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Consortia of bioactives in supercritical carbon dioxide extracts of mustard and small cardamom seeds lower serum cholesterol levels in rats: new leads for hypocholesterolaemic supplements from spices.

Chakraborty S, Paul K, Mallick P, Pradhan S, Das K, Chakrabarti S, Nandi DK, Bhattacharjee P.

J Nutr Sci. 2019 Sep 24;8:e32. doi: 10.1017/jns.2019.28. eCollection 2019.


Development and Application of a Life-Stage Physiologically-Based Pharmacokinetic (PBPK) Model to the Assessment of Internal Dose of Pyrethroids in Humans.

Mallick P, Moreau M, Song G, Efremenko AY, Pendse SN, Creek MR, Osimitz TG, Hines RN, Hinderliter P, Clewell HJ, Lake BG, Yoon M.

Toxicol Sci. 2019 Oct 8. pii: kfz211. doi: 10.1093/toxsci/kfz211. [Epub ahead of print]


Molecular characterization of Orf virus isolates from Kodai hills, Tamil Nadu, India.

Nagarajan G, Pourouchottamane R, Reddy GBM, Yogisharadhya R, Sumana K, Rajapandi S, Murali G, Thirumaran SMK, Mallick PK, Rajendiran AS.

Vet World. 2019 Jul;12(7):1022-1027. doi: 10.14202/vetworld.2019.1022-1027. Epub 2019 Jul 12.


Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility.

Srivastava A, Adusumilli R, Boyce H, Garijo D, Ratnakar V, Mayani R, Yu T, Machiraju R, Gil Y, Mallick P.

Pac Symp Biocomput. 2019;24:208-219.


Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows.

Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ.

J Am Soc Mass Spectrom. 2019 Apr;30(4):669-684. doi: 10.1007/s13361-018-2122-8. Epub 2019 Jan 22.


Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis.

Tiemann K, Garri C, Lee SB, Malihi PD, Park M, Alvarez RM, Yap LP, Mallick P, Katz JE, Gross ME, Kani K.

Oncogene. 2019 Apr;38(16):3003-3018. doi: 10.1038/s41388-018-0638-9. Epub 2018 Dec 21.


PCSeg: Color model driven probabilistic multiphase level set based tool for plasma cell segmentation in multiple myeloma.

Gupta A, Mallick P, Sharma O, Gupta R, Duggal R.

PLoS One. 2018 Dec 12;13(12):e0207908. doi: 10.1371/journal.pone.0207908. eCollection 2018.


Imitating Pathologist Based Assessment With Interpretable and Context Based Neural Network Modeling of Histology Images.

Srivastava A, Kulkarni C, Huang K, Parwani A, Mallick P, Machiraju R.

Biomed Inform Insights. 2018 Oct 31;10:1178222618807481. doi: 10.1177/1178222618807481. eCollection 2018.


Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma.

Sharpnack MF, Ranbaduge N, Srivastava A, Cerciello F, Codreanu SG, Liebler DC, Mascaux C, Miles WO, Morris R, McDermott JE, Sharpnack JL, Amann J, Maher CA, Machiraju R, Wysocki VH, Govindan R, Mallick P, Coombes KR, Huang K, Carbone DP.

J Thorac Oncol. 2018 Oct;13(10):1519-1529. doi: 10.1016/j.jtho.2018.06.025. Epub 2018 Jul 11.


A Bayesian Active Learning Experimental Design for Inferring Signaling Networks.

Ness RO, Sachs K, Mallick P, Vitek O.

J Comput Biol. 2018 Jul;25(7):709-725. doi: 10.1089/cmb.2017.0247. Epub 2018 Jun 21.


Impact of diet on irinotecan toxicity in mice.

Mallick P, Shah P, Ittmann MM, Trivedi M, Hu M, Gao S, Ghose R.

Chem Biol Interact. 2018 Aug 1;291:87-94. doi: 10.1016/j.cbi.2018.06.018. Epub 2018 Jun 18.


