| Year |
Citation |
Score |
| 2019 |
Amodei D, Egertson J, MacLean BX, Johnson R, Merrihew GE, Keller A, Marsh D, Vitek O, Mallick P, MacCoss MJ. Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping Windows. Journal of the American Society For Mass Spectrometry. PMID 30671891 DOI: 10.1007/S13361-018-2122-8 |
0.356 |
|
| 2019 |
Nikolov M, White B, Pegoraro A, Hope D, Eljanne M, Eddy J, Janmey P, Mallick P, Dang K. Abstract 2451: Physical, genomic, and proteomic characterization of a cancer cell line panel in an integrated dataset Cancer Research. 79: 2451-2451. DOI: 10.1158/1538-7445.Am2019-2451 |
0.369 |
|
| 2018 |
Tiemann K, Garri C, Lee SB, Malihi PD, Park M, Alvarez RM, Yap LP, Mallick P, Katz JE, Gross ME, Kani K. Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasis. Oncogene. PMID 30575818 DOI: 10.1038/S41388-018-0638-9 |
0.594 |
|
| 2018 |
Hughes NP, Xu L, Nielsen CH, Chang E, Hori SS, Natarajan A, Lee S, Kjær A, Kani K, Wang SX, Mallick P, Gambhir SS. A blood biomarker for monitoring response to anti-EGFR therapy. Cancer Biomarkers : Section a of Disease Markers. PMID 29689709 DOI: 10.3233/Cbm-171149 |
0.528 |
|
| 2018 |
Sylman JL, Mitrugno A, Atallah M, Tormoen GW, Shatzel JJ, Tassi Yunga S, Wagner TH, Leppert JT, Mallick P, McCarty OJT. The Predictive Value of Inflammation-Related Peripheral Blood Measurements in Cancer Staging and Prognosis. Frontiers in Oncology. 8: 78. PMID 29619344 DOI: 10.3389/Fonc.2018.00078 |
0.305 |
|
| 2018 |
Lee JR, Appelmann I, Miething C, Shultz TO, Ruderman D, Kim D, Mallick P, Lowe SW, Wang SX. Longitudinal Multiplexed Measurement of Quantitative Proteomic Signatures in Mouse Lymphoma Models Using Magneto-Nanosensors. Theranostics. 8: 1389-1398. PMID 29507628 DOI: 10.7150/Thno.20706 |
0.361 |
|
| 2018 |
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, ... ... Mallick P, et al. How many human proteoforms are there? Nature Chemical Biology. 14: 206-214. PMID 29443976 DOI: 10.1038/Nchembio.2576 |
0.612 |
|
| 2017 |
Sharpnack MF, Chen B, Aran D, Kosti I, Sharpnack DD, Carbone DP, Mallick P, Huang K. Global Transcriptome Analysis of RNA Abundance Regulation by ADAR in Lung Adenocarcinoma. Ebiomedicine. PMID 29273356 DOI: 10.1016/J.Ebiom.2017.12.005 |
0.34 |
|
| 2017 |
Yeh CY, Adusumilli R, Kullolli M, Mallick P, John EM, Pitteri SJ. Assessing biological and technological variability in protein levels measured in pre-diagnostic plasma samples of women with breast cancer. Biomarker Research. 5: 30. PMID 29075496 DOI: 10.1186/S40364-017-0110-Y |
0.333 |
|
| 2017 |
Lee JR, Chan CT, Ruderman D, Chuang HY, Gaster RS, Atallah M, Mallick P, Lowe SW, Gambhir SS, Wang SX. Longitudinal monitoring of antibody responses against tumor cells using magneto-nanosensors with a nanoliter of blood. Nano Letters. PMID 28990786 DOI: 10.1021/Acs.Nanolett.7B02591 |
0.3 |
|
| 2017 |
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. JUN-Mediated downregulation of EGFR signaling is associated with resistance to gefitinib in EGFR-mutant NSCLC cell lines. Molecular Cancer Therapeutics. PMID 28566434 DOI: 10.1158/1535-7163.Mct-16-0564 |
0.565 |
|
| 2017 |
