Ran Zhang, Mu Yang, Jacob Schreiber, Diana R. O'Day, James Turner, Jay
Shendure, Christine M. Disteche, Xinxian Deng, William S. Noble.
"Cross-species imputation and comparison of single-cell transcriptomic
profiles." bioRxiv.
|
Borislav Hristov, William Stafford Noble, Alessandro Bertero.
Systematic
identification of inter-chromosomal interaction networks supports
the existence of specialized RNA factories."
|
|
|
Andy Lin, Donovan See, Uri Keich, Wiliam E. Fondrie, William Stafford
Noble.
"Target-decoy
false discovery rate estimation using Crema."
|
Crema |
|
He Fang, Ana R. Tronco, Giancarlo Bonora, Truong Nguyen, Jitendra
Thakur, Joel B. Berletch, Galina N. Filippova, Steven Henikoff, Jay
Shendure, William S. Noble, Christine M. Disteche, Xinxian Deng.
"CTCF-mediated
insulation and chromatin environment modulate Car5b escape from X
inactivation." bioRxiv
|
|
|
Jack Freestone, William Stafford Noble, Uri Keich.
"Analysis
of tandem mass spectrometry data with CONGA: Combining Open and
Narrow searches with Group-wise Analysis." bioRxiv
|
|
|
Jack Freestone, William Stafford Noble, Uri Keich.
"Re-investigating
the correctness of decoy-based false discovery rate control in
proteomics tandem mass spectrometry." bioRxiv
|
|
|
Anupama Jha, Stephanie C. Bohaczuk, Yizi Mao, Jane Ranchalis,
Benjamin J. Mallory, Alan T. Min, Morgan O. Hamm, Elliott Swanson,
Connor Finkbeiner, Tony Li, Dale Whittington, William Stafford
Noble, Andrew B. Stergachis, Mitchell R. Vollger.
"Fibertools:
fast and accurate DNA-m6A calling using single-molecule long-read
sequencing."
bioRxiv.
|
Fibertools |
|
Lincoln Harris, William Fondrie, Sewoong Oh, William Noble.
"Evaluating
proteomics imputation methods with improved criteria"
bioRxiv.
|
|
| Robin Aguilar, Conor K. Camplisson, Qiaoyi Lin, Karen H.
Miga, William S. Noble, Brian J. Beliveau.
"Tigerfish
designs oligonucleotide-based in situ hybridization probes targeting
intervals of highly repetitive DNA at the scale of genomes"
bioRxiv.
|
|
|
Vikram Agarwal, Fumitaka Inoue, Max Schubach, Beth K.\ Martin,
Pyaree Mohan Dash, Zicong Zhang, Ajuni Sohota, William Stafford
Noble, Galip Gurkan Yardimci, Martin Kircher, Jay Shendure,
Nadav Ahituv. "Massively parallel characterization of
transcriptional regulatory elements in three diverse human cell
types.". bioRxiv.
|
|
|
Arya Ebadi, Dong Luo, Jack Freestone, William Stafford Noble, Uri Keich.
"Bounding the FDP in
competition-based control of the FDR." arXiv.
|
|
|
Melih Yilmaz, William E. Fondrie, Wout Bittremieux, Rowan
Nelson, Varun Ananth, Sewoong Oh, William Stafford Noble.
"Sequence-to-sequence translation from mass spectra to peptides
with a transformer model." bioRxiv.
|
Casanovo |
|
Gayani Batugedara, Xueqing M. Lu, Steven Abel, Zeinab Chahine,
Borislav Hristov, Desiree Williams, Thomas Hollin, Tina Wang, Anthony
Cort, Todd Lenz, Trevor Thompson, Jacques Prudhomme, Abai K. Tripathi,
Guoyue Xu, Juliana Cudini, Sunil Dogga, Mara Lawniczak, William
Stafford Noble, Photini Sinnis, Karine G Le Roch.
"Deciphering
the non-coding code of pathogenicity and sexual differentiation in
the human malaria parasite."
bioRxiv.
|
|
|
Ricard A. Rodriguez-Mias, Kyle N. Hess, Bianca Y. Ruiz, Ian R. Smith,
Anthony S. Barente, Sarah M. Zimmerman, Yang Y. Lu, William Stafford
Noble, Stanley Fields, Judit Villen.
"Proteome-wide
identification of amino acid substitutions deleterious for protein
function."
bioRxiv.
|
|
| In press |
|
Daniel Mar, Ilona Babenko, Ran Zhang, William Stafford Noble, Oleg
Denisenko, Tomas Vaisar, Karol Bomsztyk.
"MultiomicsTracks96:
A high throughput PIXUL-Matrix-based toolbox to profile frozen and
FFPE tissues multiomes."
Laboratory Investigation.
|
|
|
Suchen Zheng, Nitya Thakkar, Hannah Harris, Megan Zhang, Susanna
Liu, Mark Gerstein, Erez Lieberman-Aiden, M. Jordan Rowley,
William Stafford Noble, Gamze Gursoy, Ritambhara Singh.
"Predicting
A/B compartments from histone modifications using
deep learning."
ACM-BCB '23: Proceedings of the 14th ACM International Conference
on Bioinformatics, Computational Biology and Health
Informatics..
|
|
|
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 Lawniczak,
William Stafford Noble, Photini Sinnis and Karine G. Le Roch.
"Novel insights into the role of long non-coding RNA in the
human malaria parasite, Plasmodium falciparum.
Nature Communications.
|
|
|
Laetitia Meng-Papaxanthos, Ran Zhang, Gang Li, Marco Cuturi, William
Stafford Noble, Jean-Philippe Vert.
"LSMMD-MA:
Scaling multimodal data integration for single-cell genomics data
analysis." Bioinformatics.
|
LSMMD-MA |
|
Brittany Baur, Jacob Schreiber, Junha Shin, Shilu Zhang, Yi Zhang,
Mohith Manjunath, Jun S. Song, William Stafford Noble, Sushmita Roy.
"Leveraging public epigenomic
datasets to examine the role of regulatory variation in the
three-dimensional organization of the genome."
PLOS Computational Biology.
|
|
|
Arya Ebadi, Jack Freestone, William Stafford Noble, Uri Keich.
"Bridging the false discovery gap."
Journal of Proteome Research.
|
|
|
Huiya Gu, Hannah Harris, Moshe Olshansky, Yossi Eliaz, Akshay
Krishna, Achyuth Kalluchi, Mozes Jacobs, Gesine Cauer, Melanie Pham,
Suhas S.P. Rao, Olga Dudchenko, Arina Omer, Kiana Mohajeri, Sungjae
Kim, Michael H Nichols, Eric S Davis, Devika Udupa, Aviva Presser
Aiden, Victor G Corces, Douglas H Phanstiel, William Stafford Noble,
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.
|
|
|
Rui Yang, Arnav Das, Vianne R. Gao, Alirezah Karbalayghareh, William Stafford
Noble, Jeff A. Bilmes, Christina S. Leslie.
"Epiphany:
predicting Hi-C contact maps from 1D epigenomic
signals." Genome Biology.
|
|
|
Alan Min, Timothy J. Durham, Louis Gevirtzmann, William Stafford
Noble.
Matrix
prior for data transfer between single cell data types in latent
Dirichlet allocation
PLOS Computational Biology.
|
lda_matrix_prior |
|
J Rozowsky, J Drenkow, YT Yang, G Gursoy, T Galeev, B Borsari,
CB Epstein, K Xiong, J Xu, J Gao, K Yu, A Berthel, Z Chen, F
Navarro, J Liu, MS Sun, J Wright, J Chang, CJF Cameron, N Shoresh, E
Gaskell, J Adrian, S Aganezov, G Balderrama-Gutierrez, S Banskota,
GB Corona, S Chee, SB Chhetri, GCC Martins, C Danyko, CA Davis, D
Farid, NP Farrell, I Gabdank, Y Gofin, DU Gorkin, M Gu, V Hecht, BC
Hitz, R Issner, M Kirsche, X Kong, BR Lam, S Li, B Li, T Li, X Li, K
Zin Lin, R Luo, M Mackiewicz, JE Moore, J Mudge, N Nelson, C
Nusbaum, I Popov, HE Pratt, Y Qiu, S Ramakrishnan, J Raymond, L
Salichos, A Scavelli, JM Schreiber, FJ Sedlazeck, LH See, RM
Sherman, X Shi, M Shi, CA Sloan, JS Strattan, Z Tan, FY Tanaka, A
Vlasova, J Wang, J Werner, B Williams, MXu, C Yan, L Yu, C Zaleski,
J Zhang, JM Cherry, EM Mendenhall, WS Noble, Z Weng, ME
Levine, A Dobin, B Wold, A Mortazavi, B Ren, J Gillis, RM Myers, MP
Snyder, J Choudhary, A Milosavljevic, MC Schatz, R Guigo, BE
Bernstein, TR Gingeras, M Gerstein.
"Multi-tissue
integrative analysis of personal epigenomes."
Cell
|
|
|
Dong Luo, Yilun He, Kristen Emery, William Stafford Noble, Uri Keich.
"Competition-based
control of the false discovery proportion." Biometrics.
| |
| 2023 |
|
Job Dekker, Frank Alber, Sarah Aufmkolk, Brian J. Beliveau,
Benoit G Bruneau, Andrew Belmont, Lacramioara Bintu, Alistair
Boettiger, Riccardo Calandrelli, Christine Disteche, David M
Gilbert, Thomas Gregor, Anders S Hansen, Bo Huang, Danwei Huangfu,
Reza Kalhor, Christina Leslie, Wenbo Li, Yun Li, Jian Ma,
William S Noble, Peter J Park, Jennifer E Phillips-Cremins,
Katherine S Pollard, Susanne Rafelski, Bing Ren, Yijun Ruan, Yaron
Shav-Tal, Yin Shen, Jay Shendure, Xiaokun Shu, Caterina
Strambio-De-Castillia, Anastassiia Vertii, Huaiying Zhang, Sheng
Zhong.
"Spatial
and temporal organization of the genome: current state and future
aims of the 4D Nucleome Project."
Molecular Cell.
|
|
|
Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li,
Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex
Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas
Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco
Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y.
Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun
Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi,
Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow,
Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth
Strattan, Michael Snyder, Manolis Kellis, William Stafford Noble,
Anshul Kundaje, ENCODE Imputation Challenge Participants.
"The
ENCODE Imputation Challenge: A critical assessment of methods for
cross-cell type imputation of epigenomic profiles."
Genome Biology. 24(9), 2023. |
|
|
Kris G. Alavattam, Katie A. Mitzelfelt, Giancarlo Bonora, Paul
A. Fields, Xiulan Yang, Han S. Chiu, Lil Pabon, Alessandro Bertero,
Nicholas J. Palpant, William Stafford Noble, Charles E. Murry.
"Dynamic
chromatin organization and regulatory interactions in human
endothelial cell differentiation." Stem Cell Reports.
18(1):159-174, 2023. |
|
|
Syamand Hasam, Kristen Emery, William Stafford Noble, Uri Keich.
"A
pipeline for peptide detection using multiple decoys." Methods
in Molecular Biology. 2426:25-34, 2023.
|
|
|
Nelle Varoquaux, William Stafford Noble, Jean-Phillipe Vert.
"Inference
of genome 3D architecture by modeling overdispersion of Hi-C
data."
Bioinformatics. 39(1):btac838, 2023.
|
PASTIS |
|
Andy Lin, Brooke L. Deatherage Kaiser, Janine R. Hutchison, Jeffrey A.
Bilmes, William Stafford Noble.
"MS1Connect:
a mass spectrometry run similarity
measure".
Bioinformatics. 39(2):btad058, 2023.
|
MS1Connect |
|
William Stafford Noble.
"Ten
simple rules for defining a computational biology project." PLOS
Computational Biology. 19(1):e1010786, 2023.
|
|
|
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye,
Kishankumar Bimani, Jimmy K. Eng, William E. Fondrie, Charles E.
Grant, Michael 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):561-569,
2023. |
Crux |
|
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):577-584, 2023.
|
Crux |
| 2022 |
|
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert,
William Stafford Noble.
"Multimodal
Single-Cell Translation and Alignment with Semi-Supervised
Learning." Journal of Computational Biology.
29(11):1198-1212, 2022. |
Polarbear |
|
Andy Lin, Temana Short, William Stafford Noble, Uri Keich.
"Improving peptide-level mass spectrometry analysis via double competition"
Journal of Proteome Research. 21(10):2412-2420, 2022.
|
|
|
Borislav Hristov, Jeffrey A. Bilmes, William Stafford Noble.
"Linking
cells across single-cell modalities by synergistic matching of
neighborhood structure." Bioinformatics (Proceedings of the
European Conference on Computational Biology).
8(Suppl_2):ii148-ii154, 2022. |
Synmatch |
|
Kayvon Mazooji, Sreeram Kannan, William Stafford Noble, Ilan Shomorony.
"Fundamental
limits of multi-sample flow graph decomposition."
Proceedings of the IEEE International Symposium on Information
Theory. 2403-2408, 2022.
|
|
|
Jack Freestone, Temana Short, William Stafford Noble, Uri Keich.
"Group-walk,
a rigorous approach to separate FDR analysis by TDC."
