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List of works by David Haussler

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

29 Mammalian Genomes Reveal Novel Exaptations of Mobile Elements for Likely Regulatory Functions in the Human Genome ⬇️

scientific article published on August 27, 2012

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part one

scientific article (publication date: November 2016)

A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer

scientific article published on January 2016

A draft human pangenome reference

scientific article published on 10 May 2023

A graph-theoretic generalization of the Sauer-Shelah lemma

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A physical map of the human genome

scientific article

A population genetic hidden Markov model for detecting genomic regions under selection

scientific article

A unifying model of genome evolution under parsimony

scientific article

A user guide for the online exploration and visualization of PCAWG data

scientific article published on 07 July 2020

Abstract 2985: Predicting the impact of mutations in cancer using an integrated pathway approach

Abstract 5087: UCSC Cancer Genomics Browser 2.0

Abstract 60: The MedBook network for cancer precision medical care

Abstract A39: The UCSC Cancer Genomics Browser

Alignathon: a competitive assessment of whole-genome alignment methods

scientific article

An RNA gene expressed during cortical development evolved rapidly in humans

scientific article

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

scientific article

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing

scientific article published on October 2004

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2

scientific article published on 26 December 2018

Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion

scientific article

Blockchain-Authenticated Sharing of Genomic and Clinical Outcomes Data of Patients With Cancer: A Prospective Cohort Study

scientific article published on 20 March 2020

Building a pan-genome reference for a population

scientific article published on 7 January 2015

Building the minimal DFA for the set of all subwords of a word on-line in linear time ⬇️

scholarly article by Blumer et al. which introduced DAWG

Cactus Graphs for Genome Comparisons

scientific article (publication date: 2010)

Cactus graphs for genome comparisons

scientific article published in March 2011

Cactus: Algorithms for genome multiple sequence alignment

scientific article published on 10 June 2011

Canonical, stable, general mapping using context schemes ⬇️

scientific article published on 27 July 2015

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage ⬇️

scientific article published on 4 February 2016

Classifying G-protein coupled receptors with support vector machines

scientific journal article

Coding exon detection using comparative sequences

scientific article published in July 2006

Combining phylogenetic and hidden Markov models in biosequence analysis

scientific article published in January 2004

Combining phylogenetic and hidden Markov models in biosequence analysis

scholarly article published 2003

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

article published in 2017

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation

Comparative Genomic Analysis Using the UCSC Genome Browser

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparative assembly hubs: web-accessible browsers for comparative genomics

scientific article published on 18 August 2014

Comparative genomic analysis using the UCSC genome browser

scientific article published in January 2007

Comparative genomics reveals insights into avian genome evolution and adaptation

scientific article

Comparative genomics search for losses of long-established genes on the human lineage

scientific article published in December 2007

Comparative recombination rates in the rat, mouse, and human genomes

scientific article published on April 2004

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.

scientific article

Complete inverted files for efficient text retrieval and analysis ⬇️

scholarly article by Blumer et al.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

scientific article published on 4 November 2015

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

article

Computational identification of evolutionarily conserved exons

Computational reconstruction of ancestral DNA sequences

scientific article published in January 2008

Computational screening of conserved genomic DNA in search of functional noncoding elements

scientific article published in July 2005

Counterexample to a claim about the reconstruction of ancestral character states

scientific article published in August 2005

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

scientific article

DUPCAR: reconstructing contiguous ancestral regions with duplications

scientific article

David Haussler ⬇️

scientific article published on March 1, 2011

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Detecting coevolution in and among protein domains

scientific article

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

scientific article published on 27 August 2013

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons

scientific article published on 12 August 2013

ENCODE data in the UCSC Genome Browser: year 5 update

scientific article

ENCODE whole-genome data in the UCSC Genome Browser

scientific article

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

scientific article

ENCODE whole-genome data in the UCSC genome browser (2011 update)

scientific article

Earth BioGenome Project: Sequencing life for the future of life

scientific article published on 23 April 2018

Editing modifies the GABA(A) receptor subunit alpha3

scientific article

Efficient approximations for learning phylogenetic HMM models from data

scientific article

Endangered species hold clues to human evolution

scientific article (publication date: 2010)

Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes

scientific article

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Exploring TCGA Pan-Cancer data at the UCSC Cancer Genomics Browser

scientific article

Exploring relationships and mining data with the UCSC Gene Sorter

scientific article

Facilitating a culture of responsible and effective sharing of cancer genome data

scientific article

Feather development genes and associated regulatory innovation predate the origin of Dinosauria

scientific article

Forces Shaping the Fastest Evolving Regions in the Human Genome

Forces shaping the fastest evolving regions in the human genome

scientific article

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GC-biased evolution near human accelerated regions

scientific article

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Gene isoform specificity through enhancer-associated antisense transcription

scientific article

Gene structure-based splice variant deconvolution using a microarray platform

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome wide screens in yeast to identify potential binding sites and target genes of DNA-binding proteins

scientific article

HAL: a hierarchical format for storing and analyzing multiple genome alignments

scientific article

High-resolution comparative analysis of great ape genomes

scientific article published in Science

Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules

scientific article

Hotspots of mammalian chromosomal evolution

scientific article

How to use expert advice

How to use expert advice

Human genome ultraconserved elements are ultraselected

scientific article

Human tRNA genes function as chromatin insulators

scientific article published on 15 November 2011

Human-mouse alignments with BLASTZ

scientific article

Identification and Classification of Conserved RNA Secondary Structures in the Human Genome

scientific article published on 07 March 2006

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification and characterization of multi-species conserved sequences

scientific article

Identification and classification of conserved RNA secondary structures in the human genome

scientific article

Increased mutation and gene conversion within human segmental duplications

scientific article published on 10 May 2023

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM.

scientific article

Information-theoretic dissection of pairwise contact potentials.

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular and interleukin signaling

scientific article published on 9 September 2011

Integration of the cytogenetic map with the draft human genome sequence

scientific article

International network of cancer genome projects

scientific article

Into the heart of darkness: large-scale clustering of human non-coding DNA.

scientific article published in August 2004

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

scientific article

Learnability and the Vapnik-Chervonenkis dimension

Life, the Universe, and Everything: An Interview with David Haussler ⬇️

scientific article published on January 31, 2013

Light-weight electrophysiology hardware and software platform for cloud-based neural recording experiments

scientific article published on 20 October 2021

Long-read sequence assembly of the gorilla genome

scientific article published on April 2016

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma

scientific article

Low cost cloud based remote microscopy for biological sciences

scientific article published on 11 September 2021

Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization ⬇️

scientific article

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma

scientific article published on January 2016

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

scientific article published on 04 May 2020

Navigating protected genomics data with UCSC Genome Browser in a Box.

scientific article

New Methods for Detecting Lineage-Specific Selection

Ongoing GC-Biased Evolution Is Widespread in the Human Genome and Enriched Near Recombination Hot Spots ⬇️

scientific article published on June 21, 2011

Online resources for PCAWG data exploration, visualization, and discovery

scholarly article published 14 July 2017

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis

scientific article

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes

scientific article published on April 2004

Phylogenetic Hidden Markov Models

article

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

scientific article

Phylogenomic resources at the UCSC Genome Browser

scientific article published in January 2008

Picroscope: low-cost system for simultaneous longitudinal biological imaging

scientific article published on 04 November 2021

Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans

Posttranscriptional crossregulation between Drosha and DGCR8.