A Temporal Examination of Platelet Counts as a Predictor of Prognosis in Lung, Prostate, and Colon Cancer Patients.

Sylman JL, Boyce HB, Mitrugno A, Tormoen GW, Thomas IC, Wagner TH, Lee JS, Leppert JT, McCarty OJT, Mallick P.

Sci Rep. 2018 Apr 26;8(1):6564. doi: 10.1038/s41598-018-25019-1.


Multi-lectin Affinity Chromatography and Quantitative Proteomic Analysis Reveal Differential Glycoform Levels between Prostate Cancer and Benign Prostatic Hyperplasia Sera.

Totten SM, Adusumilli R, Kullolli M, Tanimoto C, Brooks JD, Mallick P, Pitteri SJ.

Sci Rep. 2018 Apr 25;8(1):6509. doi: 10.1038/s41598-018-24270-w.


A blood biomarker for monitoring response to anti-EGFR therapy.

Hughes NP, Xu L, Nielsen CH, Chang E, Hori SS, Natarajan A, Lee S, Kjær A, Kani K, Wang SX, Mallick P, Gambhir SS.

Cancer Biomark. 2018;22(2):333-344. doi: 10.3233/CBM-171149.


The Predictive Value of Inflammation-Related Peripheral Blood Measurements in Cancer Staging and Prognosis.

Sylman JL, Mitrugno A, Atallah M, Tormoen GW, Shatzel JJ, Tassi Yunga S, Wagner TH, Leppert JT, Mallick P, McCarty OJT.

Front Oncol. 2018 Mar 21;8:78. doi: 10.3389/fonc.2018.00078. eCollection 2018. Review.


Longitudinal Multiplexed Measurement of Quantitative Proteomic Signatures in Mouse Lymphoma Models Using Magneto-Nanosensors.

Lee JR, Appelmann I, Miething C, Shultz TO, Ruderman D, Kim D, Mallick P, Lowe SW, Wang SX.

Theranostics. 2018 Feb 3;8(5):1389-1398. doi: 10.7150/thno.20706. eCollection 2018.


How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.


Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma.

Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K.

EBioMedicine. 2018 Jan;27:167-175. doi: 10.1016/j.ebiom.2017.12.005. Epub 2017 Dec 6.


Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles.

Srivastava A, Kulkarni C, Mallick P, Huang K, Machiraju R.

Pac Symp Biocomput. 2018;23:377-387.


Platelet count as a predictor of metastasis and venous thromboembolism in patients with cancer.

Sylman JL, Mitrugno A, Tormoen GW, Wagner TH, Mallick P, McCarty OJT.

Converg Sci Phys Oncol. 2017 Jun;3(2). pii: 023001. doi: 10.1088/2057-1739/aa6c05. Epub 2017 May 17.


Assessing biological and technological variability in protein levels measured in pre-diagnostic plasma samples of women with breast cancer.

Yeh CY, Adusumilli R, Kullolli M, Mallick P, John EM, Pitteri SJ.

Biomark Res. 2017 Oct 17;5:30. doi: 10.1186/s40364-017-0110-y. eCollection 2017.


Longitudinal Monitoring of Antibody Responses against Tumor Cells Using Magneto-nanosensors with a Nanoliter of Blood.

Lee JR, Chan CT, Ruderman D, Chuang HY, Gaster RS, Atallah M, Mallick P, Lowe SW, Gambhir SS, Wang SX.

Nano Lett. 2017 Nov 8;17(11):6644-6652. doi: 10.1021/acs.nanolett.7b02591. Epub 2017 Oct 20.


JUN-Mediated Downregulation of EGFR Signaling Is Associated with Resistance to Gefitinib in EGFR-mutant NSCLC Cell Lines.

Kani K, Garri C, Tiemann K, Malihi PD, Punj V, Nguyen AL, Lee J, Hughes LD, Alvarez RM, Wood DM, Joo AY, Katz JE, Agus DB, Mallick P.