Bioinformatics (Proceedings of the European Conference on
Computational Biology).
38(Supplement_2):ii82-ii88, 2022. |
|
|
Lilian R. Heil, William E. Fondrie, Christopher D. McGann, Alexander
J. Federation, William Stafford Noble, Michael J. MacCoss, Uri Keich.
"A
flexible workflow for building spectral libraries from narrow window
data independent acquisition mass spectrometry
data." Journal of Proteome Research. 21(6):1382-1391, 2022.
|
|
|
Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert,
William Stafford Noble.
"Semi-supervised
single-cell cross-modality translation using Polarbear."
Proceedings of the International Conference
on Research in Computational Biology (RECOMB).
|
Polarbear |
|
Melih Yilmaz, William Fondrie, Wout Bittremieux, Sewoong Oh, William
Stafford Noble.
"De
novo mass spectrometry peptide sequencing with a
transformer model."
Proceedings of the International Conference on Machine
Learning. 162:25514-25522, 2022.
|
Casanovo
Talk |
|
Wout Bittremieux, William Stafford Noble.
"A
neural network for large-scale clustering of peptide mass
spectra." Nature Methods. 19(6):658-659, 2022.
|
GLEAMS
|
|
Wout Bittremieux, Damon H. May, Jeff Bilmes, and William Stafford Noble.
"A learned
embedding for efficient joint analysis of millions of mass spectra."
Nature Methods. 19(6):675-678, 2022.
|
GLEAMS
|
|
Ayse Berceste Dincer, Yang Lu, Devin Schweppe, Sewoong Oh, William
Stafford Noble.
"Reducing
peptide sequence bias in quantitative mass spectrometry data with
machine learning."
Journal of Proteome Research. 21(7):1771-1782, 2022.
|
Pepper |
|
Aakash Sur, William Stafford Noble, Peter J. Myler.
"A
benchmark of Hi-C scaffolders using reference genomes and de novo
assemblies."
bioRxiv.
|
|
|
Aakash Sur, William Stafford Noble, Shawn Sullivan, Peter Myler.
"Edison:
measuring scaffolding accuracy with edit distance."
bioRxiv.
|
Edison |
|
William S. Phipps, Kelly D. Smith, Han-Yin Yang, Clark M.
Henderson, Hannah Pflaum, Melissa L. Lerch,
William E. Fondrie, Michelle Emrick, Michael J. MacCoss, William
Stafford Noble, Andy N. Hoofnagle.
"Tandem
mass spectrometry-based amyloid typing using
manual microdissection and open-source data processing."
American Journal of Clinical Pathology. 157(5):748-757,
2022.
|
|
|
Chengxiang Qiu, Junyue Cao, Tony Li, Sanjay Srivatsan, Xingfan Huang,
Diego Calderon, William Stafford Noble, Christine M. Disteche, Malte
Spielmann, Cecilia B. Moens, Cole Trapnell, Jay Shendure.
"Systematic
reconstruction of the cellular trajectories of mammalian
embryogenesis."
Nature Genetics. 54:328-341, 2022.
|
|
|
Magnus Palmblad, Sebastian Boecker, Sven Degroeve,
Oliver Kohlbacher, Lukas Kall, William Stafford Noble, Matthias
Wilhelm.
"Interpretation of the DOME recommendations for machine
learning in proteomics and metabolomics." Journal of Proteome
Research. 21(4):1204-1207, 2022.
|
|
|
Sean Whalen, Jacob Schreiber*, William Stafford Noble,
Katherine Pollard.
"Navigating
the pitfalls of applying machine learning in genomics." Nature
Reviews Genetics. 23(3):169-181, 2022.
(featured article)
| talk |
|
Pilar Demetci, R Santorella, Brian Sandstede, William Stafford Noble, Ritambhara Singh.
"SCOT:
single-cell multi-omics alignment with optimal transport."
Journal of Computational Biology. 29(1):3-18, 2022.
| SCOT |
|
Pilar Demetci, R Santorella, Brian Sandstede, William Stafford Noble, Ritambhara Singh.
"Single-Cell
Multiomics Integration by SCOT."
Journal of Computational Biology. 29(1):19-22, 2022.
| SCOT |
| 2021 |
|
Timothy J. Durham, Riza M. Daza, Lou Gevirtzman, Darren
A. Cusanovich, William Stafford Noble, Jay Shendure, Robert
H. Waterston. "Comprehensive characterization
of tissue-specific chromatin accessibility in L2 Caenorhabditis
elegans nematodes."
Genome Research. 31:1952-1969, 2021.
| |
|
Dejun Lin, Justin Sanders, William Stafford Noble.
"HiCRep.py:
Fast comparison of Hi-C contact matrices in Python."
Bioinformatics. 37(18):2996-2997, 2021.
| HiCrep.py |
|
Sarah G. Swygert, Dejun Li, Stephanie Portillo-Ledesma,
Po-Yen Lin, Dakota R. Hunt, Cheng-Fu Kao, Tamar Schlick, William
Stafford Noble, Toshio Tsukiyama.
"Chromatin
fiber folding represses transcription and loop extrusion in
quiescent cells." eLife. e72062, 2021.
| |
|
Wout Bittremieux, Kris Laukens, William Stafford Noble, Pieter C. Dorrestein.
"Large-scale
tandem mass spectrum clustering using fast nearest neighbor
searching." Rapid Communications in Mass
Spectrometry. e9153, 2021.
| falcon |
|
Yang Young Lu, Jeff Bilmes, Ricard A. Rodriguez-Mias, Judit
Villen, William Stafford Noble.
"DIAmeter:
Matching peptides to data-independent acquisition mass spectrometry data".
Bioinformatics (Proceedings of the
ISMB). 37(Supplement_1):i434-i442, 2021.
| DIAmeter |
|
Yang Young Lu, Timothy C. Yu, Giancarlo Bonora, William Stafford
Noble.
"ACE:
Explaining cluster from an adversarial perspective."
Proceedings of the International Conference on Machine Learning
(ICML). 139:7156-7167, 2021.
|
ACE
Supplement
|
|
Yang Y. Lu, Wenbo Guo, Xinyu Xing, William Stafford Noble.
"DANCE: Enhancing
saliency maps using decoys." Proceedings of the
International Conference on Machine Learning (ICML).
139:7124-7133, 2021.
| |
|
Andy Lin, Deanna 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):4153-4164, 2021.
| Subset neighbor search |
| Giancarlo Bonora, Vijay Ramani, Ritambhara Singh, He
Fang, D Jackson, Sanjay Srivatsan, Ruolan Qiu, Choli Lee, Cole
Trapnell, Jay Shendure, Zhijun Duan, Xinxian Deng, William Stafford
Noble, Christine
M. Disteche. "Single-cell
landscape of nuclear configuration and gene expression during stem
cell differentiation and X inactivation." Genome Biology. 22:279, 2021.
| Supplement |
Yang Young Lu, William Stafford Noble. "A wider field of view to
predict expression." Nature Methods. 18:1155-1160, 2021
| | |
William E. Fondrie, Wout Bittremieux, William Stafford Noble.
"ppx:
Programmatic access to proteomics data
repositories." Journal of Proteome Research.
20(9):4621-4624, 2021.
| ppx | |
|
William E. Fondrie, William Stafford Noble.
mokapot:
Fast and flexible semi-supervised learning for peptide
detection." Journal of Proteome Research. 20(4):1966-1971, 2021.
| mokapot |
|
Jacob Schreiber, Jeff Bilmes, William Stafford Noble.
"Prioritizing
transcriptomic and epigenomic experiments by using an optimization
strategy that leverages imputed data." Bioinformatics,
37(4):439-447, 2021. | |
|
Miranda Mudge, Brook L. Nunn, Erin Firth, Marcela Ewert,
Kianna Hales, William E. Fondrie, William Stafford Noble, Jonathan
Toner, Bonnie Light, Karen A. Junge.
"Subzero,
saline incubations of Colwellia psychrerythraea reveal strategies and
biomarkers for sustained life in extreme icy
environments." Environmental
Microbiology. 23(7):3840-3866, 2021.
| |
| 2020 |
|
He Fang,* Giancarlo Bonora,*, JP Lewandowski,
J Thakur, Galina N Filippova, Steve Henikoff, Jay Shendure, Zhijun
Duan, Jonathan L. Rinn, Xinxian Deng, William Stafford Noble,
Christime M. Disteche.
"Trans-
and cis-acting effects of the lncRNA
Firre on epigenetic and structural
features of the inactive X chromosome." Nature
Communications.
11(1):6053, 2020. |
|
|
Jacob Schreiber, Deepthi Hegde, William Stafford Noble.
"Zero-shot
imputations across species are enabled through joint modeling
of human and mouse epigenomics." BCB '20: Proceedings
of the 11th ACM International Conference on Bioinformatics,
Computational Biology and Health Informatics,
article 39, pages 1-9, 2020.
| Best paper award |
|
Jacob Schreiber, Yang Y. Lu, William Stafford Noble.
"Ledidi:
Designing genomic edits that induce functional activity."
bioRxiv, 2020.
| Ledidi |
|
Ritambhara Singh, Pilar Demetci, Giancarlo Bonora, Vijay Ramani, Choli
Lee, He Fang, Zhijun Duan, Xinxian Deng, Jay Shendure, Christine
Disteche, William Stafford Noble.
"Unsupervised
manifold alignment for single-cell multi-omics data."
BCB '20: Proceedings of the 11th ACM International Conference on
Bioinformatics, Computational Biology and Health
Informatics, article 40, pages 1-10, 2020.
| MMD-MA
Talk |
|
Wei Yang, Jeff Bilmes, William Stafford Noble.
"Submodular
sketches of single-cell RNA-seq measurements".
BCB '20: Proceedings of the 11th ACM International Conference on
Bioinformatics, Computational Biology and Health
Informatics, article 61, pages 1-6, 2020.
| Talk |
|
Hyeon-Jin Kim, Galip Gurkan Yardimci, Giancarlo Bonora, Vijay
Ramani, Jie Liu, Ruolan Qiu, Choli Lee, Jennifer Hesson, Carol
B. Ware, Jay Shendure, Zhijun Duan and William Stafford Noble.
"Capturing
cell type-specific chromatin structural patterns by
applying topic modeling to single-cell Hi-C data."
PLOS Computational Biology, 16(9):e1008173, 2020.
| |
|
Jacob Schreiber, Ritambhara Singh, Jeff Bilmes, William Stafford
Noble.
"A
pitfall for machine learning methods aiming to predict across
cell types."
Genome Biology. 21(1):282, 2020.
| |
|
ENCODE Consortium.
"Expanded
encyclopedias of DNA elements in the human and mouse
genomes." Nature. 583(7818):699-710, 2020.
| |
|
Ariel Erijman, Lukasz Kozlowski, Salma Sohrabi-Jahromi, James
Fishburn, Linda Warfield, Jacob Schreiber, William Stafford Noble,
Johannes Soeding, Steven Hahn.
"A high-throughput screen for transcription activation domains reveals their sequence
characteristics and permits reliable prediction by deep learning."
Molecular Cell. 78(5):P890-P892, 2020.
| |
|
Jacob Schreiber, Jeff Bilmes, William Stafford Noble.
"apricot:
Submodular selection for data summarization in Python."
Journal of Machine Learning Research, 21(161):1-6, 2020. |
apricot |
|
Kristen Emery, S Hasan, Uri Keich and William Stafford Noble.
"Multiple
competition based FDR control and peptide
detection." Proceedings of the International on Research in
Computational Biology (RECOMB). 24:54-71, 2020.
| Supplement
Talk
|
|
Jacob Schreiber, Timothy J. Durham, Jeff Bilmes, William Stafford
Noble.
"Multi-scale
deep tensor factorization learns a latent representation of the
human epigenome". Genome Biology. 81:21, 2020. |
Avocado
Supplement
GenomeWeb
|
| Jacob Schreiber, Jeff Bilmes, and William Stafford
Noble.
"Completing the ENCODE3 compendium yields accurate
imputations across a variety of assays and human biosamples."
Genome Biology. 81:22, 2020.
| |
|
Sheng Pan, Meredith A. J. Hullar, Lisa A. Lai, Hong Peng, Damon
May, William Stafford Noble, Daniel Raftery, Sandi L. Navarro,
Marina L. Neuhouser, Paul D. Lampe, Joanna W. Lampe, Ru Chen.
"Gut microbial
protein expression in response to dietary patterns
in a controlled feeding study: a metaproteomic approach."
Microorganisms. 8(3):379, 2020.
| |
|
Kate Cook, Borislav Hristov, Karine Le Roch, Jean-Philippe Vert, William Stafford Noble.
"Measuring
significant changes in chromatin conformation with ACCOST."
Nucleic Acids Research. 48(5):2303-2311, 2020.
| ACCOST |
|
Brook Nunn, Molly Mikan, H. Harvey, Emma Timmins-Schiffman, Michael
Riffle, Damon May, William Stafford Noble, and Ian Salter.
"Metaproteomics reveal that rapid perturbations in organic matter
prioritize functional restructuring over taxonomy in Western Arctic
Ocean microbiomes." The ISME Journal. 14:39-52, 2020.
| |
|
Lindsay 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):1147-1153, 2020.
| |
|
Will Fondrie, William Stafford Noble.
