Publications



2017

Pei W.; Feyerabend T.B.; Roessler J.; Wang X.; Postrach D.; Busch K.; Rode I.; Klapproth K.; Dietlein N.; Quedenau C.; Chen W.; Sauer S.; Wolf S.; Hoefer T.; Rodewald H.Re.
Polylox barcoding reveals haematopoietic stem cell fates realized in vivo
Nature : (2017-08-16)



Piwecka M.; Glazar Petar; Hernandez-Miranda L.R.; Memczak S.; Wolf S.A.; Rybak-Wolf A.; Filipchyk A.; Klironomos F.; Cerda Jara C.A.; Fenske P.; Trimbuch T.; Zywitza V.; Plass M.; Schreyer L.; Ayoub S.; Kocks C.; Kuehn R.; Rosenmund C.; Birchmeier C.; Rajewsky N.
Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function
Science : (2017-08-10)



Hadizadeh F.; Bonfiglio F.; Belheouane M.; Vallier M.; Sauer S.; Bang C.; Bujanda L.; Andreasson A.; Agreus L.; Engstrand L.; Talley N.J.; Rafter J.; Baines J.F.; Walter S.; Franke A.; D'Amato M.
Faecal microbiota composition associates with abdominal pain in the general population
Gut : (2017-08-01)



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)



Lacraz G.P.A.; Junker J.P.; Gladka M.M.; Molenaar B.; Scholman K.T.; Vigil-Garcia M.; Versteeg D.; de Ruiter H.; Vermunt M.W.; Creyghton M.P.; Huibers M.M.H.; de Jonge N.; van Oudenaarden A.; van Rooij E.
Tomo-seq identifies SOX9 as a key regulator of cardiac fibrosis during ischemic injury
Circulation : (2017-07-19)



Beagrie R.A.; Pombo A.
Cell cycle: continuous chromatin changes
Nature 547 (7661): 34-35 (2017-07-06)



Dejure F.R.; Royla N.; Herold S.; Kalb J.; Walz S.; Ade C.P.; Mastrobuoni G.; Vanselow J.T.; Schlosser A.; Wolf E.; Kempa S.; Eilers M.
The MYCmRNA3'-UTR couples RNA polymerase II function to glutamine and ribonucleotide levels
EMBO Journal 36 (13): 1854-1868 (2017-07-03)



Xu X.; Meng Q.; Erben U.; Wang P.; Glauben R.; Kuehl A.A.; Wu H.; Ma C.W.; Hu M.; Wang Y.; Sun W.; Jia J.; Wu X.; Chen W.; Siegmund B.; Qin Z.
Myeloid-derived suppressor cells promote B-cell production of IgA in a TNFR2-dependent manner
Cellular and Molecular Immunology 14 (7): 597-606 (2017-07)



Kar G.; Kim J.K.; Kolodziejczyk A.A.; Natarajan K.N.; Torlai Triglia E.; Mifsud B.; Elderkin S.; Marioni J.C.; Pombo A.; Teichmann S.A.
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Nature Communications 8 (1): 36 (2017-06-26)



Varano G.; Raffel S.; Sormani M.; Zanardi F.; Lonardi S.; Zasada C.; Perucho L.; Petrocelli V.; Haake A.; Lee A.K.; Bugatti M.; Paul U.; Van Anken E.; Pasqualucci L.; Rabadan R.; Siebert R.; Kempa S.; Ponzoni M.; Facchetti F.; Rajewsky K.; Casola S.
The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3{beta} inhibition
Nature 546 (7657): 302-306 (2017-06-08)



Gruening B.A.; Fallmann J.; Yusuf D.; Will S.; Erxleben A.; Eggenhofer F.; Houwaart T.; Batut B.; Videm P.; Bagnacani A.; Wolfien M.; Lott S.C.; Hoogstrate Y.; Hess W.R.; Wolkenhauer O.; Hoffmann S.; Akalin A.; Ohler U.; Stadler P.F.; Backofen R.
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Nucleic Acids Research : (2017-06-05)



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)



Jamal-Hanjani M.; Wilson G.A.; McGranahan N.; Birkbak N.J.; Watkins T.B.K.; Veeriah S.; Shafi S.; Johnson D.H.; Mitter R.; Rosenthal R.; Salm M.; Horswell S.; Escudero M.; Matthews N.; Rowan A.; Chambers T.; Moore D.A.; Turajlic S.; Xu H.; Lee S.-M.; Forster M.D.; Ahmad T.; Hiley C.T.; Abbosh C.; Falzon M.; Borg E.; Marafioti T.; Lawrence D.; Hayward M.; Kolvekar S.; Panagiotopoulos N.; Janes S.M.; Thakrar R.; Ahmed A.; Blackhall F.; Summers Y.; Shah R.; Joseph L.; Quinn A.M.; Crosbie P.A.; Naidu B.; Middleton G.; Langman G.; Trotter S.; Nicolson M.; Remmen H.; Kerr K.; Chetty M.; Gomersall L.; Fennell D.A.; Nakas A.; Rathinam S.; Anand G.; Khan S.; Russell P.; Ezhil V.; Ismail B.; Irvin-Sellers M.; Prakash V.; Lester J.F.; Kornaszewska M.; Attanoos R.; Adams H.; Davies H.; Dentro S.; Taniere P.; O'Sullivan B.; Lowe H.L.; Hartley J.A.; Iles N.; Bell H.; Ngai Y.; Shaw J.A.; Herrero J.; Szallasi Z.; Schwarz R.F.; Stewart A.; Quezada S.A.; Le Quesne J.; Van Loo P.; Dive C.; Hackshaw A.; Swanton C.
Tracking the evolution of non-small-cell lung cancer
New England Journal of Medicine 376 (22): 2109-2121 (2017-06-01)