Atallah M, Flory MR, Mallick P. A Robust Protocol for Protein Extraction and Digestion. Methods of Molecular Biology. 1550: 1-10. PMID 28188518 DOI: 10.1007/978-1-4939-6747-6_1 |
0.368 |
|
| 2016 |
Patsch K, Chiu CL, Engeln M, Agus DB, Mallick P, Mumenthaler SM, Ruderman D. Single cell dynamic phenotyping. Scientific Reports. 6: 34785. PMID 27708391 DOI: 10.1038/Srep34785 |
0.631 |
|
| 2016 |
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. Dual transcript and protein quantification in a massive single cell array. Lab On a Chip. PMID 27546183 DOI: 10.1039/C6Lc00762G |
0.675 |
|
| 2016 |
Garvey CM, Spiller E, Lindsay D, Chiang CT, Choi NC, Agus DB, Mallick P, Foo J, Mumenthaler SM. A high-content image-based method for quantitatively studying context-dependent cell population dynamics. Scientific Reports. 6: 29752. PMID 27452732 DOI: 10.1038/Srep29752 |
0.652 |
|
| 2016 |
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. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Medicine. 8: 54. PMID 27146673 DOI: 10.1186/S13073-016-0305-0 |
0.67 |
|
| 2016 |
van de Ven S, Bemis KD, Lau K, Adusumilli R, Kota U, Stolowitz M, Vitek O, Mallick P, Gambhir SS. Protein biomarkers on tissue as imaged via MALDI mass spectrometry: A systematic approach to study the limits of detection. Proteomics. PMID 26970438 DOI: 10.1002/Pmic.201500515 |
0.358 |
|
| 2016 |
Liu S, Bainer R, Yui Y, Flinders C, Mallick P, Weaver V, Mumenthaler S. Abstract A23: Characterization of diverging molecular and phenotypic responses under changing extracellular matrix stiffness in MCF10A cells Cancer Research. 76. DOI: 10.1158/1538-7445.Tme16-A23 |
0.767 |
|
| 2015 |
Frieboes HB, Curtis LT, Wu M, Kani K, Mallick P. Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor. Cancer Informatics. 14: 163-75. PMID 26715830 DOI: 10.4137/Cin.S35374 |
0.587 |
|
| 2015 |
Chang E, Pohling C, Natarajan A, Witney TH, Kaur J, Xu L, Gowrishankar G, L D'Souza A, Murty S, Schick S, Chen L, Wu N, Khaw P, Mischel P, Abbasi T, ... ... Mallick P, et al. AshwaMAX and Withaferin A inhibits gliomas in cellular and murine orthotopic models. Journal of Neuro-Oncology. PMID 26650066 DOI: 10.1007/S11060-015-1972-1 |
0.32 |
|
| 2015 |
Mumenthaler SM, Foo J, Choi NC, Heise N, Leder K, Agus DB, Pao W, Michor F, Mallick P. The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells. Cancer Informatics. 14: 19-31. PMID 26244007 DOI: 10.4137/Cin.S19338 |
0.665 |
|
| 2015 |
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. Predictive Modeling of Drug Response in Non-Hodgkin's Lymphoma. Plos One. 10: e0129433. PMID 26061425 DOI: 10.1371/Journal.Pone.0129433 |
0.752 |
|
| 2015 |
Schubert OT, Gillet LC, Collins BC, Navarro P, Rosenberger G, Wolski WE, Lam H, Amodei D, Mallick P, MacLean B, Aebersold R. Building high-quality assay libraries for targeted analysis of SWATH MS data. Nature Protocols. 10: 426-41. PMID 25675208 DOI: 10.1038/Nprot.2015.015 |
0.454 |
|
| 2015 |
Bainer R, Yui Y, Mumenthaler S, Mallick P, Liu L, Wu H, Podlaha O, Michor F, Liphardt J, Licht J, Weaver V. Abstract PR09: Extracellular stiffness cues drive spatial reorganization of the genome to globally constrain RNA abundance Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr09 |
