Edward M Marcotte

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 63

Top Venues

bioRxiv : the preprint server for biology

PLoS computational biology

Molecular systems biology

Molecular biology of the cell

University of Texas at Austin

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Texas at Austin

United States

Professor :: Department of Molecular Biosciences

Publications

Riddhiman K Garge, Renee C Geck, Joseph O Armstrong, Barbara L Dunn, Daniel R Boutz, Anna M Battenhouse, Mario Leutert, Vy Dang, Pengyao Jiang, Dusan Kwiatkowski, Thorin Peiser, Hoyt McElroy, Edward M Marcotte, Maitreya J Dunham
Systematic profiling of ale yeast protein dynamics across fermentation and repitching. G3 (Bethesda, Md.) 14 (3) (2024)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. PLoS computational biology 20 (7) (2024)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Molecular biology of the cell 35 (3) (2024)
Meghana Venkata Palukuri, Edward M Marcotte
DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations. bioRxiv : the preprint server for biology (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology (2024)
Riddhiman K Garge, Renee C Geck, Joseph O Armstrong, Barbara L Dunn, Daniel R Boutz, Anna M Battenhouse, Mario Leutert, Vy Dang, Pengyao Jiang, Dusan Kwiatkowski, Thorin Peiser, Hoyt McElroy, Edward M Marcotte, Maitreya J Dunham
Systematic profiling of ale yeast protein dynamics across fermentation and repitching. G3 (Bethesda, Md.) 14 (3) (2024)
Colleen J Mulvihill, Joshua D Lutgens, Jimmy D Gollihar, Petra Bachanová, Caitlin Tramont, Edward M Marcotte, Andrew D Ellington, Elizabeth C Gardner
A Humanized CB1R Yeast Biosensor Enables Facile Screening of Cannabinoid Compounds. International journal of molecular sciences 25 (11) (2024)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Molecular biology of the cell 35 (3) (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Rosamaria Y Moreno, Svetlana B Panina, Seema Irani, Haley A Hardtke, Renee Stephenson, Brendan M Floyd, Edward M Marcotte, Qian Zhang, Y Jessie Zhang
Thr 4 phosphorylation on RNA Pol II occurs at early transcription regulating 3'-end processing. Science advances 10 (36) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. PLoS computational biology 20 (7) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Colleen J Mulvihill, Joshua D Lutgens, Jimmy D Gollihar, Petra Bachanová, Caitlin Tramont, Edward M Marcotte, Andrew D Ellington, Elizabeth C Gardner
A Humanized CB1R Yeast Biosensor Enables Facile Screening of Cannabinoid Compounds. International journal of molecular sciences 25 (11) (2024)
Rachael M Cox, Ophelia Papoulas, Shirlee Shril, Chanjae Lee, Tynan Gardner, Anna M Battenhouse, Muyoung Lee, Kevin Drew, Claire Darnell McWhite, David Yang, Janelle C Leggere, Dannie Durand, Friedhelm Hildebrandt, John B Wallingford, Edward M Marcotte
Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders. bioRxiv : the preprint server for biology (2024)
Claire Darnell McWhite, Wisath Sae-Lee, Yaning Yuan, Anna L Mallam, Nicolas A Gort-Freitas, Silvia Ramundo, Masayuki Onishi, Edward M Marcotte
Alternative proteoforms and proteoform-dependent assemblies in humans and plants. Molecular systems biology 20 (8) (2024)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. PLoS computational biology 20 (7) (2024)
Rachael M Cox, Ophelia Papoulas, Shirlee Shril, Chanjae Lee, Tynan Gardner, Anna M Battenhouse, Muyoung Lee, Kevin Drew, Claire Darnell McWhite, David Yang, Janelle C Leggere, Dannie Durand, Friedhelm Hildebrandt, John B Wallingford, Edward M Marcotte
Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders. bioRxiv : the preprint server for biology (2024)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. PLoS computational biology 20 (7) (2024)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. PLoS computational biology 20 (7) (2024)
Colleen J Mulvihill, Joshua D Lutgens, Jimmy D Gollihar, Petra Bachanová, Caitlin Tramont, Edward M Marcotte, Andrew D Ellington, Elizabeth C Gardner
A Humanized CB1R Yeast Biosensor Enables Facile Screening of Cannabinoid Compounds. International journal of molecular sciences 25 (11) (2024)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Molecular biology of the cell 35 (3) (2024)
Meghana Venkata Palukuri, Edward M Marcotte
DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations. bioRxiv : the preprint server for biology (2024)
Meghana Venkata Palukuri, Edward M Marcotte