Barbieri M.; Xie S.Q.; Torlai Triglia E.; Chiariello A.M.; Bianco S.; de Santiago I.; Branco M.R.; Rueda D.; Nicodemi M.; Pombo A.
Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells
Nature Structural & Molecular Biology 24 (6): 515-524 (2017-06)



Abbosh C.; Birkbak N.J.; Wilson G.A.; Jamal-Hanjani M.; Constantin T.; Salari R.; Quesne J.L.; Moore D.A.; Veeriah S.; Rosenthal R.; Marafioti T.; Kirkizlar E.; Watkins T.B.K.; McGranahan N.; Ward S.; Martinson L.; Riley J.; Fraioli F.; Bakir M.A.; Groenroos E.; Zambrana F.; Endozo R.; Bi W.L.; Fennessy F.M.; Sponer N.; Johnson D.; Laycock J.; Shafi S.; Czyzewska-Khan J.; Rowan A.; Chambers T.; Matthews N.; Turajlic S.; Hiley C.; Lee S.M.; Forster M.D.; Ahmad T.; Falzon M.; Borg E.; Lawrence D.; Hayward M.; Kolvekar S.; Panagiotopoulos N.; Janes S.M.; Thakrar R.; Ahmed A.; Blackhall F.; Summers Y.; Hafez D.; Naik A.; Ganguly A.; Kareht S.; Shah R.; Joseph L.; Quinn A.M.; Crosbie P.; Naidu B.; Middleton G.; Langman G.; Trotter S.; Nicolson M.; Remmen H.; Kerr K.; Chetty M.; Gomersall L.; Fennell D.A.; Nakas A.; Rathinam S.; Anand G.; Khan S.; Russell P.; Ezhil V.; Ismail B.; Irvin-Sellers M.; Prakash V.; Lester J.F.; Kornaszewska M.; Attanoos R.; Adams H.; Davies H.; Oukrif D.; Akarca A.U.; Hartley J.A.; Lowe H.L.; Lock S.; Iles N.; Bell H.; Ngai Y.; Elgar G.; Szallasi Z.; Schwarz R.F.; Herrero J.; Stewart A.; Quezada S.A.; Van Loo P.; Dive C.; Lin C.J.; Rabinowitz M.; Aerts H.J.W.L.; Hackshaw A.; Shaw J.A.; Zimmermann B.G.; Swanton C.
Phylogenetic ctDNA analysis depicts early stage lung cancer evolution
Nature 545 (7655): 446-451 (2017-05-25)



Alles J.; Karaiskos N.; Praktiknjo S.D.; Grosswendt S.; Wahle P.; Ruffault P.L.; Ayoub S.; Schreyer L.; Boltengagen A.; Birchmeier C.; Zinzen R.; Kocks C.; Rajewsky N.
Cell fixation and preservation for droplet-based single-cell transcriptomics
BMC Biology 15 (1): 44 (2017-05-19)



Caglio Giulia; Torlai Triglia E.; Pombo A.
Keep them close: PRC2 poises enhancer-promoter interactions at anterior neuronal genes
Cell Stem Cell 20 (5): 573-575 (2017-05-04)



Uhlitz F.; Sieber A.; Wyler E.; Fritsche-Guenther R.; Meisig J.; Landthaler M.; Klinger B.; Bluethgen N.
An immediate-late gene expression module decodes ERK signal duration
Molecular Systems Biology 13 (5): 928 (2017-05-03)



Buonocore F.; Kuehnen P.; Suntharalingham J.P.; Del Valle I.; Digweed M.; Stachelscheid H.; Khajavi N.; Didi M.; Brady A.F.; Blankenstein O.; Procter A.M.; Dimitri P.; Wales J.K.H.; Ghirri P.; Knoebl D.; Strahm B.; Erlacher M.; Wlodarski M.W.; Chen W.; Kokai G.K.; Anderson G.; Morrogh D.; Moulding D.A.; McKee S. A.; Niemeyer C.M.; Grueters A.; Achermann J.C.
Somatic mutations and progressive monosomy modify SAMD9-related phenotypes in humans
Journal of Clinical Investigation 127 (5): 1700-1713 (2017-05-01)



Park T.J.; Reznick J.; Peterson B.L.; Blass G.; Omerbasic D.; Bennett N.C.; Kuich P.H.J.L.; Zasada C.; Browe B.M.; Hamann W.; Applegate D.T.; Radke M.H.; Kosten T.; Lutermann H.; Gavaghan V.; Eigenbrod O.; Begay V.; Amoroso V. G.; Govind V.; Minshall R.D.; Smith E.S.J.; Larson J.; Gotthardt M.; Kempa S.; Lewin G.R.
Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat
Science 356 (6335): 307-311 (2017-04-21)



