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List of works by William S. Noble

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

scientific article published on 03 January 2019

A New Algorithm for the Evaluation of Shotgun Peptide Sequencing in Proteomics: Support Vector Machine Classification of Peptide MS/MS Spectra and SEQUEST Scores ⬇️

scientific article published on March 1, 2003

A Unified Multitask Architecture for Predicting Local Protein Properties ⬇️

scientific article published on March 26, 2012

A cross-validation scheme for machine learning algorithms in shotgun proteomics

scientific article

A learned embedding for efficient joint analysis of millions of mass spectra

scientific article published in 2022

A learned embedding for efficient joint analysis of millions of mass spectra:

A pitfall for machine learning methods aiming to predict across cell types

scholarly article published 4 January 2019

A quick guide to organizing computational biology projects

scientific article

A statistical framework for genomic data fusion

scientific article

A structural alignment kernel for protein structures

scientific article published on 18 January 2007

A thermodynamic approach to PCR primer design

scientific article published on 15 June 2009

A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types

scientific article published on 28 August 2019

An Integrative Framework For Detecting Structural Variations In Cancer Genomes

An averaging strategy to reduce variability in target-decoy estimates of false discovery rate

article

Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries

scientific article

Assessing computational tools for the discovery of transcription factor binding sites

scientific article

Assessing phylogenetic motif models for predicting transcription factor binding sites

scientific article published in June 2009

Assigning significance to peptides identified by tandem mass spectrometry using decoy databases

scientific article published on 08 December 2007

Automated mapping of large-scale chromatin structure in ENCODE

scientific article published on 30 June 2008

Automated validation of polymerase chain reaction amplicon melting curves

scientific article published in April 2006

Automated validation of polymerase chain reactions using amplicon melting curves.

scientific article published in January 2005

Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate

article

Calibration using a single-point external reference material harmonizes quantitative mass spectrometry proteomics data between platforms and laboratories

article by Lindsay K. Pino et al published 11 October 2018 in Analytical Chemistry

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

scientific article published on 18 September 2020

Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.

scientific article

Choosing negative examples for the prediction of protein-protein interactions

scientific article published on 20 March 2006

Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization

scientific article published on 18 January 2018

Choosing panels of genomics assays using submodular optimization

scientific article

Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data

scientific article published on 18 October 2018

Combining high resolution and exact calibration to boost statistical power: A well-calibrated score function for high-resolution MS2 data

Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships

scientific article published in January 2003

Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

scientific article published on 22 April 2021

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies

scientific article published on 5 December 2017

Computational and Statistical Analysis of Protein Mass Spectrometry Data ⬇️

scientific article published on January 26, 2012

Computing exact p-values for a cross-correlation shotgun proteomics score function

scientific article

Consistent probabilistic outputs for protein function prediction

scientific article published on 27 June 2008

Correction to "Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics".

scientific article published on 21 October 2016

Correction to "On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra".

scientific article published on 21 October 2016

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns

scientific article

Crux: rapid open source protein tandem mass spectrometry analysis

scientific article published on 9 September 2014

DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding

scientific article published on 24 May 2017

DeepPINK: reproducible feature selection in deep neural networks ⬇️

article by Yang Lu et al published 2018 in Advances in Neural Information Processing Systems 31

Detecting Modifications in Proteomics Experiments with Param-Medic

article

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding ⬇️

scientific article (publication date: 27 January 2011)

Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs

scientific article

Detecting modifications in proteomics experiments with Param-Medic

Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics

scientific article published on 23 December 2012

Direct Maximization of Protein Identifications from Tandem Mass Spectra ⬇️

scientific article published on November 3, 2011

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

scientific article published on 04 April 2019

Efficient identification of DNA hybridization partners in a sequence database

scientific article published on July 2006

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data

scientific article

Empirical comparison of web-based antimicrobial peptide prediction tools

scientific article published on 15 February 2017

Epigenetic priors for identifying active transcription factor binding sites

scientific article

Estimating relative abundances of proteins from shotgun proteomics data ⬇️

scientific article published on November 19, 2012

Exploratory analysis of genomic segmentations with Segtools

scientific article

Exploring gene expression data with class scores.