DeepSLICEM: Clustering CryoEM particles using deep image and similarity graph representations. bioRxiv : the preprint server for biology (2024)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Molecular biology of the cell 35 (3) (2024)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and nonciliary phenotypes of IFT-A mutants. Molecular biology of the cell 35 (3) (2024)
Clayton W Kosonocky, Claus O Wilke, Edward M Marcotte, Andrew D Ellington
Mining patents with large language models elucidates the chemical function landscape. Digital discovery 3 (6) (2024)
Rachael M Cox, Ophelia Papoulas, Shirlee Shril, Chanjae Lee, Tynan Gardner, Anna M Battenhouse, Muyoung Lee, Kevin Drew, Claire Darnell McWhite, David Yang, Janelle C Leggere, Dannie Durand, Friedhelm Hildebrandt, John B Wallingford, Edward M Marcotte
Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders. bioRxiv : the preprint server for biology (2024)
Meghana Venkata Palukuri, Ridhi S Patil, Edward M Marcotte
Molecular complex detection in protein interaction networks through reinforcement learning. BMC bioinformatics 24 (1) (2023)
Avrin Ghanaeian, Sumita Majhi, Caitlyn L McCafferty, Babak Nami, Corbin Steven Black, Shun Kai Yang, Thibault Legal, Ophelia Papoulas, Martyna Janowska, Melissa Valente-Paterno, Edward M Marcotte, Dorota Wloga, Khanh Huy Bui
Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism. Nature communications 14 (1) (2023)
Caitlyn L McCafferty, Erin L Pennington, Ophelia Papoulas, David W Taylor, Edward M Marcotte
Does AlphaFold2 model proteins' intracellular conformations? An experimental test using cross-linking mass spectrometry of endogenous ciliary proteins. Communications biology 6 (1) (2023)
Matthew Beauregard Smith, Kent VanderVelden, Thomas Blom, Heather D Stout, James H Mapes, Tucker M Folsom, Christopher Martin, Angela M Bardo, Edward M Marcotte
Estimating error rates for single molecule protein sequencing experiments. bioRxiv : the preprint server for biology (2023)
James H Mapes, Julia Stover, Heather D Stout, Tucker M Folsom, Emily Babcock, Sandra Loudwig, Christopher Martin, Mariah J Austin, Fan Tu, Casey J Howdieshell, Zachary B Simpson, Thomas Blom, Daniel Weaver, Daniel Winkler, Kent Vander Velden, Parham M Ossareh, John M Beierle, Talli Somekh, Angela M Bardo, Eric V Anslyn, Edward M Marcotte, Jagannath Swaminathan
Robust and scalable single-molecule protein sequencing with fluorosequencing. bioRxiv : the preprint server for biology (2023)
Shintaroh Kubo, Corbin Steven Black, Ewa Joachimiak, Shun Kai Yang, Thibault Legal, Katya Peri, Ahmad Abdelzaher Zaki Khalifa, Avrin Ghanaeian, Caitlyn L McCafferty, Melissa Valente-Paterno, Chelsea De Bellis, Phuong M Huynh, Zhe Fan, Edward M Marcotte, Dorota Wloga, Khanh Huy Bui
Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins. Nature communications 14 (1) (2023)
Jule Goike, Ching-Lin Hsieh, Andrew P Horton, Elizabeth C Gardner, Ling Zhou, Foteini Bartzoka, Nianshuang Wang, Kamyab Javanmardi, Andrew Herbert, Shawn Abbassi, Xuping Xie, Hongjie Xia, Pei-Yong Shi, Rebecca L Renberg, Thomas H Segall-Shapiro, Cynthia I Terrace, Wesley Wu, Raghav Shroff, Michelle Byrom, Andrew D Ellington, Edward M Marcotte, James M Musser, Suresh V Kuchipudi, Vivek Kapur, George Georgiou, Scott C Weaver, John M Dye, Daniel R Boutz, Jason S Mclellan, Jimmy D Gollihar
SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Communications biology 6 (1) (2023)
Riddhiman K Garge, Renee C Geck, Joseph O Armstrong, Barbara L Dunn, Daniel R Boutz, Anna M Battenhouse, Mario Leutert, Vy Dang, Pengyao Jiang, Dusan Kwiatkowski, Thorin Peiser, Hoyt McElroy, Edward M Marcotte, Maitreya J Dunham
Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching. bioRxiv : the preprint server for biology (2023)
Matthew Beauregard Smith, Zack Booth Simpson, Edward M Marcotte
Amino acid sequence assignment from single molecule peptide sequencing data using a two-stage classifier. PLoS computational biology 19 (5) (2023)
Avrin Ghanaeian, Sumita Majhi, Caitie L McCaffrey, Babak Nami, Corbin S Black, Shun Kai Yang, Thibault Legal, Ophelia Papoulas, Martyna Janowska, Melissa Valente-Paterno, Edward M Marcotte, Dorota Wloga, Khanh Huy Bui
Integrated modeling of the Nexin-dynein regulatory complex reveals its regulatory mechanism. bioRxiv : the preprint server for biology (2023)
Janelle C Leggere, Jaime V K Hibbard, Ophelia Papoulas, Chanjae Lee, Chad G Pearson, Edward M Marcotte, John B Wallingford
Label-free proteomic comparison reveals ciliary and non-ciliary phenotypes of IFT-A mutants. bioRxiv : the preprint server for biology (2023)
Caitlyn L McCafferty, Ophelia Papoulas, Chanjae Lee, Khanh Huy Bui, David W Taylor, Edward M Marcotte, John B Wallingford