Pamudurti NR.; Bartok O.; Jens M.; Ashwal-Fluss R.; Stottmeister C.; Ruhe L.; Hanan M.; Wyler E.; Perez-Hernandez D.; Ramberger E.; Shenzis S.; Samson M.; Dittmar G.; Landthaler M.; Chekulaeva M.; Rajewsky N.; Kadener S.
Translation of circRNAs
Molecular Cell 66 (1): 9-21.e7 (2017-04-06)



Legnini I.; Di Timoteo G.; Rossi F.; Morlando M.; Briganti F.; Sthandier O.; Fatica A.; Santini T.; Andronache A.; Wade M.; Laneve P.; Rajewsky N.; Bozzoni I.
Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis
Molecular Cell 66 (1): 22-37.e9 (2017-04-06)



Beagrie R.A.; Scialdone A.; Schueler M.; Kraemer D.C.A.; Chotalia M.; Xie S.Q.; Barbieri M.; de Santiago I.; Lavitas L.M.; Branco M.R.; Fraser J.; Dostie J.; Game L.; Dillon N.; Edwards P.A.W.; Nicodemi M.; Pombo A.
Complex multi-enhancer contacts captured by genome architecture mapping
Nature 543 (7646): 519-524 (2017-03-23)



Meszaros B.; Kumar M.; Gibson T.J.; Uyar B.; Dosztanyi Z.
Degrons in cancer
Science Signaling 10 (470): eaak9982 (2017-03-14)



Bielow C.; Mastrobuoni G.; Orioli M.; Kempa S.
On mass ambiguities in high-resolution shotgun lipidomics
Analytical Chemistry 89 (5): 2986-2994 (2017-03-07)



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)



Torlai Triglia E.; Rito Tiago; Pombo A.
A finer print than TADs: PRC1-mediated domains
Molecular Cell 65 (3): 373-375 (2017-02-02)



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)



Schmidt F.; Gasparoni N.; Gasparoni G.; Gianmoena K.; Cadenas C.; Polansky J.K.; Ebert P.; Nordstroem K.; Barann M.; Sinha A.; Froehler S.; Xiong J.; Dehghani Amirabad A.; Behjati Ardakani F.; Hutter B.; Zipprich G.; Felder B.; Eils J.; Brors B.; Chen W.; Hengstler J.G.; Hamann A.; Lengauer T.; Rosenstiel P.; Walter J.; Schulz M.H.
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
Nucleic Acids Research 45 (1): 54-66 (2017-01-09)



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)



Adolphe C.; Junker J.P.; Lyubimova A.; van Oudenaarden A.; Wainwright B.
Patched receptors sense, interpret and establish an epidermal Hedgehog signalling gradient
Journal of Investigative Dermatology 137 (1): 179-186 (2017-01)



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)



2016

Xiao M.S.; Zhang B.; Li Y.S.; Gao Q.; Sun W.; Chen W.
Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
Molecular Systems Biology 12 (12): 890 (2016-12-08)



Beagrie R.A.; Pombo A.
Examining topological domain influence on enhancer function
Developmental Cell 39 (5): 523-524 (2016-12-05)



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)



Durek P.; Nordstroem K.; Gasparoni G.; Salhab A.; Kressler C.; de Almeida M.; Bassler K.; Ulas T.; Schmidt F.; Xiong J.; Glazar P.; Klironomos F.; Sinha A.; Kinkley S.; Yang X.; Arrigoni L.; Amirabad A..; Ardakani F.B.; Feuerbach L.; Gorka O.; Ebert P.; Mueller F.; Li N.; Frischbutter S.; Schlickeiser S.; Cendon C.; Froehler S.; Felder B.; Gasparoni N.; Imbusch C.D.; Hutter B.; Zipprich G.; Tauchmann Y.; Reinke S.; Wassilew G.; Hoffmann U.; Richter A.S.; Sieverling L.; Chang H.D.; Syrbe U.; Kalus U.; Eils J.; Brors B.; Manke T.; Ruland J.; Lengauer T.; Rajewsky N.; Chen W.; Dong J.; Sawitzki B.; Chung H.R.; Rosenstiel P.; Schulz M.H.; Schultze J.L.; Radbruch A.; Walter J.; Hamann A.; Polansky J.K.
Epigenomic profiling of human CD4+ T cells supports a linear differentiation model and highlights molecular regulators of memory development
Immunity 45 (5): 1148-1161 (2016-11-15)



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)



Kaplan O.I.; Berber B.; Hekim N.; Doluca O.
G-quadruplex prediction in E. coli genome reveals a conserved putative G-quadruplex-hairpin-duplex switch
Nucleic Acids Research 44 (19): 9083-9095 (2016-11-02)



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)



McShane E.; Sin C.; Zauber H.; Wells J.N.; Donnelly N.; Wang X.; Hou J.; Chen W.; Storchova Z.; Marsh J.A.; Valleriani A.; Selbach M.
Kinetic analysis of protein stability reveals age-dependent degradation
Cell 167 (3): 803-815 (2016-10-20)