scientific article

Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units

scientific article published on 30 August 2019

FIMO: scanning for occurrences of a given motif ⬇️

scientific article published on February 16, 2011

Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

scientific article published on 13 September 2018

Fast open modification spectral library searching through approximate nearest neighbor indexing

Faster Mass Spectrometry-Based Protein Inference: Junction Trees Are More Efficient than Sampling and Marginalization by Enumeration ⬇️

scientific article published on May 1, 2012

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra ⬇️

scientific article published on July 29, 2011

Finding the optimal bayesian network given a constraint graph

Finding the optimal bayesian network given a constraint graph

GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs

GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs

scholarly article by Oana Ursu published in August 2018

HiCRep.py: fast comparison of Hi-C contact matrices in Python

scientific article published in 2021

HiCRep: assessing the reproducibility of Hi-C data using a stratum- adjusted correlation coefficient

scientific article published on 30 August 2017

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions ⬇️

scientific article published on September 9, 2010

Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics

scientific article

Improved network-based identification of protein orthologs

scientific article published in August 2008

Improved similarity scores for comparing motifs ⬇️

scientific article published on May 4, 2011

Improvements to the percolator algorithm for Peptide identification from shotgun proteomics data sets

scientific article

Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions

scientific article published on 11 July 2007

Inferring clonal composition from multiple sections of a breast cancer

scientific article

Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism.

scientific article

Integrating Information for Protein Function Prediction

Integrative annotation of chromatin elements from ENCODE data

scientific article

Integrative detection and analysis of structural variation in cancer genomes

scientific article published on 10 September 2018

Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

scientific article

Joint precursor elution profile inference via regression for peptide detection in data-independent acquisition mass spectra

Kernel hierarchical gene clustering from microarray expression data

scientific article published in November 2003

Kernel methods for predicting protein-protein interactions

scientific article published on June 2005

Large-scale identification of yeast integral membrane protein interactions

scientific article

Learning a weighted sequence model of the nucleosome core and linker yields more accurate predictions in Saccharomyces cerevisiae and Homo sapiens

scientific article

Learning gene functional classifications from multiple data types

scientific article

Learning kernels from biological networks by maximizing entropy

scientific article published in August 2004

Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments

scientific article published on 15 August 2012

Learning to predict protein-protein interactions from protein sequences

scientific article

MCAST: scanning for cis-regulatory motif clusters

scientific article published on 24 December 2015

Machine Learning Strategy That Leverages Large Data sets to Boost Statistical Power in Small-Scale Experiments

scientific article published on 17 February 2020

Machine learning applications in genetics and genomics

scientific article published on 07 May 2015

Mass spectrometrists should search only for peptides they care about

scientific article

Massively multiplex single-cell Hi-C.

scientific article

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

Matrix-Matched Calibration Curves for Assessing Analytical Figures of Merit in Quantitative Proteomics

scientific article published on 24 February 2020

Matrix2png: a utility for visualizing matrix data

scientific article

Measuring significant changes in chromatin conformation with ACCOST

scientific article published on 01 March 2020

MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

scientific article

Metaproteomics reveal that rapid perturbations in organic matter prioritize functional restructuring over taxonomy in western Arctic Ocean microbiomes

scientific article published on 06 September 2019

Mismatch string kernels for discriminative protein classification

scientific article published on 22 January 2004

MoMo: discovery of statistically significant post-translational modification motifs

article

Modeling peptide fragmentation with dynamic Bayesian networks for peptide identification

scientific article

Motif-based protein ranking by network propagation

scientific article published on 2 August 2005

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum

scientific article

Multiple functional categories of proteins identified in an in vitro cellular ubiquitin affinity extract using shotgun peptide sequencing

scientific article published in July 2003

NIPS workshop on New Problems and Methods in Computational Biology

scientific article

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

scientific article published on August 2008

Nucleosome positioning signals in genomic DNA

scientific article published on 9 July 2007

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

scientific article

On the importance of well-calibrated scores for identifying shotgun proteomics spectra

scientific article published on 17 December 2014

On using samples of known protein content to assess the statistical calibration of scores assigned to peptide-spectrum matches in shotgun proteomics

scientific article published on 24 March 2011

Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.

