Heller D.; Krestel R.; Ohler U.; Vingron M.; Marsico A.
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data
Nucleic Acids Research 45 (19): 11004-11018 (2017-11-02)

Hafez D.; Karabacak A.; Krueger S.; Hwang Y.C.; Wang L.S.; Zinzen R.P.; Ohler U.
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Genome Biology 18 (1): 199 (2017-10-26)

Calviello L.; Ohler U.
Beyond read-counts: Ribo-seq data analysis to understand the functions of the transcriptome
Trends in Genetics 33 (10): 728-744 (2017-10)

Zappulo A.; van den Bruck D.; Ciolli Mattioli C.; Franke V.; Imami K.; McShane E.; Moreno-Estelles M.; Calviello L.; Filipchyk A.; Peguero-Sanchez E.; Mueller T.; Woehler A.; Birchmeier C.; Merino E.; Rajewsky N.; Ohler U.; Mazzoni E.O.; Selbach M.; Akalin A.; Chekulaeva M.
RNA localization is a key determinant of neurite-enriched proteome
Nature Communications 8 (1): 583 (2017-09-19)

Milek M.; Imami K.; Mukherjee N.; De Bortoli F.; Zinnall U.; Hazapis O.; Trahan C.; Oeffinger M.; Heyd F.; Ohler U.; Selbach M.; Landthaler M.
DDX54 regulates transcriptome dynamics during DNA damage response
Genome Research 27 (8): 1344-1359 (2017-08)

Uyar B.; Yusuf D.; Wurmus R.; Rajewsky N.; Ohler U.; Akalin A.
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
Nucleic Acids Research 45 (10): e91 (2017-06-02)

Maatouk D.M.; Natarajan A.; Shibata Y.; Song L.; Crawford G.E.; Ohler U.; Capel B.
Genome-wide identification of regulatory elements in Sertoli cells
Development 144 (4): 720-730 (2017-02-15)

Velasco S.; Ibrahim M.M.; Kakumanu A.; Garipler G.; Aydin B.; Al-Sayegh M.A.; Hirsekorn A.; Abdul-Rahman F.; Satija R.; Ohler U.; Mahony S.; Mazzoni E.O.
A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells
Cell Stem Cell 20 (2): 205-217 (2017-02-02)

Schuelke M.; Oien N.C.; Oldfors A.
Myopathology in the times of modern genetics
Neuropathology and Applied Neurobiology 43 (1): 44-61 (2017-02)

Mukherjee N.; Calviello L.; Hirsekorn A.; de Pretis S.; Pelizzola M.; Ohler U.
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
Nature Structural & Molecular Biology 24 (1): 86-96 (2017-01)

Zhong Y.; Karaletsos T.; Drewe P.; Sreedharan V.T.; Kuo D.; Singh K.; Wendel H.G.; Raetsch G.
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints
Bioinformatics 33 (1): 139-141 (2017-01-01)


Li S.; Yamada M.; Han X.; Ohler U.; Benfey P.N.
High-resolution expression map of the arabidopsis root reveals alternative splicing and lincRNA regulation
Developmental Cell 39 (4): 508-522 (2016-11-21)

Hsu P.Y.; Calviello L.; Wu H.Y.L.; Li F.W.; Rothfels C.J.; Ohler U.; Benfey P.N.
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.
Proceedings of the National Academy of Sciences of the United States of America 113 (45): E7126-E7135 (2016-11-08)

Hartmann L.; Drewe-Boss P.; Wiessner T.; Wagner G.; Geue S.; Lee H.C.; Obermueller D.M.; Kahles A.; Behr J.; Sinz F.H.; Raetsch G.; Wachter A.
Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in arabidopsis
Plant Cell 28 (11): 2715-2734 (2016-11)

Wessels H.H.; Imami K.; Baltz A.G.; Kolinksi M.; Beldovskaya A.; Selbach M.; Small S.; Ohler U.; Landthaler M.
The mRNA-bound proteome of the early fly embryo
Genome Research 26 (7): 1000-1009 (2016-07)

Vucicevic D.; Gehre M.; Dhamija S.; Friis-Hansen L.; Meierhofer D.; Sauer S.; Orom U.A.
The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation
Oncotarget 7 (23): 33934-33947 (2016-06-07)

Huang Y.H.; Peng W.; Furuuchi N.; Gerhart J.; Rhodes K.; Mukherjee N.; Jimbo M.; Gonye G.E.; Brody J.R.; Getts R.C.; Sawicki J.A.
Delivery of therapeutics targeting the mRNA-binding protein HuR using 3DNA nanocarriers suppresses ovarian tumor growth
Cancer Research 76 (6): 1549-1559 (2016-03-15)

