Recent Publications

2024

Cover of the issue. Photographs by Nicholas Gompel.

HOX GENES: THE ORIGINAL BODY BUILDERS

A consortium of Hoxologists

2022

Transcription factor paralogs orchestrate alternative gene regulatory networks by context dependent cooperation with multiple cofactors

Siqian Feng

Chaitanya Rastogi

Ryan Loker

William Glassford

Tomas Rube

Harmen Bussemaker

Richard Mann

Post-transcriptional regulation of transcription factor codes in immature neurons drives neuronal diversity

Guan, W. et al.

Richard Mann

Jonathan Enriquez

SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

Siqian Feng

Richard Mann

Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning

Tomas Rube, et al.

Richard Mann

Harmen Bussemaker

An example of fluorescent labeling of endogenous loci

Fluorescent labeling of genomic loci in Drosophila imaginal discs with heterologous DNA-binding proteins

Delker RK

Munce RH

Hu M

Richard Mann

2021

An abx bx pbx/DfP2 four winged mutant. Photograph by Nicolas Gompel, University of Munich

Cell-type-specific Hox regulatory strategies orchestrate tissue identity

Ryan Loker

Jordyn Sanner

Richard S. Mann

Homothorax controls a binary Rhodopsin switch in Drosophila ocelli

Abhishek Kumar Mishra, Cornelia Fritsch, Roumen Voutev, Richard S Mann, Simon G Sprecher

Scarless engineering of the Drosophila genome near any site-specific integration site.

Siqian Feng

Shan Lu

Wesley B Grueber

Richard S Mann

2020

Types of changes to CRM activities after random mutagenesis

Dense and pleiotropic regulatory information in a developmental enhancer

Timothy Fuqua, Jeff Jordan, Maria Elize van Breugel, Aliaksandr Halavatyi, Christian Tischer, Peter Polidoro, Namiko Abe, Albert Tsai, Richard S. Mann, David L. Stern & Justin Crocker

Major neuropils and organization of the Drosophila Ventral Nerve Cord

A Systematic Nomenclature for the Drosophila Ventral Nerve Cord

Robert Court

Shigehiro Namiki

J. Douglas Armstrong

Jana Bo ̈ rner

Gwyneth Card

Marta Costa

Michael Dickinson

Carsten Duch

Wyatt Korff

Richard Mann

David Merritt

Rod K. Murphey

Andrew M. Seeds

Troy Shirangi

Julie H. Simpson

James W. Truman

John C. Tuthill

Darren W. Williams

David Shepherd

A size principle for recruitment of Drosophila leg motor neurons

Azevedo AW

Dickinson ES

Gurung P

Venkatasubramanian L

Mann RS

Tuthill JC

Control of tissue morphogenesis by the HOX gene Ultrabithorax

Diaz-de-la-Loza MD

Loker R

Mann RS

Thompson BJ

A variety of protein-DNA structures can form between Hox-Exd-DNA

Context-Dependent Gene Regulation by Homeodomain Transcription Factor

Judith F. Kribelbauer, Ryan E. Loker, Siqian Feng, Chaitanya Rastogi, Namiko Abe, H. Tomas Rube, Harmen J. Bussemaker, and Richard S. Mann

2019

A summary showing the effects of serotonin on walking

Serotonergic Modulation of Walking in Drosophila

Clare E. Howard

Chin-Lin Chen, Tanya Tabachnik, Rick Hormigo, Pavan Ramdya

Richard S. Mann

A role for low affinity binding sites in fine tuning the levels of transcription

Rebecca K. Delker, Vikram Ranade, Ryan Loker, Roumen Voutev, Richard S. Mann

In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module

Carlos Sánchez-Higueras, Chaitanya Rastogi, Roumen Voutev, Harmen J. Bussemaker, Richard S. Mann & James C.-G. Hombría

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes

Judith Kribelbauer

Chaitanya Rastogi

Harmen Bussemaker

Richard S. Mann

The development and assembly of the Drosophila adult ventral nerve cord

Lalanti Venkatasubramanian

Richard S. Mann

Stereotyped terminal axon branching of leg motor neurons mediated by IgSF proteins DIP-α and Dpr10

Venkatasubramanian L, Guo Z, Xu S, Tan L, Xiao Q, Nagarkar-Jaiswal S, Mann RS.

2018

Hox complexes in A. aegypti (our contribution)

An improved genome assembly for Aedes aegypti

Benjamin J. Matthews, Olga Dudchenko, [LOTS]... Leslie B. Vosshall

Graphical abstract showing how DNA shape influences affinity

DNA shape fine tunes TF-DNA affinities

Tim Zeiske, Nithya Baburajendran, Anna Kaczynska, Julia Brasch, Arthur G. Palmer III, Lawrence Shapiro, Barry Honig, Richard S. Mann

A leg imaginal disc stained for markers along the proximal-distal axis

The role of EGFR in patterning the distal leg

Susan Newcomb, Roumen Voutev, Aurelie Jory, Rebecca K. Delker, Matthew Slattery, Richard S. Mann

Accurate and sensitive quantification of protein-DNA binding affinity

Chaitanya Rastogi, H. Tomas Rube, Judith F. Kribelbauer, Justin Crocker, Ryan E. Loker, Gabriella D. Martini, Oleg Laptenko, William A. Freed-Pastor, Carol Prives, David L. Stern, Richard S. Mann and Harmen J. Bussemaker

Robust ΦC31-Mediated Genome Engineering in Drosophila melanogaster Using Minimal attP/attB Phage Sites

Roumen Voutev and Richard S. Mann

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding

Satyanarayan Rao, Tsu-Pei Chiu, Judith F. Kribelbauer, Richard S. Mann, Harmen J. Bussemaker, Remo Rohs

A single stem cell clone in which both motor neurons (green) and glia (red) are labeled

Building a CNS

Jonathan Enriquez, Laura Quintana Rio, Richard Blazeski, Stephanie Bellemin, Pierre Godement, Carol Mason, Richard S. Mann

2017

Origins and Specification of the Drosophila Wing

David Requena, Jose Andres Álvarez, Hugo Gabilondo, Ryan Loker, Richard S. Mann, Carlos Estella

Using genome engineering to better understand animal development

Rebecca Delker & Richard S. Mann

Calculating electrostatic potentials in DNA grooves

Still thinking about electrostatic potentials

Tsu-Pei Chiu, Satyanarayan Rao, Richard S. Mann, Barry Honig, Remo Rohs

2024

HOX GENES: THE ORIGINAL BODY BUILDERS

2022

Transcription factor paralogs orchestrate alternative gene regulatory networks by context dependent cooperation with multiple cofactors

SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues

2021

Cell-type-specific Hox regulatory strategies orchestrate tissue identity

Homothorax controls a binary Rhodopsin switch in Drosophila ocelli

Scarless engineering of the Drosophila genome near any site-specific integration site.

2020

Dense and pleiotropic regulatory information in a developmental enhancer

A size principle for recruitment of Drosophila leg motor neurons

Control of tissue morphogenesis by the HOX gene Ultrabithorax

2019

A role for low affinity binding sites in fine tuning the levels of transcription

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes

2018

2017

Using genome engineering to better understand animal development

Still thinking about electrostatic potentials

No results

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