Franke M.; Ibrahim D.M.; Andrey G.; Schwarzer W.; Heinrich V.; Schoepflin R.; Kraft K.; Kempfer R.; Jerkovic I.; Chan W.L.; Spielmann M.; Timmermann B.; Wittler L.; Kurth I.; Cambiaso P.; Zuffardi O.; Houge G.; Lambie L.; Brancati F.; Pombo A.; Vingron M.; Spitz F.; Mundlos S.
Formation of new chromatin domains determines pathogenicity of genomic duplications
Nature 538 (7624): 265-269 (2016-10-13)



Grunert M.; Dorn C.; Cui H.; Dunkel I.; Schulz K.; Schoenhals S.; Sun W.; Berger F.; Chen W.; Sperling S.R.
Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases
Cardiovascular Research 112 (1): 464-477 (2016-10-01)



Stellos K.; Gatsiou A.; Stamatelopoulos K.; Perisic Matic L.; John D.; Lunella F.F.; Jae N.; Rossbach O.; Amrhein C.; Sigala F.; Boon R.A.; Fuertig B.; Manavski Y.; You X.; Uchida S.; Keller T.; Boeckel J.N.; Franco-Cereceda A.; Maegdefessel L.; Chen W.; Schwalbe H.; Bindereif A.; Eriksson P.; Hedin U.; Zeiher A.M.; Dimmeler S.
Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation
Nature Medicine 22 (10): 1140-1150 (2016-10)



Plauth A.; Geikowski A.; Cichon S.; Wowro S.J.; Liedgens L.; Rousseau M.; Weidner C.; Fuhr L.; Kliem M.; Jenkins G.; Lotito S.; Wainwright L.J.; Sauer S.
Hormetic shifting of redox environment by pro-oxidative resveratrol protects cells against stress
Free Radical Biology and Medicine 99: 608-622 (2016-10)



Chekulaeva M.; Landthaler M.
Eyes on translation
Molecular Cell 63 (6): 918-925 (2016-09-15)



Seelk S.; Adrian-Kalchhauser I.; Hargitai B.; Hajduskova M.; Gutnik S.; Tursun B.; Ciosk R.
Increasing Notch signaling antagonizes PRC2-mediated silencing to promote reprograming of germ cells into neurons
eLife 5: e15477 (2016-09-07)



Mauri M.; Kirchner M.; Aharoni R.; Ciolli Mattioli C.; van den Bruck D.; Gutkovitch N.; Modepalli V.; Selbach M.; Moran Y.; Chekulaeva M.
Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution
Nucleic Acids Research 45 (2): 938-950 (2016-09-06)



Roest H.L.; Sachsenberg T.; Aiche S.; Bielow C.; Weisser H.; Aicheler F.; Andreotti S.; Ehrlich H.C.; Gutenbrunner P.; Kenar E.; Liang X.; Nahnsen S.; Nilse L.; Pfeuffer J.; Rosenberger G.; Rurik M.; Schmitt U.; Veit J.; Walzer M.; Wojnar D.; Wolski W.E.; Schilling O.; Choudhary J.S.; Malmstroem L.; Aebersold R.; Reinert K.; Kohlbacher O.
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Nature Methods 13 (9): 741-748 (2016-09)



Chen W.; Schuman E.
Circular RNAs in brain and other tissues: a functional enigma
Trends in Neurosciences 39 (9): 597-604 (2016-09)



Simandi Z.; Horvath A.; Wright L.C.; Cuaranta-Monroy I.; De Luca I.; Karolyi K.; Sauer S.; Deleuze J.F.; Gudas L.J.; Cowley S.M.; Nagy L.
OCT4 acts as an integrator of pluripotency and signal-induced differentiation
Molecular Cell 63 (4): 647-661 (2016-08-18)



Kinkley S.; Helmuth J.; Polansky J.K.; Dunkel I.; Gasparoni G.; Froehler S.; Chen W.; Walter J.; Hamann A.; Chung H.R.
reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells
Nature Communications 7: 12514 (2016-08-17)



Waaijers S.; Munoz J.; Berends C.; Ramalho J.J.; Goerdayal S.S.; Low T.Y.; Zoumaro-Djayoon A.D.; Hoffmann M.; Koorman T.; Tas R.P.; Harterink M.; Seelk S.; Kerver J.; Hoogenraad C.C.; Bossinger O.; Tursun B.; van den Heuvel S.; Heck A.J.R.; Boxem M.
A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large
BMC Biology 14 (1): 66 (2016-08-09)



Solana J.; Irimia M.; Ayoub S.; Orejuela M.R.; Zywitza V.; Jens M.; Tapial J.; Ray D.; Morris Q.D.; Hughes T.R.; Blencowe B.J.; Rajewsky N.
Conserved functional antagonism of CELF 1 and MBNL proteins controls stem cell-specific alternative splicing in planarians
eLife 5: e16797 (2016-08-09)



Wallmeier J.; Shiratori H.; Dougherty G.W.; Edelbusch C.; Hjeij R.; Loges N.T.; Menchen T.; Olbrich H.; Pennekamp P.; Raidt J.; Werner C.; Minegishi K.; Shinohara K.; Asai Y.; Takaoka K.; Lee C.; Griese M.; Memari Y.; Durbin R.; Kolb-Kokocinski A.; Sauer S.; Wallingford J.B.; Hamada H.; Omran H.
TTC25 deficiency results in defects of the outer dynein arm docking machinery and primary ciliary dyskinesia with left-right body asymmetry randomization
American Journal of Human Genetics 99 (2): 460-469 (2016-08-04)



