William Stafford Noble (William S Noble, Galip Gürkan Yardımcı, W S Noble)

Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 124

Top Venues

Journal of proteome research

bioRxiv : the preprint server for biology

Nature communications

PLoS computational biology

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

Publications

Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Bo Wen, Jack Freestone, Michael Riffle, Michael J MacCoss, William Stafford Noble, Uri Keich
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. bioRxiv : the preprint server for biology (2024)
Robin Aguilar, Conor K Camplisson, Qiaoyi Lin, Karen H Miga, William Stafford Noble, Brian J Beliveau
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nature communications 15 (1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Gang Li, Eva K Nichols, Valentino E Browning, Nicolas J Longhi, Conor Camplisson, Brian J Beliveau, William Stafford Noble
Predicting cell cycle stage from 3D single-cell nuclear-stained images. bioRxiv : the preprint server for biology (2024)
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, Previn Naicker, Ireshyn Govender, Sindisiwe Buthelezi, Stoyan Stoychev, Justin Jordaan, Gennifer E Merrihew, Eric Huang, Edward D Parker, Michael Riffle, Andrew N Hoofnagle, William Stafford Noble, Kathleen L Poston, Thomas J Montine, Michael J MacCoss
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv : the preprint server for biology (2024)
Thomas Hollin, Steven Abel, Charles Banks, Borislav Hristov, Jacques Prudhomme, Kianna Hales, Laurence A Florens, William Stafford Noble, Karine Le Roch
Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nature communications 15 (1) (2024)
William Stafford Noble
Response to "The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a 'scientist'". Nature biotechnology (2024)
Jack Freestone, William Stafford Noble, Uri Keich
Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis. Journal of proteome research (2024)
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, Previn Naicker, Ireshyn Govender, Sindisiwe Buthelezi, Stoyan Stoychev, Justin Jordaan, Gennifer E Merrihew, Eric Huang, Edward D Parker, Michael Riffle, Andrew N Hoofnagle, William Stafford Noble, Kathleen L Poston, Thomas J Montine, Michael J MacCoss
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv : the preprint server for biology (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine M Disteche, William Stafford Noble
Multi-condition and multi-modal temporal profile inference during mouse embryonic development. bioRxiv : the preprint server for biology (2024)
Jack Freestone, William Stafford Noble, Uri Keich
Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis. Journal of proteome research 23 (6) (2024)
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, Previn Naicker, Ireshyn Govender, Sindisiwe Buthelezi, Stoyan Stoychev, Justin Jordaan, Gennifer E Merrihew, Eric Huang, Edward D Parker, Michael Riffle, Andrew N Hoofnagle, William Stafford Noble, Kathleen L Poston, Thomas J Montine, Michael J MacCoss
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv : the preprint server for biology (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Andy Lin, Donavan See, William E Fondrie, Uri Keich, William Stafford Noble
Target-decoy false discovery rate estimation using Crema. Proteomics 24 (8) (2024)
William Stafford Noble
Response to "The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a 'scientist'". Nature biotechnology 42 (6) (2024)
Ran Zhang, Chengxiang Qiu, Gala Filippova, Gang Li, Jay Shendure, Jean-Philippe Vert, Xinxian Deng, Christine M Disteche, William Stafford Noble
Multi-condition and multi-modal temporal profile inference during mouse embryonic development. bioRxiv : the preprint server for biology (2024)
Jack Freestone, William Stafford Noble, Uri Keich
Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry. Journal of proteome research (2024)
Carlo Melendez, Justin Sanders, Melih Yilmaz, Wout Bittremieux, William E Fondrie, Sewoong Oh, William Stafford Noble
Accounting for Digestion Enzyme Bias in Casanovo. Journal of proteome research (2024)
Alan Min, Jacob Schreiber, Anshul Kundaje, William Stafford Noble
Predicting chromatin conformation contact maps. bioRxiv : the preprint server for biology (2024)
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, Previn Naicker, Ireshyn Govender, Sindisiwe Buthelezi, Stoyan Stoychev, Justin Jordaan, Gennifer E Merrihew, Eric Huang, Edward D Parker, Michael Riffle, Andrew N Hoofnagle, William Stafford Noble, Kathleen L Poston, Thomas J Montine, Michael J MacCoss
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv : the preprint server for biology (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Bo Wen, Jack Freestone, Michael Riffle, Michael J MacCoss, William Stafford Noble, Uri Keich
