M. Niepel

发表

Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

D. Lauffenburger, William W. Chen, P. Sorger, 2009, Molecular systems biology.

The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome

B. Chait, M. Niepel, M. Rout, 2013, Molecular biology of the cell.

Classic and contemporary approaches to modeling biochemical reactions.

William W. Chen, P. Sorger, M. Niepel, 2010, Genes & development.

Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks

P. Sorger, D. Vitkup, M. Niepel, 2020, eLife.

Receptor-Based Mechanism of Cell Memory and Relative Sensing in Mammalian Signaling Networks

Peter K. Sorger, Eugenia Lyashenko, Purushottam D. Dixit, 2017, bioRxiv.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

Peter K. Sorger, Jason E. McDermott, Carrie D. Nicora, 2016, Science Signaling.

Non-genetic Cell-to-cell Variability and the Consequences for Pharmacology This Review Comes from a Themed Issue on Omics Edited the Distribution of Protein Abundance and Resulting Variability in Phenotype Measuring Cell-to-cell Variation

Sabrina L Spencer, Mario Niepel, Peter K Sorger, 2022 .

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

Marc Hafner, Peter K. Sorger, Todd R. Golub, 2017, Nature Communications.

A multi-center study on factors influencing the reproducibility of in vitro drug-response studies

Elizabeth H. Williams, Laura M. Heiser, Alan D. Stern, 2017, bioRxiv.

The nuclear pore complex: bridging nuclear transport and gene regulation

M. Niepel, M. Rout, C. Strambio-De-Castillia, 2010, Nature Reviews Molecular Cell Biology.

Adaptive informatics for multi-factorial and high content biological data

Mario Niepel, Peter K Sorger, Michael P Menden, 2011, Nature Methods.

Mass spectrometry based method to increase throughput for kinome analyses using ATP probes.

S. Gygi, P. Sorger, M. Niepel, 2013, Analytical chemistry.

Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs

P. Sorger, M. Niepel, M. Hafner, 2016, Nature Methods.

Dissecting Variability in Responses to Cancer Chemotherapy Through Systems Pharmacology

P. Sorger, M. Niepel, P K Sorger, 2010, Clinical pharmacology and therapeutics.

Analysis of growth factor signaling in genetically diverse breast cancer lines

Marc Hafner, Birgit Schoeberl, Mario Niepel, 2014, BMC Biology.

Identification and Characterization of the Functional Elements within the Tobacco Etch Virus 5′ Leader Required for Cap-Independent Translation

M. Niepel, D. Gallie, 1999, Journal of Virology.

Systematic analysis of BRAFV 600 E melanomas reveals a role for JNK / c-Jun pathway in adaptive resistance to drug-induced apoptosis

P. Sorger, M. Fallahi-Sichani, M. Niepel, 2015 .

Maximum Entropy Framework For Inference Of Cell Population Heterogeneity In Signaling Networks

D. Vitkup, M. Niepel, P. Dixit, 2017 .

Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines

Marc Hafner, Birgit Schoeberl, Peter K. Sorger, 2013, Science Signaling.

ADP-ribosyltransferases, an update on function and nomenclature

A. Ashworth, D. Corda, I. Matic, 2021, The FEBS journal.

Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells

Marc Hafner, Mario Niepel, Peter K Sorger, 2017, Current protocols in chemical biology.

Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method

Benjamin L. Gaudio, P. Sorger, M. Niepel, 2021, bioRxiv.

Selective pharmaceutical inhibition of PARP14 mitigates allergen-induced IgE and mucus overproduction in a mouse model of pulmonary allergic response

Kevin C. Chen, M. Niepel, K. Swinger, 2021, bioRxiv.

DeepDyeDrop: an image-based approach to quantify the phenotypic response of cancer cells to therapeutics (Conference Presentation)

P. Sorger, M. Niepel, M. Hafner, 2018 .

Targeted Degradation of PARP14 Using a Heterobifunctional Small Molecule

Tim J. Wigle, M. Niepel, K. Swinger, 2021, Chembiochem : a European journal of chemical biology.

Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop

Benjamin L. Gaudio, P. Sorger, M. Niepel, 2022, Nature Communications.

PARP7 negatively regulates the type I interferon response in cancer cells and its inhibition triggers antitumor immunity.

Tim J. Wigle, M. Niepel, K. Swinger, 2021, Cancer cell.

Secondary structure in the 5′‐leader or 3′‐untranslated region reduces protein yield but does not affect the functional interaction between the 5′‐cap and the poly(A) tail

M. Niepel, D. Gallie, J. Ling, 1999, FEBS letters.

In Vitro and Cellular Probes to Study PARP Enzyme Target Engagement.

M. Niepel, K. Swinger, A. Lu, 2020, Cell chemical biology.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

Andrew D. Rouillard, Avi Ma'ayan, Marc Hafner, 2014, Nucleic Acids Res..

PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven adaptive resistance

M. Niepel, K. Kunii, B. Telfer, 2022, bioRxiv.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

David Haussler, Peter K. Sorger, Evan O. Paull, 2013, Bioinform..

Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR.

S. Elledge, D. Sabatini, M. Niepel, 2013, Cancer research.

Characterization of Torin 2 , an ATP-Competitive Inhibitor of mTOR , ATM , and ATR Citation

S. Elledge, D. Sabatini, M. Niepel, 2013 .

ATM , and ATR Characterization of Torin 2 , an ATP-Competitive Inhibitor of mTOR

S. Elledge, D. Sabatini, M. Niepel, 2013 .

mTOR , ATM and ATR Characterization of Torin 2 , an ATP-competitive inhibitor of

S. Elledge, D. Sabatini, M. Niepel, 2013 .

Therapeutics , Targets , and Chemical Biology Characterization of Torin 2 , an ATP-Competitive Inhibitor of mTOR , ATM , and ATR

S. Elledge, D. Sabatini, M. Niepel, 2013 .

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

Evan O. Paull, Joshua M. Stuart, T. Golub, 2017, Nature Communications.