"A
machine learning strategy that leverages large datasets to boost
statistical power in small-scale experiments."
Journal of Proteome Research, 19(3):1267-1274, 2020.
|
Percolator
GenomeWeb |
|
Vijay Ramani, Xinxian Deng, Ruolan Qiu, Christine Disteche, William
Stafford Noble, Jay Shendure, Zhijun Duan.
"Sci-Hi-C:
a single-cell Hi-C method for mapping 3D genome organization in
large numbers of single cells." Methods. 170:61-68, 2020.
| |
| 2019 |
|
Alessandro Bertero, Paul A. Fields, AST Smith, A Leonard, K Beussman,
NJ Sniadecki, D-H Kim, HF Tse, Lil Pabon, Jay Shendure, William
Stafford Noble, Charles E. Murry.
"Chromatin
compartment dynamics in a haploinsufficient model of cardiac
laminopathy."
Journal of Cell Biology. 218(9):2919-2944, 2019.
| data |
|
Yi Yin, Yue Jian, Kwan-Wood G. Lam, Joel B. Berletch, Christine
M. Disteche, William Stafford Noble,
Frank J. J Steemers, R. Daniel Camerini-Otero, Andrew C. Adey, Jay Shendure.
"High-throughput single cell genome sequencing reveals
cell-autonomous equational segregation in meiosis I."
Molecular Cell. 76(4):676-690, 2019.
| |
|
David F. Read, Kate Cook, Yang Y. Lu, Karine Le Roch, and William
Stafford Noble.
"Predicting
gene expression in the human malaria parasite Plasmodium
falciparum." PLOS Computational Biology. 15(9):e1007329, 2019.
| Supplement |
| Wei Chen, Aaron McKenna, Jacob Schreiber, Maximilian
Haeussler, Yi Yin, Vikram Agarwal, William Stafford Noble, Jay
Shendure.
"Massively
parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated
double-strand break repair."
Nucleic Acids Research. 47(15):7989-8003, 2019.
| Lindel |
|
Jung-Sik Kim, Xiaoyuan He, Jie Liu, Zhijun Duan, Taeyeon Kim, Julia
Gerard, Brian Kim, William S. Lane, William S. Noble, Bogdan Budnik,
Todd Waldman.
"Cohesin interacts
with a panoply of splicing factors required for cell
cycle progression and genomic organization".
Journal of Biological Chemistry. 294(22):8760-8772,
2019. | |
|
John T. Halloran, Hantian Zhang, Kaan Kara, Cedric Renggli, Matthew
The, Ce Zhang, David M. Rocke, Lukas Kall, William Stafford Noble.
"Speeding
up Percolator." Journal of Proteome
Research. 18(9):3353-3359, 2019.
| |
|
Wout Bittremieux, Kris Laukens, William Stafford Noble.
"Extremely
fast and accurate open modification spectral library searching of
high-resolution mass spectra using feature hashing and graphics
processing units".
Journal of Proteome Research, 18(10):3972-3799, 2019. |
ANN-SoLo |
|
Alice Cheng, Charles E. Grant, William Stafford Noble, and Timothy L. Bailey.
"MoMo:
Discovery of statistically significant post-translational
modification motifs."
Bioinformatics. 35(16):2774-2782, 2019.
| MEME Suite |
|
Wenruo Bai, Jeff Bilmes, William Stafford Noble.
"Submodular
generalized matching for peptide identification in tandem mass spectrometry."
IEEE Transactions in Computational Biology and
Bioinformatics. 16(4):1168-1181, 2019.
| |
|
Maxwell W. Libbrecht, Oscar Rodriguez, Zhiping Weng, Jeff 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. 20:180, 2019.
|
Encyclopedia Segway
SAGA interpretation |
|
Gesine Cauer, Gurkan Yardimci, Jean-Philippe Vert, Nelle Varoquaux,
William Stafford
Noble. "Inferring
diploid 3D chromatin structures from Hi-C data."
19th International Workshop on Algorithms in Bioinformatics (WABI 2019),
143(11):1-13, 2019.
|
PASTIS |
|
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, William
Stafford
Noble. "Jointly
embedding multiple single-cell omics measurements."
19th International Workshop on Algorithms in Bioinformatics (WABI
2019),
143(10):1-13, 2019. |
Supplement,
Source code |
|
Damon May, Kaipo Tamura, William Stafford Noble.
"Detecting
modifications in proteomics experiments with Param-Medic".
Journal of Proteome Research. 18(4):1902-1906, 2019.
|
Param-medic
Crux |
|
Alessandro Bertero, Paul A. Fields, Vijay Ramani, Giancarlo Bonora,
Gurkan Yardimci, Hans Reinecke, Lil Pabon, William Stafford Noble, Jay
Shendure, Charles E. Murry.
"Dynamics
of genome reorganization during human cardiogenesis
reveal an RBM20-dependent splicing factory." Nature
Communications. 10(1):1538, 2019.
| data |
|
Molly Gasperini, Andrew J. Hill, Jose L. McFaline-Figueroa, Beth
Martin, Seungsoo Kim, M. D. Kim, Dana Jackson, Anh Leith, Jacob Schreiber,
William S. Noble, Cole Trapnell, Nadav Ahituv, Jay Shendure.
"A
genome-wide framework for mapping gene regulation via cellular
genetic screens." Cell. 176(1-2):377-390, 2019.
| |
| Gurkan Galip Yardimci, Hakan Ozadam, Michael
E. G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit
Chakraborty, Arya Kaul, Bryan R Lajoie, Fan Song, Ye Zhan, Ferhat
Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng
Yue, Job Dekker, William S Noble.
"Measuring
the reproducibility and quality of Hi-C data." Genome
Biology, 20(1):57, 2019. |
3D
Chromatin ReplicateQC |
|
Uri Keich, Kaipo Tamura, and William Stafford Noble.
"Averaging
strategy to reduce variability in target-decoy estimates of false
discovery rate." Journal of Proteome Research,
18(2):585-593, 2019.
|
Protocol
|
|
Alex Hu, Yang Lu, Jeff A. Bilmes, William Stafford Noble.
"Joint
precursor elution profile inference via regression for
peptide detection in data-independent acquisition mass spectra."
Journal of Proteome Research, 18(1):86-94, 2019.
| Siren |
| Dejun Lin, Giancarlo Bonora, Gurkam Yardimci, and William
Stafford Noble.
"Computational
methods for analyzing and modeling genome structure and
organization." WIREs Systems Biology. 11(1):e1435, 2019. | |
| 2018 |
|
Lindsay Pino, Brian Searle, E Huang, William Stafford Noble,
Andy Hoofnagle, Michael J. MacCoss.
"Calibration using a
single-point external reference material harmonizes quantitative
mass spectrometry proteomics data between platforms and
laboratories." Analytical Chemistry. 90(21):13112-13117,
2018.
| |
|
Yang Lu, Yinging Fan, Jinchi Lv, and William Stafford Noble.
"DeepPINK:
reproducible feature selection in deep neural networks."
Advances in Neural Information Processing Systems.
31:8690-8700, 2018.
| DeepPINK
Supplement
|
|
Andy Lin, J. Jeffry Howbert, William Stafford Noble.
"Combining high resolution and exact calibration to boost statistical power:
A well-calibrated score function for high-resolution MS2 data".
Journal of Proteome Research. 17(11):3644-3656, 2018.
|
Crux |
|
Wenruo Bai, William Stafford Noble, Jeffrey A. Bilmes.
"Submodular
maximization via gradient ascent: The case of deep submodular
functions."
Advances in Neural Information Processing
Systems. 31:7989-7999, 2018.
| |
|
Wenxiu Ma, Giancarlo Bonora, J. B. Berletch, Xinxian Deng, William
Stafford Noble, Christine M. Disteche.
"X-chromosome
inactivation and escape from X inactivation in
mouse." Methods in Molecular Biology. 1861:205-219,
2018.
| |
|
Jesse Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria
T. Le, Galip Gurkan Yardimci, Abhijit Chakraborty, Darrin V. Bann,
Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu,
Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan
Carlos Rivera Mulia, Hakan Ozadam, Bryan R. Lajoie, Rajinder Kaul,
Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic,
Christina Ernst, Suzana Hadjur, Duncan T. Odom, John
A. Stamatoyannopoulos, James R. Broach, Ross Hardison, Ferhat Ay,
William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue.
"Integrative
detection and analysis of structural variation in cancer
genomes." Nature Genetics. 50(10):1388-1398, 2018.
| |
|
Wout Bittremieux, Pieter Meysman, William Stafford Noble, Kris
Laukens.
"Fast open modification spectral library searching through
approximate nearest neighbor indexing".
Journal of Proteome Research. 17(10):3463-3474, 2018. |
ANN-SoLo |
|
Giancarlo Bonora, Xinxian Deng, He Fang, Vijay Ramani, Ruolan Qiu, Joel Berletch,
Gala N. Filippova, ZhiJun Duan, Jay Schendure, William S. Noble, Christine M. Disteche.
"Orientation-dependent
Dxz4 contacts shape the 3D structure of the inactive X
chromosome." Nature Communications. 9(1):1445, 2018. |
data |
|
Maxwell W. Libbrecht, Jeffrey A. Bilmes and William Stafford Noble.
"Choosing
non-redundant representative subsets of protein sequence data sets
using submodular optimization." Proteins. 86(4):454-466,
2018 |
Source code |
|
Wenxiu Ma, Ferhat Ay, Cholie Lee, G Gulsoy, Xinxian Deng, S
Cook, J Hesson, C Cavanaugh, Carol B. Ware, Anton Krumm, Jay
Shendure, C. Anthony Blau, Christin M. Disteche, William
Stafford Noble, Zhijun Duan.
"Using
DNase Hi-C techniques to map global and local three-dimensional
genome architecture at high resolution." Methods.
142:59-73, 2018.
| |
|
Timothy J. Durham, Maxwell W. Libbrecht, J. Jeffry Howbert, Jeff Bilmes and
William Stafford Noble.
"PREDICTD:
PaRallel Epigenomics Data Imputation with Cloud-based Tensor
Decomposition". Nature Communications. 9(1):1402, 2018 |
PREDICTD |
| Evelien M. Bunnik, Kate B. Cook, Nelle Varoquaux, Gayani
Batugedara, Jacques Prudhomme, A. Cort, Lirong Shi, Chiara Andolina,
Leila S. Ross, Declan Brady, David A. Fidock, Francois Nosten, Rita
Tewari, Photini Sinnis, Ferhat Ay, Jean-Philippe Vert, William
Stafford Noble, Karine G. Le Roch
"Changes in genome organization of parasite-specific gene
families during the Plasmodium transmission
stages." Nature Communications, 9(1):1910, 2018. |
Web Supplement |
| Jie Liu, Dejun Lin, Gurkan Yardimci and William Stafford
Noble.
"Unsupervised
embedding of single-cell Hi-C data". Bioinformatics
(Proceedings of the ISMB). 34(13):i96-i104, 2018. | |
| Oana Ursu, Nathan Boley, M Taranova, Y X. R. Wang, Gurkan
Yardimci, William Stafford Noble, and Anshul Kundaje.
"GenomeDISCO:
A concordance score for chromosome conformation capture experiments
using random walks on contact map
graphs." Bioinformatics, 34(16):2701-2707,
2018. |
GenomeDISCO |
|
Uri Keich and William Stafford Noble.
"Controlling
the FDR in imperfect matches to an incomplete database."
Journal of the American Statistical Association.
113(523):973-982, 2018.
| |
|
Rachel C. W. Chan, Maxwell W. Libbrecht, Eric G. Roberts, Jeffrey
A. Bilmes, William Stafford Noble, and Michael M. Hoffman.
"Segway
2.0: Gaussian mixture models and minibatch
training." Bioinformatics. 34(4):669-671, 2018. |
Segway |
| 2017 |
|
Z. E. Sychev, Alex Hu, T. DiMaio, Anthony Gitter, N. D. Camp,
William Stafford Noble, Alejandro Wolf-Yadlin, M. Lagunoff.
"Integrated systems biology analysis of KSHV latent
infection reveals viral induction and reliance on peroxisome mediated
lipid metabolism."
PLOS Pathogens. 13(3):e1006256, 2017.
| |
|
Mike Riffle, Damon H. May, Emma Timmins-Schiffman,
M. P. Mikan, Daniel Jaschob, William Stafford Noble, and Brook L
Nunn.
MetaGOmics: A
web-based tool for peptide-centric functional and taxonomic
analysis of metaproteomics data."
Proteomes. 6(1), 2017.
| |
| Jacob Schreiber, Maxwell W. Libbrecht, Jeff Bilmes,
William Stafford
Noble. "Nucleotide
sequence and DNaseI sensitivity are predictive of 3D chromatin
architecture"
bioRxiv, 2017 |
Rambutan |
| Tao Yang, Feiping Zhang, G. Gurkan Yardimci, F. Song,
Ross C. Hardison, William Stafford Noble, Feng Yue, and Qunhua
Li. "HiCRep:
assessing the reproducibility of Hi-C data using a stratum-adjusted
correlation coefficient."