Calviello L.; Mukherjee N.; Wyler E.; Zauber H.; Hirsekorn A.; Selbach M.; Landthaler M.; Obermayer B.; Ohler U.
Detecting actively translated open reading frames in ribosome profiling data
Nature Methods 13 (2): 165-170 (2016-02)


Duttke S.H.C.; Lacadie S.A.; Ibrahim M.M.; Glass C.K.; Corcoran D.L.; Benner C.; Heinz S.; Kadonaga J.T.; Ohler U.
Perspectives on unidirectional versus divergent transcription
Molecular Cell 60 (3): 348-349 (2015-11-05)

Moreno-Risueno M.A.; Sozzani R.; Yardimci G.G.; Petricka J.J.; Vernoux T.; Blilou I.; Alonso J.; Winter C.M.; Ohler U.; Scheres B.; Benfey P.N.
Transcriptional control of tissue formation throughout root development
Science 350 (6259): 426-430 (2015-10-23)

Mackowiak S.D.; Zauber H.; Bielow C.; Thiel D.; Kutz K.; Calviello L.; Mastrobuoni G.; Rajewsky N.; Kempa S.; Selbach M.; Obermayer B.
Extensive identification and analysis of conserved small ORFs in animals
Genome Biology 16: 179 (2015-09-14)

Mino T.; Murakawa Y.; Fukao A.; Vandenbon A.; Wessels H.H.; Ori D.; Uehata T.; Tartey S.; Akira S.; Suzuki Y.; Vinuesa C.G.; Ohler U.; Standley D.M.; Landthaler M.; Fujiwara T.; Takeuchi O.
Regnase-1 and roquin regulate a common element in inflammatory mRNAs by spatiotemporally distinct mechanisms
Cell 161 (5): 1058-1073 (2015-05-21)

Duttke S.H.C.; Lacadie S.A.; Ibrahim M.M.; Glass C.K.; Corcoran D.L.; Benner C.; Heinz S.; Kadonaga J.T.; Ohler U.
Human promoters are intrinsically directional
Molecular Cell 57 (4): 674-684 (2015-02-19)

Ibrahim M.M.; Lacadie S.A.; Ohler U.
JAMM: a peak finder for joint analysis of NGS replicates
Bioinformatics 31 (1): 48-55 (2015-01-01)


Yardimci G.G.; Frank C.L.; Crawford G.E.; Ohler U.
Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection
Nucleic Acids Research 42 (19): 11865-11878 (2014-10-29)

Zemojtel T.; Koehler S.; Mackenroth L.; Jaeger M.; Hecht J.; Krawitz P.; Graul-Neumann L.; Doelken S.; Ehmke N.; Spielmann M.; Oien N.C.; Schweiger M.R.; Krueger U.; Frommer G.; Fischer B.; Kornak U.; Floettmann R.; Ardeshirdavani A.; Moreau Y.; Lewis S.E.; Haendel M.; Smedley D.; Horn D.; Mundlos S.; Robinson P.N.
Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome
Science Translational Medicine 6 (252): 252ra123 (2014-09-03)

Morton T.; Petricka J.; Corcoran D.L.; Li S.; Winter C.M.; Carda A.; Benfey P.N.; Ohler U.; Megraw M.
Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures
Plant Cell 26 (7): 2746-2760 (2014-07)

Munteanu A.; Ohler U.; Gordan R.
COUGER-co-factors associated with uniquely-bound genomic regions
Nucleic Acids Research 42 (Web Server issue): W461-W467 (2014-07)

Mukherjee N.; Jacobs N.C.; Hafner M.; Kennington E.A.; Nusbaum J.D.; Tuschl T.; Blackshear P.J.; Ohler U.
Global target mRNA specification and regulation by the RNA-binding protein ZFP36
Genome Biology 15 (1): R12 (2014-01-08)


Li S.; Liberman L.; Mukherjee N.; Benfey P.; Ohler U.
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
Genome Research 23 (10): 1730-1739 (2013-10)

Ohler U.
Using machine learning to identify disease-relevant regulatory RNAs
Proceedings of the National Academy of Sciences of the United States of America 110 (39): 15516-15517 (2013-09-24)

Megraw M.; Mukherjee S.; Ohler U.
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits
Genome Biology 14 (8): R85 (2013-08-23)

Munger S.C.; Natarajan A.; Looger L.L.; Ohler U.; Capel B.
Fine time course expression analysis identifies cascades of activation and repression and maps a putative regulator of Mammalian sex determination
PLoS Genetics 9 (7): e1003630 (2013-07-11)

