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Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines.
Published in:
Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-06886-1
By:
- Demirhan, Deniz;
- Kumar, Amit;
- Zhu, Jie;
- Poulsen, Pi Camilla;
- Majewska, Natalia I.;
- Sebastian, Yinong;
- Chaerkady, Raghothama;
- Yu, Wen;
- Zhu, Wei;
- Zhuang, Li;
- Shah, Punit;
- Lekstrom, Kristen;
- Cole, Robert N.;
- Zhang, Hui;
- Betenbaugh, Michael J.;
- Bowen, Michael A.
Publication type:
Article
Identification of putative biomarkers for HIV-associated neurocognitive impairment in the CSF of HIV-infected patients under cART therapy determined by mass spectrometry.
Published in:
Journal of NeuroVirology, 2014, v. 20, n. 5, p. 457, doi. 10.1007/s13365-014-0263-5
By:
- Bora, Adriana;
- Mohien, Ceereena;
- Chaerkady, Raghothama;
- Chang, Linda;
- Moxley, Richard;
- Sacktor, Ned;
- Haughey, Norman;
- McArthur, Justin;
- Cotter, Robert;
- Nath, Avindra;
- Graham, David
Publication type:
Article
A multi-omic analysis of human naïve CD4+ T cells.
Published in:
BMC Systems Biology, 2015, v. 9, p. 1, doi. 10.1186/s12918-015-0225-4
By:
- Mitchell, Christopher J.;
- Getnet, Derese;
- Min-Sik Kim;
- Manda, Srikanth S.;
- Kumar, Praveen;
- Tai-Chung Huang;
- Pinto, Sneha M.;
- Nirujogi, Raja Sekhar;
- Mio Iwasaki;
- Shaw, Patrick G.;
- Xinyan Wu;
- Jun Zhong;
- Chaerkady, Raghothama;
- Marimuthu, Arivusudar;
- Muthusamy, Babylakshmi;
- Sahasrabuddhe, Nandini A.;
- Raju, Rajesh;
- Bowman, Caitlyn;
- Danilova, Ludmila;
- Cutler, Jevon
Publication type:
Article
The NHERF2 sequence adjacent and upstream of the ERM-binding domain affects NHERF2-ezrin binding and dexamethasone stimulated NHE3 activity.
Published in:
Biochemical Journal, 2015, v. 470, n. 1, p. 77, doi. 10.1042/BJ20150238
By:
- Jianbo Yang;
- Sarker, Rafiquel;
- Singh, Varsha;
- Sarker, Prateeti;
- Jianyi Yin;
- Tian-E Chen;
- Chaerkady, Raghothama;
- Xuhang Li;
- Tse, C. Ming;
- Donowitz, Mark
Publication type:
Article
USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 2, p. 823, doi. 10.1093/nar/gkx1226
By:
- Li, Zengxia;
- Cheng, Zhao;
- Raghothama, Chaerkady;
- Cui, Zhaomeng;
- Liu, Kaiyu;
- Li, Xiaojing;
- Jiang, Chenxiao;
- Jiang, Wei;
- Tan, Minjia;
- Ni, Xiaohua
Publication type:
Article
Human Proteinpedia: a unified discovery resource for proteomics research.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D773, doi. 10.1093/nar/gkn701
By:
- Kandasamy, Kumaran;
- Keerthikumar, Shivakumar;
- Goel, Renu;
- Mathivanan, Suresh;
- Patankar, Nandini;
- Shafreen, Beema;
- Renuse, Santosh;
- Pawar, Harsh;
- Ramachandra, Y. L.;
- Acharya, Pradip Kumar;
- Ranganathan, Prathibha;
- Chaerkady, Raghothama;
- Keshava Prasad, T. S.;
- Pandey, Akhilesh
Publication type:
Article
Bioinformatics and Proteomics Approaches for Aging Research.
Published in:
Biogerontology, 2005, v. 6, n. 4, p. 227, doi. 10.1007/s10522-005-2617-0
By:
- Raghothama, Chaerkady;
- Harsha, H.;
- Prasad, C.;
- Pandey, Akhilesh
Publication type:
Article
Actomyosin contraction during cellularization is regulated in part by Src64 control of Actin 5C protein levels.
