Debora S Marks (Debora Marks)

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 56

Top Topics

Genome Wide Association

Artificial Intelligence

Protein Protein

Top Venues

Nature structural & molecular biology

Nature communications

bioRxiv : the preprint server for biology

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

Publications

David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham, Alessandro Passera, Eve Napier, Nicole N Thadani, Samuel Lim, Kristen Roberts, Gurleen Kaur, Michael A Stiffler, Debora S Marks, Christopher D Bahl, Amir R Khan, Chris Sander, Nicholas P Gauthier
Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature communications 15 (1) (2024)
Pascal Notin, Nathan Rollins, Yarin Gal, Chris Sander, Debora S Marks
Machine learning for functional protein design. Nature biotechnology 42 (2) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
Pascal Notin, Nathan Rollins, Yarin Gal, Chris Sander, Debora S Marks
Machine learning for functional protein design. Nature biotechnology 42 (2) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
Pascal Notin, Nathan Rollins, Yarin Gal, Chris Sander, Debora S Marks
Machine learning for functional protein design. Nature biotechnology 42 (2) (2024)
Stefan Peidli, Tessa D Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J Schumacher, Jake P Taylor-King, Debora S Marks, Augustin Luna, Nils Blüthgen, Chris Sander
scPerturb: harmonized single-cell perturbation data. Nature methods 21 (3) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology (2024)
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham, Alessandro Passera, Eve Napier, Nicole N Thadani, Samuel Lim, Kristen Roberts, Gurleen Kaur, Michael A Stiffler, Debora S Marks, Christopher D Bahl, Amir R Khan, Chris Sander, Nicholas P Gauthier
Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature communications 15 (1) (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham, Alessandro Passera, Eve Napier, Nicole N Thadani, Samuel Lim, Kristen Roberts, Gurleen Kaur, Michael A Stiffler, Debora S Marks, Christopher D Bahl, Amir R Khan, Chris Sander, Nicholas P Gauthier
Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature communications 15 (1) (2024)
Pascal Notin, Nathan Rollins, Yarin Gal, Chris Sander, Debora S Marks
Machine learning for functional protein design. Nature biotechnology 42 (2) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology (2024)
Stefan Peidli, Tessa D Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J Schumacher, Jake P Taylor-King, Debora S Marks, Augustin Luna, Nils Blüthgen, Chris Sander
scPerturb: harmonized single-cell perturbation data. Nature methods 21 (3) (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Benjamin Fram, Yang Su, Ian Truebridge, Adam J Riesselman, John B Ingraham, Alessandro Passera, Eve Napier, Nicole N Thadani, Samuel Lim, Kristen Roberts, Gurleen Kaur, Michael A Stiffler, Debora S Marks, Christopher D Bahl, Amir R Khan, Chris Sander, Nicholas P Gauthier
Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature communications 15 (1) (2024)
Debora S Marks, Rose Orenbuch, Aaron Kollasch, Hansen Spinner, Courtney Shearer, Thomas A Hopf, Dinko Franceschi, Mafalda Dias, Jonathan Frazer
Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. Research square (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
Stefan Peidli, Tessa D Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J Schumacher, Jake P Taylor-King, Debora S Marks, Augustin Luna, Nils Blüthgen, Chris Sander
scPerturb: harmonized single-cell perturbation data. Nature methods (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology (2024)
Stefan Peidli, Tessa D Green, Ciyue Shen, Torsten Gross, Joseph Min, Samuele Garda, Bo Yuan, Linus J Schumacher, Jake P Taylor-King, Debora S Marks, Augustin Luna, Nils Blüthgen, Chris Sander