0.64 |
|
| 2015 |
Mumenthaler S, Foo J, Choi N, Pao W, Agus D, Michor F, Mallick P. Abstract PR16: Spatio-temporal heterogeneity in the tumor microenvironment influences the evolutionary dynamics of drug resistance Cancer Research. 75. DOI: 10.1158/1538-7445.Chtme14-Pr16 |
0.655 |
|
| 2015 |
Chang E, Pohling C, Natarajan A, Witney T, Kaur J, Xu L, Gowrishankar G, de Souza A, Schick S, Chan L, Wu N, Khaw P, Mischel P, Abbasi T, Usmani S, ... Mallick P, et al. DDEL-04AshwaMAX AND WITHAFERIN A INHIBITS GLIOMAS IN CELLULAR AND MURINE ORTHOTOPIC MODELS Neuro-Oncology. 17: v73.4-v73. DOI: 10.1093/Neuonc/Nov212.04 |
0.315 |
|
| 2014 |
Li K, Tavaré R, Zettlitz KA, Mumenthaler SM, Mallick P, Zhou Y, Marks JD, Wu AM. Anti-MET immunoPET for non-small cell lung cancer using novel fully human antibody fragments. Molecular Cancer Therapeutics. 13: 2607-17. PMID 25143449 DOI: 10.1158/1535-7163.Mct-14-0363 |
0.649 |
|
| 2014 |
Bainer R, Yui Y, Mumenthaler S, Mallick P, Podlaha O, Michor F, Liphardt J, Licht J, Weaver V. Abstract 2344: 3D extracellular stiffness cues drive localized changes in gene expression Cancer Research. 74: 2344-2344. DOI: 10.1158/1538-7445.Am2014-2344 |
0.656 |
|
| 2014 |
Chang E, Abbasi T, D'Souza A, Gowrishankar G, Mallick P, Gambhir SS. DD-03 * THE NATURALLY OCCURRING STEROID, WITHAFERIN A, IN SYNERGISTIC CONCERT WITH HER2/EGFR INHIBITORS ABROGATES PROLIFERATION OF HUMAN GLIOBLASTOMA CELL CULTURES AT NANOMOLAR CONCENTRATIONS Neuro-Oncology. 16: v60-v60. DOI: 10.1093/Neuonc/Nou246.3 |
0.309 |
|
| 2013 |
Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, ... ... Mallick P, et al. A physical sciences network characterization of non-tumorigenic and metastatic cells. Scientific Reports. 3: 1449. PMID 23618955 DOI: 10.1038/Srep01449 |
0.642 |
|
| 2013 |
Byun S, Son S, Amodei D, Cermak N, Shaw J, Kang JH, Hecht VC, Winslow MM, Jacks T, Mallick P, Manalis SR. Characterizing deformability and surface friction of cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 110: 7580-5. PMID 23610435 DOI: 10.1073/Pnas.1218806110 |
0.317 |
|
| 2013 |
Kani K, Malihi PD, Jiang Y, Wang H, Wang Y, Ruderman DL, Agus DB, Mallick P, Gross ME. Anterior gradient 2 (AGR2): blood-based biomarker elevated in metastatic prostate cancer associated with the neuroendocrine phenotype. The Prostate. 73: 306-15. PMID 22911164 DOI: 10.1002/Pros.22569 |
0.535 |
|
| 2013 |
Park S, Lee JY, Hong S, Dimov IK, Li K, Wu AM, Mumenthaler S, Mallick P, Lee LP. Concurrent Transcript and Protein Quantification in a Massive Single Cell Array Enables Population-Wide Observation of Oncogene Escape Biophysical Journal. 104: 686a. DOI: 10.1016/J.Bpj.2012.11.3790 |
0.679 |
|
| 2012 |
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J, Hoff K, Kessner D, Tasman N, Shulman N, Frewen B, ... ... Mallick P, et al. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology. 30: 918-20. PMID 23051804 DOI: 10.1038/Nbt.2377 |
0.577 |
|
| 2012 |