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. bioRxiv : the preprint server for biology (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Christine C Wu, Kristine A Tsantilas, Jea Park, Deanna Plubell, Justin A Sanders, Previn Naicker, Ireshyn Govender, Sindisiwe Buthelezi, Stoyan Stoychev, Justin Jordaan, Gennifer E Merrihew, Eric Huang, Edward D Parker, Michael Riffle, Andrew N Hoofnagle, William Stafford Noble, Kathleen L Poston, Thomas J Montine, Michael J MacCoss
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. bioRxiv : the preprint server for biology (2024)
Robin Aguilar, Conor K Camplisson, Qiaoyi Lin, Karen H Miga, William Stafford Noble, Brian J Beliveau
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nature communications 15 (1) (2024)
Robin Aguilar, Conor K Camplisson, Qiaoyi Lin, Karen H Miga, William Stafford Noble, Brian J Beliveau
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nature communications 15 (1) (2024)
Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Robin Aguilar, Conor K Camplisson, Qiaoyi Lin, Karen H Miga, William Stafford Noble, Brian J Beliveau
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nature communications 15 (1) (2024)
Lincoln Harris, William Stafford Noble
Imputation of cancer proteomics data with a deep model that learns from many datasets. bioRxiv : the preprint server for biology (2024)
Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble
A learned score function improves the power of mass spectrometry database search. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature (2024)
Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble
A learned score function improves the power of mass spectrometry database search. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Melih Yilmaz, William E Fondrie, Wout Bittremieux, Carlo F Melendez, Rowan Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble
Sequence-to-sequence translation from mass spectra to peptides with a transformer model. Nature communications 15 (1) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Alan Min, Jacob Schreiber, Anshul Kundaje, William Stafford Noble
Predicting chromatin conformation contact maps. bioRxiv : the preprint server for biology (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
William Stafford Noble
Response to "The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a 'scientist'". Nature biotechnology 42 (6) (2024)
Robin Aguilar, Conor K Camplisson, Qiaoyi Lin, Karen H Miga, William Stafford Noble, Brian J Beliveau
Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nature communications 15 (1) (2024)
Bo Wen, Jack Freestone, Michael Riffle, Michael J MacCoss, William Stafford Noble, Uri Keich
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment. bioRxiv : the preprint server for biology (2024)
Jack Freestone, William Stafford Noble, Uri Keich
Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry. Journal of proteome research 23 (6) (2024)
Chengxiang Qiu, Beth K Martin, Ian C Welsh, Riza M Daza, Truc-Mai Le, Xingfan Huang, Eva K Nichols, Megan L Taylor, Olivia Fulton, Diana R O'Day, Anne Roshella Gomes, Saskia Ilcisin, Sanjay Srivatsan, Xinxian Deng, Christine M Disteche, William Stafford Noble, Nobuhiko Hamazaki, Cecilia B Moens, David Kimelman, Junyue Cao, Alexander F Schier, Malte Spielmann, Stephen A Murray, Cole Trapnell, Jay Shendure
A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 626 (8001) (2024)
Thomas Hollin, Steven Abel, Charles Banks, Borislav Hristov, Jacques Prudhomme, Kianna Hales, Laurence A Florens, William Stafford Noble, Karine Le Roch
Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nature communications 15 (1) (2024)
Andy Lin, Donavan See, William E Fondrie, Uri Keich, William Stafford Noble
Target-decoy false discovery rate estimation using Crema. Proteomics 24 (8) (2024)
Andy Lin, Donavan See, William E Fondrie, Uri Keich, William Stafford Noble
Target-decoy false discovery rate estimation using Crema. Proteomics (2024)
Varun Ananth, Justin Sanders, Melih Yilmaz, Bo Wen, Sewoong Oh, William Stafford Noble
A learned score function improves the power of mass spectrometry database search. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
William Stafford Noble
Response to "The perpetual motion machine of AI-generated data and the distraction of ChatGPT as a 'scientist'". Nature biotechnology 42 (6) (2024)
Thomas Hollin, Steven Abel, Charles Banks, Borislav Hristov, Jacques Prudhomme, Kianna Hales, Laurence A Florens, William Stafford Noble, Karine Le Roch
Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nature communications 15 (1) (2024)
Alan Min, Jacob Schreiber, Anshul Kundaje, William Stafford Noble