Majoros W.H.; Lekprasert P.; Mukherjee N.; Skalsky R.L.; Corcoran D.L.; Cullen B.R.; Ohler U.
MicroRNA target site identification by integrating sequence and binding information
Nature Methods 10 (7): 630-633 (2013-07)

Lacadie S.A.
NextGen speaks
Science 340 (6128): 29 (2013-04)


Ascano M.; Mukherjee N.; Bandaru P.; Miller J.B.; Nusbaum J.D.; Corcoran D.L.; Langlois C.; Munschauer M.; Dewell S.; Hafner M.; Williams Z.; Ohler U.; Tuschl T.
FMRP targets distinct mRNA sequence elements to regulate protein expression
Nature 492 (7429): 382-386 (2012-12-20)

Busch W.; Moore B.T.; Martsberger B.; Mace D.L.; Twigg R.W.; Jung J.; Pruteanu-Malinici I.; Kennedy S.J.; Fricke G.K.; Clark R.L.; Ohler U.; Benfey P.N.
A microfluidic device and computational platform for high-throughput live imaging of gene expression
Nature Methods 9 (11): 1101-1106 (2012-11)

Tewari A.K.; Yardimci G.G.; Shibata Y.; Sheffield N.C.; Song L.; Taylor B.S.; Georgiev S.G.; Coetzee GA.; Ohler U.; Furey T.S.; Crawford G.E.; Febbo P.G.
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Genome Biology 13 (10): R88 (2012-10-03)

Natarajan A.; Yardimci G.G.; Sheffield N.C.; Crawford G.E.; Ohler U.
Predicting cell-type-specific gene expression from regions of open chromatin
Genome Research 22 (9): 1711-1722 (2012-09)

Lamonte G.; Philip N.; Reardon J.; Lacsina J.R.; Majoros W.; Chapman L.; Thornburg C.D.; Telen M.J.; Ohler U.; Nicchitta C.V.; Haystead T.; Chi J.T.
Translocation of sickle cell erythrocyte microRNAs into plasmodium falciparum inhibits parasite rranslation and contributes to malaria resistance
Cell Host & Microbe 12 (2): 187-199 (2012-08-16)

Petricka J.J.; Schauer M.A.; Megraw M.; Breakfield N.W.; Thompson J.W.; Georgiev S.; Soderblom E.J.; Ohler U.; Moseley M.A.; Grossniklaus U.; Benfey P.N.
The protein expression landscape of the Arabidopsis root
Proceedings of the National Academy of Sciences of the United States of America 109 (18): 6811-6818 (2012-05-01)

Skalsky R.L.; Corcoran D.L.; Gottwein E.; Frank C.L.; Kang D.; Hafner M.; Nusbaum J.D.; Feederle R.; Delecluse H.J.; Luftig M.A.; Tuschl T.; Ohler U.; Cullen B.R.
The viral and cellular microRNA targetome in lymphoblastoid cell lines
PLoS Pathogens 8 (1): e1002484 (2012-01-26)

Breakfield N.W.; Corcoran D.L.; Petricka J.J.; Shen J.; Sae-Seaw J.; Rubio-Somoza I.; Weigel D.; Ohler U.; Benfey P.N.
High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis
Genome Research 22 (1): 163-176 (2012-01)


Gottwein E.; Corcoran D.L.; Mukherjee N.; Skalsky R.L.; Hafner M.; Nusbaum J.D.; Shamulailatpam P.; Love C.L.; Dave S.S.; Tuschl T.; Ohler U.; Cullen B.R.
Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines
Cell Host & Microbe 10 (5): 515-526 (2011-11-17)

Corcoran D.L.; Georgiev S.; Mukherjee N.; Gottwein E.; Skalsky R.L.; Keene J.D.; Ohler U.
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data
Genome Biology 12 (8): R79 (2011-08-18)

Mukherjee N.; Corcoran D.L.; Nusbaum J.D.; Reid D.W.; Georgiev S.; Hafner M.; Ascano M.; Tuschl T.; Ohler U.; Keene J.D.
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability
Molecular Cell 43 (3): 327-339 (2011-08-05)

Pruteanu-Malinici I.; Mace D.L.; Ohler U.
Automatic annotation of spatial expression patterns via sparse Bayesian factor models
PLoS Computational Biology 7 (7): e1002098 (2011-07)

Brady S.M.; Zhang L.; Megraw M.; Martinez N.J.; Jiang E.; Yi C.S.; Liu W.; Zeng A.; Taylor-Teeples M.; Kim D.; Ahnert S.; Ohler U.; Ware D.; Walhout A.J.M.; Benfey P.N.
A stele-enriched gene regulatory network in the Arabidopsis root
Molecular Systems Biology 7: 459 (2011-01-18)

