhao; Simon Lee; Shrey Sukhadia; Vignesh Arunachalam; Eileen Roulis; Robert Flower; Lyn Griffiths; Shivashankar Nagaraj
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Machine Learning-Based Prediction of Distant Recurrence in Invasive Breast Carcinoma Using Clinicopathological Data: A Cross-Institutional Study

Cancers
2023-08-03 | Journal article
DOI: 10.3390/cancers15153960
Contributors: Shrey S. Sukhadia; Kristen E. Muller; Adrienne A. Workman; Shivashankar H. Nagaraj
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BGvar: A comprehensive resource for blood group immunogenetics

Transfusion medicine (Oxford, England)
2022 | Journal article
DOI: 10.1111/tme.12844
Part of ISSN: 0958-7578
Contributors: Rophina, Mercy; Pandhare, Kavita; Jadhao, Sudhir; Nagaraj, Shivashankar H; Scaria, Vinod
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Unlocking capacities of genomics for the COVID-19 response and future pandemics

Nature methods
2022 | Journal article
DOI: 10.1038/s41592-022-01444-z
Part of ISSN: 1548-7091
Contributors: Knyazev, Sergey; Chhugani, Karishma; Sarwal, Varuni; Ayyala, Ram; Singh, Harman; Karthikeyan, Smruthi; Deshpande, Dhrithi; Baykal, Pelin Icer; Comarova, Zoia; Lu, Angela et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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ImaGene: A web-based software platform for tumor radiogenomic evaluation and reporting

2022-11-09 | Other
DOI: 10.1093/bioadv/vbac079
Contributors: Shrey Sukhadia; Aayush Tyagi; Pritam Mukherjee; Vivek venkatram; Prathosh A Prasad; Shivashankar Hiriyur Nagaraj; Olivier Gevaert
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Using whole-genome sequencing to characterize clinically significant blood groups among healthy older Australians.

Blood advances
2022-08-01 | Journal article | Author
DOI: 10.1182/bloodadvances.2022007505
PMID: 35420653
PMC: PMC9636324
Contributors: Jadhao S; Candice L. Davison; Eileen Roulis; Lee S; Paul Lacaze; Riaz M; John James McNeil; David Thomas; Natalie Pecheniuk; Hyland CA et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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The genomic landscape of blood groups in Indigenous Australians in remote communities.

Transfusion
2022-04-11 | Journal article
DOI: 10.1111/trf.16873
PMID: 35403234
PMC: PMC9544628
Contributors: Sudhir Jadhao; Hoy W; Lee S; Patel HR; Brendan McMorran; Flower RL; Nagaraj SH
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Pharmacogenomic analysis of a genetically distinct Indigenous population

The Pharmacogenomics Journal
2022-03 | Journal article
DOI: 10.1038/s41397-021-00262-4
Contributors: Arvind Jaya Shankar; Sudhir Jadhao; Wendy Hoy; Simon J. Foote; Hardip R. Patel; Vinod Scaria; Brendan J. McMorran; Shivashankar H. Nagaraj
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Deep Learning-Based Pan-Cancer Classification Model Reveals Tissue-of-Origin Specific Gene Expression Signatures

Cancers
2022-02-24 | Journal article
DOI: 10.3390/cancers14051185
Contributors: Mayur Divate; Aayush Tyagi; Derek J. Richard; Prathosh A. Prasad; Harsha Gowda; Shivashankar H. Nagaraj
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RBCeq: A robust and scalable algorithm for accurate genetic blood typing.

EBioMedicine
2022-01-14 | Journal article
DOI: 10.1016/j.ebiom.2021.103759
PMID: 35033986
PMC: PMC8763639
Contributors: Jadhao S; Candice L. Davison; Eileen Roulis; Elizna Schoeman; Divate M; Haring M; Williams C; Shankar AJ; Lee S; Natalie Pecheniuk et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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The Gene-Drug Duality: Exploring the Pharmacogenomics of Indigenous Populations.

Frontiers in genetics
2021-09-20 | Journal article
DOI: 10.3389/fgene.2021.687116
PMID: 34616423
PMC: PMC8488351
Contributors: Nagaraj SH; Toombs M
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping

Briefings in bioinformatics
2020 | Journal article
DOI: 10.1093/bib/bbz121
Part of ISSN: 1467-5463
Contributors: Sathyanarayanan, Anita; Gupta, Rohit; Thompson, Erik W; Nyholt, Dale R; Bauer, Denis C; Bauer, Denis C; Nagaraj, Shivashankar H
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Analysis of the <i>F2LR3</i> (PAR4) Single Nucleotide Polymorphism (<i>rs773902</i>) in an Indigenous Australian Population

Frontiers in genetics
2020 | Journal article
DOI: 10.3389/fgene.2020.00432
Part of ISSN: 1664-8021
Contributors: Ningtyas, Dian; Ningtyas, Dian; Thomson, Russell J; Tarlac, Volga; Nagaraj, Shivashankar H; Hoy, Wendy; Mathews, John D; Foote, Simon J; Gardiner, Elizabeth E; Hamilton, Justin R et al.
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Shivashankar Hiriyur Nagaraj
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Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms

PLoS neglected tropical diseases
2020 | Journal article
DOI: 10.1371/journal.pntd.0008237
Part of ISSN: 1935-2727
Contributors: Logan, Jayden; Pearson, Mark S; Manda, Srikanth S; Choi, Young-Jun; Field, Matthew; Eichenberger, Ramon M; Mulvenna, Jason; Nagaraj, Shivashankar H; Fujiwara, Ricardo T; Gazzinelli-Guimaraes, Pedro et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Equitable Expanded Carrier Screening Needs Indigenous Clinical and Population Genomic Data

American journal of human genetics
2020 | Journal article
DOI: 10.1016/j.ajhg.2020.06.005
Part of ISSN: 0002-9297
Contributors: Easteal, Simon; Arkell, Ruth M; Balboa, Renzo F; Bellingham, Shayne A; Brown, Alex D; Calma, Tom; Cook, Matthew C; Davis, Megan; Dawkins, Hugh J S; Dinger, Marcel E et al.
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Shivashankar Hiriyur Nagaraj
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Limiting Self-Renewal of the Basal Compartment by PKA Activation Induces Differentiation and Alters the Evolution of Mammary Tumors

Developmental cell
2020 | Journal article
DOI: 10.1016/j.devcel.2020.10.004
Part of ISSN: 1534-5807
Contributors: Ognjenovic, Nevena B; Bagheri, Meisam; Mohamed, Gadisti Aisha; Xu, Ke; Chen, Youdinghuan; Mohamed Saleem, Mohamed Ashick; Brown, Meredith S; Nagaraj, Shivashankar H; Muller, Kristen E; Gerber, Scott A et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Identifying Therapies to Combat Epithelial Mesenchymal Plasticity-Associated Chemoresistance to Conventional Breast Cancer Therapies Using An shRNA Library Screen

Cancers
2020-04 | Journal article | Author
DOI: 10.3390/cancers12051123
Contributors: Sugandha Bhatia; Tony Blick; Cletus Pinto; Mark Waltham; james monkman; Ekaterina Ivanova; Pamela M. Pollock; Shivashankar Hiriyur Nagaraj; Adrian P. Wiegmans; Izhak Haviv et al.
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Multidisciplinary Digital Publishing Institute
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Interrogation of Phenotypic Plasticity between Epithelial and Mesenchymal States in Breast Cancer

Journal of clinical medicine
2019 | Journal article
DOI: 10.3390/jcm8060893
Part of ISSN: 2077-0383
Contributors: Bhatia, Sugandha; Monkman, James; Blick, Tony; Pinto, Cletus; Waltham, Mark; Nagaraj, Shivashankar H; Thompson, Erik W
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Multi-Omics Characterization of the Spontaneous Mesenchymal-Epithelial Transition in the PMC42 Breast Cancer Cell Lines

Journal of clinical medicine
2019 | Journal article
DOI: 10.3390/jcm8081253
Part of ISSN: 2077-0383
Contributors: Bhatia, Sugandha; Monkman, James; Blick, Tony; Duijf, Pascal Hg; Nagaraj, Shivashankar H; Thompson, Erik W
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Targeting Epithelial Mesenchymal Plasticity in Pancreatic Cancer: A Compendium of Preclinical Discovery in a Heterogeneous Disease

Cancers
2019 | Journal article
DOI: 10.3390/cancers11111745
Part of ISSN: 2072-6694
Contributors: Monkman, James H; Thompson, Erik W; Nagaraj, Shivashankar H
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Transition states that allow cancer to spread

Nature
2018 | Journal article
DOI: 10.1038/d41586-018-04403-x
Part of ISSN: 0028-0836
Contributors: Thompson, Erik W; Nagaraj, Shivashankar H
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Targeting epithelial-mesenchymal plasticity in cancer: clinical and preclinical advances in therapy and monitoring

The Biochemical journal
2017 | Journal article
DOI: 10.1042/bcj20160782
Part of ISSN: 0264-6021
Contributors: Bhatia, Sugandha; Monkman, James; Toh, Alan Kie Leong; Nagaraj, Shivashankar H; Thompson, Erik W
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Whole-genome landscape of pancreatic neuroendocrine tumours

Nature
2017 | Journal article
DOI: 10.1038/nature21063
Part of ISSN: 0028-0836
Contributors: Scarpa, Aldo; Chang, David K; Nones, Katia; Corbo, Vincenzo; Patch, Ann-Marie; Bailey, Peter; Lawlor, Rita T; Johns, Amber L; Miller, David K; Mafficini, Andrea et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

Journal of proteome research
2015 | Journal article
DOI: 10.1021/acs.jproteome.5b00029
Part of ISSN: 1535-3893
Contributors: Nagaraj, Shivashankar H; Waddell, Nicola; Madugundu, Anil K; Wood, Scott; Jones, Alun; Mandyam, Ramya A; Nones, Katia; Pearson, John V; Grimmond, Sean M
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Whole-genome characterization of chemoresistant ovarian cancer