Genome Research, 27(11):1939-1949,
2017. |
HiCRep |
|
Umut Eser, Devon Chandler-Brown, Ferha Ay, Aaron F. Straight,
Zhijun Duan, William Stafford Noble, Jan M. Skotheim.
"Form and function of topologically
associating genomic domains in budding yeast". Proceedings of
the National Academy of Science. 114(15):E3061-E3070,
2017.
| |
|
Jie Liu, John T. Halloran, Jeffrey A. Bilmes, Riza M. Daza, Choli
Lee, Elisabeth M. Mahen, Donna Prunkard, Chaozhong Song, Sibel Blau,
Michael O. Dorschner, Vijayakrishna K. Gadi, Jay Shendure,
C. Anthony Blau, and William S. Noble.
"Comprehensive
statistical inference of the clonal structure of cancer from
multiple biopsies". Scientific Reports. 7(1):16943, 2017 |
THEMIS |
|
Giancarlo Bonora and Christine M. Disteche.
"Structural aspects of the inactive X chromosome."
Philosophical Transactions of the Royal Society B.,
372(1733), 2017. |
|
|
William Stafford Noble.
"Ten simple rules for writing a response to
reviewers." PLOS Computational Biology. 13(10):e1005730, 2017. | |
| Jacob Schreiber and William Stafford Noble.
"Finding the optimal
Bayesian network given a constraint graph." PeerJ Computer
Science. 3:e122, 2017.
| |
|
Wenxiu Ma, Lin Yang, Remo Rohs and William Stafford
Noble.
"DNA
sequence+shape kernel enables alignment-free modeling of
transcription factor binding." Bioinformatics.
33(19):3003-3010, 2017.
| |
|
Koon-Kiu Yan, Gurkan Yardimci, C. Yan, William Stafford Noble, and Mark
Gerstein.
"HiC-Spector:
a matrix library for spectral and reproducibility analysis of Hi-C
contact maps." Bioinformatics. 33(14):2199-2201,
2017. |
HiC-Spector |
| Hitomi Sakano, DAR Zorio, X. Wang, Ying Sonia Ting,
William Stafford Noble, Michael J. MacCoss, Edwin W. Rubel, Y
Wang. "Proteomic analyses of nucleus laminaris
identified candidate targets of the fragile X mental retardation
protein." Journal of Comparative
Neurology. 525(15):3341-3359,
2017. | |
|
Shengjie Wang, Haoran Cai, Jeff Bilmes, William Stafford
Noble. "Training
compressed fully-connected networks with a density-diversity
penalty". Proceedings of the 5th International
Conference on Learning Representations.
| |
|
Seungsoo Kim, Ivan Liachko, DG Brickner, Kate Cook, William Stafford
Noble, JH Brickner, Jay Shendure, and Maitreya J. Dunham.
"The
dynamic three-dimensional organization of the diploid yeast
genome." eLife. 6:e23623, 2017. | |
|
Uri Keich and William Stafford Noble.
"Progressive
calibration and averaging for tandem mass spectrometry statistical confidence
estimation: Why settle for a single decoy?" Proceedings of
the International on Research in Computational Biology
(RECOMB). 10229:99-116, 2017.
| |
|
William Stafford Noble and Uri Keich.
Response
to 'Mass spectrometrists should search for all peptides, but assess
only the ones they care about.'" Nature Methods. 14(7):644, 2017. |
|
|
Musa N. Gabere and William Stafford Noble.
"Empirical
comparison of web-based antimicrobial peptide prediction
tools." Bioinformatics. 33(13):1921-1929,
2017. | |
|
Damon H. May, Kaipo Tamura, William Stafford Noble.
"Param-Medic:
A tool for improving MS/MS database search yield by optimizing
parameter settings."
Journal of Proteome Research. 16(4):1817-1824,
2017. Supporting
Information |
Param-Medic,
Crux |
| Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor
O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh
C. O'Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay
Shendure, Sheng Zhong and the 4D Nucleome
Network. "The
4D nucleome project". Nature 549(7671):219-226,
2017. | |
|
Ying Sonia Ting, Jarrett D. Egertson, James Bollinger, Brian
C. Searle, SH
Payne, William Stafford Noble and Michael J MacCoss.
"PECAN:
library-free peptide detection for data-independent acquisition
tandem mass spectrometry data." Nature Methods.
14(9):903-908, 2017.
| PECAN |
|
Vijay Ramani, Xinxian Deng, Ruolan Qiu, KL Gunderson, FJ Steemers,
Christine M. Disteche,
William Stafford Noble, Zhijun Duan, Jay Shendure.
"Massively
multiplex single-cell Hi-C." Nature Methods. 14(3):263-266, 2017.
| |
|
Gurkan Yardimci and William Stafford Noble.
"Software
tools for visualizing Hi-C data." Genome Biology,
18(1):26, 2017. | |
| Emma Timmins-Schiffman, Damon H. May, Molly Mikan,
Michael Riffle, C. Frazar, H. R. Harvey, William Stafford Noble, Brook
L. Nunn. "Critical decisions in metaproteomics: Achieving high
confidence protein annotations in a sea of unknowns." The ISME
Journal. 11(2):309-314, 2017. | |
| 2016 |
| Alex Hu, William S. Noble, Alejandro Wolf-Yadlin. "Technical advances in proteomics: new developments in data-independent acquisition." F1000Research. 5(F1000 Faculty Rev):419, 2016.
| |
| Vijay Ramani, Darren A. Cusanovich, R. J. Hause, Wenxiu
Ma, Xinxian Deng, C. Anthony Blau, C. Disteche, William Stafford
Noble, Jay Shendure, and Zhijun Duan. "Mapping
3D genome architecture through in situ DNase Hi-C." Nature
Protocols. 11(11):2014-2121, 2016.
| |
|
Nao Hiranuma, Jie Liu, Chaozhong Song, Jacob Goldsmith, Michael
Dorschner, Colin Pritchard, Kimberly Burton, Elisabeth Mahen, Sibel
Blau, Francis Senecal, Wayne Monsky, Stephanie Parker, Stephen
Schmechel, Stephen Allison, VK Gadi, Sofie Salama, Amie Radenbaugh,
Mary Goldman, Jill Johnsen, Shelly Heimfeld, Vitalina Komashko,
Marissa LaMadrid-Hermannsfeldt, Zhijun Duan, Steven Benz, Patrick
Soon-Shiong, David Haussler, Jingchun Zhu, Walter Ruzzo, William
Noble, and C. Anthony Blau.
"Cis-compound
mutations are prevalent in triple negative breast cancer and can drive
tumor progression." bioRxiv,
2016. | |
|
Arjan van der Velde, Michael Purcaro, William Stafford Noble, and
Zhiping Weng.
"LR-DNase:
Predicting TF binding prediction from DNase-seq
data." bioRxiv, 2016.
| |
|
Wenruo Bai, Jeff Bilmes and William Stafford
Noble. "Bipartite
matching generalizations for peptide identification in tandem mass
spectrometry." ACM Conference on Bioinformatics, Computational
Biology, and Health Informatics. | Best paper
award |
|
Kai Wei, Maxwell W. Libbrecht, Jeffry A. Bilmes and William
Stafford
Noble. "Choosing
panels of genomics assays using submodular
optimization." Genome Biology. 17(1):229, 2016. |
Talk
Web server |
| Matthew The, Michael J. MacCoss, William Stafford Noble
and Lukas
Käll. "Fast
and accurate protein false discovery rates on large-scale proteomics
data sets with Percolator 3.0." Journal of the American Society
of Mass Spectrometry. 27:1719, 2016.
| Percolator |
| Shengjie Wang, John Halloran, Jeff A. Bilmes and William
Stafford
Noble. "Faster
and more accurate graphical model identification of tandem mass
spectra using trellises." Bioinformatics (Proceedings of the
ISMB). 32(12):i322-i331, 2016.
| |
| O. K. Smith, R. Kim, H. Fu, M. M. Martin, K. Utani,
Y. Zhang, A. B. Marks, M. Lalande, S. Chamberlain, M. W. Libbrecht,
E. E. Bouhassira, M. C. Ryan, W. S. Noble and M. I. Aladjem.
"Distinct
epigenetic features of differentiation-regulated replication
origins." Epigenetics and Chromatin. 9(1):18,
2016. |
Data |
| John Halloran, Jeff A. Bilmes and William Stafford Noble.
"Dynamic
Bayesian network for accurate detection of peptides from tandem mass
spectra." Journal of Proteome Research. 15(8):2749-2759,
2016. | DRIP |
| Damon H. May, Emma Timmins-Schiffman, Molly P. Mikan,
H. R. Harvery, Elhanan Borenstein, Brook L. Nunn and William Stafford
Noble. "An
alignment-free 'metapeptide' strategy for metaproteomic
characterization of microbiome samples using shotgun metagenomic
sequencing." Journal of Proteome Research.
15(8):2697-2705, 2016.
|
Sixgill,
Supplement |
| 2015 |
| Joel B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure,
William Stafford Noble, and Christine
M. Disteche. "Identification
of genes escaping X inactivation by allelic expression analysis in a
novel hybrid mouse model."
Data in Brief. 5:761-769, 2015.
| |
|
Charles E. Grant, James Johnson, Timothy L. Bailey, and William
Stafford
Noble. "MCAST:
Scanning for cis-regulatory motif
clusters." Bioinformatics. 2015 |
MCAST |
|
Ferhat Ay, William Stafford Noble.
"Analysis
methods for studying the 3D architecture of the genome."
Genome Biology. 16:183, 2015. |
|
|
Xinxian Deng, Wenxiu Ma, Vijay Ramani, Andrew Hill, Fan Yang, Ferhat Ay,
Joel Berletch, Carl Blau, Jay Shendure, Zhijun Duan, William Noble, Christine Disteche
"Bipartite
structure of the inactive mouse X chromosome."
Genome Biology. 16:152, 2015. |
Supplement
data |
| Ying Sonia Ting, Jarrett D. Eggertson, Sam H. Payne, Sangtae
Kim, Brendan MacLean, Lukas Kall, Ruedi Aebersold, Richard D. Smith,
William Stafford Noble, and Michael J. MacCoss.
"Peptide-centric
proteome analysis: an alternative strategy for the analysis of tandem
mass spectrometry data." Molecular and Cellular
Proteomics. 14(9):2301-2307, 2015. |
|
| Attila Kertesz-Farkas, Uri Keich and William Stafford
Noble. "Tandem
mass spectrum identification via cascade search." Journal of
Proteome Research. 14(8):3027-3038, 2015. |
Crux |
| Uri Keich, Attila Kertesz-Farkas and William Stafford
Noble.
"Improved
false discovery rate estimation procedure for shotgun
proteomics." Journal of Proteome Research.
14(8):3148-3161, 2015.
(Correction) |
Supplement,
Crux |
|
William Stafford Noble.
"Mass
spectrometrists should search only for peptides they care
about." Nature Methods. 12(7):605-608, 2015. |
Supplement |
|
Timothy L. Bailey, James Johnson, Charles E. Grant and William
Stafford Noble.
"The MEME Suite."
Nucleic Acids Resesearch. 43(W1):W39-49, 2015. |
MEME |
|
Rachel M. Gittelman, Enna Hun, Ferhat Ay, Jennifer Madeoy, Len Pennacchio, William Stafford Noble, David R. Hawkins and Joshua M. Akey.
"Comprehensive identification and analysis of human accelerated regulatory DNA."
Genome Research, 2015. |
|
|
Vishnu Dileep, Ferhat Ay, Jiao Sima, Daniel L Vera, William Stafford Noble,
and David M Gilbert.
"Topologically-associating domains and their long-range contacts are
established during early G1 coincident with the establishment of the
replication timing program." Genome Research, 2015. |
|
| Maxwell Libbrecht and William Stafford
Noble. "Machine
learning applications in genetics and genomics". Nature
Reviews Genetics. 16(6):321-332, 2015. |
|
| Nelle Varoquaux, Ivan Liachko, Ferhat Ay, Josh Burton,
Jay Shendure, Maitreya Dunham, Jean-Philippe Vert and William Stafford
Noble.
"Accurate identification of centromere
locations in yeast genomes using Hi-C." Nucleic Acids
Research. 43(11):5331-5339, 2015.
|
Centurion,
Biotechniques article |
| Maxwell Libbrecht, Michael Hoffman, Jeff Bilmes and William Stafford Noble.
"Entropic graph-based posterior regularization." Proceedings of the International Conference on
Machine Learning, 2015. |
Source code Extended version |
| J. B. Berletch, Wenxiu Ma, Fan Yang, Jay Shendure, William
Stafford Noble, Christine M. Disteche, Xinxian
Deng. "Escape from X inactivation varies in mouse
tissues." PLOS Genetics. 18(3):e1005079, 2015. |
|
| Fan Yang, Xinxian Deng, Wenxiu Ma, Joel B. Berletch, N
Rabaia, J. M. Moore, G. N. Filippova, Y. Liu, William Stafford
Noble, Jay Shendure and Christine M. Disteche.