Le H.Q.; Ghatak S.; Yeung C.Y.C.; Tellkamp F.; Guenschmann C.; Dieterich C.; Yeroslaviz A.; Habermann B.; Pombo A.; Niessen C.M.; Wickstroem S.A.
Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment
Nature Cell Biology 18 (8): 864-875 (2016-08)



Wallner S.; Schroeder C.; Leitao E.; Berulava T.; Haak C.; Beisser D.; Rahmann S.; Richter A.S.; Manke T.; Boenisch U.; Arrigoni L.; Froehler S.; Klironomos F.; Chen W.; Rajewsky N.; Mueller F.; Ebert P.; Lengauer T.; Barann M.; Rosenstiel P.; Gasparoni G.; Nordstroem K.; Walter J.; Brors B.; Zipprich G.; Felder B.; Klein-Hitpass L.; Attenberger C.; Schmitz G.; Horsthemke B.
Epigenetic dynamics of monocyte-to-macrophage differentiation
Epigenetics & Chromatin 9: 33 (2016-07-29)



Wang X.; Hou J.; Quedenau C.; Chen W.
Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals
Molecular Systems Biology 12 (7): 875 (2016-07-18)



Hasler D.; Lehmann G.; Murakawa Y.; Klironomos F.; Jakob L.; Graesser F.A.; Rajewsky N.; Landthaler M.; Meister G.
The Lupus autoantigen La prevents Mis-channeling of tRNA fragments into the human microRNA pathway
Molecular Cell 63 (1): 110-124 (2016-07-07)



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)



Schmidt V.; Schulz N.; Yan X.; Schuermann A.; Kempa S.; Kern M.; Blueher M.; Poy M.N.; Olivecrona G.; Willnow T.E.
SORLA facilitates insulin receptor signaling in adipocytes and exacerbates obesity
Journal of Clinical Investigation 126 (7): 2706-2720 (2016-07-01)



Van Haute L.; Dietmann S.; Kremer L.; Hussain S.; Pearce S.F.; Powell C.A.; Rorbach J.; Lantaff R.; Blanco S.; Sauer S.; Kotzaeridou U.; Hoffmann G.F.; Memari Y.; Kolb-Kokocinski A.; Durbin R.; Mayr J.A.; Frye M.; Prokisch H.; Minczuk M.
Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3
Nature Communications 7: 12039 (2016-06-30)



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)



Brachs M.; Wiegand S.; Leupelt V.; Ernert A.; Kintscher U.; Jumpertz von Schwarzenberg R.; Decker A.M.; Bobbert T.; Huebner N.; Chen W.; Krude H.; Spranger J.; Mai K.
ANP system activity predicts variability of fat mass reduction and insulin sensitivity during weight loss
Metabolism 65 (6): 935-943 (2016-06)



Bertelsen B.; Nazaryan-Petersen L.; Sun W.; Mehrjouy M.M.; Xie G.; Chen W.; Hjermind L.E.; Taschner P.E.M.; Tuemer Z.
A germline chromothripsis event stably segregating in 11 individuals through three generations
Genetics in Medicine 18 (5): 494-500 (2016-05)



Schmied C.; Steinbach P.; Pietzsch T.; Preibisch S.; Tomancak P.
An automated workflow for parallel processing of large multiview SPIM recordings
Bioinformatics 32 (7): 1112-1114 (2016-04-01)



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)



Gogol-Doering A.; Ammar I.; Gupta S.; Bunse M.; Miskey C.; Chen W.; Uckert W.; Schulz T.F.; Izsvak Z.; Ivics Z.
Genome-wide profiling reveals remarkable parallels between insertion site selection properties of the MLV retrovirus and the piggyBac transposon in primary human CD4+ T cells
Molecular Therapy 24 (3): 592-606 (2016-03)



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)



Naujoks J.; Tabeling C.; Dill B.D.; Hoffmann C.; Brown A.S.; Kunze M.; Kempa S.; Peter A.; Mollenkopf H.J.; Dorhoi A.; Kershaw O.; Gruber A.D.; Sander L.E.; Witzenrath M.; Herold S.; Nerlich A.; Hocke A.C.; van Driel I.; Suttorp N.; Bedoui S.; Hilbi H.; Trost M.; Opitz B.
IFNs modify the proteome of Legionella-containing vacuoles and restrict infection via IRG1-derived itaconic acid
PLoS Pathogens 12 (2): e1005408 (2016-02-01)



Cheng Z.; Teo G.; Krueger S.; Rock T.M.; Koh H.W.L.; Choi H.; Vogel C.
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
Molecular Systems Biology 12 (1): 855 (2016-01-20)



Fritsche-Guenther R.; Witzel F.; Kempa S.; Brummer T.; Sers C.; Bluethgen N.
Effects of RAF inhibitors on PI3K/AKT signalling depend on mutational status of the RAS/RAF signalling axis
Oncotarget 7 (7): 7960-7969 (2016-01-20)



Glahs A.; Zinzen R.P.
Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions
EMBO Journal 35 (1): 1-3 (2016-01-04)