Mol Cancer Ther. 2017 Aug;16(8):1645-1657. doi: 10.1158/1535-7163.MCT-16-0564. Epub 2017 May 31.


Regulation of drug-metabolizing enzymes in infectious and inflammatory disease: implications for biologics-small molecule drug interactions.

Mallick P, Taneja G, Moorthy B, Ghose R.

Expert Opin Drug Metab Toxicol. 2017 Jun;13(6):605-616. doi: 10.1080/17425255.2017.1292251. Epub 2017 Feb 22. Review.


Role of Toll-like receptor 4 in drug-drug interaction between paclitaxel and irinotecan in vitro.

Mallick P, Basu S, Moorthy B, Ghose R.

Toxicol In Vitro. 2017 Jun;41:75-82. doi: 10.1016/j.tiv.2017.02.019. Epub 2017 Feb 27.


Data Conversion with ProteoWizard msConvert.

Adusumilli R, Mallick P.

Methods Mol Biol. 2017;1550:339-368. doi: 10.1007/978-1-4939-6747-6_23.


A Robust Protocol for Protein Extraction and Digestion.

Atallah M, Flory MR, Mallick P.

Methods Mol Biol. 2017;1550:1-10. doi: 10.1007/978-1-4939-6747-6_1.


Emerging polymorphisms in falciparum Kelch 13 gene in Northeastern region of India.

Mishra N, Bharti RS, Mallick P, Singh OP, Srivastava B, Rana R, Phookan S, Gupta HP, Ringwald P, Valecha N.

Malar J. 2016 Dec 3;15(1):583.


Single cell dynamic phenotyping.

Patsch K, Chiu CL, Engeln M, Agus DB, Mallick P, Mumenthaler SM, Ruderman D.

Sci Rep. 2016 Oct 6;6:34785. doi: 10.1038/srep34785.


Dual transcript and protein quantification in a massive single cell array.

Park SM, Lee JY, Hong S, Lee SH, Dimov IK, Lee H, Suh S, Pan Q, Li K, Wu AM, Mumenthaler SM, Mallick P, Lee LP.

Lab Chip. 2016 Oct 7;16(19):3682-8. doi: 10.1039/c6lc00762g. Epub 2016 Aug 22.


A high-content image-based method for quantitatively studying context-dependent cell population dynamics.

Garvey CM, Spiller E, Lindsay D, Chiang CT, Choi NC, Agus DB, Mallick P, Foo J, Mumenthaler SM.

Sci Rep. 2016 Jul 25;6:29752. doi: 10.1038/srep29752.


Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma.

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M.

Genome Med. 2016 May 4;8(1):54. doi: 10.1186/s13073-016-0305-0.


Genetic trend for growth and wool performance in a closed flock of Bharat Merino sheep at sub temperate region of Kodai hills, Tamil Nadu.

Mallick PK, Thirumaran SM, Pourouchottamane R, Rajapandi S, Venkataramanan R, Nagarajan G, Murali G, Rajendiran AS.

Vet World. 2016 Mar;9(3):276-80. doi: 10.14202/vetworld.2016.276-280. Epub 2016 Mar 16.


A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India.

Rao PN, Uplekar S, Kayal S, Mallick PK, Bandyopadhyay N, Kale S, Singh OP, Mohanty A, Mohanty S, Wassmer SC, Carlton JM.

J Clin Microbiol. 2016 Jun;54(6):1500-1511. doi: 10.1128/JCM.00235-16. Epub 2016 Mar 23.


Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection.

van de Ven SM, Bemis KD, Lau K, Adusumilli R, Kota U, Stolowitz M, Vitek O, Mallick P, Gambhir SS.

Proteomics. 2016 Jun;16(11-12):1660-9. doi: 10.1002/pmic.201500515. Epub 2016 May 11.


In Vitro Approaches to Study Regulation of Hepatic Cytochrome P450 (CYP) 3A Expression by Paclitaxel and Rifampicin.