"The
lncRNA Firre anchors the inactive X chromosome to the nucleolus by
binding CTCF and maintains H3K27me3 methylation." Genome
Biology. 16(1):52, 2015. |
|
| Ferhat Ay, Thanh H Vu, Michael J. Zeitz, Nelle Varoquaux,
Jan E. Carette, Jean-Philippe Vert, Andrew R. Hoffman and William
Stafford Noble.
"Identifying
multi-locus chromatin contacts in human cells using tethered multiple
3C." BMC Genomics. 16:121, 2015. | |
| Zafer Aydin, David Baker and William Stafford Noble.
"Constructing structural profiles for protein torsion angle
prediction." Proceedings of the International Conference on
Bioinformatics Models, Methods and Algorithms
(BIOINFORMATICS-2015). Lisbon, Portugal, pp. 26-35,
2015. |
|
| Uri Keich and William Stafford Noble.
"On
the importance of well calibrated scores for identifying shotgun
proteomics spectra." Journal of Proteome Research.
14(2):1147-1160, 2015.
(Correction) |
Supplementary data |
| Maxwell Libbrecht, Ferhat Ay, Michael Hoffman, David
M. Gilbert, Jeff Bilmes and William Stafford Noble.
"Joint annotation
of chromatin state and chromatin conformation reveals relationships
among domain types and identifies domains of cell type-specific
expression." Genome
Research. 25(2):544-557, 2015. |
Source code |
| Wenxiu Ma, Ferhat Ay, Cholie Lee, Gunhan Gulsoy, Xinxian
Deng, Savannah Cook, Jennifer Hesson, Christopher Cavanagh, Carol
B. Ware, Anton Krumm, Jay Shendure, C. Anthony Blau, Christine
Disteche, William Stafford Noble, Zhijun
Duan. "Fine-scale
chromatin interaction maps reveal the cis-regulatory landscape of
lincRNA genes in human cells." Nature
Methods. 12(1):71-78, 2015. |
Supplementary data |
| Jimmy K. Eng, Michael R. Hoopmann, T. A. Jahan, Jarrett
D. Egertson, William Stafford Noble, and Michael J. MacCoss.
"A
deeper look into Comet — implementation and
features." Journal of Proteome Research.
26(11):1865-1874, 2015. |
|
Michael Riffle, Gennifer E. Merrihew, D. Jaschob, Vagisha
Sharma, Trisah N. Davis, William Stafford
Noble, and Michael J. MacCoss. "Visualization and dissemination of
multidimensional proteomics data comparing protein abundance during
Caenorhabditis elegans development." Journal of the
American Society for Mass Spectrometry. 26(11):1827-1836,
2015. |
| 2014 |
|
Ferhat Ay, Evelien M. Bunnik, Nelle Varoquaux, Jean-Philippe Vert,
William Stafford Noble and Karine G. Le Roch.
"Multiple dimensions of epigenetic gene regulation in the malaria
parasite Plasmodium falciparum."
Bioessays. Early online, 2014. |
Supplement |
| Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas,
Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry
Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael
J. MacCoss and William Stafford
Noble. "Crux:
rapid open source protein tandem mass spectrometry
analysis." Journal of Proteome Research.
13(10):4488-4491, 2014. |
Supplementary
data |
| J. Jeffry Howbert and William Stafford Noble.
"Computing
exact p-values for a cross-correlation shotgun proteomics scoring
function."
Molecular and Cellular Proteomics. 13(9):2467-2479,
2014. | Supplementary data
Blog post |
| P Park, J Ho, Y Jung, T Liu, B Alver, S Lee, K Ikegami, K
Sohn, A Minoda, M Tolstorukov, A Appert, S Parker, T Gu, A Kundaje, N
Riddle, E Bishop, T Egelhofer, S Hu, A Alekseyenko, Y Schwartz, D
Asker, J Belsky, S Bowman, Q Chen, R Chen, D Day, Y Dong, X Duan, C
Epstein, S Ercan, E Feingold, F Ferrari, J Garrigues, N Gehlenborg, P
Good, P Haseley, D He, M Herrmann, M Hoffman, T Jeffers, P Kharchenko,
P Kolasinska-Zwierz, C Kotwaliwale, N Kumar, S Langley, E Larschan, I
Latorre, M Libbrecht, X Lin, R Park, M Pazin, H Pham, A Plachetka, B
Qin, N Shoresh, P Stempor, A Vielle, C Wang, C Whittle, H Xue, R
Kingston, JH Kim, B Bernstein, A Dernburg, V Pirrotta, M Kuroda, WS
Noble, T Tullius, M Kellis, D MacAlpine, S Strome, S Elgin, XS Liu, J
Lieb, J Ahringer, G Karpen, A Rechtsteiner and A
Dose. "Comparative
analysis of metazoan chromatin organization." Nature.
512:449-452, 2014. |
|
Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie
Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau and William
Stafford Noble. "Inferring clonal composition from multiple sections
of a breast cancer." PLOS Computational Biology.
10(7):e1003703,
2014. | Supplementary data
Clomial
Biomedical
Computation Review
|
|
John Halloran, Jeff Bilmes and William Stafford Noble.
"Learning
peptide-spectrum alignment models for tandem mass spectrometry."
Thirtieth Conference on Uncertainty in Artificial Intelligence (UAI
2014). Ed. Nevin Zhang and Jin Tian. AUAI Press, Corvallis,
OR. pp. 320-329, 2014 | Supplementary
data |
|
Nelle Varoquaux, Ferhat Ay, William Stafford Noble and Jean-Philippe
Vert. "A
statistical approach for inferring the 3D structure of the
genome." Bioinformatics (Proceedings of the ISMB).
30(12):i26-i33, 2014. |
PASTIS |
|
Wenxiu Ma, William Stafford Noble and Timothy
L. Bailey. "Motif-based
analysis of large nucleotide datasets using MEME-ChIP." Nature
Protocols. 9(6):1428-1450,
2014. | Supplementary
data |
|
Ferhat Ay, Evelien M. Bunnik, Nelle Varoquaux, Sebastian M. Bol,
Jacques Prudhomme, Jean-Philippe Vert, William Stafford Noble and
Karine G. Le Roch.
"Three-dimensional modeling of the P. falciparum
genome during the erythrocytic cycle reveals a strong connection
between genome architecture and gene expression."
Genome Research. 24(6):974-988, 2014. |
Supplementary data,
Press coverage
|
|
Ferhat Ay, Timothy L. Bailey and William Stafford Noble.
"Statistical
confidence estimation for Hi-C data reveals regulatory chromatin
contacts." Genome
Research. 24(6):999-1011, 2014.
| Fit-Hi-C software and supplementary
data |
| 2013 |
|
Michael J. Zeitz, Paula L. Lerner, Ferhat Ay, Eric Van Nostrand,
Juilia D. Heidmann, William Stafford Noble and Andrew
R. Hoffman. "Implications
of COMT long-range interactions on the phenotypic variability of
22q11.2 deletion syndrome." Nucleus. 4(6):487-493,
2013. |
|
Michael J. Zeitz, Ferhat Ay, Julia D. Heidmann, Paula L. Lerner,
William Stafford Noble, Brandon N. Steelman and Andrew R.
Hoffman. "Genomic
interaction profiles in breast cancer reveal altered chromatin
architecture." PLoS One. 8(9):e73974, 2013. |
|
Brittany S. Sexton, Denis Avey, Brooke R. Druliner, Justin A. Fincher,
Daniel L. Vera, Daniel J. Grau, Mark L. Borowsky, Shobhit Gupta,
Senthil Girimurugan, Eric Chicken, Jinfeng Zhang, William S. Noble,
Fanxiu Zhu, Robert E. Kingston, and Jonathan Hancock
Dennis. "The
spring-loaded genome: Nucleosome redistributions are widespread,
transient, and DNA-directed." Genome
Research. 24(2):251-259, 2013. |
|
Daniel A. Skelly, Gennifer E. Merrihew, Michael Riffle, Caitlin F.
Connelly, Emily O. Kerr, Marnie Johansson, Daniel Jaschob, Beth
Graczyk, Nicholas J. Shulman, Jon Wakefield, Sara J. Cooper, Stanley
Fields, William S. Noble, Eric G. D. Muller, Trisha N. Davis, Maitreya
J. Dunham, Michael J. MacCoss, and Joshua M
Akey. "Integrative
phenomics reveals insight into the structure of phenotypic diversity
in budding yeast." Genome Research. 23(9):1496-1504,
2013. |
|
Xianxin Deng, Joel B. Berletch, Wenxiu Ma, Di K. Nguyen, Joseph
B. Hiatt, William Stafford Noble, Jay Shendure and Christine
M. Disteche. "Mammalian
X upregulation is associated with enhanced transcription initiation,
RNA half-life, and MOF-mediated H4K16
acetylation." Developmental Cell. 25(1):55-68, 2013. |
|
Michael Hoffman, Jason Ernst, Steve P Wilder, Anshul Kundaje, Robert
S. Harris, Max Libbrecht, Belinda Giardine, Paul Ellenbogen, Jeff
A. Bilmes, Ewan Birney, Ross C. Hardison, Ian Dunham, Manolis Kellis
and William Stafford Noble.
"Integrative annotation
of chromatin elements from ENCODE data."
Nucleic Acids Research. 41(2):827-841, 2013. |
|
MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, S Talukder, A Vedenko,
DREAM5 consortium, QD Morris, ML Bulyk, G Stolovitzky and TR
Hughes. "An
evaluation of methods for the modeling of transcription factor
sequence specificity." Nature Biotechnology.
31(2):126-34, 2013. |
| 2012 |
|
Viktor Granholm, William Stafford Noble and Lukas Käll.
"Determining
the calibration of confidence estimation procedures for unique
peptides in shotgun proteomics." Journal of
Proteomics. 80:123-131, 2012. |
|
Zhi-jun Duan, Mirela Andronescu, Kevin Schutz, C Lee, Jay Shendure,
Stanley Fields, William Stafford Noble and C. Anthony
Blau. "A
genome-wide 3C-method for characterizing the three-dimensional
architectures of genomes." Methods. 58(3):277-288,
2012. |
|
Viktor Granholm, William Stafford Noble and Lukas
Käll. "A
cross-validation scheme for machine learning algorithms in shotgun
proteomics." BMC Bioinformatics. 13(Suppl 16):S3,
2012. |
|
Sean McIlwain, Michael Mathews, Michael Bereman, Edwin W. Rubel,
Michael J. MacCoss and William Stafford
Noble. "Estimating
relative abundances of proteins from shotgun proteomics
data." BMC Bioinformatics. 13:308,
2012. | Supplement |
|
Sara C. Di Rienzi, Kim C. Lindstrom, Tobias Mann, William Stafford
Noble, MK Raghuraman and Bonita
J. Brewer. "Maintaining
replication origins in the face of genomic change." Genome
Research. 22(10):1940-1952, 2012. |
|
Ajit P. Singh, John Halloran, Jeff Bilmes and William Stafford
Noble. "Spectrum
identification using a dynamic Bayesian network model of tandem mass
spectra." Uncertainty in Artificial Intelligence: Proceedings
of the Twenty-Eighth Conference. Aug. 15-17, 2012. pp.
775-784. |
|
Soyoung Ryu, David R. Goodlett, William Stafford Noble and Vladimir
N. Minin. "A
statistical approach to peptide identification from clustered tandem
mass spectrometry data." Proceedings of the International
Workshop on Computational Proteomics, IEEE BIBM. |
|
Zafer Aydin, James Thompson, Jeff Bilmes, David Baker and William
Stafford Noble. "Protein
torsion angle class prediction by a hybrid architecture of Bayesian
and neural networks." Proceedings of the 13th International
Conference on Bioinformatics and Computational Biology.
pp. 2012-2018. |
|
Mariana Fioramonte, Aline Mara dos Santos, Sean McIlwain, William
Stafford Noble, Kleber Gomes Franchini and Fabio Cesar Gozzo.
"Analysis
of secondary structure in proteins by chemical cross-linking coupled
to mass spectrometry." Proteomics. 12(17):2746-52,
2012. |
|
Marina Spivak, Michael S. Berriman, Michael J. MacCoss and William
Stafford
Noble. "Learning
score function parameters for improved spectrum identification in
tandem mass spectrometry experiments." Journal of Proteome
Research. 11(9):4499-508, 2012. |
|
The ENCODE Project
Consortium. "An
integrated encylopedia of DNA elements in the human
genome." Nature. 489(7414):57-74, 2012. |
|
Jie Wang, Jiali Zhuang, Sowmya Iyer, XinYing Lin, Troy W. Whitfield,
Melissa Greven, Xianjun Dong, Anshul Kundaje, Yong Cheng, Ewan Birney,
Richard M. Myers, William S. Noble, Michael Snyder and Zhiping Weng.
"Sequence
features and chromatin structure around the genomic regions bound by
119 human transcription factors." Genome Research.
22(9):1798-812, 2012. |
|
Aaron Arvey, Phaedra Agius, William Stafford Noble and Christina
Leslie. "Sequence and
chromatin determinants of cell-type specific transcription factor
binding." Genome Research. 22(9):1723-34, 2012. |
|
Oliver Serang and William Stafford
Noble. "Faster
mass spectrometry-based protein inference: junction trees are more
efficient than sampling and marginalization by
enumeration." IEEE Transactions on Computational Biology and
Bioinformatics. 9(3):809-817,
2012. | Fido |
|
Daniela M. Witten and William Stafford
Noble. "On the assessment
of statistical significance of three-dimensional colocalization of
sets of genomic elements." Nucleic Acids
Research. 40(9):3849-3855, 2012. |
Code |
|
Benjamin J. Diament, Michael J. MacCoss, William Stafford Noble.
