A. Stark

发表

Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks

T. Gibson, R. Russell, Victor Neduva, 2005, PLoS biology.

Evolution of genes and genomes on the Drosophila phylogeny

Melanie A. Huntley, Sonja J. Prohaska, Albert J. Vilella, 2007, Nature.

Reliable prediction of regulator targets using 12 Drosophila genomes.

Manolis Kellis, P. Kheradpour, A. Stark, 2007, Genome research.

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.

Manolis Kellis, J. Zeitlinger, R. Young, 2007, Genes & development.

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Nathaniel D. Heintzman, Manolis Kellis, R. Stewart, 2009, Nature.

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

B. Dickson, A. Stark, E. Kvon, 2014, Nature.

The relationship between sequence and interaction divergence in proteins.

R. Russell, P. Aloy, A. Stark, 2003, Journal of molecular biology.

bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila

R. Russell, S. Cohen, A. Stark, 2003, Cell.

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

Colin N. Dewey, Mira V. Han, Matthew D. Rasmussen, 2007, Nature.

Combinatorial function of transcription factors and cofactors.

A. Stark, F. Reiter, Sebastian Wienerroither, 2017, Current opinion in genetics & development.

Transcriptional enhancers: from properties to genome-wide predictions

A. Stark, G. Stampfel, Daria Shlyueva, 2014, Nature Reviews Genetics.

Functional Sites in Structure and Sequence. Protein Active Sites and miRNA Target Recognition

A. Stark, A. Stark, 2004 .

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

A. Stark, Rui R Catarino, A. Stark, 2018, Genes & development.

Identification of Drosophila MicroRNA Targets

Julius Brennecke, Robert B Russell, Alexander Stark, 2003, PLoS biology.

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

Cosmas D. Arnold, N. Lau, A. Stark, 2014, Nature Genetics.

Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution

Martina Rath, Muhammad A. Zabidi, Michaela Pagani, 2016, Nature Biotechnology.

Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation

A. Stark, Michaela Pagani, Daria Shlyueva, 2014, bioRxiv.

Transcriptional regulators form diverse groups with context-dependent regulatory functions

Gerald Stampfel, Tomáš Kazmar, Alexander Stark, 2015, Nature.

Genome-wide Ultrabithorax binding analysis reveals highly targeted genomic loci at developmental regulators and a potential connection to Polycomb-mediated regulation

A. Stark, Michaela Pagani, Daria Shlyueva, 2014, bioRxiv.

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

Gerald Stampfel, Łukasz M. Boryń, Martina Rath, 2014, Genome research.

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Łukasz M. Boryń, Cosmas D. Arnold, A. Stark, 2013, Science.

Deciphering the transcriptional cis-regulatory code.

A. Stark, E. Kvon, J. O. Yáñez-Cuna, 2013, Trends in genetics : TIG.

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature.

Barry J Dickson, Gerald Stampfel, Alexander Stark, 2012, Genes & development.

Neural-specific elongation of 3′ UTRs during Drosophila development

M. Levine, A. Stark, D. Hendrix, 2011, Proceedings of the National Academy of Sciences.

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

Manolis Kellis, R. Sachidanandam, G. Hannon, 2007, Cell.

An endogenous small interfering RNA pathway in Drosophila

N. Perrimon, Manolis Kellis, R. Sachidanandam, 2008, Nature.

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

Martina Rath, Muhammad A. Zabidi, Michaela Pagani, 2014, Nature.

Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary

Julius Brennecke, W. Richard McCombie, Ravi Sachidanandam, 2009, Cell.

Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile

Thomas Franz, Alexander Stark, A. Stark, 2009, Nature Structural &Molecular Biology.

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs.

Manolis Kellis, Eric C Lai, Alexander Stark, 2007, Genome research.

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.

Manolis Kellis, G. Hannon, P. Kheradpour, 2007, Genome research.

