Leah Schaffer

Title(s)	Postdoctoral Scholar, Medicine
School	Vc-health Sciences-schools
Address	9500 Gilman Drive # La Jolla CA 92093
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Bibliographic

Publications

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.

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State of the interactomes: an evaluation of molecular networks for generating biological insights. Mol Syst Biol. 2024 Dec 09. Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. PMID: 39653848.

View in: PubMed Mentions:
Multi-modal contrastive learning of subcellular organization using DICE. Bioinformatics. 2024 09 01; 40(Suppl 2):ii105-ii110. Nasser R, Schaffer LV, Ideker T, Sharan R. PMID: 39230695; PMCID: PMC11520230.

View in: PubMed Mentions: Fields:
Com Computational Biology
Translation:Humans Cells
Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes. Annu Rev Biomed Data Sci. 2024 Aug; 7(1):369-389. Cesnik A, Schaffer LV, Gaur I, Jain M, Ideker T, Lundberg E. PMID: 38748859; PMCID: PMC11343683.

View in: PubMed Mentions: 1 Fields:
Com Computational Biology
Translation:Humans
Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. bioRxiv. 2024 May 24. Clark T, Mohan J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A, Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S, Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P, Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. PMID: 38826258; PMCID: PMC11142054.

View in: PubMed Mentions:
State of the Interactomes: an evaluation of molecular networks for generating biological insights. bioRxiv. 2024 Apr 29. Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. PMID: 38746239; PMCID: PMC11092493.

View in: PubMed Mentions:
Proteoform Analysis and Construction of Proteoform Families in Proteoform Suite. Methods Mol Biol. 2022; 2500:67-81. Schaffer LV, Shortreed MR, Smith LM. PMID: 35657588; PMCID: PMC9694099.

View in: PubMed Mentions: Fields:
Mol Molecular Biology
Translation:Humans Cells
A multi-scale map of cell structure fusing protein images and interactions. Nature. 2021 12; 600(7889):536-542. Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. PMID: 34819669; PMCID: PMC9053732.

View in: PubMed Mentions: 28 Fields:
Sci Science
Translation:Humans Cells
Advanced Strategies for Proton-Transfer Reactions Coupled with Parallel Ion Parking on a 21 T FT-ICR MS for Intact Protein Analysis. Anal Chem. 2021 07 06; 93(26):9119-9128. Weisbrod CR, Anderson LC, Hendrickson CL, Schaffer LV, Shortreed MR, Smith LM, Shabanowitz J, Hunt DF. PMID: 34165955; PMCID: PMC8388574.

View in: PubMed Mentions: 8 Fields:
Che Chemistry Techniques
Mapping the multiscale structure of biological systems. Cell Syst. 2021 06 16; 12(6):622-635. Schaffer LV, Ideker T. PMID: 34139169; PMCID: PMC8245186.

View in: PubMed Mentions: 11 Fields:
Cel Cell Biology Com Computational Biology Mol Molecular Biology
Binary Classifier for Computing Posterior Error Probabilities in MetaMorpheus. J Proteome Res. 2021 04 02; 20(4):1997-2004. Shortreed MR, Millikin RJ, Liu L, Rolfs Z, Miller RM, Schaffer LV, Frey BL, Smith LM. PMID: 33683901; PMCID: PMC8377504.

View in: PubMed Mentions: 1 Fields:
Bio Biochemistry
Construction of Human Proteoform Families from 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Top-Down Proteomic Data. J Proteome Res. 2021 01 01; 20(1):317-325. Schaffer LV, Anderson LC, Butcher DS, Shortreed MR, Miller RM, Pavelec C, Smith LM. PMID: 33074679; PMCID: PMC7775878.

View in: PubMed Mentions: 2 Fields:
Bio Biochemistry
Translation:Humans
Improving Proteoform Identifications in Complex Systems Through Integration of Bottom-Up and Top-Down Data. J Proteome Res. 2020 08 07; 19(8):3510-3517. Schaffer LV, Millikin RJ, Shortreed MR, Scalf M, Smith LM. PMID: 32584579; PMCID: PMC7490796.

View in: PubMed Mentions: 17 Fields:
Bio Biochemistry
Translation:Humans Cells
Micromolded Carbon Paste Microelectrodes for Electrogenerated Chemiluminescent Detection on Microfluidic Devices. ChemElectroChem. 2020 Aug 03; 7(15):3244-3252. Gross EM, Porter LR, Stukel NR, Lowry ER, Schaffer LV, Maddipati SS, Hoyt DJ, Stombaugh SE, Peila SR, Henry CS. PMID: 33542892; PMCID: PMC7853645.