"On the feasibility and
utility of exploiting real time database search to improve adaptive
peak selection." arXiv:1207.5848v1. |
|
Yanjun Qi, Merja Oja, Jason Weston and William Stafford
Noble. "A unified multitask
architecture for predicting local protein properties." PLoS
One. 7(3):e32235, 2012. | Supplementary data |
|
Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Jeff A. Bilmes and
William Stafford
Noble. "Unsupervised
pattern discovery in human chromatin structure through genomic
segmentation." Nature Methods. 9(5):473-476, 2012. |
The Scientist |
|
Marina Spivak, Jason Weston, Michael J. MacCoss and William Stafford
Noble. "Direct
maximization of protein identifications from tandem mass
spectra." Molecular and Cellular Proteomics.
11(2):M111.012161, 2012. | Supplement |
|
William Stafford Noble, C. Anthony Blau, Job Dekker, Zhi-jun Duan and
Yi Mao. "The structure and
function of chromatin and chromosomes." Proceedings of the
Pacific Symposium on Biocomputing. 17:434-440, 2012. |
|
William Stafford Noble and Michael
J. MacCoss. "Computational
and statistical analysis of protein mass spectrometry
data." PLoS Computational Biology. 8(1):e1002296,
2012. |
|
Oliver Serang and William Stafford
Noble. "A review of
statistical methods for protein identification using tandem mass
spectrometry." Statistics and its Interface. 5:3-20,
2012. |
|
Gabriel Cuellar-Partida, Fabian A. Buske, R C. McLeay, Tom Whitington,
William Stafford Noble and Timothy
L. Bailey. "Epigenetic
priors for identifying active transcription factor binding sites."
Bioinformatics. 28:56-62, 2012. | Supplementary
data |
| 2011 |
|
Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine Le Roch and
William Stafford
Noble. "Exploratory
analysis of genomic segmentations with Segtools." BMC
Bioinformatics. 12:415, 2011. |
|
Benjamin J. Diament and William Stafford
Noble. "Faster SEQUEST
searching for peptide identification from tandem mass
spectra." Journal of Proteome Research.
10(9):3871-9, 2011. |
|
Yanjun Qi and William Stafford Noble. "Protein interaction networks:
protein domain interaction and protein function prediction." In
Handbook of Statistical Bioinformatics. Ed. by HH Lu, B
Schoelkopf and H. Zhao. Springer Verlag, 2011. |
|
Emily Tanaka, Timothy L. Bailey, Charles E. Grant, William Stafford
Noble and Uri
Keich. "Improved similarity
scores for comparing
motifs." Bioinformatics. 27(12):1603-1609, 2011. |
|
Viktor Granholm, William Stafford Noble and Lukas
Käll. "On using samples
of known protein content to assess the statistical calibration of
scores assigned to peptide-spectrum matches in shotgun
proteomics." Journal of Proteome Research. 10(5):2671-2678,
2011. |
|
The ENCODE Project
Consortium. "A user's guide to
the Encylopedia of DNA Elements (ENCODE)." PLoS Biology.
9(4):e1001046, 2011. |
|
Zafer Aydin, Ajit Singh, Jeff Bilmes and William Stafford Noble.
"Learning sparse models for a
dynamic Bayesian network classifier of protein secondary
structure." BMC Bioinformatics. 12:154, 2011. |
|
Charles E. Grant, Timothy L. Bailey and William Stafford Noble.
"FIMO: Scanning for occurrences of
a given motif." Bioinformatics. 27(7):1017-1018,
2011. |
|
Iain Melvin, Jason Weston, William Stafford Noble and Christina
Leslie. "Detecting remote
evolutionary relationships among proteins by large-scale semantic
embedding." PLoS Computational Biology. 7(1):e1001047,
2011 | Supplement |
|
William Stafford Noble and Christina Leslie. "Learning models of
biological sequences." In Encyclopedia of Machine Learning.
Ed. by C Sammut and GI Webb. Springer Verlag, 2011. |
|
Emmet Hirsch, Courtney Lim, Debra Dobrez, MG Adams and William
Stafford
Noble. "Meteorological
factors and the timing of the initiating event of
parturition." International Journal of Biometeorology.
55(2):265, 2011. |
| 2010 |
|
Vagisha Sharma, Jimmy K. Eng, Sergey Feldman, Priska von Haller,
Michael J. MacCoss and William Stafford
Noble. "Precursor charge
state prediction for electron transfer dissociation tandem mass
spectra." Journal of Proteome Research. 9(10):5438-5444,
2010. |
|
Oliver Serang, Michael J. MacCoss and William Stafford Noble.
"Efficient marginalization
to compute protein posterior probabilities from shotgun mass
spectrometry data." Journal of Proteome
Research. 9(10):5346-5357, 2010. |
|
Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble and
Christina Leslie. "High
resolution models of transcription factor-DNA affinities improve in
vitro and in vivo binding predictions." PLoS Computational
Biology. 6(9):e10000916, 2010. |
|
Sheila Moore Reynolds, Jeffrey A. Bilmes and William Stafford Noble.
"Learning a weighted
sequence model of the nucleosome core and linker yields more accurate
predictions in Saccharomyces cerevisiae and Homo
sapiens". PLoS Computational Biology. 6(7):e10000834,
2010. |
|
Sheila Reynolds, Zhiping Weng, Jeffrey Bilmes and William Stafford
Noble. "Predicting
nucleosome positioning using multiple evidence
tracks." Proceedings of the International Conference on
Research in Computational Biology (RECOMB). Lecture Notes in
Computer Science, 2010, Volume 6044/2010, pp. 441-455. |
|
Zhijun Duan, Mirela Andronescu, Kevin Schutz, Sean McIlwain, Yoo Jung
Kim, Choli Lee, Jay Shendure, Stanley Fields, C. Anthony Blau and
William S. Noble. "A
three-dimensional model of the yeast genome". Nature.
465:363-367, 2010. |
Supplementary
materials
"Genome
Blossoms" in The Scientist |
|
Xiaoyu Chen, Michael Hoffman, Jeffrey A. Bilmes, Jay R. Hesselberth
and William Stafford Noble. "A
dynamic Bayesian network for identifying protein binding footprints
from single molecule based sequencing data." Bioinformatics
(Proceedings of the ISMB). 26(12):i334-i342, 2010. |
|
Michael M. Hoffman, Orion J. Buske and William Stafford Noble.
"The Genomedata format for
storing large-scale functional genomics data."
Bioinformatics. 26(11):1458-1459, 2010. |
|
Sean McIlwain, Paul Draghicescu, Pragya Singh, Dave R. Goodlett and
William Stafford
Noble. "Detecting
cross-linked peptides by searching against a database of cross-linked
peptide pairs." Journal of Proteome Research.
9(5):2488-2495, 2010. |
Supplement |
|
Nir Yosef, Jens Gramm, Qian-fei Wang, William Stafford Noble, Richard
M. Karp and Roded
Sharan. "Prediction of
phenotype information from genotype data." Communications in
Information and Systems. 10(2):99-114, 2010. |
|
Martial Hue, Michael Riffle, Jean-Philippe Vert and William Stafford
Noble. "Large-scale
prediction of protein-protein interactions from
structures." BMC Bioinformatics. 11:144, 2010. |
|
Zafer Aydin, John I. Murray, Robert H. Waterston and William Stafford
Noble. "Using machine learning
to speed up manual image annotation: application to a 3D imaging
protocol for measuring single cell gene expression in the
developing C. elegans embryo." BMC Bioinformatics.
11(1):84, 2010. |
| 2009 |
William Stafford Noble. "How does
multiple testing correction work?" Nature Biotechnology.
27(12):1135-1137,
2009.
 | |
|
William Stafford Noble. "A quick
guide to organizing computational biology experiments." PLoS
Computational Biology. 5(7):e1000424, 2009.
|
Software
Carpentry slides on Data Management by Orion Buske, based in
part on ideas from this article. |
|
Tobias Mann, Rich Humbert, Michael Dorschner, John
A. Stamatoyannopoulos and William Stafford
Noble. "A thermodynamic
approach to PCR primer design."
Nucleic Acids Research. 25(12):i339-347,
2009. | Pythia |
|
John Hawkins, Charles E. Grant, William Stafford Noble and Timothy
L. Bailey. "Assessing
phylogenetic motif models for predicting transcription factor binding
sites." Bioinformatics (Proceedings of the ISMB).
25(12):i339-347, 2009. |
|
Timothy L. Bailey, Michael Boden, Fabian A. Buske, Martin Frith,
Charles E. Grant, Luca Clementi, Jane Ren, Wilfred W. Li and William
Stafford Noble. "MEME Suite:
tools for motif discovery and searching." Nucleic Acids
Research. 37(Web server issue):W202-208, 2009. |
MEME |
|
Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William
Stafford Noble. "Improvements to
the Percolator algorithm for peptide identification from shotgun
proteomics data sets." Journal of Proteome Research.
8(7):3737-3745, 2009. |
|
Sheila Reynolds, Jeffrey A. Bilmes and William Stafford
Noble. "On the
relationship between DNA periodicity and local chromatin
structure." Proceedings of the International Conference on
Research in Computational Biology (RECOMB). May 18-21, 2009.
pp. 434-450. |
|
Aaron A. Klammer, Christopher Y. Park and William Stafford Noble.
"Statistical calibration
of the SEQUEST XCorr function." Journal of Proteome
Research. 8(4):2106-2113, 2009. |
|
Jay Hesselberth, Xiaoyu Chen, Zhihong Zhang, Pete J. Sabo, Richard
Sandstrom, Alex P. Reynolds, Robert E. Thurman, Shane Neph, Michael
S. Kuehn, William Stafford Noble, Stanley Fields and John
A. Stamatoyannopoulos. "Global
mapping of protein-DNA interactions in vivo by digital genomic
footprinting." Nature Methods. 6(4):283-289, 2009. |
Supplementary data |
|
Lukas Käll, John D. Storey and William Stafford
Noble. "QVALITY: Nonparametric
estimation of q values and posterior error
probabilities." Bioinformatics. 25(7):964-966, 2009. |
Qvality
software and web server |
|
Iian Melvin, Jason Weston, Christina Leslie and William Stafford
Noble. "Rankprop: a web
server for protein remote homology
detection." Bioinformatics. 25(1):121-122, 2009. |
Web server |
| 2008 |
|
Sheila M. Reynolds, Lukas Käll, Jeff A. Bilmes and William Stafford Noble.
"Transmembrane
topology and signal peptide prediction using dynamic Bayesian
networks." PLoS Computational Biology. 4(11):e1000213, 2008. |
|
Gennifer E. Merrihew, Colleen Davis, Brent Ewing, Gary Williams, Lukas
Käll, Barbara E. Frewen, William Stafford Noble, Phil Green,
James H. Thomas, Michael J. MacCoss.
"Use of shotgun
proteomics for the identification, confirmation and correction
of C. elegans gene annotations." Genome
Research. 18(10):1660-1669, 2008. |
|
Iain Melvin, Jason Weston, Christina Leslie and William Stafford
Noble. Combining
classifiers for improved classification of proteins from
sequence or structure BMC Bioinformatics. 9:389,
2008. |
Supplement |
|
Heng Lian, William Thompson, Robert E. Thurman, John
A. Stamatoyannpoulos, William Stafford Noble and Charles Lawrence. "Automated mapping of large-scale
chromatin structure in ENCODE."
Bioinformatics. 24(17):1911-1916, 2008. |
Supplementary data
Source code |
| Shobhit Gupta, Jonathan Dennis, Robert E. Thurman, Robert
Kingston, John A. Stamatoyannopoulos and William Stafford
Noble. "Predicting
human nucleosome occupancy from primary sequence." PLoS
Computational Biology. 4(8):e10000134, 2008. |
Supplement |
|
Nir Yosef, Roded Sharan and William Stafford
Noble. "Improved
network-based identification of protein
orthologs." Bioinformatics (Proceedings of the ECCB).
24(16):i200-i206, 2008. |
|
Lukas Käll, John Storey and William Stafford
Noble. "Non-parametric
estimation of posterior error probabilities associated with peptides
identified by tandem mass spectrometry." Bioinformatics
(Proceedings of the ECCB). 24(16):i42-i48, 2008. |
Qvality software,
web server and supplement |
|
Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael J. MacCoss and
William Stafford Noble. "Rapid
and accurate peptide identification from tandem mass spectra."
Journal of Proteome Research. 7(7):3022-3027, 2008. |
Crux |
|
Aaron A. Klammer, Sheila M. Reynolds, Jeff A. Bilmes, Michael
J. MacCoss and William Stafford Noble. "Modeling peptide fragmentation
with dynamic Bayesian networks for peptide identification."
