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De novo gene birth and the conundrum of ORFan genes in bacteria

Md. Hassan uz-Zaman
Howard Ochman

First Published July 10, 2025

k-mer approaches for biodiversity genomics" > k-mer approaches for biodiversity genomics

Katharine M. Jenike
Lucía Campos-Domínguez
Marilou Boddé
José Cerca
Christina N. Hodson
Michael C. Schatz
Kamil S. Jaron

First Published January 31, 2025

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics

W.H. Adrian Tsui
Spencer C. Ding
Peiyong Jiang
Y.M. Dennis Lo

First Published January 22, 2025

Advancements in prospective single-cell lineage barcoding and their applications in research

Xiaoli Zhang
Yirui Huang
Yajing Yang
Qi-En Wang
Lang Li

First Published November 21, 2024

Leveraging the power of long reads for targeted sequencing

Shruti V. Iyer
Sara Goodwin
William Richard McCombie

First Published November 20, 2024

Challenges in identifying mRNA transcript starts and ends from long-read sequencing data

Ezequiel Calvo-Roitberg
Rachel F. Daniels
Athma A. Pai

First Published November 20, 2024

Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics

Natan Belchikov
Justine Hsu
Xiang Jennie Li
Julien Jarroux
Wen Hu
Anoushka Joglekar
Hagen U. Tilgner

First Published November 20, 2024

The chromatin tapestry as a framework for neurodevelopment

Ben Nolan
Timothy E. Reznicek
Christopher T. Cummings
M. Jordan Rowley

First Published October 29, 2024

Diversifying the genomic data science research community

Rosa Alcazar
Maria Alvarez
Rachel Arnold
Mentewab Ayalew
Lyle G. Best
Michael C. Campbell Kamal Chowdhury Katherine E.L. Cox Christina Daulton Youping Deng Carla Easter Karla Fuller Shazia Tabassum Hakim Ava M. Hoffman Natalie Kucher Andrew Lee Joslynn Lee Jeffrey T. Leek Robert Meller Loyda B. Méndez Miguel P. Méndez-González Stephen Mosher Michele Nishiguchi Siddharth Pratap Tiffany Rolle Sourav Roy Rachel Saidi Michael C. Schatz Shurjo K. Sen James Sniezek Edu Suarez Martinez Frederick J. Tan Jennifer Vessio Karriem Watson
... [+29 authors] ...,
Wendy Westbroek
Joseph Wilcox
Carrie Wright
Xianfa Xie

First Published July 20, 2022

Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences

Terence Gall-Duncan
Nozomu Sato
Ryan K.C. Yuen
Christopher E. Pearson

First Published December 29, 2021

k-mers for querying large collections of sequencing data sets" > Data structures based on k-mers for querying large collections of sequencing data sets

Camille Marchet
Christina Boucher
Simon J. Puglisi
Paul Medvedev
Mikaël Salson
Rayan Chikhi

First Published December 16, 2020

Accurate and complete genomes from metagenomes

Lin-Xing Chen
Karthik Anantharaman
Alon Shaiber
A. Murat Eren
Jillian F. Banfield

First Published March 18, 2020

Genome graphs and the evolution of genome inference

Benedict Paten
Adam M. Novak
Jordan M. Eizenga
Erik Garrison

First Published March 30, 2017

Contrasting genetic architectures in different mouse reference populations used for studying complex traits

David A. Buchner
Joseph H. Nadeau

First Published May 7, 2015

Origins, evolution, and phenotypic impact of new genes

Henrik Kaessmann

First Published July 22, 2010

Population genetic inference from genomic sequence variation

John E. Pool
Ines Hellmann
Jeffrey D. Jensen
Rasmus Nielsen

First Published January 12, 2010

Darwinian alchemy: Human genes from noncoding DNA

Adam Siepel

First Published October 1, 2009

Every genome sequence needs a good map

Harris A. Lewin
Denis M. Larkin
Joan Pontius
Stephen J. O'Brien

First Published July 13, 2009

On the origin of prokaryotic species

W. Ford Doolittle
Olga Zhaxybayeva

First Published May 1, 2009

‘Why genomes in pieces?’ revisited: Sucking lice do their own thing in mtDNA circle game

David M. Rand

First Published May 1, 2009

Non-Darwinian estimation: My ancestors, my genes' ancestors

Kenneth M. Weiss
Jeffrey C. Long

First Published May 1, 2009

Constructing genomic maps of positive selection in humans: Where do we go from here?