Nature
2015 | Journal article
DOI: 10.1038/nature14410
Part of ISSN: 0028-0836
Contributors: Patch, Ann-Marie; Christie, Elizabeth L; Etemadmoghadam, Dariush; Garsed, Dale W; George, Joshy; Fereday, Sian; Nones, Katia; Cowin, Prue; Alsop, Kathryn; Bailey, Peter J et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Cloning and tissue distribution of novel splice variants of the ovine ghrelin gene

BMC veterinary research
2014 | Journal article
DOI: 10.1186/s12917-014-0211-x
Part of ISSN: 1746-6148
Contributors: Menzies, Moira; Seim, Inge; Josh, Peter; Nagaraj, Shivashankar H; Lees, Michael; Walpole, Carina; Chopin, Lisa K; Colgrave, Michelle; Ingham, Aaron
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Shivashankar Hiriyur Nagaraj
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Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline

Molecular & cellular proteomics : MCP
2013 | Journal article
DOI: 10.1074/mcp.m112.027169
Part of ISSN: 1535-9476
Contributors: Kumar, Dhirendra; Yadav, Amit Kumar; Kadimi, Puneet Kumar; Nagaraj, Shivashankar H; Grimmond, Sean M; Dash, Debasis
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Gene network analyses of first service conception in Brangus heifers: use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors

Journal of animal science
2012 | Journal article
DOI: 10.2527/jas.2011-4601
Part of ISSN: 0021-8812
Contributors: Fortes, M R S; Snelling, WM; Reverter, A; Nagaraj, SH; Lehnert, SA; Hawken, RJ; DeAtley, KL; Peters, SO; Silver, GA; Rincon, G et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Proteomic analysis of the abomasal mucosal response following infection by the nematode, Haemonchus contortus, in genetically resistant and susceptible sheep

Journal of proteomics
2012 | Journal article
DOI: 10.1016/j.jprot.2012.01.016
Part of ISSN: 1874-3919
Contributors: Nagaraj, Shivashankar H; Harsha, HC; Reverter, Antonio; Colgrave, Michelle L; Sharma, Rakesh; Andronicos, Nicholas; Hunt, Peter; Menzies, Moira; Lees, Michael S; Sekhar, Nirujogi R et al.
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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A Boolean-based systems biology approach to predict novel genes associated with cancer: Application to colorectal cancer

BMC systems biology
2011 | Journal article
DOI: 10.1186/1752-0509-5-35
Part of ISSN: 1752-0509
Contributors: Nagaraj, Shivashankar H; Reverter, Antonio
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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A single nucleotide polymorphism-derived regulatory gene network underlying puberty in 2 tropical breeds of beef cattle

Journal of animal science
2011 | Journal article
DOI: 10.2527/jas.2010-3681
Part of ISSN: 0021-8812
Contributors: Fortes, M R S; Reverter, A; Nagaraj, SH; Zhang, Y; Jonsson, NN; Barris, W; Lehnert, S; Boe-Hansen, GB; Hawken, RJ
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Chronic exposure to anabolic steroids induces the muscle expression of oxytocin and a more than fiftyfold increase in circulating oxytocin in cattle

Physiological genomics
2011 | Journal article
DOI: 10.1152/physiolgenomics.00226.2010
Part of ISSN: 1094-8341
Contributors: De Jager, Nadia; Hudson, Nicholas J; Reverter, Antonio; Wang, Yong-Hong; Nagaraj, Shivashankar H; Cafe, Linda M; Greenwood, Paul L; Barnard, Ross T; Kongsuwan, Kritaya P; Dalrymple, Brian P
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins

PloS one
2011 | Journal article
DOI: 10.1371/journal.pone.0025457
Part of ISSN: 1932-6203
Contributors: Hudson, Nicholas J; Gu, Quan; Nagaraj, Shivashankar H; Ding, Yong-Sheng; Dalrymple, Brian P; Reverter, Antonio
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
grade
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Genome-wide patterns of promoter sharing and co-expression in bovine skeletal muscle

BMC genomics
2011 | Journal article
DOI: 10.1186/1471-2164-12-23
Part of ISSN: 1471-2164
Contributors: Gu, Quan; Nagaraj, Shivashankar H; Hudson, Nicholas J; Dalrymple, Brian P; Reverter, Antonio
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
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Association weight matrix for the genetic dissection of puberty in beef cattle

Proceedings of the National Academy of Sciences of the United States of America
2010 | Journal article
DOI: 10.1073/pnas.1002044107
Part of ISSN: 0027-8424
Contributors: Fortes, Marina R S; Reverter, Antonio; Zhang, Yuandan; Collis, Eliza; Nagaraj, Shivashankar H; Jonsson, Nick N; Prayaga, Kishore C; Barris, Wes; Hawken, Rachel J
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
grade
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Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data

Bioinformatics (Oxford, England)
2010 | Journal article
DOI: 10.1093/bioinformatics/btq051
Part of ISSN: 1367-4803
Contributors: Reverter, Antonio; Hudson, Nicholas J; Nagaraj, Shivashankar H; Pérez-Enciso, Miguel; Dalrymple, Brian P
Source: Self-asserted source
Shivashankar Hiriyur Nagaraj
grade
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