Bioinformatics (Proceedings of the ISMB). 24(13):i345-i356,
2008. |
|
L Pena-Castillo, M Tasan, CL Myers, H Lee, T Joshi, C Zhang, Y Guan, M
Leone, A Pagnani, WK Kim, C Krumpelman, W Tian, G Obozinski, Y Qi, S
Mostafavi, GN Lin, G Berriz, F Gibbons, G Lanckriet, J Qiu, C Grant, Z
Barutcuoglu, DP Hill, D Warde-Farely, C Grouios, D Ray, JA Blake, M
Deng, M Jordan, WS Noble, Q Morris, J Klein-Seetharaman, Z Bar-Joseph,
T Chen, F Sun, OG Troyanskaya, EM Marcotte, D Xu, TR Hughes and FP
Roth. "A critical
assessment of M. musculus gene function prediction using
integrated genomic evidence." Genome Biology. 9(Suppl
1):S2, 2008. |
|
Guillaume Obozinski, Gert Lanckriet, Charles E. Grant, Michael
I. Jordan and William Stafford Noble. "Consistent probabilistic
outputs for protein function prediction." Genome Biology.
9(Suppl 1):S6, 2008. |
|
Jian Qiu and William Stafford Noble. "Predicting co-complexed protein
pairs from heterogeneous data." PLoS Computational
Biology. 4(4):e1000054, 2008. |
|
Robert E. Thurman, William Stafford Noble and John
A. Stamatoyannopoulos. "Multi-scale correlations in
continuous genomic data." Proceedings of the Pacific Symposium
on Biocomputing. January 4-8, 2008. pp. 201-215. |
|
Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford
Noble. "Assigning significance
to peptides identified by tandem mass spectrometry using decoy
databases." Journal of Proteome Research. 7(1):29-34,
2008 |
|
Lukas Käll, John D. Storey, Michael J. MacCoss and William Stafford
Noble. "Posterior error
probabilities and false discovery rates: two sides of the same
coin." Journal of Proteome Research. 7(1):40-44, 2008. |
| 2007 |
|
Jean-Philippe Vert, Jian Qiu and William Stafford Noble. "A new pairwise kernel for biological
network inference with support vector machines." BMC
Bioinformatics. 8(Suppl. 10):S8, 2007. |
|
Jian Qiu, Will Sheffler, David Baker and William Stafford Noble. "Ranking predicted protein
structures with support vector regression." Proteins:
Structure, Function, and Bioinformatics. 71(3):1175-1182,
2007. |
|
Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and
Michael J. MacCoss. "Semi-supervised
learning for peptide identification from shotgun proteomics datasets."
Nature Methods. 4(11):923-925,
2007. | Supplement Percolator |
|
Jason Weston, Gokhan Bakir, Olivier Bousquet, Tobias Mann, William
Stafford Noble and Bernhard Scholkopf. "Joint kernel maps." In
Predicting Structured Data. Ed. by Gokhan Bakir, Thomas
Hofmann, Bernhard Scholkopf, Alex J. Smola, Ben Taskar and
V. S. N. Vishwanathan. MIT Press, 2007. |
|
Aaron A. Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford
Noble. "Improving tandem
mass spectrum identification using peptide retention time prediction
across diverse chromatography conditions."
Analytical Chemistry. 79(16):6111-6118, 2007. |
|
Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford
Noble and Christina Leslie. "SVM-fold: a tool for
discriminative multi-class protein fold and superfamily
recognition." BMC Bioinformatics. 8(Suppl 4):S2,
2007. |
|
Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble and
Christina Leslie. "Multi-class protein
classification using adaptive codes." Journal of Machine
Learning Research. 8(Jul):1557-1581, 2007 |
| Heather E. Peckham, Robert E. Thurman, Yutao Fu, John
A. Stamatoyannopoulos, William Stafford Noble, Kevin Struhl and
Zhiping
Weng. "Nucleosome
positioning signals in genomic DNA."
Genome Research. 17(8):1170-1177,
2007. | Supplement |
|
Saurabh Asthana, William Stafford Noble, Grigory Kryukov, Charles
E. Grant, Shamil Sunyaev and John A. Stamatoyannopoulos. "Widely distributed non-coding
selection in the human genome." Proceedings of the National
Academy of Science. 104(30):12410-12415, 2007. |
|
The ENCODE Project Consortium. "Identification and
analysis of functional elements in 1% of the human genome by the
ENCODE project." Nature. 447:779-816, 2007. |
|
Robert E. Thurman, Nathan Day, William Stafford Noble and John
A. Stamatoyannopoulos. "Identification of
higher-order functional domains in the human ENCODE regions."
Genome Research. 17(6):917-927, 2007. |
|
Nathan Day, Andrew Hemmaplardh, Robert E. Thurman, John
A. Stamatoyannopoulos and William Stafford Noble. "Unsupervised segmentation of
continuous genomic data."
Bioinformatics. 23(11):1424-1426, 2007 |
|
Jonathan H. Dennis, Hua-Ying Fan, Sheila R. Reynolds, Guocheng Yuan,
Jim Meldrim, Daniel J. Richter, Daniel G. Peterson, Oliver J. Rando,
William Stafford Noble and Robert E. Kingston. "Independent and
complementary methods for large-scale structural analysis of
mammalian chromatin." Genome Research. 17(6):928-939,
2007. |
Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert and William
Stafford Noble. "A structural
alignment kernel for protein structures." Bioinformatics.
23(9):1090-1098, 2007.
|
Aaron Klammer, Xianhua Yi, Michael J. MacCoss and William Stafford
Noble. "Peptide retention
time prediction yields improved tandem mass spectrum identification
for diverse chromatography conditions."
Proceedings of the International Conference on Research in
Computational Biology (RECOMB). April 21-25, 2007.
pp. 459-472. |
ChargeCzar |
|
Shobhit Gupta, John A. Stamatoyannopoulos, Timothy L. Bailey and
William Stafford
Noble. "Quantifying
similarity between motifs."
Genome Biology. 8:R24, 2007. | Supplement |
|
William Stafford Noble and Asa Ben-Hur. "Integrating information for
protein function prediction." In Bioinformatics - From Genomes
to Therapies. T. Lenguaer, ed. Vol. 3. pp. 1297-1314. |
| 2006 |
|
William Stafford Noble. "What is a
support vector machine?" Nature Biotechnology.
24(12):1565-1567,
2006. | Extended version |
|
Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Support vector machine learning from
heterogeneous data: an empirical analysis using protein sequence and
structure." Bioinformatics. 22(22):2753-2760, 2006. |
Supplement |
|
Barbara E. Frewen, Gennifer E. Merrihew, William Stafford Noble and
Michael J. MacCoss. "Analysis
of peptide MS/MS spectra from large-scale proteomics experiments using
spectrum libraries." Analytical Chemistry.
78(16):5678-5684, 2006. |
|
Tata Pramila, Wei Wu, William Stafford Noble and Linda L. Breeden. "The Forkhead transcription factor
Hcm1 regulates chromosome segregation genes and fills the S phase gap
in the transcriptional circuitry of the cell cycle." Genes and
Development. 20(16):2266-2278, 2006. |
|
Jean-Philippe Vert, Robert Thurman and William Stafford Noble. "Kernels for gene regulatory
regions." Advances in Neural Information Processing Systems
18, 2006. |
|
Tobias Mann and William Stafford Noble. "Efficient identification of DNA
binding partners in a sequence database." Bioinformatics
(Proceedings of the Intelligent Systems for Molecular Biology
Conference). 22:e350-e358, 2006. |
|
Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William
Stafford Noble. "Automated
validation of polymerase chain reactions using amplicon melting
curves." Journal of Bioinformatics and Computational
Biology. 22(14):350-358, 2006. |
|
PJ Sabo, MS Kuehn, R Thurman, B Johnson, EM Johnson, H Cao, M Yu, J
Goldy, E Rosenzweigh, J Goldy, A Haydock, M Weaver, A Shafer, K Lee, F
Neri, R Humbert, MA Singer, TA Richmond, MO Dorschner, M McArthur, M
Hawrylycz, RD Green, PA Navas, WS Noble and JA
Stamatoyannopoulos. "Genome-scale
mapping of DNase I sensitivity in vivo using tiling DNA
microarrays."
Nature Methods. 3(7):511-518, 2006. |
|
Darrin P. Lewis, Tony Jebara and William Stafford Noble. "Nonstationary kernel
combination." Proceedings of the International Conference on
Machine Learning, June 25-29, 2006, Pittsburgh, PA. |
|
Asa Ben-Hur and William Stafford Noble. "Choosing negative examples for
the prediction of protein-protein interactions." BMC
Bioinformatics. 7(Suppl 1):S2, 2006. |
|
Jason Weston, Rui Kuang, Christina Leslie, William Stafford Noble. "Protein ranking by semi-supervised
network propagation." BMC Bioinformatics. 7(Suppl 1):S10,
2006. |
| 2005 |
|
Jason Weston, Christina Leslie, Eugene Ie and William Stafford
Noble. "Semi-supervised protein classification using cluster kernels."
Semi-supervised Learning. O Chapelle, B Schoelkopf and A Zien,
ed. MIT Press, 2005. pp. 321-338. |
Supplement |
|
William Stafford Noble, Rui Kuang, Christina Leslie and Jason Weston.
"Identifying remote protein
homologs by network propagation."
FEBS Journal. 272(20):5119-5128, 2005. |
|
Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie.
"Motif-based protein ranking by
network propagation." Bioinformatics. 21(19):3711-3718,
2005. |
|
Eugene Ie, Jason Weston, William Stafford Noble and Christina Leslie.
"Adaptive codes for multi-class
protein classification."
Proceedings of the International Conference on Machine
Learning, August 7-11, 2005, Bonn, Germany. |
|
Aaron Klammer, Christine C. Wu, Michael J. MacCoss, William Stafford
Noble. "Peptide charge state
determination for low-resolution tandem mass spectra."
Proceedings of the Computational Systems Bioinformatics
Conference, August 8-11, 2005, Stanford, CA. pp. 175-185. |
|
Tobias Mann, Richard Humbert, John Stamatoyannopoulos and William
Stafford Noble. "Automated
validation of polymerase chain reactions using amplicon melting
curves." Proceedings of the Computational Systems
Bioinformatics Conference, August 8-11, 2005, Stanford,
CA. pp. 377-385. |
|
Will Sheffler, Eli Upfal, John Sedivy and William Stafford
Noble. "A learned comparative
expression measure for Affymetrix GeneChip DNA
microarrays." Proceedings of the Computational Systems
Bioinformatics Conference, August 8-11, 2005, Stanford,
CA. pp. 144-154. |
|
John P. Miller, Russel S. Lo, Asa Ben-Hur, Cynthia Desmarais, Igor
Stagljar, William Stafford Noble and Stanley Fields. "Large-scale identification of yeast
integral membrane protein interactions." Proceedings of the
National Academy of Science. 102(34):12123-12128, 2005. |
|
Jason Weston, Christina Leslie, Eugene Ie, Dengyong Zhou, Andre
Eliseeff and William Stafford Noble. "Semi-supervised protein classification
using cluster kernels." Bioinformatics. 21(15):3241-3247,
2005. |
Supplement |
|
Asa Ben-Hur and William Stafford Noble. "Kernel methods for predicting
protein-protein interactions."
Bioinformatics (Proceedings of the Intelligent Systems for
Molecular Biology Conference). 21(Suppl 1):i38-i46, 2005. |
|
William Stafford Noble, Scott Kuehn, Robert Thurman, Richard Humbert,
James C. Wallace, Man Yu, Michael Hawrylycz and John
Stamatoyannopoulos. "Predicting the in vivo
signature of human gene regulatory sequences." Bioinformatics
(Proceedings of the Intelligent Systems for Molecular Biology
Conference). 21(Suppl 1):i338-i343, 2005. |
Supplement |
|
M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov,
MC Frith, Y Fu, WJ Kent, VJ Makeev, AA Mironov, WS Noble, G Pavesi, G
Pesole, M Regnier, N Simonis, S Sinha, G Thijs, J van Helden, M
Vandenbogaert, Z Weng, C Workman, C Ye and Z Zhu. "Assessing
computational tools for the discovery of transcription factor binding
sites." Nature Biotechnology. 23(1):137-144, 2005. |
| 2004 |
|
E Feingold, PJ Good, ..., WS Noble, ..., FS Collins.
"The
ENCODE (Encyclopedia of DNA Elements) Project."
Science. 306:636-640, 2004. |
|
Lanckriet, Gert R. G., Tijl De Bie, Nello Cristianini, Michael
I. Jordan and William Stafford Noble. "A statistical framework for
genomic data fusion." Bioinformatics. 20(16):2626-2635,
2004. |
|
Noble, William Stafford. "Data
hoarding is harming proteomics."
Nature Biotechnology. 22(10):1209. |
|
Noble, William Stafford. "Support
vector machine applications in computational biology." Kernel
Methods in Computational Biology. B. Schoelkopf, K. Tsuda and
J.-P. Vert, ed. MIT Press, 2004. pp. 71-92. |
|
Weston, Jason, Christina Leslie, Denyong Zhou and William Stafford
Noble. "Semi-supervised protein
classification using cluster kernels." Advances in Neural
Information Processing Systems 16, 2004. pp. 595-602. |
|
Tsuda, Koji and William Stafford Noble. "Learning kernels from biological
networks by maximizing entropy." Bioinformatics (Proceedings of
the ISMB/ECCB). 20(Suppl. 1):i326-i333, 2004. |
|
Lu, Henry, Weiqun Li, William Stafford Noble, Donald Payan and D. C.