GRcalculator: an online tool for calculating and mining dose–response data

Elizabeth H. Williams, Nicholas A. Clark, Jeremy L. Muhlich, 2017, BMC Cancer.

Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics

Marc Hafner, Mario Niepel, Peter K Sorger, 2017, Nature Biotechnology.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

Ravi Iyengar, Vasileios Stathias, Amar Koleti, 2017, Cell systems.

A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

Marc Hafner, Elizabeth H. Williams, Kartik Subramanian, 2019, Cell systems.

Discovery of potent and selective covalent inhibitors of JNK.

Taebo Sim, Mario Niepel, Scott B Ficarro, 2012, Chemistry & biology.

The nuclear pore complex–associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly

B. Chait, M. Niepel, M. Rout, 2005, The Journal of cell biology.

Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells

P. Sorger, M. Niepel, N. Gray, 2019, bioRxiv.

Myosin-Like Proteins in S. cerevisiae: Multifunctional, Structural Components of the Nuclear Envelope

M. Niepel, 2005 .

The role of 5'-leader length, secondary structure and PABP concentration on cap and poly(A) tail function during translation in Xenopus oocytes.

M. Niepel, V. M. Pain, D. Gallie, 2000, Nucleic acids research.

Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis

Mohammad Fallahi-Sichani, Mario Niepel, Nathanael S Gray, 2015 .

A Cell Cycle Phosphoproteome of the Yeast Centrosome

Arend Sidow, John R. Yates, Jonathan Binkley, 2011, Science.

Identification and Characterization of the Functional Elements within the Tobacco Etch Virus 5′ Leader Required for Cap-Independent Translation

M. Niepel, D. Gallie, 1999, Journal of Virology.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine

Marc Hafner, Rachel Hodos, Ben Readhead, 2016, npj Systems Biology and Applications.

GRcalculator: an online tool for calculating and mining dose–response data

Elizabeth H. Williams, Nicholas A. Clark, Jeremy L. Muhlich, 2017, BMC Cancer.

Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.

Eugenia Lyashenko, Mario Niepel, Dennis Vitkup, 2019, Cell systems.

Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells.

P. Sorger, M. Niepel, N. Gray, 2019, Cell systems.

Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics

Marc Hafner, Elizabeth H. Williams, Laura M. Heiser, 2017, Scientific Data.

Designing Drug‐Response Experiments and Quantifying their Results

Marc Hafner, Kartik Subramanian, Mario Niepel, 2017, Current protocols in chemical biology.

Other Positions and Employment

M. Niepel, F. Kreuzaler, 2015 .

A potent and selective PARP14 inhibitor decreases protumor macrophage gene expression and elicits inflammatory responses in tumor explants.

M. Niepel, K. Swinger, K. Kunii, 2021, Cell chemical biology.

Enabling drug discovery for the PARP protein family through the detection of mono-ADP-ribosylation.

M. Niepel, B. Gui, R. Abo, 2019, Biochemical pharmacology.

The nuclear basket proteins Mlp 1 p and Mlp 2 p are part of a dynamic interactome including Esc 1 p and the proteaosme

B. Chait, M. Niepel, M. Rout, 2013 .

Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer

Heather A. Harrington, Birgit Schoeberl, Mariano Beguerisse-Díaz, 2016, Journal of the Royal Society Interface.

Kinome-wide Selectivity Profiling of ATP-competitive Mammalian Target of Rapamycin (mTOR) Inhibitors and Characterization of Their Binding Kinetics*

P. Sorger, D. Sabatini, A. Look, 2012, The Journal of Biological Chemistry.

Rapid isolation of functionally intact nuclei from the yeast Saccharomyces

M. Niepel, M. Rout, Julia C. Farr, 2017, bioRxiv.

Abstract 1344: Small molecule inhibitor of CD38 modulates its intra- and extracellular functions leading to antitumor activity

M. Niepel, K. Kunii, V. Richon, 2021, Experimental and Molecular Therapeutics.

Receptor-Based Mechanism of Cell Memory and Relative Sensing in Mammalian Signaling Networks

P. Sorger, M. Niepel, P. Dixit, 2017, bioRxiv.

Receptor-Based Mechanism of Relative Sensing in Mammalian Signaling Networks

P. Sorger, M. Niepel, P. Dixit, 2017 .

PARP14 inhibition restores PD-1 immune checkpoint inhibitor response following IFNγ-driven acquired resistance in preclinical cancer models

M. Niepel, B. Telfer, K. Williams, 2023, Nature communications.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

Evan O. Paull, Joshua M. Stuart, Daniel E. Carlin, 2013, Bioinform..

Mass spectrometry based method to increase throughput for kinome analyses using ATP probes.

Edward L. Huttlin, S. Gygi, P. Sorger, 2013, Analytical chemistry.

Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis

P. Sorger, M. Fallahi-Sichani, M. Niepel, 2015, Molecular systems biology.

Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells

P. Sorger, M. Niepel, M. Hafner, 2017, Current protocols in chemical biology.

MIT Open Access Articles Characterization of Torin2, an ATP-Competitive Inhibitor of mTOR, ATM, and ATR

M. Niepel, K. Westover, W. Hur, 2022 .

Molecular Systems Biology Peer Review Process File Systematic Analysis of Braf V600e Melanomas Reveals a Role for Jnk/c-jun Pathway in Adaptive Resistance to Drug- Induced Apoptosis Transaction Report

P. Sorger, M. Fallahi-Sichani, M. Niepel, 2022 .