scPerturb: harmonized single-cell perturbation data. Nature methods 21 (3) (2024)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Ziwei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nature structural & molecular biology 31 (4) (2024)
David Ding, Ada Y Shaw, Sam Sinai, Nathan Rollins, Noam Prywes, David F Savage, Michael T Laub, Debora S Marks
Protein design using structure-based residue preferences. Nature communications 15 (1) (2024)
Rose Orenbuch, Aaron W Kollasch, Hansen D Spinner, Courtney A Shearer, Thomas A Hopf, Dinko Franceschi, Mafalda Dias, Jonathan Frazer, Debora S Marks
Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. Research square (2024)
Gordon Rix, Rory L Williams, Hansen Spinner, Vincent J Hu, Debora S Marks, Chang C Liu
Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. bioRxiv : the preprint server for biology (2023)
Katherine R Hummels, Samuel P Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt
Coordination of bacterial cell wall and outer membrane biosynthesis. Nature 615 (7951) (2023)
Rose Orenbuch, Aaron W Kollasch, Hansen D Spinner, Courtney A Shearer, Thomas A Hopf, Dinko Franceschi, Mafalda Dias, Jonathan Frazer, Debora S Marks
Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. medRxiv : the preprint server for health sciences (2023)
Pascal Notin, Debora S Marks, Ruben Weitzman, Yarin Gal
ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers. bioRxiv : the preprint server for biology (2023)
Davide Placido, Bo Yuan, Jessica X Hjaltelin, Chunlei Zheng, Amalie Dahl Haue, Piotr J Chmura, Chen Yuan, Jihye Kim, Renato Umeton, Gregory Antell, Alexander Chowdhury, Alexandra Franz, Lauren Brais, Elizabeth Andrews, Debora S Marks, Aviv Regev, Siamack Ayandeh, Mary T Brophy, Nhan V Do, Peter Kraft, Brian M Wolpin, Michael H Rosenthal, Nathanael R Fillmore, Soren Brunak, Chris Sander
A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories. Nature medicine 29 (5) (2023)
Pascal Notin, Aaron W Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Hansen Spinner, Nathan Rollins, Ada Shaw, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Rose Orenbuch, Yarin Gal, Debora S Marks
ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. bioRxiv : the preprint server for biology (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W Coley, Yoshua Bengio, Marinka Zitnik
Scientific discovery in the age of artificial intelligence. Nature 620 (7972) (2023)
Katherine R Hummels, Samuel P Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt
Coordination of bacterial cell wall and outer membrane biosynthesis. Nature 615 (7951) (2023)
Pascal Notin, Ruben Weitzman, Debora S Marks, Yarin Gal
ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers. bioRxiv : the preprint server for biology (2023)
Katherine R Hummels, Samuel P Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt
Coordination of bacterial cell wall and outer membrane biosynthesis. Nature (2023)
Katherine R Hummels, Samuel P Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt
Coordination of bacterial cell wall and outer membrane biosynthesis. Nature 615 (7951) (2023)
Katherine R Hummels, Samuel P Berry, Zhaoqi Li, Atsushi Taguchi, Joseph K Min, Suzanne Walker, Debora S Marks, Thomas G Bernhardt
Coordination of bacterial cell wall and outer membrane biosynthesis. Nature 615 (7951) (2023)
Nicholas Hoppe, Simone Harrison, Sun-Hee Hwang, Zi-Wei Chen, Masha Karelina, Ishan Deshpande, Carl-Mikael Suomivuori, Vivek R Palicharla, Samuel P Berry, Philipp Tschaikner, Dominik Regele, Douglas F Covey, Eduard Stefan, Debora S Marks, Jeremy F Reiter, Ron O Dror, Alex S Evers, Saikat Mukhopadhyay, Aashish Manglik
GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. bioRxiv : the preprint server for biology (2023)
Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora S Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W Coley, Yoshua Bengio, Marinka Zitnik