scientific article

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data.

scientific article published on 07 August 2017

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.

scientific article published on 11 April 2018

PREDICTD: PaRallel Epigenomics Data Imputation With Cloud-based Tensor Decomposition

Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings

scientific article published on 6 March 2017

Peptide charge state determination for low-resolution tandem mass spectra.

scientific article published in January 2005

Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data

scientific article published on 27 July 2015

Posterior error probabilities and false discovery rates: two sides of the same coin

scientific article published on 04 December 2007

Predicting co-complexed protein pairs from heterogeneous data

scientific article

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

scientific article published on 11 September 2019

Predicting human nucleosome occupancy from primary sequence

scientific article

Predicting the in vivo signature of human gene regulatory sequences

scientific article published in June 2005

Predictive model of 3D domain formation via CTCF-mediated extrusion

scientific article

Protein family classification using sparse markov transducers

scientific article

Protein ranking by semi-supervised network propagation

scientific article published on 20 March 2006

Protein ranking: from local to global structure in the protein similarity network

scientific article

Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes

scientific article published in 2024

QVALITY: non-parametric estimation of q-values and posterior error probabilities

scientific article published on 4 February 2009

Quantifying similarity between motifs

scientific article

RANKPROP: a web server for protein remote homology detection

scientific article

Ranking predicted protein structures with support vector regression.

scientific article

Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about".

scientific article published in June 2017

Response to comments on ‘Empirical comparison of web-based antimicrobial peptide prediction tools’

scientific article published on 01 August 2019

Riboproteomics of the hepatitis C virus internal ribosomal entry site

scientific article

Searching for statistically significant regulatory modules

scientific article published in October 2003

Segway 2.0: Gaussian mixture models and minibatch training

scientific article

Segway 2.0: Gaussian mixture models and minibatch training

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

scientific article

Semi-supervised protein classification using cluster kernels

scientific article published on 19 May 2005

Sequence and chromatin determinants of cell-type-specific transcription factor binding

scientific article

Software tools for visualizing Hi-C data

scientific article

Speeding Up Percolator

scientific article published on 23 August 2019

Statistical calibration of the SEQUEST XCorr function

scientific article published on April 2009

Submodular Maximization via Gradient Ascent: The Case of Deep Submodular Functions ⬇️

Support vector machine classification on the web.

scientific article

Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure

scientific article

Systematic reconstruction of cellular trajectories across mouse embryogenesis

scientific article published on 14 March 2022

Tandem Mass Spectrum Identification via Cascaded Search

scientific article

Ten simple rules for defining a computational biology project

scientific article published in 2023

Ten simple rules for writing a response to reviewers

scientific article published on 12 October 2017

The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle

scientific article

The Genomedata format for storing large-scale functional genomics data

scientific article

The effect of replication on gene expression microarray experiments

scientific article published in September 2003

The spectrum kernel: a string kernel for SVM protein classification

scientific article published in January 2002

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

scientific article

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

scientific article published on 27 November 2020

Transmembrane topology and signal peptide prediction using dynamic bayesian networks

scientific article

Unsupervised embedding of single-cell Hi-C data.

scientific article published in July 2018

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

scientific article published on 18 March 2012

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

scientific article published on 24 July 2008

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

scientific article published on 27 January 2018

Using substitution matrices to estimate probability distributions for biological sequences

scientific article published in January 2002

ppx: Programmatic Access to Proteomics Data Repositories

scientific article published on 03 August 2021

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