Rach E.A.; Winter D.R.; Benjamin A.M.; Corcoran D.L.; Ni T.; Zhu J.; Ohler U.
Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level
PLoS Genetics 7 (1): e1001274 (2011-01-13)


Majoros W.H.; Ohler U.
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs
PLoS Computational Biology 6 (12): e1001037 (2010-12-16)

Kalinka A.T.; Varga K.M.; Gerrard D.T.; Preibisch S.; Corcoran D.L.; Jarrells J.; Ohler U.; Bergman C.M.; Tomancak P.
Gene expression divergence recapitulates the developmental hourglass model
Nature 468 (7325): 811-814 (2010-12-09)

Parry T.J.; Theisen J.W.M.; Hsu J.Y.; Wang Y.L.; Corcoran D.L.; Eustice M.; Ohler U.; Kadonaga J.T.
The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery
Genes & Development 24 (18): 2013-2018 (2010-09-15)

Ni T.; Corcoran D.L.; Rach E.A.; Song S.; Spana E.P.; Gao Y.; Ohler U.; Zhu J.
A paired-end sequencing strategy to map the complex landscape of transcription initiation
Nature Methods 7 (7): 521-527 (2010-07)

Tomancak P.; Ohler U.
Mapping the complexity of transcription control in higher eukaryotes
Genome Biology 11 (4): 115 (2010-04-30)

Georgiev S.; Boyle A.P.; Jayasurya K.; Ding X.; Mukherjee S.; Ohler U.
Evidence-ranked motif identification
Genome Biology 11 (2): R19 (2010-02-15)

Ohler U.; Wassarman D.A.
Promoting developmental transcription
Development 137 (1): 15-26 (2010-01)


Rach E.A.; Yuan H.Y.; Majoros W.H.; Tomancak P.; Ohler U.
Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome
Genome Biology 10 (7): R73 (2009-07-09)

Yokoyama K.D.; Ohler U.; Wray G.A.
Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships
Nucleic Acids Research 37 (13): e92 (2009-07)

Megraw M.; Pereira F.; Jensen S.T.; Ohler U.; Hatzigeorgiou A.G.
A transcription factor affinity-based code for mammalian transcription initiation
Genome Research 19 (4): 644-656 (2009-04)


Holste D.; Ohler U.
Strategies for identifying RNA splicing regulatory motifs and predicting alternative splicing events
PLoS Computational Biology 4 (1): e21 (2008-01-25)


Gottwein E.; Mukherjee N.; Sachse C.; Frenzel C.; Majoros W.H.; Chi J.T.A.; Braich R.; Manoharan M.; Soutschek J.; Ohler U.; Cullen B.R.
A viral microRNA functions as an orthologue of cellular miR-155
Nature 450 (7172): 1096-1099 (2007-12-13)

Brady S.M.; Orlando D.A.; Lee J.Y.; Wang J.Y.; Koch J.; Dinneny J.R.; Mace D.; Ohler U.; Benfey P.N.
A high-resolution root spatiotemporal map reveals dominant expression patterns
Science 318 (5851): 801-806 (2007-11-02)

Huang W.; Nevins J.R.; Ohler U.
Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools
Genome Biology 8 (10): R225 (2007-10-24)


Ohler U.
Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction
Nucleic Acids Research 34 (20): 5943-5950 (2006-11)

Lee J.Y.; Colinas J.; Wang J.Y.; Mace D.; Ohler U.; Benfey P.N.
Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots
Proceedings of the National Academy of Sciences of the United States of America 103 (15): 6055-6060 (2006-04-11)

Bajic V.B.; Brent M.R.; Brown R.H.; Frankish A.; Harrow J.; Ohler U.; Solovyev V.V.; Tan S.L.
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment
Genome Biology 7 Suppl 1: S3.1-13 (2006)


Ohler U.; Yekta S.; Lim L.P.; Bartel D.P.; Burge C.B.
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
RNA 10 (9): 1309-1322 (2004-09)

Lim C.Y.; Santoso B.; Boulay T.; Dong E.; Ohler U.; Kadonaga J.T.
The MTE, a new core promoter element for transcription by RNA polymerase II
Genes & Development 18 (13): 1606-1617 (2004-07-01)


Ohler U.; Niemann H.
Identification and analysis of eukaryotic promoters: recent computational approaches
Trends in Genetics 17 (2): 56-60 (2001-02)


Ohler U.
Promoter prediction on a genomic scale-the Adh experience
Genome Research 10 (4): 539-542 (2000-04)

Reese M.G.; Hartzell G.; Harris N.L.; Ohler U.; Abril J.F.; Lewis S.E.
Genome annotation assessment in Drosophila melanogaster
Genome Research 10 (4): 483-501 (2000-04)