Kani K, Faca VM, Hughes LD, Zhang W, Fang Q, Shahbaba B, Luethy R, Erde J, Schmidt J, Pitteri SJ, Zhang Q, Katz JE, Gross ME, Plevritis SK, McIntosh MW, ... ... Mallick P, et al. Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibition. Molecular Cancer Therapeutics. 11: 1071-81. PMID 22411897 DOI: 10.1158/1535-7163.Mct-11-0852 |
0.609 |
|
| 2012 |
Kani K, Sordella R, Mallick P. Investigation of acquired resistance to EGFR-targeted therapies in lung cancer using cDNA microarrays. Methods in Molecular Biology (Clifton, N.J.). 795: 233-53. PMID 21960227 DOI: 10.1007/978-1-61779-337-0_16 |
0.558 |
|
| 2011 |
Mumenthaler SM, Foo J, Leder K, Choi NC, Agus DB, Pao W, Mallick P, Michor F. Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer. Molecular Pharmaceutics. 8: 2069-79. PMID 21995722 DOI: 10.1021/Mp200270V |
0.655 |
|
| 2011 |
Fang Q, Kani K, Faca VM, Zhang W, Zhang Q, Jain A, Hanash S, Agus DB, McIntosh MW, Mallick P. Impact of protein stability, cellular localization, and abundance on proteomic detection of tumor-derived proteins in plasma. Plos One. 6: e23090. PMID 21829587 DOI: 10.1371/Journal.Pone.0023090 |
0.583 |
|
| 2011 |
Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Molecular & Cellular Proteomics : McP. 10: M110.006353. PMID 21632744 DOI: 10.1074/Mcp.M110.006353 |
0.503 |
|
| 2011 |
Vogelsang MS, Kani K, Katz JE, Mallick P. Model-based discovery of circulating biomarkers. Methods in Molecular Biology (Clifton, N.J.). 728: 87-107. PMID 21468942 DOI: 10.1007/978-1-61779-068-3_5 |
0.583 |
|
| 2010 |
Mallick P, Kuster B. Proteomics: A pragmatic perspective Nature Biotechnology. 28: 695-709. PMID 20622844 DOI: 10.1038/Nbt.1658 |
0.347 |
|
| 2008 |
Luethy R, Kessner DE, Katz JE, Maclean B, Grothe R, Kani K, Faça V, Pitteri S, Hanash S, Agus DB, Mallick P. Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. Journal of Proteome Research. 7: 4031-9. PMID 18707148 DOI: 10.1021/Pr800307M |
0.552 |
|
| 2008 |
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of Proteome Research. 7: 3755-64. PMID 18652504 DOI: 10.1021/Pr800031F |
0.351 |
|
| 2008 |
Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H, Schmidt A, Ossola R, Eng JK, Aebersold R, Martin DB. The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. Journal of Proteome Research. 7: 96-103. PMID 17711323 DOI: 10.1021/Pr070244J |
0.478 |
|
| 2007 |
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R. Computational prediction of proteotypic peptides for quantitative proteomics. Nature Biotechnology. 25: 125-31. PMID 17195840 DOI: 10.1038/Nbt1275 |
0.6 |
|
| 2006 |
Flory MR, Lee H, Bonneau R, Mallick P, Serikawa K, Morris DR, Aebersold R. Quantitative proteomic analysis of the budding yeast cell cycle using acid-cleavable isotope-coded affinity tag reagents. Proteomics. 6: 6146-57. PMID 17133367 DOI: 10.1002/Pmic.200600159 |
0.502 |
|
| 2006 |
King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biology. 7: R106. PMID 17101051 DOI: 10.1186/Gb-2006-7-11-R106 |
0.486 |
|
| 2006 |
Seebacher J, Mallick P, Zhang N, Eddes JS, Aebersold R, Gelb MH. Protein cross-linking analysis using mass spectrometry, isotope-coded cross-linkers, and integrated computational data processing. Journal of Proteome Research. 5: 2270-82. PMID 16944939 DOI: 10.1021/Pr060154Z |