View in: PubMed Mentions: 2
A five-level classification system for proteoform identifications. Nat Methods. 2019 10; 16(10):939-940. Smith LM, Thomas PM, Shortreed MR, Schaffer LV, Fellers RT, LeDuc RD, Tucholski T, Ge Y, Agar JN, Anderson LC, Chamot-Rooke J, Gault J, Loo JA, Paša-Tolic L, Robinson CV, Schlüter H, Tsybin YO, Vilaseca M, Vizcaíno JA, Danis PO, Kelleher NL. PMID: 31451767; PMCID: PMC6857706.

View in: PubMed Mentions: 33 Fields:
Cli Clinical Laboratory Techniques
Constructing Human Proteoform Families Using Intact-Mass and Top-Down Proteomics with a Multi-Protease Global Post-Translational Modification Discovery Database. J Proteome Res. 2019 10 04; 18(10):3671-3680. Dai Y, Buxton KE, Schaffer LV, Miller RM, Millikin RJ, Scalf M, Frey BL, Shortreed MR, Smith LM. PMID: 31479276; PMCID: PMC6890418.

View in: PubMed Mentions: 15 Fields:
Bio Biochemistry
Translation:Humans Cells
Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms. Anal Chem. 2019 09 03; 91(17):10937-10942. Schaffer LV, Tucholski T, Shortreed MR, Ge Y, Smith LM. PMID: 31393705; PMCID: PMC6722015.

View in: PubMed Mentions: 10 Fields:
Che Chemistry Techniques
Translation:Humans Cells
Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics. 2019 05; 19(10):e1800361. Schaffer LV, Millikin RJ, Miller RM, Anderson LC, Fellers RT, Ge Y, Kelleher NL, LeDuc RD, Liu X, Payne SH, Sun L, Thomas PM, Tucholski T, Wang Z, Wu S, Wu Z, Yu D, Shortreed MR, Smith LM. PMID: 31050378; PMCID: PMC6602557.

View in: PubMed Mentions: 89 Fields:
Bio Biochemistry
Translation:Humans Animals Cells
Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. J Proteome Res. 2018 10 05; 17(10):3526-3536. Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, Frey BL, Pagliarini DJ, Smith LM. PMID: 30180576; PMCID: PMC6201694.

View in: PubMed Mentions: 15 Fields:
Bio Biochemistry
Translation:Animals Cells
Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance. Stem Cell Reports. 2018 02 13; 10(2):627-641. Zaidan NZ, Walker KJ, Brown JE, Schaffer LV, Scalf M, Shortreed MR, Iyer G, Smith LM, Sridharan R. PMID: 29358085; PMCID: PMC5830946.

View in: PubMed Mentions: 15 Fields:
Cel Cell Biology
Translation:Humans Animals Cells
Expanding Proteoform Identifications in Top-Down Proteomic Analyses by Constructing Proteoform Families. Anal Chem. 2018 01 16; 90(2):1325-1333. Schaffer LV, Shortreed MR, Cesnik AJ, Frey BL, Solntsev SK, Scalf M, Smith LM. PMID: 29227670; PMCID: PMC5807004.

View in: PubMed Mentions: 15 Fields:
Che Chemistry Techniques
Translation:Animals
Proteoform Suite: Software for Constructing, Quantifying, and Visualizing Proteoform Families. J Proteome Res. 2018 01 05; 17(1):568-578. Cesnik AJ, Shortreed MR, Schaffer LV, Knoener RA, Frey BL, Scalf M, Solntsev SK, Dai Y, Gasch AP, Smith LM. PMID: 29195273; PMCID: PMC5770237.

View in: PubMed Mentions: 22 Fields:
Bio Biochemistry
Elucidating Escherichia coli Proteoform Families Using Intact-Mass Proteomics and a Global PTM Discovery Database. J Proteome Res. 2017 11 03; 16(11):4156-4165. Dai Y, Shortreed MR, Scalf M, Frey BL, Cesnik AJ, Solntsev S, Schaffer LV, Smith LM. PMID: 28968100; PMCID: PMC5679780.

View in: PubMed Mentions: 26 Fields:
Bio Biochemistry
Translation:Cells
Global Post-Translational Modification Discovery. J Proteome Res. 2017 04 07; 16(4):1383-1390. Li Q, Shortreed MR, Wenger CD, Frey BL, Schaffer LV, Scalf M, Smith LM. PMID: 28248113; PMCID: PMC5387672.

View in: PubMed Mentions: 44 Fields:
Bio Biochemistry
Translation:Humans Cells