Systematic genetic analysis of muscle morphogenesis and function in Drosophila

Cornelia Schönbauer, Frank Schnorrer, Barry J Dickson, 2010, Nature.

Principles of MicroRNA–Target Recognition

R. Russell, S. Cohen, A. Stark, 2005, PLoS biology.

Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution

R. Russell, S. Cohen, A. Stark, 2005, Cell.

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

Manolis Kellis, Richard A Young, Michael Levine, 2007, Nature Genetics.

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

Albert J. Vilella, Matthew D. Rasmussen, André L. Martins, 2011, Nature.

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway

R. Sachidanandam, A. Stark, K. Mclaughlin, 2010, Proceedings of the National Academy of Sciences.

Conservation of small RNA pathways in platypus Material Supplemental

Manolis Kellis, R. Sachidanandam, Z. Xuan, 2008 .

from opposite DNA strands produces functional microRNAs Drosophila A single Hox locus in

Manolis Kellis, D. Bartel, S. Cohen, 2008 .

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.

Manolis Kellis, Pouya Kheradpour, Julius Brennecke, 2008, Genes & development.

Small RNA pathways in platypus

Manolis Kellis, R. Sachidanandam, Z. Xuan, 2007 .

A computational pipeline for comparative ChIP-seq analyses

J. Zeitlinger, A. Stark, Qiye He, 2011, Nature Protocols.

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

J. Zeitlinger, A. Stark, Qiye He, 2011, Nature Genetics.

Crystal Structure of an Archaeal Class I Aldolase and the Evolution of (βα)8 Barrel Proteins*

P. Zwart, R. Russell, A. Stark, 2003, Journal of Biological Chemistry.

mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.

P. Bork, T. Doerks, A. Stark, 2006, Genes & development.

Genome analysis of the platypus reveals unique signatures of evolution

Miriam K. Konkel, Tom H. Pringle, Robert S. Harris, 2008, Nature.

Genome analysis of the platypus reveals unique signatures of evolution

Miriam K. Konkel, Tom H. Pringle, Robert S. Harris, 2008, Nature.

The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer

Manolis Kellis, J. Graves, T. Harkins, 2009, Science.

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

A. Stark, E. Kvon, J. O. Yáñez-Cuna, 2012, Genome research.

Accurate Prediction of Peptide Binding Sites on Protein Surfaces

Eduardo Garcia Urdiales, R. Russell, A. Stark, 2009, PLoS Comput. Biol..

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

Łukasz M. Boryń, J. Zuber, A. Stark, 2015, Nature.

cis-Regulatory Requirements for Tissue-Specific Programs of the Circadian Clock

A. Stark, G. Stampfel, J. O. Yáñez-Cuna, 2014, Current Biology.

Comparative Genomics of Gene Regulation—conservation and Divergence of Cis-regulatory Information This Review Comes from a Themed Issue on Genomes and Evolution Edited Main Text Conflict of Interest

Alexander Stark, M. Bulyk, A. Stark, 2022 .

Learning the transcriptional regulatory code

A. Stark, 2009, Molecular systems biology.

A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis

Anaïs F. Bardet, Alexander Stark, Karl Kuchler, 2012, PLoS genetics.

Overall Performance of Functional Site Comparison Cutoffs Number of Matches Dali Z Score PINTS E Value Dali PINTS Both Only Dali Only

R. Russell, A. Stark, A. Shkumatov, 2004 .

Cancer Schwann Cell Origins of a Clonally Transmissible The Tasmanian Devil Transcriptome Reveals

Manolis Kellis, T. Harkins, G. Hannon, 2010 .

A high‐throughput method to identify trans‐activation domains within transcription factor sequences

Ashley R. Woodfin, Cosmas D. Arnold, A. Stark, 2018, The EMBO journal.

Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.