Publisher Correction: Scientific discovery in the age of artificial intelligence. Nature (2023)
Douglas M Fowler, David J Adams, Anna L Gloyn, William C Hahn, Debora S Marks, Lara A Muffley, James T Neal, Frederick P Roth, Alan F Rubin, Joshua T Schiffer, Matthew E Hurles
An Atlas of Variant Effects to understand the genome at nucleotide resolution. Genome biology 24 (1) (2023)
Nicole N Thadani, Sarah F Gurev, Pascal Notin, Noor Youssef, Nathan J Rollins, Daniel Ritter, Chris Sander, Yarin Gal, Debora S Marks
Learning from prepandemic data to forecast viral escape. Nature (2023)
Davide Placido, Bo Yuan, Jessica X Hjaltelin, Chunlei Zheng, Amalie Dahl Haue, Piotr J Chmura, Chen Yuan, Jihye Kim, Renato Umeton, Gregory Antell, Alexander Chowdhury, Alexandra Franz, Lauren Brais, Elizabeth Andrews, Debora S Marks, Aviv Regev, Siamack Ayandeh, Mary T Brophy, Nhan V Do, Peter Kraft, Brian M Wolpin, Michael H Rosenthal, Nathanael R Fillmore, Soren Brunak, Chris Sander
A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories. Nature medicine (2023)
Pascal Notin, Aaron W Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Hansen Spinner, Nathan Rollins, Ada Shaw, Ruben Weitzman, Jonathan Frazer, Mafalda Dias, Dinko Franceschi, Rose Orenbuch, Yarin Gal, Debora S Marks
ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. bioRxiv : the preprint server for biology (2023)
Edward P Harvey, Jung-Eun Shin, Meredith A Skiba, Genevieve R Nemeth, Joseph D Hurley, Alon Wellner, Ada Y Shaw, Victor G Miranda, Joseph K Min, Chang C Liu, Debora S Marks, Andrew C Kruse
An in silico method to assess antibody fragment polyreactivity. Nature communications 13 (1) (2022)
Jonathan Frazer, Pascal Notin, Mafalda Dias, Aidan Gomez, Joseph K Min, Kelly Brock, Yarin Gal, Debora S Marks
Disease variant prediction with deep generative models of evolutionary data. Nature 599 (7883) (2021)
Jung-Eun Shin, Adam J Riesselman, Aaron W Kollasch, Conor McMahon, Elana Simon, Chris Sander, Aashish Manglik, Andrew C Kruse, Debora S Marks
Protein design and variant prediction using autoregressive generative models. Nature communications 12 (1) (2021)
Anna G Green, Hadeer Elhabashy, Kelly P Brock, Rohan Maddamsetti, Oliver Kohlbacher, Debora S Marks
Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences. Nature communications 12 (1) (2021)
Melissa A Chiasson, Nathan J Rollins, Jason J Stephany, Katherine A Sitko, Kenneth A Matreyek, Marta Verby, Song Sun, Frederick P Roth, Daniel DeSloover, Debora S Marks, Allan E Rettie, Douglas M Fowler
Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 9 (2020)
Alon Wellner, Conor McMahon, Morgan S A Gilman, Jonathan R Clements, Sarah Clark, Kianna M Nguyen, Ming H Ho, Jung-Eun Shin, Jared Feldman, Blake M Hauser, Timothy M Caradonna, Laura M Wingler, Aaron G Schmidt, Debora S Marks, Jonathan Abraham, Andrew C Kruse, Chang C Liu
Rapid generation of potent antibodies by autonomous hypermutation in yeast. bioRxiv : the preprint server for biology (2020)
Nathan J Rollins, Kelly P Brock, Frank J Poelwijk, Michael A Stiffler, Nicholas P Gauthier, Chris Sander, Debora S Marks
Inferring protein 3D structure from deep mutation scans. Nature genetics 51 (7) (2019)
Benjamin Schubert, Rohan Maddamsetti, Jackson Nyman, Maha R Farhat, Debora S Marks
Genome-wide discovery of epistatic loci affecting antibiotic resistance in Neisseria gonorrhoeae using evolutionary couplings. Nature microbiology 4 (2) (2018)
Adam J Riesselman, John B Ingraham, Debora S Marks
Deep generative models of genetic variation capture the effects of mutations. Nature methods 15 (10) (2018)
Thomas A Hopf, Charlotta P I Schärfe, João P G L M Rodrigues, Anna G Green, Oliver Kohlbacher, Chris Sander, Alexandre M J J Bonvin, Debora S Marks
Sequence co-evolution gives 3D contacts and structures of protein complexes. eLife 3 (2014)