Predicting chromatin conformation contact maps. bioRxiv : the preprint server for biology (2024)
Lincoln Harris, William E Fondrie, Sewoong Oh, William Stafford Noble
Evaluating Proteomics Imputation Methods with Improved Criteria. Journal of proteome research (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Ran Zhang, Mu Yang, Jacob Schreiber, Diana R O'Day, James M A Turner, Jay Shendure, Christine M Disteche, Xinxian Deng, William Stafford Noble
Cross-species imputation and comparison of single-cell transcriptomic profiles. bioRxiv : the preprint server for biology (2023)
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Efficient Indexing of Peptides for Database Search Using Tide. Journal of proteome research (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Vikram Agarwal, Fumitaka Inoue, Max Schubach, Beth K Martin, Pyaree Mohan Dash, Zicong Zhang, Ajuni Sohota, William Stafford Noble, Galip Gürkan Yardimci, Martin Kircher, Jay Shendure, Nadav Ahituv
Massively parallel characterization of transcriptional regulatory elements in three diverse human cell types. bioRxiv : the preprint server for biology (2023)
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Efficient Indexing of Peptides for Database Search Using Tide. Journal of proteome research 22 (2) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, William Stafford Noble
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of proteome research 22 (2) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Anupama Jha, Stephanie C Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J Mallory, Alan T Min, Morgan O Hamm, Elliott G Swanson, Connor Finkbeiner, Tony Li, Dale Whittington, William Stafford Noble, Andrew Ben Stergachis, Mitchell R Vollger
Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing. bioRxiv : the preprint server for biology (2023)
Nelle Varoquaux, William Stafford Noble, Jean-Philippe Vert
Inference of 3D genome architecture by modeling overdispersion of Hi-C data. Bioinformatics (Oxford, England) 39 (1) (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, William Stafford Noble
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of proteome research 22 (2) (2023)
Hannah L Harris, Huiya Gu, Moshe Olshansky, Ailun Wang, Irene Farabella, Yossi Eliaz, Achyuth Kalluchi, Akshay Krishna, Mozes Jacobs, Gesine Cauer, Melanie Pham, Suhas S P Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae Kim, Michael H Nichols, Eric S Davis, Dimos Gkountaroulis, Devika Udupa, Aviva Presser Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble, Guy Nir, Michele Di Pierro, Jeong-Sun Seo, Michael E Talkowski, Erez Lieberman Aiden, M Jordan Rowley
Chromatin alternates between A and B compartments at kilobase scale for subgenic organization. Nature communications 14 (1) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, William Stafford Noble
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of proteome research (2023)
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Efficient Indexing of Peptides for Database Search Using Tide. Journal of proteome research 22 (2) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Andy Lin, Brooke L Deatherage Kaiser, Janine R Hutchison, Jeffrey A Bilmes, William Stafford Noble
MS1Connect: a mass spectrometry run similarity measure. Bioinformatics (Oxford, England) 39 (2) (2023)
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Efficient Indexing of Peptides for Database Search Using Tide. Journal of proteome research 22 (2) (2023)
Arya Ebadi, Jack Freestone, William Stafford Noble, Uri Keich
Bridging the False Discovery Gap. Journal of proteome research (2023)
Anupama Jha, Stephanie C Bohaczuk, Yizi Mao, Jane Ranchalis, Benjamin J Mallory, Alan T Min, Morgan O Hamm, Elliott G Swanson, Connor Finkbeiner, Tony Li, Dale Whittington, William Stafford Noble, Andrew Ben Stergachis, Mitchell R Vollger
Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing. bioRxiv : the preprint server for biology (2023)
Andy Lin, Brooke L Deatherage Kaiser, Janine R Hutchison, Jeffrey A Bilmes, William Stafford Noble
MS1Connect: a mass spectrometry run similarity measure. Bioinformatics (Oxford, England) 39 (2) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, William Stafford Noble
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of proteome research 22 (2) (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K Eng, William E Fondrie, Charles Grant, Michael R Hoopmann, Andy Lin, Yang Y Lu, Robert L Moritz, Michael J MacCoss, William Stafford Noble
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data. Journal of proteome research 22 (2) (2023)
William Stafford Noble
Ten simple rules for defining a computational biology project. PLoS computational biology 19 (1) (2023)
Borislav Hrisimirov Hristov, William Stafford Noble, Alessandro Bertero
Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. bioRxiv : the preprint server for biology (2023)
Alan Min, Timothy Durham, Louis Gevirtzman, William Stafford Noble
Matrix prior for data transfer between single cell data types in latent Dirichlet allocation. PLoS computational biology 19 (5) (2023)
Gayani Batugedara, Xueqing M Lu, Borislav Hristov, Steven Abel, Zeinab Chahine, Thomas Hollin, Desiree Williams, Tina Wang, Anthony Cort, Todd Lenz, Trevor A Thompson, Jacques Prudhomme, Abhai K Tripathi, Guoyue Xu, Juliana Cudini, Sunil Dogga, Mara N K Lawniczak, William Stafford Noble, Photini Sinnis, Karine Le Roch
Novel insights into the role of long non-coding RNA in the human malaria parasite, Plasmodium falciparum. Nature communications 14 (1) (2023)
Andy Lin, Temana Short, William Stafford Noble, Uri Keich
Improving Peptide-Level Mass Spectrometry Analysis via Double Competition. Journal of proteome research 21 (10) (2022)
Chengxiang Qiu, Junyue Cao, Beth K Martin, Tony Li, Ian C Welsh, Sanjay Srivatsan, Xingfan Huang, Diego Calderon, William Stafford Noble, Christine M Disteche, Stephen A Murray, Malte Spielmann, Cecilia B Moens, Cole Trapnell, Jay Shendure
Systematic reconstruction of cellular trajectories across mouse embryogenesis. Nature genetics 54 (3) (2022)
Ayse B Dincer, Yang Lu, Devin K Schweppe, Sewoong Oh, William Stafford Noble
Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning. Journal of proteome research 21 (7) (2022)
Wout Bittremieux, Damon H May, Jeffrey Bilmes, William Stafford Noble
A learned embedding for efficient joint analysis of millions of mass spectra. Nature methods 19 (6) (2022)
Magnus Palmblad, Sebastian Böcker, Sven Degroeve, Oliver Kohlbacher, Lukas Käll, William Stafford Noble, Mathias Wilhelm
Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics. Journal of proteome research 21 (4) (2022)
Sean Whalen, Jacob Schreiber, William Stafford Noble, Katherine S Pollard
Navigating the pitfalls of applying machine learning in genomics. Nature reviews. Genetics (2021)
Jacob Schreiber, Jeffrey Bilmes, William Stafford Noble
Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data. Bioinformatics (Oxford, England) 37 (4) (2021)
Yang Young Lu, William Stafford Noble
A wider field of view to predict expression. Nature methods 18 (10) (2021)
William E Fondrie, Wout Bittremieux, William Stafford Noble
ppx: Programmatic Access to Proteomics Data Repositories. Journal of proteome research 20 (9) (2021)
Timothy J Durham, Riza M Daza, Louis Gevirtzman, Darren A Cusanovich, Olubusayo Bolonduro, William Stafford Noble, Jay Shendure, Robert H Waterston
Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes. Genome research 31 (10) (2021)
Andy Lin, Deanna L Plubell, Uri Keich, William Stafford Noble
Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant. Journal of proteome research 20 (8) (2021)
William E Fondrie, William Stafford Noble
mokapot: Fast and Flexible Semisupervised Learning for Peptide Detection. Journal of proteome research 20 (4) (2021)
He Fang, Giancarlo Bonora, Jordan P Lewandowski, Jitendra Thakur, Galina N Filippova, Steven Henikoff, Jay Shendure, Zhijun Duan, John L Rinn, Xinxian Deng, William Stafford Noble, Christine M Disteche
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nature communications 11 (1) (2020)
Lindsay K Pino, Brian C Searle, Han-Yin Yang, Andrew N Hoofnagle, William Stafford Noble, Michael J MacCoss
Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics. Journal of proteome research 19 (3) (2020)
Hyeon-Jin Kim, Galip Gürkan Yardimci, Giancarlo Bonora, Vijay Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol B Ware, Jay Shendure, Zhijun Duan, William Stafford Noble
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data. PLoS computational biology 16 (9) (2020)
William E Fondrie, William Stafford Noble
Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments. Journal of proteome research 19 (3) (2020)
Damon H May, Kaipo Tamura, William Stafford Noble
Detecting Modifications in Proteomics Experiments with Param-Medic. Journal of proteome research 18 (4) (2019)
Maxwell W Libbrecht, Oscar L Rodriguez, Zhiping Weng, Jeffrey A Bilmes, Michael M Hoffman, William Stafford Noble
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types. Genome biology 20 (1) (2019)
David F Read, Kate Cook, Yang Young Lu, Karine G Le Roch, William Stafford Noble
Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features. PLoS computational biology 15 (9) (2019)

William Stafford Noble.css-eqlu8i{font-size:small;padding-left:4px;} (William S Noble, Galip Gürkan Yardımcı, W S Noble)

Publication Activity (10 Years)

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William Stafford Noble (William S Noble, Galip Gürkan Yardımcı, W S Noble)