A. Stark, M. A. Zabidi, A. Stark, 2016, Trends in genetics : TIG.

Genome-Wide Analysis of mRNAs Regulated by Drosha and Argonaute Proteins in Drosophila melanogaster

S. Cohen, A. Stark, J. Brennecke, 2006, Molecular and Cellular Biology.

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

A. Stark, Michaela Pagani, F. Reiter, 2022, Nature Genetics.

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

A. Stark, K. Mechtler, A. Akalin, 2020, Nature Communications.

STARR‐seq and UMI‐STARR‐seq: Assessing Enhancer Activities for Genome‐Wide‐, High‐, and Low‐Complexity Candidate Libraries

Cosmas D. Arnold, A. Stark, Michaela Pagani, 2019, Current protocols in molecular biology.

Differential cofactor dependencies define distinct types of human enhancers

Cosmas D. Arnold, A. Stark, K. Mechtler, 2022, Nature.

RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2

A. Stark, Daniel Gerlach, K. Keleman, 2016, Proceedings of the National Academy of Sciences.

Systematic identification and characterization of repressive domains in Drosophila transcription factors

A. Stark, Martina Rath, A. Schleiffer, 2022, bioRxiv.

Somatostatin inhibits glucagon-like peptide-1-induced insulin secretion and proliferation of RINm5F insulinoma cells

A. Stark, R. Mentlein, 2002, Regulatory Peptides.

Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

A. Stark, Michaela Pagani, Jelle Jacobs, 2022, bioRxiv.

Probing the canonicity of the Wnt/Wingless signaling pathway

A. Stark, E. Brunner, Daria Shlyueva, 2017, PLoS genetics.

Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns

L. Pleyer, A. Stark, K. Mechtler, 2022, bioRxiv.

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases.

Gregory J. Hannon, Fedor V. Karginov, Alexander Stark, 2010, Molecular cell.

, from opposite DNA strands produces functional microRNAsDrosophilaA single Hox locus in data

Manolis Kellis, D. Bartel, S. Cohen, 2007 .

Principles of MicroRNATarget Recognition

Robert B. Russell, Julius Brennecke, Alexander Stark, 2005 .

Genome-Wide Analysis of mRNAs Regulated by Drosha and Argonaute Proteins in Drosophila melanogaster

S. Cohen, A. Stark, J. Brennecke, 2006, Molecular and Cellular Biology.

The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline.

A. Stark, Tsutomu Suzuki, N. Nakatsuji, 2009, Developmental cell.

Forward and reverse genetics through derivation of haploid mouse embryonic stem cells.

J. Zuber, R. O’Malley, J. Ecker, 2011, Cell stem cell.

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

A. Stark, Michaela Pagani, F. Reiter, 2021, bioRxiv.

Denoising feedback loops by thresholding--a new role for microRNAs.

Julius Brennecke, Alexander Stark, S. Cohen, 2006, Genes & development.

Insights into gene regulation: From regulatory genomic elements to DNA-protein and protein-protein interactions.

A. Stark, Leonid Serebreni, A. Stark, 2020, Current opinion in cell biology.

Coherent but overlapping expression of microRNAs and their targets during vertebrate development.

Hazel Sive, Alexander Stark, D. Bartel, 2009, Genes & development.

Transcriptional cofactors display specificity for distinct types of core promoters

Cosmas D. Arnold, A. Stark, Martina Rath, 2019, Nature.

Eukaryotic core promoters and the functional basis of transcription initiation

A. Stark, Vanja Haberle, A. Stark, 2018, Nature Reviews Molecular Cell Biology.

Resolving systematic errors in widely-used enhancer activity assays in human cells

Łukasz M. Boryń, Ashley R. Woodfin, Cosmas D. Arnold, 2017, Nature Methods.

A systematic analysis of Drosophila TUDOR domain‐containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors

R. Sachidanandam, A. Stark, K. Mechtler, 2011, The EMBO journal.

Temporal Reciprocity of miRNAs and Their Targets during the Maternal-to-Zygotic Transition in Drosophila

S. Cohen, A. Stark, Natascha Bushati, 2008, Current Biology.

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

R. Sachidanandam, G. Hannon, A. Aravin, 2008, Science.

Developmental gene regulation in the era of genomics.