Ghose R, Mallick P, Taneja G, Chu C, Moorthy B.

Methods Mol Biol. 2016;1395:55-68. doi: 10.1007/978-1-4939-3347-1_4.


Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments.

Bemis KD, Harry A, Eberlin LS, Ferreira CR, van de Ven SM, Mallick P, Stolowitz M, Vitek O.

Mol Cell Proteomics. 2016 May;15(5):1761-72. doi: 10.1074/mcp.O115.053918. Epub 2016 Jan 21.


Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor.

Frieboes HB, Curtis LT, Wu M, Kani K, Mallick P.

Cancer Inform. 2015 Dec 20;14:163-75. doi: 10.4137/CIN.S35374. eCollection 2015.


Nanostructured Anodic Multilayer Dielectric Stacked Metal-Insulator-Metal Capacitors.

Karthik R, Kannadassan D, Baghini MS, Mallick PS.

J Nanosci Nanotechnol. 2015 Dec;15(12):9938-43.


AshwaMAX and Withaferin A inhibits gliomas in cellular and murine orthotopic models.

Chang E, Pohling C, Natarajan A, Witney TH, Kaur J, Xu L, Gowrishankar G, D'Souza AL, Murty S, Schick S, Chen L, Wu N, Khaw P, Mischel P, Abbasi T, Usmani S, Mallick P, Gambhir SS.

J Neurooncol. 2016 Jan;126(2):253-64. doi: 10.1007/s11060-015-1972-1. Epub 2015 Dec 9.


A rare case of unusual migrated foreign bodies in kidney and their successful extraction using retrograde percutaneous nephrostomy.

Upadhyay SP, Zahir M, Al Muttari H, Mallick PN.

Qatar Med J. 2015 Jul 2;2015(1):7. doi: 10.5339/qmj.2015.7. eCollection 2015.


Polymorphism in drug resistance genes dihydrofolate reductase and dihydropteroate synthase in Plasmodium falciparum in some states of India.

Sharma D, Lather M, Mallick PK, Adak T, Dang AS, Valecha N, Singh OP.

Parasit Vectors. 2015 Sep 17;8:471. doi: 10.1186/s13071-015-1080-2.


Impact of obesity on accumulation of the toxic irinotecan metabolite, SN-38, in mice.

Mallick P, Shah P, Gandhi A, Ghose R.

Life Sci. 2015 Oct 15;139:132-8. doi: 10.1016/j.lfs.2015.08.017. Epub 2015 Sep 1.


The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells.

Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P.

Cancer Inform. 2015 Jul 15;14(Suppl 4):19-31. doi: 10.4137/CIN.S19338. eCollection 2015.


Predictive Modeling of Drug Response in Non-Hodgkin's Lymphoma.

Frieboes HB, Smith BR, Wang Z, Kotsuma M, Ito K, Day A, Cahill B, Flinders C, Mumenthaler SM, Mallick P, Simbawa E, Al-Fhaid AS, Mahmoud SR, Gambhir SS, Cristini V.

PLoS One. 2015 Jun 10;10(6):e0129433. doi: 10.1371/journal.pone.0129433. eCollection 2015.


A fully human scFv phage display library for rapid antibody fragment reformatting.

Li K, Zettlitz KA, Lipianskaya J, Zhou Y, Marks JD, Mallick P, Reiter RE, Wu AM.

Protein Eng Des Sel. 2015 Oct;28(10):307-16. doi: 10.1093/protein/gzv024. Epub 2015 May 19.


Impact of Oxidative Stress Biomarkers and Carboxymethyllysine (an Advanced Glycation End Product) on Prostate Cancer: A Prospective Study.

Yang S, Pinney SM, Mallick P, Ho SM, Bracken B, Wu T.

Clin Genitourin Cancer. 2015 Oct;13(5):e347-51. doi: 10.1016/j.clgc.2015.04.004. Epub 2015 Apr 18.

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