2015

Rohwer N.; Bindel F.; Grimm C.; Lin S.J.; Wappler J.; Klinger B.; Bluethgen N.; Du Bois I.; Schmeck B.; Lehrach H.; de Graauw M.; Goncalves E.; Saez-Rodriguez J.; Tan P.; Grabsch H.I.; Prigione A.; Kempa S.; Cramer T.
Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1A
Oncotarget 7 (6): 6693-6710 (2015-12-29)



Fraser J.; Ferrai C.; Chiariello A.M.; Schueler M.; Rito T.; Laudanno G.; Barbieri M.; Moore B.L.; Kraemer D.C.A.; Aitken S.; Xie S.Q.; Morris K.J.; Itoh M.; Kawaji H.; Jaeger I.; Hayashizaki Y.; Carninci P.; Forrest A.R.R.; Semple C.A.; Dostie J.; Pombo A.; Nicodemi M.
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
Molecular Systems Biology 11 (12): 852 (2015-12-23)



Dias J.D.; Rito T.; Torlai Triglia E.; Kukalev A.; Ferrai C.; Chotalia M.; Brookes E.; Kimura H.; Pombo A.
Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells
eLife 4: e11215 (2015-12-19)



von Eyss B.; Jaenicke L.A.; Kortlever R.M.; Royla N.; Wiese K.E.; Letschert S.; McDuffus L.A.; Sauer M.; Rosenwald A.; Evan G.I.; Kempa S.; Eilers M.
A MYC-driven change in mitochondrial dynamics limits YAP/TAZ function in mammary epithelial cells and breast cancer
Cancer Cell 28 (6): 743-757 (2015-12-14)



Shen S.Q.; Wei H.X.; Fu Y.H.; Zhang H.; Mo Q.Y.; Wang X.J.; Deng S.Q.; Zhao W.; Liu Y.; Feng X.S.; Chen W.; Peng H.J.
Multiple sources of infection and potential endemic characteristics of the large outbreak of dengue in Guangdong in 2014
Scientific Reports 5: 16913 (2015-11-23)



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)



Aue A.; Hinze C.; Walentin K.; Ruffert J.; Yurtdas Y.; Werth M.; Chen W.; Rabien A.; Kilic E.; Schulzke J.D.; Schumann M.; Schmidt-Ott K.M.
A grainyhead-like 2/Ovo-like 2 pathway regulates renal epithelial barrier function and lumen expansion
Journal of the American Society of Nephrology 26 (11): 2704-2715 (2015-11)



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)



Boeckel J.N.; Jae N.; Heumueller A.W.; Chen W.; Boon R.A.; Stellos K.; Zeiher A.M.; John D.; Uchida S.; Dimmeler S.
Identification and characterization of hypoxia-regulated endothelial circular RNA
Circulation Research 117 (10): 884-890 (2015-10-23)



Haghikia A.; Joerg S.; Duscha A.; Berg J.; Manzel A.; Waschbisch A.; Hammer A.; Lee D.H.; May C.; Wilck N.; Balogh A.; Ostermann A.I.; Schebb N.H.; Akkad D.A.; Grohme D.A.; Kleinewietfeld M.; Kempa S.; Thoene J.; Demir S.; Mueller D.N.; Gold R.; Linker R.A.
Dietary fatty acids directly impact central nervous system autoimmunity via the small intestine
Immunity 43 (4): 817-829 (2015-10-20)



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)



Witzel F.; Fritsche-Guenther R.; Lehmann N.; Sieber A.; Bluethgen N.
Analysis of impedance-based cellular growth assays
Bioinformatics 31 (16): 2705-2712 (2015-08-15)



Hou J.; Wang X.; McShane E.; Zauber H.; Sun W.; Selbach M.; Chen W.
Extensive allele-specific translational regulation in hybrid mice
Molecular Systems Biology 11 (8): 825 (2015-08-07)



Hartmann L.; Pedrotti L.; Weiste C.; Fekete A.; Schierstaedt J.; Goettler J.; Kempa S.; Krischke M.; Dietrich K.; Mueller M.J.; Vicente-Carbajosa J.; Hanson J.; Droege-Laser W.
Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in arabidopsis roots
Plant Cell 27 (8): 2244-2260 (2015-08)



Murakawa Y.; Hinz M.; Mothes J.; Schuetz A.; Uhl M.; Wyler E.; Yasuda T.; Mastrobuoni G.; Friedel C.C.; Doelken L.; Kempa S.; Schmidt-Supprian M.; Bluethgen N.; Backofen R.; Heinemann U.; Wolf J.; Scheidereit C.; Landthaler M.
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-{kappa}B pathway
Nature Communications 6: 7367 (2015-07-14)



Gao Q.; Sun W.; Ballegeer M.; Libert C.; Chen W.
Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing
Molecular Systems Biology 11 (7): 816 (2015-07-01)



Rybak-Wolf A.; Stottmeister C.; Glazar P.; Jens M.; Pino N.; Giusti S.; Hanan M.; Behm M.; Bartok O.; Ashwal-Fluss R.; Herzog M.; Schreyer L.; Papavasileiou P.; Ivanov A.; Oehman M.; Refojo D.; Kadener S.; Rajewsky N.
Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed
Molecular Cell 58 (5): 870-885 (2015-06-04)