Published in:
Genesis: The Journal of Genetics & Development, 2019, v. 57, n. 6, p. N.PAG, doi. 10.1002/dvg.23297
By:
- Carter, Tammy Y.;
- Gadwala, Swetha;
- Chougule, Ashish B.;
- Bui, Anh P. N.;
- Sanders, Alex C.;
- Chaerkady, Raghothama;
- Cormier, Nathaly;
- Cole, Robert N.;
- Thomas, Jeffrey H.
Publication type:
Article
A TRIM21-based bioPROTAC highlights the therapeutic benefit of HuR degradation.
Published in:
Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-42546-2
By:
- Fletcher, Alice;
- Clift, Dean;
- de Vries, Emma;
- Martinez Cuesta, Sergio;
- Malcolm, Timothy;
- Meghini, Francesco;
- Chaerkady, Raghothama;
- Wang, Junmin;
- Chiang, Abby;
- Weng, Shao Huan Samuel;
- Tart, Jonathan;
- Wong, Edmond;
- Donohoe, Gerard;
- Rawlins, Philip;
- Gordon, Euan;
- Taylor, Jonathan D.;
- James, Leo;
- Hunt, James
Publication type:
Article
Integrated Proteomic and Metabolic Analysis of Breast Cancer Progression.
Published in:
PLoS ONE, 2013, v. 8, n. 9, p. 1, doi. 10.1371/journal.pone.0076220
By:
- Shaw, Patrick G.;
- Chaerkady, Raghothama;
- Wang, Tao;
- Vasilatos, Shauna;
- Huang, Yi;
- Van Houten, Bennett;
- Pandey, Akhilesh;
- Davidson, Nancy E.
Publication type:
Article
Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells.
Published in:
PLoS ONE, 2012, v. 7, n. 6, p. 1, doi. 10.1371/journal.pone.0039088
By:
- Pashai, Nikta;
- Hao, Haiping;
- All, Angelo;
- Gupta, Siddharth;
- Chaerkady, Raghothama;
- Los Angeles, Alejandro De;
- Gearhart, John D.;
- Kerr, Candace L.
Publication type:
Article
Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway.
Published in:
Proteomics, 2015, v. 15, n. 2/3, p. 591, doi. 10.1002/pmic.201400339
By:
- Zhong, Jun;
- Martinez, Marissa;
- Sengupta, Srona;
- Lee, Albert;
- Wu, Xinyan;
- Chaerkady, Raghothama;
- Chatterjee, Aditi;
- O'Meally, Robert N.;
- Cole, Robert N.;
- Pandey, Akhilesh;
- Zachara, Natasha E.
Publication type:
Article
Identifying novel targets of oncogenic EGF receptor signaling in lung cancer through global phosphoproteomics.
Published in:
Proteomics, 2015, v. 15, n. 2/3, p. 340, doi. 10.1002/pmic.201400315
By:
- Zhang, Xu;
- Belkina, Natalya;
- Jacob, Harrys Kishore Charles;
- Maity, Tapan;
- Biswas, Romi;
- Venugopalan, Abhilash;
- Shaw, Patrick G.;
- Kim, Min‐Sik;
- Chaerkady, Raghothama;
- Pandey, Akhilesh;
- Guha, Udayan
Publication type:
Article
A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.
Published in:
Proteomics, 2012, v. 12, n. 6, p. 832, doi. 10.1002/pmic.201100505
By:
- Pawar, Harsh;
- Sahasrabuddhe, Nandini A.;
- Renuse, Santosh;
- Keerthikumar, Shivakumar;
- Sharma, Jyoti;
- Kumar, Ghantasala. S. Sameer;
- Venugopal, Abhilash;
- Sekhar, Nirujogi Raja;
- Kelkar, Dhanashree S.;
- Nemade, Harshal;
- Khobragade, Sweta N.;
- Muthusamy, Babylakshmi;
- Kandasamy, Kumaran;
- Harsha, H. C.;
- Chaerkady, Raghothama;
- Patole, Milind S.;
- Pandey, Akhilesh
Publication type:
Article
Comprehensive proteomic analysis of human bile.
Published in:
Proteomics, 2011, v. 11, n. 23, p. 4443, doi. 10.1002/pmic.201100197
By:
- Barbhuiya, Mustafa A.;
- Sahasrabuddhe, Nandini A.;
- Pinto, Sneha M.;
- Muthusamy, Babylakshmi;
- Singh, Tekcham D.;
- Nanjappa, Vishalakshi;
- Keerthikumar, Shivakumar;
- Delanghe, Bernard;
- Harsha, H. C.;
- Chaerkady, Raghothama;
- Jalaj, Visvajit;
- Gupta, Sanjeev;
- Shrivastav, Braj R.;
- Tiwari, Pramod K.;
- Pandey, Akhilesh
Publication type:
Article
Quantitative temporal proteomic analysis of human embryonic stem cell differentiation into oligodendrocyte progenitor cells.