scientific article published on January 2009

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

scientific article published on 11 November 2020

Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era

scientific article published on 9 August 2019

RADIA: RNA and DNA integrated analysis for somatic mutation detection

scientific article

Reconstructing contiguous regions of an ancestral genome

scientific article

Reconstructing large regions of an ancestral mammalian genome in silico

scientific article

Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs

scientific article

Retrocopy contributions to the evolution of the human genome

scientific article

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

scientific article

Scale-sensitive dimensions, uniform convergence, and learnability

Score functions for determining regional conservation in two-species local alignments

scientific article published in January 2004

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions

scientific article

Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.

scholarly article

Spiking neural state machine for gait frequency entrainment in a flexible modular robot

scientific article published on 21 October 2020

Stability of SARS-CoV-2 phylogenies

scientific article published on 18 November 2020

Subtype and pathway specific responses to anticancer compounds in breast cancer

scientific article published on 14 October 2011

Targeted discovery of novel human exons by comparative genomics

scientific article

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data

scientific article

The ENCODE Project at UC Santa Cruz

scientific article

The Earth BioGenome Project 2020: Starting the clock

scientific article published on 25 January 2022

The Human Epigenome Browser at Washington University

scientific article

The Human Pangenome Project: a global resource to map genomic diversity

scientific article published in April 2022

The NIH BD2K center for big data in translational genomics

scientific article

The Somatic Genomic Landscape of Glioblastoma

article

The UCSC Cancer Genomics Browser

scientific article (publication date: April 2009)

The UCSC Cancer Genomics Browser: update 2011

scientific article

The UCSC Cancer Genomics Browser: update 2013.

scientific article

The UCSC Cancer Genomics Browser: update 2015

scientific article

The UCSC Ebola Genome Portal

scientific article published on 7 November 2014

The UCSC Genome Browser database: 2014 update

scientific article

The UCSC Genome Browser database: 2015 update

scientific article

The UCSC Genome Browser database: 2016 update

scientific article

The UCSC Genome Browser database: 2017 update

scientific article

The UCSC Genome Browser database: 2018 update

scientific article published on 2 November 2017

The UCSC Genome Browser database: extensions and updates 2011.

scientific article

The UCSC Genome Browser database: extensions and updates 2013.

scientific article

The UCSC Genome Browser database: update 2011

scientific article

The UCSC Interaction Browser: multidimensional data views in pathway context

scientific article

The UCSC Known Genes

scientific article

The UCSC Proteome Browser

scientific article

The UCSC SARS-CoV-2 Genome Browser

scientific article published on 09 September 2020

The UCSC genome browser and associated tools ⬇️

scientific article published on August 20, 2012

The birds of Genome10K

scientific article

The completion of the Mammalian Gene Collection (MGC).

scientific article published on 18 September 2009

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The fishes of Genome 10K.

scientific article

The genome of the green anole lizard and a comparative analysis with birds and mammals ⬇️

scientific article

The human genome browser at UCSC

scientific article

The infinite sites model of genome evolution

scholarly article

The somatic genomic landscape of glioblastoma

scientific article

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

scientific article

The structure and evolution of centromeric transition regions within the human genome

scientific article published on 01 August 2004

The structure of a rigorously conserved RNA element within the SARS virus genome

scientific article published in January 2005

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

scientific article (publication date: 8 May 2007)

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

scientific article

Three periods of regulatory innovation during vertebrate evolution ⬇️

scientific article

Tissue sampling methods and standards for vertebrate genomics

scientific article (publication date: 12 July 2012)

Toil enables reproducible, open source, big biomedical data analyses

scientific article

Towards complete and error-free genome assemblies of all vertebrate species

scientific article

UCSC Data Integrator and Variant Annotation Integrator

scientific article published on 6 January 2016

UCSC genome browser tutorial

scientific article published on 02 June 2008

Unusual intron conservation near tissue-regulated exons found by splicing microarrays

scientific article

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

scientific article

Variation resources at UC Santa Cruz

scientific article published on 6 December 2006

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

epsilon-Nets and Simplex Range Queries

journal article from 'Discrete & Computational Geometry' published in 1987

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