Schafer S.; Adami E.; Heinig M.; Costa Rodrigues K.E.; Kreuchwig F.; Silhavy J.; van Heesch S.; Simaite D.; Rajewsky N.; Cuppen E.; Pravenec M.; Vingron M.; Cook S.A.; Hubner N.
Translational regulation shapes the molecular landscape of complex disease phenotypes
Nature Communications 6: 7200 (2015-05-26)



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)



Junker J.P.; van Oudenaarden A.
Single-cell transcriptomics enters the age of mass production
Molecular Cell 58 (4): 563-564 (2015-05-21)



Hosp F.; Vossfeldt H.; Heinig M.; Vasiljevic D.; Arumughan A.; Wyler E.; Landthaler M.; Hubner N.; Wanker E.E.; Lannfelt L.; Ingelsson M.; Lalowski M.; Voigt A.; Selbach M.
Quantitative interaction proteomics of neurodegenerative disease proteins
Cell Reports 11 (7): 1134-1146 (2015-05-19)



Jia S.; Ivanov A.; Blasevic D.; Mueller T.; Purfuerst B.; Sun W.; Chen W.; Poy M.N.; Rajewsky N.; Birchmeier C.
Insm1 cooperates with Neurod1 and Foxa2 to maintain mature pancreatic {beta}-cell function
EMBO Journal 34 (10): 1417-1433 (2015-05-12)



Zhang B.; Calado D.P.; Wang Z.; Froehler S.; Koechert K.; Qian Y.; Koralov S.B.; Schmidt-Supprian M.; Sasaki Y.; Unitt C.; Rodig S.; Chen W.; Dalla-Favera R.; Alt F.W.; Pasqualucci L.; Rajewsky K.
An oncogenic role for alternative NF-{kappa}B signaling in DLBCL revealed upon deregulated BCL6 expression
Cell Reports 11 (5): 715-726 (2015-05-05)



You X.; Vlatkovic I.; Babic A.; Will T.; Epstein I.; Tushev G.; Akbalik G.; Wang M.; Glock C.; Quedenau C.; Wang X.; Hou J.; Liu H.; Sun W.; Sambandan S.; Chen T.; Schuman E.M.; Chen W.
Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity
Nature Neuroscience 18 (4): 603-610 (2015-04)



Pombo A.; Dillon N.
Three-dimensional genome architecture: players and mechanisms
Nature Reviews Molecular Cell Biology 16 (4): 245-257 (2015-04)



Drenckhahn J.D.; Strasen J.; Heinecke K.; Langner P.; Yin K.V.; Skole F.; Hennig M.; Spallek B.; Fischer R.; Blaschke F.; Heuser A.; Cox T.C.; Black M.J.; Thierfelder L.
Impaired myocardial development resulting in neonatal cardiac hypoplasia alters postnatal growth and stress response in the heart
Cardiovascular Research 106 (1): 43-54 (2015-04-01)



Moussaieff A.; Rouleau M.; Kitsberg D.; Cohen M.; Levy G.; Barasch D.; Nemirovski A.; Shen-Orr S.; Laevsky I.; Amit M.; Bomze D.; Elena-Herrmann B.; Scherf T.; Nissim-Rafinia M.; Kempa S.; Itskovitz-Eldor J.; Meshorer E.; Aberdam D.; Nahmias Y.
Glycolysis-mediated changes in acetyl-CoA and histone acetylation control the early differentiation of embryonic stem cells
Cell Metabolism 21 (3): 392-402 (2015-03-03)



Arner E.; Daub C.O.; Vitting-Seerup K.; Andersson R.; Lilje B.; Drablos F.; Lennartsson A.; Roennerblad M.; Hrydziuszko O.; Vitezic M.; Freeman T.C.; Alhendi A.; Arner P.; Axton R.; Baillie J.K.; Beckhouse A.; Bodega B.; Briggs J.; Brombacher F.; Davis M.; Detmar M.; Ehrlund A.; Endoh M.; Eslami A.; Fagiolini M.; Fairbairn L.; Faulkner G.J.; Ferrai C.; Fisher M.E.; Forrester L.; Goldowitz D.; Guler R.; Ha T.; Hara M.; Herlyn M.; Ikawa T.; Kai C.; Kawamoto H.; Khachigian L.; Klinken P.S.; Kojima S.; Koseki H.; Klein S.; Mejhert N.; Miyaguchi K.; Mizuno Y.; Morimoto M.; Morris K.J.; Mummery C.; Nakachi Y.; Ogishima S.; Okada-Hatakeyama M.; Okazaki Y.; Orlando V.; Ovchinnikov D.; Passier R.; Patrikakis M.; Pombo A.; Qin X.Y.; Roy S.; Sato H.; Savvi S.; Saxena A.; Schwegmann A.; Sugiyama D.; Swoboda R.; Tanaka H.; Tomoiu A.; Winteringham L.N.; Wolvetang E.; Yanagi-Mizuochi C.; Yoneda M.; Zabierowski S.; Zhang P.; Abugessaisa I.; Bertin N.; Diehl A.D.; Fukuda S.; Furuno M.; Harshbarger J.; Hasegawa A.; Hori F.; Ishikawa-Kato S.; Ishizu Y.; Itoh M.; Kawashima T.; Kojima M.; Kondo N.; Lizio M.; Meehan T.F.; Mungall C.J.; Murata M.; Nishiyori-Sueki H.; Sahin S.; Sato-Nagao S.; Severin J.; de Hoon M.J.; Kawai J.; Kasukawa T.; Lassmann T.; Suzuki H.; Kawaji H.; Summers K.M.; Wells C.; Hume D.A.; Forrest A.R.R.; Sandelin A.; Carninci P.; Hayashizaki Y.
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Science 347 (6225): 1010-1014 (2015-02-27)