Published in:
Proteomics, 2011, v. 11, n. 20, p. 4007, doi. 10.1002/pmic.201100107
By:
- Chaerkady, Raghothama;
- Letzen, Brian;
- Renuse, Santosh;
- Sahasrabuddhe, Nandini A.;
- Kumar, Praveen;
- All, Angelo H.;
- Thakor, Nitish V.;
- Delanghe, Bernard;
- Gearhart, John D.;
- Pandey, Akhilesh;
- Kerr, Candace L.
Publication type:
Article
Proteogenomics.
Published in:
Proteomics, 2011, v. 11, n. 4, p. 620, doi. 10.1002/pmic.201000615
By:
- Renuse, Santosh;
- Chaerkady, Raghothama;
- Pandey, Akhilesh
Publication type:
Article
Proteomic characterization of Her2/neu-overexpressing breast cancer cells.
Published in:
Proteomics, 2010, v. 10, n. 21, p. 3800, doi. 10.1002/pmic.201000297
By:
- Chen, Hexin;
- Pimienta, Genaro;
- Gu, Yiben;
- Sun, Xu;
- Hu, Jianjun;
- Kim, Min-Sik;
- Chaerkady, Raghothama;
- Gucek, Marjan;
- Cole, Robert N.;
- Sukumar, Saraswati;
- Pandey, Akhilesh
Publication type:
Article
Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells.
Published in:
Proteomics, 2010, v. 10, n. 7, p. 1359, doi. 10.1002/pmic.200900483
By:
- Chaerkady, Raghothama;
- Kerr, Candace L.;
- Kandasamy, Kumaran;
- Marimuthu, Arivusudar;
- Gearhart, John D.;
- Pandey, Akhilesh
Publication type:
Article
Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells.
Published in:
Proteomics, 2010, v. 10, n. 5, p. 1029, doi. 10.1002/pmic.200900602
By:
- Zhou, Qun;
- Chaerkady, Raghothama;
- Shaw, Patrick G.;
- Kensler, Thomas W.;
- Pandey, Akhilesh;
- Davidson, Nancy E.
Publication type:
Article
Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.
Published in:
Proteomics, 2009, v. 9, n. 5, p. 1374, doi. 10.1002/pmic.200800551
By:
- Yang, Yi;
- Chaerkady, Raghothama;
- Beer, Michael A.;
- Mendell, Joshua T.;
- Pandey, Akhilesh
Publication type:
Article
A functional annotation of subproteomes in human plasma.
Published in:
Proteomics, 2005, v. 5, n. 13, p. 3506, doi. 10.1002/pmic.200500140
By:
- Peipei Ping;
- Thomas M. Vondriska;
- Chad J. Creighton;
- TKB Gandhi;
- Ziping Yang;
- Rajasree Menon;
- Min-Seok Kwon;
- Sang Yun Cho;
- Garry Drwal;
- Markus Kellmann;
- Suraj Peri;
- Shubha Suresh;
- Mads Gronborg;
- Henrik Molina;
- Raghothama Chaerkady;
- B. Rekha;
- Arun S. Shet;
- Robert E. Gerszten;
- Haifeng Wu;
- Mark Raftery
Publication type:
Article
Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles.
Published in:
Breast Cancer Research & Treatment, 2012, v. 132, n. 1, p. 175, doi. 10.1007/s10549-011-1536-9
By:
- Agyeman, Abena;
- Chaerkady, Raghothama;
- Shaw, Patrick;
- Davidson, Nancy;
- Visvanathan, Kala;
- Pandey, Akhilesh;
- Kensler, Thomas
Publication type:
Article
Correction to: Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts.
Published in:
2018
By:
- Wu, Xinyan;
- Zahari, Muhammad Saddiq;
- Renuse, Santosh;
- Sahasrabuddhe, Nandini A.;
- Chaerkady, Raghothama;
- Kim, Mi-Sik;
- Fackler, Mary Jo;
- Stampfer, Martha;
- Gabrielson, Edward;
- Sukumar, Saraswati;
- Pandey, Akhilesh
Publication type:
Correction Notice
Quantitative phosphoproteomic analysis reveals reciprocal activation of receptor tyrosine kinases between cancer epithelial cells and stromal fibroblasts.