Joshua M. Akey

First Published May 1, 2009

Genetic architecture of quantitative traits in mice, flies, and humans

Jonathan Flint
Trudy F.C. Mackay

First Published May 1, 2009

Evolution under canalization and the dual roles of microRNAs—A hypothesis

Chung-I Wu
Yang Shen
Tian Tang

First Published May 1, 2009

One hundred fifty years without Darwin are enough!

Francisco J. Ayala

First Published May 1, 2009

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

Micah Hamady
Rob Knight

First Published April 21, 2009

Finding the fifth base: Genome-wide sequencing of cytosine methylation

Ryan Lister
Joseph R. Ecker

First Published March 9, 2009

Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1

Edward J. Hollox
John C.K. Barber
Anthony J. Brookes
John A.L. Armour

First Published October 30, 2008

The biological effects of simple tandem repeats: Lessons from the repeat expansion diseases

Karen Usdin

First Published July 1, 2008

The new paradigm of flow cell sequencing

Robert A. Holt
Steven J.M. Jones

First Published June 2, 2008

Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs

Jürgen Schmitz
Anja Zemann
Gennady Churakov
Heiner Kuhl
Frank Grützner
Richard Reinhardt
Jürgen Brosius

First Published May 7, 2008

Protein networks in disease

Trey Ideker
Roded Sharan

First Published April 1, 2008

Panel construction for mapping in admixed populations via expected mutual information

Sivan Bercovici
Dan Geiger
Liran Shlush
Karl Skorecki
Alan Templeton

First Published March 18, 2008

Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information

Eleazar Eskin

First Published March 18, 2008

On the inference of ancestries in admixed populations

Sriram Sankararaman
Gad Kimmel
Eran Halperin
Michael I. Jordan

First Published March 18, 2008

Effect of genetic divergence in identifying ancestral origin using HAPAA

Andreas Sundquist
Eugene Fratkin
Chuong B. Do
Serafim Batzoglou

First Published March 18, 2008

Mammalian non-LTR retrotransposons: For better or worse, in sickness and in health

Victoria P. Belancio
Dale J. Hedges
Prescott Deininger

First Published February 6, 2008

The influence of genetic variation on gene expression

Rohan B.H. Williams
Eva K.F. Chan
Mark J. Cowley
Peter F.R. Little

First Published December 3, 2007

Multiple sequence alignment: In pursuit of homologous DNA positions

Sudhir Kumar
Alan Filipski

First Published February 1, 2007

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Nathan M. Springer
Robert M. Stupar

First Published January 25, 2007

Synthetic biology projects in vitro

Anthony C. Forster
George M. Church

First Published December 6, 2006

Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping

Albertha J.M. Walhout

First Published October 19, 2006

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

Laura Elnitski
Victor X. Jin
Peggy J. Farnham
Steven J.M. Jones

First Published October 19, 2006

Copy number variation: New insights in genome diversity

Jennifer L. Freeman
George H. Perry
Lars Feuk
Richard Redon
Steven A. McCarroll
David M. Altshuler Hiroyuki Aburatani Keith W. Jones Chris Tyler-Smith
... [+4 authors] ...,
Matthew E. Hurles
Nigel P. Carter
Stephen W. Scherer
Charles Lee

First Published June 29, 2006

Many Paths to Many Clones: A Comparative Look at High-Throughput Cloning Methods

Gerald Marsischky
Joshua LaBaer

First Published October 15, 2004

From ORFeomes to Protein Interaction Maps in Viruses

Peter Uetz
Seesandra V. Rajagopala
Yu-An Dong
Jürgen Haas

First Published October 15, 2004

The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis

Jef D. Boeke

First Published September 2, 2003

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources

Kelly A. Frazer
Laura Elnitski
Deanna M. Church
Inna Dubchak
Ross C. Hardison

First Published January 1, 2003

Mammalian Retroelements

Prescott L. Deininger
Mark A. Batzer

First Published October 1, 2002

Biomedical Applications and Studies of Molecular Evolution: A Proposal for a Primate Genomic Library Resource

Evan E. Eichler
Pieter J. DeJong

First Published May 1, 2002

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