Anderson. "Riboproteomics of
the hepatitis C virus internal ribosomal entry site." Journal of
Proteome Research Web Release Date: 17-Jul-2004; (Article) DOI:
10.1021/pr0499592 |
|
Wu, Wei and William Stafford Noble. "Genomic data visualization on the
web." Bioinformatics. 20(11):1804-1805, 2004. |
|
Weston, Jason, Andre Eliseeff, Dengyong Zhou, Christina Leslie and
William Stafford Noble. "Protein
ranking: from local to global structure in the protein similarity
network." Proceedings of the National Academy of Science.
101(17):6559-6563, 2004. |
Supplement |
|
Leslie, Christina, Eleazar Eskin, Adiel Cohen, Jason Weston and
William Stafford Noble. "Mismatch string kernels for
discriminative protein classification." Bioinformatics.
20(4):467-476, 2004. |
String
kernel software |
|
Pavlidis, Paul, Ilan Wapinski and WS Noble. "Support vector machine
classification on the web." Bioinformatics. 20(4):586-587,
2004. |
|
Lanckriet, Gert R. G., Minghua Deng, Nello Cristianini, Michael
I. Jordan and William Stafford Noble. "Kernel-based data fusion and its
application to protein function prediction in yeast."
Proceedings of the Pacific Symposium on Biocomputing, January
3-8, 2004. pp. 300-311. |
| 2003 |
|
Liao, Li and William Stafford Noble. "Combining pairwise sequence
similarity and support vector machines for detecting remote protein
evolutionary and structural relationships." Journal of
Computational Biology. 10(6):857-868, 2003. |
|
Qin, Jie, Darrin Lewis and William Stafford Noble. "Kernel hierarchical clustering of
microarray gene expression data."
Bioinformatics. 19(16):2097-2104, 2003. |
|
Eskin, Eleazar, William Stafford Noble and Yoram Singer. "Protein family classification using
sparse Markov transducers." Journal of Computational
Biology. 10(2):187-213, 2003. |
|
Gomez, Shawn M., William Stafford Noble and Andrey Rzhetsky. "Learning to predict protein-protein
interactions from protein sequences." Bioinformatics
(Proceedings of the Georgia Tech International Conference on
Bioinformatics). 19:1875-1881, 2003. |
|
Leslie, Christina, Eleazar Eskin, Jason Weston and William Stafford
Noble. "Mismatch string kernels
for SVM protein classification." Neural Information Processing
Systems 15, 2003. pp. 1441-1448. |
String
kernel oftware |
|
Bailey, Timothy and William Stafford Noble. "Searching for statistically
significant regulatory modules" Bioinformatics (Proceedings of
the European Conference on Computational Biology).
19(Suppl. 2):ii16-ii25, 2003. |
|
Pavlidis, Paul, Qinghong Li and William Stafford Noble. "The effect of replication on gene
expression microarray experiments." Bioinformatics.
19(13):1620-1627, 2003. |
|
Gururaja, Tarikere, Weiqun Li, William Stafford Noble, Donald G. Payan
and D. C. Anderson. "Multiple
functional categories of proteins identified in an
in vitro cellular ubiquitin affinity extract using shotgun
peptide sequencing." Journal of Proteome Research.
2:394-404, 2003. |
|
Segal, Neil H., Paul Pavlidis, Cristina R. Antonescu, Robert G. Maki,
William Stafford Noble, James M. Woodruff, Jonathan J. Lewis, Murray
F. Brennan, Alan N. Houghton and Carlos Cordon-Cardo. "Classification and subtype
prediction of soft tissue sarcoma by functional genomics and support
vector machine analysis." American Journal of Pathology.
169:691-700, 2003. |
|
Neil H. Segal, Paul Pavlidis, William Stafford Noble, Cristina
R. Antonescu, Agnes Viale, Umadevi V. Wesley, Klaus Busam, Humilidad
Gallardo, Dianne DeSantis, Murray F. Brennan, Carlos Cordon-Cardo,
Jedd D. Wolchok and Alan N. Houghton. "Classification of clear cell
sarcoma as melanoma of soft parts by genomic profiling."
Journal of Clinical Oncology. 21:1775-1781, 2003. |
|
Pavlidis, Paul and William Stafford Noble. "Matrix2png: A utility for visualizing
matrix data." Bioinformatics. 19(2):295-296, 2003. |
|
Anderson, David C., Weiqun Li, Donald G. Payan and William Stafford
Noble. "A new algorithm for the
evaluation of shotgun peptide sequencing in proteomics: support vector
machine classification of peptide MS/MS spectra and SEQUEST
scores." Journal of Proteome Research. 2(2):137-146, 2003. |
| 2002 |
|
Eleazar Eskin, William Stafford Noble and Yoram
Singer. "Using substitution
matrices to estimate probability distributions for biological
sequences." Journal of Computational Biology. 9(6):775-91,
2002. |
|
Bernhard Schoelkopf, Jason Weston, Eleazar Eskin, Christina Leslie
and William Stafford Noble.
"A kernel
approach for learning from almost orthogonal patterns."
Proceedings of the 13th European Conference on Machine
Learning, August 19-23, 2002. pp. 511-528. |
|
Bernhard Scholkopf, Jason Weston, Eleazar Eskin, Christina Leslie and
William Stafford Noble.
"Dealing
with large diagonals in kernel matrices."
Annals of the Institute on Statistical Mathematics,
55(2):391-408, 2003.
|
|
Liao, Li and William Stafford Noble. "Combining pairwise sequence similarity and
support vector machines for remote protein homology detection".
Proceedings of the Sixth Annual International Conference on
Research in Computational Molecular Biology, April 18-21, 2002.
pp. 225-232. |
|
Pavlidis, Paul, Jason Weston, Jinsong Cai and William Stafford Noble.
"Learning gene functional
classifications from multiple data types." Journal of
Computational Biology. 9(2):401-411, 2002. |
|
Pavlidis, Paul, Darrin P. Lewis and William Stafford Noble. "Exploring gene expression data with class
scores." Proceedings of the Pacific Symposium on
Biocomputing, January 2-7, 2002. pp. 474-485. |
|
Leslie, Christina, Eleazar Eskin and William Stafford Noble. "The spectrum kernel: A string kernel for
SVM protein classification." Proceedings of the Pacific
Symposium on Biocomputing, January 2-7, 2002. pp. 564-575. |
String
kernel software |
| 2001 |
|
Pavlidis, Paul and William Stafford Noble. "Analysis of strain and regional
variation in gene expression in mouse brain." Genome
Biology. 2(10): research0042.1-0042.15, 2001. |
|
Pavlidis, Paul, Christopher Tang and William Stafford Noble. "Classification of genes using probabilistic
models of microarray expression profiles." Proceedings of
BIOKDD 2001: Workshop on Data Mining in Bioinformatics. |
|
Muhle, Rebecca A., Paul Pavlidis, William Noble Grundy and Emmet
Hirsch. "A high
throughput study of gene expression in preterm labor using a
subtractive microarray approach." American Journal of
Obstetrics and Gynecology, 185(3):716-24, 2001. |
|
Eskin, Eleazar, William Noble Grundy and Yoram Singer. "Using mixtures of common ancestors for
estimating the probabilities of discrete events in biological
sequences." Proceedings of the Ninth International Conference
on Intelligent Systems for Molecular Biology. July 21-25, 2001.
pp. 65-73. |
|
Pavlidis, Paul, Jason Weston, Jinsong Cai and William Noble Grundy.
"Gene functional classification from
heterogeneous data" Proceedings of the Fifth International
Conference on Computational Molecular Biology, April 21-24, 2001.
pp. 242-248. |
Supplement |
|
Pavlidis, Paul, Terrence S. Furey, Muriel Liberto, David Haussler and
William Noble Grundy. "Promoter
region-based classification of genes." Proceedings of the
Pacific Symposium on Biocomputing, January 3-7, 2001.
pp. 151-163. |
| 2000 |
|
Eskin, Eleazar, William Noble Grundy and Yoram Singer. "Protein family classification using sparse
Markov transducers." Proceedings of the Eighth International
Conference on Intelligent Systems for Molecular Biology. August
20-23, 2000. pp. 134-145. |
|
Brown, Michael P. S., William Noble Grundy, David Lin, Nello
Cristianini, Charles Sugnet, Terrence S. Furey, Manuel Ares, Jr., and
David Haussler. "Knowledge-based
analysis of microarray gene expression data using support vector
machines." Proceedings of the National Academy of
Science. 97(1):262-267, 2000. |
| 1999 |
|
Grundy, William Noble and Gavin J. P. Naylor. "Phylogenetic Inference from Conserved
Sites Alignments". The
Journal of Experimental Zoology: Molecular
and Developmental Evolution. 285(2):128-139, 1999. |
|
Grundy, William Noble and Timothy L. Bailey. "Family Pairwise Search with embedded motif
models". Bioinformatics. 15(6):463-470, 1999. |
|
Baker, Michael, William N. Grundy and Charles P. Elkan. "A common ancestor for a subunit in the
mitochondrial proton-translocating NADH:ubiquinone oxidoreductase
(complex I) and short-chain dehydrogenases/reductases".
Cellular and Molecular Life Sciences. 55(3):450-455, 1999. |
|
Bailey, Timothy L. and William Noble Grundy. "Classifying proteins by family using the
product of correlated p-values". Proceedings of the
Third International Conference on Computational Molecular Biology
(RECOMB99), April 11-14, 1999. pp. 10-14. |
|
Bailey, Timothy L., Michael E. Baker, Charles P. Elkan and William
N. Grundy. "MEME, MAST, and Meta-MEME: New Tools for Motif Discovery
in Protein Sequences" in Pattern Discovery in Biomolecular Data:
Tools, Techniques, and Applications. J. Wang, B. Shapiro and
D. Shasha, editors. Oxford UP, 1999. |
| 1998 |
|
Grundy, William Noble. A Bayesian
Approach to Motif-based Protein Modeling. Ph.D. dissertation.
University of California, San Diego. June, 1998. |
|
Grundy, William Noble. "Homology
Detection via Family Pairwise Search". Journal of
Computational Biology, 5(3):479-492, 1998. |
|
Baker, Michael E., William N. Grundy and Charles P. Elkan. "Spinach CSP41, an mRNA-binding protein and
ribonuclease, is homologous to nucleotide-sugar epimerases and
hydroxysteroid dehydrogenases" Biochemical and Biophysical
Research Communications, 248(2):250-254, 1998. |
|
Grundy, William Noble. "Family-based
Homology Detection via Pairwise Sequence
Comparison". Proceedings of the Second Annual International
Conference on Computational Molecular Biology, March 22-25,
1998. pp. 94-100. |
| 1997 |
|
Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael
E. Baker. "Meta-MEME: Motif-based
Hidden Markov Models of Protein Families".
Computer Applications in the Biosciences. 13(4):397-406, 1997. |
|
Grundy, William Noble. "Modeling
Biological Sequences Using HTK" Technical report prepared for
Entropic Research Laboratory, Inc. March, 1997. |
|
Grundy, William N., Timothy L. Bailey, Charles P. Elkan and Michael
E. Baker. "Hidden Markov Model
Analysis of Motifs in Steroid Dehydrogenases and their Homologs."
Biochemical and Biophysical Research
Communications. 231(3):760-766, 1997. |
| before 1997 |
|
Batali, John and William Noble Grundy. "Modeling the Evolution of
Motivation". Evolutionary Computation. 4(3):235-270,
1996. |
|
Grundy, William N., Timothy L. Bailey and Charles P. Elkan. "ParaMEME: A Parallel Implementation and a
Web Interface for a DNA and Protein Motif Discovery Tool" (with
corrections). Computer Applications in the
Biosciences. 12(4):303-310, 1996. |
|
Grundy, William Noble. "Solar Cookers
and Social Classes in Southern Africa." Techné: Journal
of Technology Studies. Gray Norton, ed. Vol. V, Winter
1995. pp. 3-7. |
|
Grundy, William. "Building a Simple Recognition System Using HTK."
Entropic Research Laboratory, Washington, DC. August, 1994. |
|
Bernstein, Jared, et al. The Latino40
Speech Database. Entropic Research Laboratory, Washington,
DC. 1994. |
|
Grundy, William and Roy Grundy "Diffusion of Innovation: Solar Oven Use
in Lesotho (Africa)."
Advances in Solar Cooking: Proceedings of the 2nd International
Conference on Solar Cooker Use and Technology. Shyam S. Nandwani,
ed. July 12-15, 1994. pp. 240-247. |
|
Grundy, Bill. Making a Thinking
Robot. Senior Honors Thesis, Symbolic Systems Program,
Stanford University, 1991. Advisor: Fred Dretske. |
|
Stanford Fleet Street Singers. curious... Bill Grundy,
Producer. 1990. |
Spotify
iTunes |
| Grundy, Bill. "The Coinage of
Sicyon." The Numismatist. November,
1986. pp. 2307-8. |
| |