0.489 |
|
| 2006 |
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Research. 34: D655-8. PMID 16381952 DOI: 10.1093/Nar/Gkj040 |
0.604 |
|
| 2006 |
Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski B. Signal maps for mass spectrometry-based comparative proteomics. Molecular & Cellular Proteomics : McP. 5: 423-32. PMID 16269421 DOI: 10.1074/Mcp.M500133-Mcp200 |
0.47 |
|
| 2005 |
Kuster B, Schirle M, Mallick P, Aebersold R. Scoring proteomes with proteotypic peptide probes. Nature Reviews. Molecular Cell Biology. 6: 577-83. PMID 15957003 DOI: 10.1038/Nrm1683 |
0.414 |
|
| 2005 |
Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biology. 6: R9. PMID 15642101 DOI: 10.1186/Gb-2004-6-1-R9 |
0.48 |
|
| 2005 |
Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp DG, Smith RD, Kemp CJ, Aebersold R. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Molecular & Cellular Proteomics : McP. 4: 144-55. PMID 15608340 DOI: 10.1074/Mcp.M400090-Mcp200 |
0.496 |
|
| 2005 |
Gurbaxani BM, Mallick P. Finding protein domain boundaries: An automated, non-homology-based method Ieee Intelligent Systems. 20: 26-33. DOI: 10.1109/Mis.2005.106 |
0.313 |
|
| 2004 |
Kleiger G, Panina EM, Mallick P, Eisenberg D. PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. Protein Science : a Publication of the Protein Society. 13: 221-9. PMID 14691237 DOI: 10.1110/Ps.03274104 |
0.701 |
|
| 2003 |
Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D. Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biology. 4: R59. PMID 12952538 DOI: 10.1186/Gb-2003-4-9-R59 |
0.644 |
|
| 2002 |
Mallick P, Weiss R, Eisenberg D. The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proceedings of the National Academy of Sciences of the United States of America. 99: 16041-6. PMID 12461172 DOI: 10.1073/Pnas.252626399 |
0.459 |
|
| 2002 |
Mallick P, Boutz DR, Eisenberg D, Yeates TO. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proceedings of the National Academy of Sciences of the United States of America. 99: 9679-84. PMID 12107280 DOI: 10.1073/Pnas.142310499 |
0.478 |
|
| 2002 |
Kleiger G, Grothe R, Mallick P, Eisenberg D. GXXXG and AXXXA: Common α-Helical Interaction Motifs in Proteins, Particularly in Extremophiles† Biochemistry. 41: 5990-5997. PMID 11993993 DOI: 10.1021/Bi0200763 |
0.699 |
|
| 2000 |
Kleiger G, Beamer LJ, Grothe R, Mallick P, Eisenberg D. The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold. Journal of Molecular Biology. 299: 1019-34. PMID 10843855 DOI: 10.1006/Jmbi.2000.3805 |
0.692 |
|
| 2000 |
Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D. Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. Proceedings of the National Academy of Sciences of the United States of America. 97: 2450-5. PMID 10706641 DOI: 10.1073/Pnas.050589297 |
0.487 |
|
| 2000 |
Goulding CW, Mallick P, Eisenberg D. Structural and Functional Studies of Proteins with Predicted “Novel” Folds in Pyrobaculum Aerophilium Biochemical Society Transactions. 28: A446-A446. DOI: 10.1042/Bst028A446B |
0.454 |
|
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