Published in:
Clinical Proteomics, 2018, v. 15, n. 1, p. N.PAG, doi. 10.1186/s12014-018-9197-x
By:
- Wu, Xinyan;
- Zahari, Muhammad Saddiq;
- Renuse, Santosh;
- Sahasrabuddhe, Nandini A.;
- Chaerkady, Raghothama;
- Kim, Min-Sik;
- Fackler, Mary Jo;
- Stampfer, Martha;
- Gabrielson, Edward;
- Sukumar, Saraswati;
- Pandey, Akhilesh
Publication type:
Article
Staphylococcus aureus drives expansion of low-density neutrophils in diabetic mice.
Published in:
2019
By:
- Cohen, Taylor S.;
- Takahashi, Virginia;
- Bonnell, Jessica;
- Tovchigrechko, Andrey;
- Chaerkady, Raghothama;
- Wen Yu;
- Jones-Nelson, Omari;
- Young Lee;
- Raja, Rajiv;
- Hess, Sonja;
- Stover, C. Kendall;
- Worthington, John J.;
- Travis, Mark A.;
- Sellman, Bret R.;
- Yu, Wen;
- Lee, Young
Publication type:
journal article
FOXE3 contributes to Peters anomaly through transcriptional regulation of an autophagy-associated protein termed DNAJB1.
Published in:
Nature Communications, 2016, v. 7, n. 4, p. 1, doi. 10.1038/ncomms10953
By:
- Khan, Shahid Y.;
- Vasanth, Shivakumar;
- Kabir, Firoz;
- Gottsch, John D.;
- Khan, Arif O.;
- Chaerkady, Raghothama;
- Mei-Chong W. Lee;
- Leitch, Carmen C.;
- Zhiwei Ma;
- Laux, Julie;
- Villasmil, Rafael;
- Khan, Shaheen N.;
- Riazuddin, Sheikh;
- Akram, Javed;
- Cole, Robert N.;
- Talbot, C. Conover;
- Pourmand, Nader;
- Zaghloul, Norann A.;
- Hejtmancik, J. Fielding;
- Riazuddin, S. Amer
Publication type:
Article
Activation of diverse signalling pathways by oncogenic PIK3CA mutations.
Published in:
Nature Communications, 2014, v. 5, n. 9, p. 4961, doi. 10.1038/ncomms5961
By:
- Wu, Xinyan;
- Renuse, Santosh;
- Sahasrabuddhe, Nandini A.;
- Zahari, Muhammad Saddiq;
- Chaerkady, Raghothama;
- Kim, Min-Sik;
- Nirujogi, Raja S.;
- Mohseni, Morassa;
- Kumar, Praveen;
- Raju, Rajesh;
- Zhong, Jun;
- Yang, Jian;
- Neiswinger, Johnathan;
- Jeong, Jun-Seop;
- Newman, Robert;
- Powers, Maureen A.;
- Somani, Babu Lal;
- Gabrielson, Edward;
- Sukumar, Saraswati;
- Stearns, Vered
Publication type:
Article
Application of mass spectrometry-based proteomics for biomarker discovery in neurological disorders.
Published in:
Annals of Indian Academy of Neurology, 2009, v. 12, n. 1, p. 3, doi. 10.4103/0972-2327.48845
By:
- Venugopal, Abhilash;
- Chaerkady, Raghothama;
- Pandey, Akhilesh
Publication type:
Article
The <i>Escherichia coli</i> Phosphotyrosine Proteome Relates to Core Pathways and Virulence.
Published in:
PLoS Pathogens, 2013, v. 9, n. 6, p. 1, doi. 10.1371/journal.ppat.1003403
By:
- Hansen, Anne-Marie;
- Chaerkady, Raghothama;
- Sharma, Jyoti;
- Díaz-Mejía, J. Javier;
- Tyagi, Nidhi;
- Renuse, Santosh;
- Jacob, Harrys K. C.;
- Pinto, Sneha M.;
- Sahasrabuddhe, Nandini A.;
- Kim, Min-Sik;
- Delanghe, Bernard;
- Srinivasan, Narayanaswamy;
- Emili, Andrew;
- Kaper, James B.;
- Pandey, Akhilesh
Publication type:
Article
Spontaneous Secretion of the Citrullination Enzyme PAD2 and Cell Surface Exposure of PAD4 by Neutrophils.