J. Zeitlinger, A. Stark, 2010, Developmental biology.

Widespread regulatory specificities between transcriptional corepressors and enhancers in Drosophila

A. Stark, Michaela Pagani, J. Jacobs, 2022, bioRxiv.

Promoting transcription over long distances

A. Stark, Rui R Catarino, Christoph Neumayr, 2017, Nature Genetics.

deadenylase and DCP 1 : DCP 2 decapping complexes mRNA degradation by miRNAs and GW 182 requires both CCR 4 : NOT Material

P. Bork, T. Doerks, A. Stark, 2006 .

Identification of transcription factor binding sites from ChIP-seq data at high resolution

Anaïs F. Bardet, Juergen A. Knoblich, Alexander Stark, 2013, Bioinform..

Not miR-ly muscular: microRNAs and muscle development.

S. Cohen, A. Stark, J. Brennecke, 2005, Genes & development.

A conserved role for Snail as a potentiator of active transcription

E. Furlong, A. Stark, R. Zinzen, 2014, Genes & development.

embryo Drosophilaintegration of diverse patterning processes in the Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail

Manolis Kellis, J. Zeitlinger, R. Young, 2007 .

embryoDrosophila suggests integration of diverse patterning processes in the Whole-genome ChIP – chip analysis of Dorsal , Twist , and Snail data

Manolis Kellis, J. Zeitlinger, R. Young, 2007 .

Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.

Łukasz M. Boryń, Cosmas D. Arnold, A. Stark, 2014, Molecular cell.

High-throughput Mutational Surveillance of the SARS-CoV-2 Spike Gene

A. Stark, L. Endler, R. Herwig, 2021, medRxiv.

Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures

Robert B. Russell, Alexander Stark, R. Russell, 2003, Nucleic Acids Res..

A model for statistical significance of local similarities in structure.

Robert B Russell, Alexander Stark, Shamil Sunyaev, 2003, Journal of molecular biology.

RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo – Supplementary Information

Manolis Kellis, J. Zeitlinger, R. Young, 2007 .

1 RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo

Manolis Kellis, J. Zeitlinger, R. Young, 2007 .

Genomics: Hiding in plain sight

A. Stark, Felix Muerdter, A. Stark, 2014, Nature.

Gene Regulation: Activation through Space

A. Stark, Felix Muerdter, A. Stark, 2016, Current Biology.

Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

P. Hufnagl, A. Stark, A. Zoufaly, 2021, Nature communications.

Predictions without templates: New folds, secondary structure, and contacts in CASP5

Patrick Aloy, Robert B Russell, Alexander Stark, 2003, Proteins.

Finding functional sites in structural genomics proteins.

Robert B Russell, Alexander Shkumatov, Alexander Stark, 2004, Structure.

A dynamic structural model for estrogen receptor-alpha activation by ligands, emphasizing the role of interactions between distant A and E domains.

R. Russell, A. Stark, F. Gannon, 2002, Molecular cell.

A reversible haploid mouse embryonic stem cell biobank resource for functional genomics

Fengtang Yang, A. Stark, H. Gerhardt, 2017, Nature.

An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo

Cosmas D. Arnold, S. Rumpel, María Méndez-Lago, 2023, Scientific reports.

SARSeq, a robust and highly multiplexed NGS assay for parallel detection of SARS-CoV2 and other respiratory infections

R. Yelagandula, A. Bykov, A. Vogt, 2020, medRxiv.

Conservation of small RNA pathways in platypus Material Supplemental

Manolis Kellis, R. Sachidanandam, Z. Xuan, 2008 .

Conservation of small RNA pathways in platypus.

Manolis Kellis, R. Sachidanandam, Z. Xuan, 2008, Genome research.