An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes. bioRxiv : the preprint server for biology (2023)
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S Lilley, Emma Lundberg, Edward M Marcotte, Markus Ralser, Juri Rappsilber
Understudied proteins: opportunities and challenges for functional proteomics. Nature methods 19 (7) (2022)
Caitlyn L McCafferty, Ophelia Papoulas, Mareike A Jordan, Gabriel Hoogerbrugge, Candice Nichols, Gaia Pigino, David W Taylor, John B Wallingford, Edward M Marcotte
Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex. eLife 11 (2022)
Björn D M Bean, Colleen J Mulvihill, Riddhiman K Garge, Daniel R Boutz, Olivier Rousseau, Brendan M Floyd, William Cheney, Elizabeth C Gardner, Andrew D Ellington, Edward M Marcotte, Jimmy D Gollihar, Malcolm Whiteway, Vincent J J Martin
Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. Nature communications 13 (1) (2022)
Kevin Drew, John B Wallingford, Edward M Marcotte
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. Molecular systems biology 17 (5) (2022)
Riddhiman K Garge, Hye Ji Cha, Chanjae Lee, Jimmy D Gollihar, Aashiq H Kachroo, John B Wallingford, Edward M Marcotte
Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast. Genetics 219 (1) (2022)
Georg Kustatscher, Tom Collins, Anne-Claude Gingras, Tiannan Guo, Henning Hermjakob, Trey Ideker, Kathryn S Lilley, Emma Lundberg, Edward M Marcotte, Markus Ralser, Juri Rappsilber
An open invitation to the Understudied Proteins Initiative. Nature biotechnology 40 (6) (2022)
Le Zhang, Brendan M Floyd, Maheshwerreddy Chilamari, James Mapes, Jagannath Swaminathan, Steven Bloom, Edward M Marcotte, Eric V Anslyn
Photoredox-Catalyzed Decarboxylative C-Terminal Differentiation for Bulk- and Single-Molecule Proteomics. ACS chemical biology 16 (11) (2021)
Meghana Venkata Palukuri, Edward M Marcotte
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PloS one 16 (12) (2021)
Meghana Venkata Palukuri, Edward M Marcotte
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. bioRxiv : the preprint server for biology (2021)
Caitlyn L McCafferty, David W Taylor, Edward M Marcotte
Improving integrative 3D modeling into low- to medium-resolution electron microscopy structures with evolutionary couplings. Protein science : a publication of the Protein Society 30 (5) (2021)
Caroline M Hinson, Angela M Bardo, Cassie E Shannon, Sebastian Rivera, Jagannath Swaminathan, Edward M Marcotte, Eric V Anslyn
Studies of Surface Preparation for the Fluorosequencing of Peptides. Langmuir : the ACS journal of surfaces and colloids 37 (51) (2021)
Jon M Laurent, Riddhiman K Garge, Ashley I Teufel, Claus O Wilke, Aashiq H Kachroo, Edward M Marcotte
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PLoS biology 18 (5) (2020)
Caitlyn L McCafferty, Edward M Marcotte, David W Taylor
Simplified geometric representations of protein structures identify complementary interaction interfaces. Proteins 89 (3) (2020)
Chanjae Lee, Rachael M Cox, Ophelia Papoulas, Amjad Horani, Kevin Drew, Caitlin C Devitt, Steven L Brody, Edward M Marcotte, John B Wallingford
Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins. eLife 9 (2020)
Riddhiman K Garge, Jon M Laurent, Aashiq H Kachroo, Edward M Marcotte
Systematic Humanization of the Yeast Cytoskeleton Discerns Functionally Replaceable from Divergent Human Genes. Genetics 215 (4) (2020)
Benjamin J Liebeskind, Richard W Aldrich, Edward M Marcotte
Ancestral reconstruction of protein interaction networks. PLoS computational biology 15 (10) (2019)
Ryan L Huizar, Chanjae Lee, Alexander A Boulgakov, Amjad Horani, Fan Tu, Edward M Marcotte, Steven L Brody, John B Wallingford
A liquid-like organelle at the root of motile ciliopathy. eLife 7 (2018)
Jagannath Swaminathan, Alexander A Boulgakov, Erik T Hernandez, Angela M Bardo, James L Bachman, Joseph Marotta, Amber M Johnson, Eric V Anslyn, Edward M Marcotte
Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nature biotechnology (2018)
Kevin Drew, Christian L Müller, Richard Bonneau, Edward M Marcotte
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS computational biology 13 (10) (2017)
Kevin Drew, Chanjae Lee, Ryan L Huizar, Fan Tu, Blake Borgeson, Claire D McWhite, Yun Ma, John B Wallingford, Edward M Marcotte
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Molecular systems biology 13 (6) (2017)
Aashiq H Kachroo, Jon M Laurent, Azat Akhmetov, Madelyn Szilagyi-Jones, Claire Darnell McWhite, Alice Zhao, Edward M Marcotte
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. eLife 6 (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Edward M Marcotte