Published in:
Frontiers in Immunology, 2017, p. 1, doi. 10.3389/fimmu.2017.01200
By:
- Yebin Zhou;
- Bo Chen;
- Mittereder, Nanette;
- Chaerkady, Raghothama;
- Strain, Martin;
- Ling-Ling An;
- Rahman, Saifur;
- Wenting Ma;
- Choon Pei Low;
- Chan, Denice;
- Neal, Frances;
- Bingham III, Clifton O.;
- Sampson, Kevon;
- Darrah, Erika;
- Siegel, Richard M.;
- Hasni, Sarfaraz;
- Andrade, Felipe;
- Vousden, Katherine A.;
- Mustelin, Tomas;
- Sims, Gary P.
Publication type:
Article
Plasma Selenium Protein P Isoform 1 (SEPP1): A Predictor of Selenium Status in Nepalese Children Detected by Plasma Proteomics.
Published in:
2017
By:
- Schulze, Kerry J.;
- Cole, Robert N.;
- Chaerkady, Raghothama;
- Wu, Lee S. F.;
- Nonyane, Bareng A. S.;
- Sun Eun Lee;
- Yager, James D.;
- Groopman, John D.;
- Christian, Parul;
- West, Jr, Keith P.
Publication type:
Abstract
A draft map of the human proteome.
Published in:
Nature, 2014, v. 509, n. 7502, p. 1, doi. 10.1038/nature13302
By:
- Min-Sik Kim;
- Pinto, Sneha M.;
- Getnet, Derese;
- Nirujogi, Raja Sekhar;
- Manda, Srikanth S.;
- Chaerkady, Raghothama;
- Madugundu, Anil K.;
- Kelkar, Dhanashree S.;
- Isserlin, Ruth;
- Jain, Shobhit;
- Thomas, Joji K.;
- Muthusamy, Babylakshmi;
- Leal-Rojas, Pamela;
- Kumar, Praveen;
- Sahasrabuddhe, Nandini A.;
- Balakrishnan, Lavanya;
- Advani, Jayshree;
- George, Bijesh;
- Renuse, Santosh;
- Selvan, Lakshmi Dhevi N.
Publication type:
Article
Evidence for a direct link between PAD4-mediated citrullination and the oxidative burst in human neutrophils.
Published in:
Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-33385-z
By:
- Zhou, Yebin;
- An, Ling-Ling;
- Chaerkady, Raghothama;
- Mittereder, Nanette;
- Clarke, Lori;
- Cohen, Taylor S.;
- Chen, Bo;
- Hess, Sonja;
- Sims, Gary P.;
- Mustelin, Tomas
Publication type:
Article
Proteomic characterization of Her2/neu-overexpressing breast cancer cells.
Published in:
Proteomics - Clinical Applications, 2011, v. 5, n. 3/4, p. 201, doi. 10.1002/prca.201190018
By:
- Chen, Hexin;
- Pimienta, Genaro;
- Gu, Yiben;
- Sun, Xu;
- Hu, Jianjun;
- Kim, Min-Sik;
- Chaerkady, Raghothama;
- Gucek, Marjan;
- Cole, Robert N.;
- Sukumar, Saraswati;
- Pandey, Akhilesh
Publication type:
Article
Comparative proteomics of human embryonic stem cells and embryonal carcinoma cells.
Published in:
Proteomics - Clinical Applications, 2010, v. 4, n. 8/9, p. 760, doi. 10.1002/prca.201090040
By:
- Chaerkady, Raghothama;
- Kerr, Candace L.;
- Kandasamy, Kumaran;
- Marimuthu, Arivusudar;
- Gearhart, John D.;
- Pandey, Akhilesh
Publication type:
Article
Screening for therapeutic targets of vorinostat by SILAC-based proteomic analysis in human breast cancer cells.
Published in:
Proteomics - Clinical Applications, 2010, v. 4, n. 8/9, p. 757, doi. 10.1002/prca.201090037
By:
- Zhou, Qun;
- Chaerkady, Raghothama;
- Shaw, Patrick G.;
- Kensler, Thomas W.;
- Pandey, Akhilesh;
- Davidson, Nancy E.
Publication type:
Article
Quantitative proteomics for identification of cancer biomarkers.
Published in:
Proteomics - Clinical Applications, 2007, v. 1, n. 9, p. 1080, doi. 10.1002/prca.200700284
By:
- Chaerkady, Raghothama;
- Pandey, Akhilesh
Publication type:
Article

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