Blevins R.; Bruno L.; Carroll T.; Elliott J.; Marcais A.; Loh C.; Hertweck A.; Krek A.; Rajewsky N.; Chen C.Z.; Fisher A.G.; Merkenschlager M.
microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes
PLoS Genetics 11 (2): e1005020 (2015-02-25)



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)



Hanack C.; Moroni M.; Lima W.C.; Wende H.; Kirchner M.; Adelfinger L.; Schrenk-Siemens K.; Tappe-Theodor A.; Wetzel C.; Kuich P.H.; Gassmann M.; Roggenkamp D.; Bettler B.; Lewin G.R.; Selbach M.; Siemens J.
GABA blocks pathological but not acute TRPV1 pain signals
Cell 160 (4): 759-770 (2015-02-12)



Jens M.; Rajewsky N.
Competition between target sites of regulators shapes post-transcriptional gene regulation
Nature Reviews Genetics 16 (2): 113-126 (2015-02)



Blin K.; Dieterich C.; Wurmus R.; Rajewsky N.; Landthaler M.; Akalin A.
DoRiNA 2.0-upgrading the doRiNA database of RNA interactions in post-transcriptional regulation
Nucleic Acids Research 43 (Database issue): D160-D167 (2015-01-28)



Ivanov A.; Memczak S.; Wyler E.; Torti F.; Porath H.T.; Orejuela M.R.; Piechotta M.; Levanon E.Y.; Landthaler M.; Dieterich C.; Rajewsky N.
Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals
Cell Reports 10 (2): 170-177 (2015-01-13)



Schrenk-Siemens K.; Wende H.; Prato V.; Song K.; Rostock C.; Loewer A.; Utikal J.; Lewin G.R.; Lechner S.G.; Siemens J.
PIEZO2 is required for mechanotransduction in human stem cell-derived touch receptors
Nature Neuroscience 18 (1): 10-16 (2015-01)



Doddaballapur A.; Michalik K.M.; Manavski Y.; Lucas T.; Houtkooper R.H.; You X.; Chen W.; Zeiher A.M.; Potente M.; Dimmeler S.; Boon R.A.
Laminar shear stress inhibits endothelial cell metabolism via Kruppel-like factor 2-mediated repression of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-3
Arteriosclerosis Thrombosis and Vascular Biology 35 (1): 137-145 (2015-01)



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)



2014

Wang J.; Xie G.; Singh M.; Ghanbarian A.T.; Rasko T.; Szvetnik A.; Cai H.; Besser D.; Prigione A.; Fuchs N.V.; Schumann G.G.; Chen W.; Lorincz M.C.; Ivics Z.; Hurst L.D.; Izsvak Z.
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells
Nature 516 (7531): 405-409 (2014-12-18)



Rampal R.; Akalin A.; Madzo J.; Vasanthakumar A.; Pronier E.; Patel J.; Li Y.; Ahn J.; Abdel-Wahab O.; Shih A.; Lu C.; Ward P.S.; Tsai J.J.; Hricik T.; Tosello V.; Tallman J.E.; Zhao X.; Daniels D.; Dai Q.; Ciminio L.; Aifantis I.; He C.; Fuks F.; Tallman M.S.; Ferrando A.; Nimer S.; Paietta E.; Thompson C.B.; Licht J.D.; Mason C.E.; Godley L.A.; Melnick A.; Figueroa M.E.; Levine R.L.
DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia
Cell Reports 9 (5): 1841-1855 (2014-12-11)



Schuetz A.; Murakawa Y.; Rosenbaum E.; Landthaler M.; Heinemann U.
Roquin binding to target mRNAs involves a winged helix-turn-helix motif
Nature Communications 5: 5701 (2014-12-11)



Ost A.; Lempradl A.; Casas E.; Weigert M.; Tiko T.; Deniz M.; Pantano L.; Boenisch U.; Itskov P.M.; Stoeckius M.; Ruf M.; Rajewsky N.; Reuter G.; Iovino N.; Ribeiro C.; Alenius M.; Heyne S.; Vavouri T.; Pospisilik J.A.
Paternal diet defines offspring chromatin state and intergenerational obesity
Cell 159 (6): 1352-1364 (2014-12-04)



Obermayer B.; Rajewsky N.
Mixed messages: re-initiation factors regulate translation of animal mRNAs
Cell Research 24 (12): 1383-1384 (2014-12)



Maaskola J.; Rajewsky N.
Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models
Nucleic Acids Research 42 (21): 12995-13011 (2014-12-01)



Borcherds W.; Theillet F.X.; Katzer A.; Finzel A.; Mishall K.M.; Powell A.T.; Wu H.; Manieri W.; Dieterich C.; Selenko P.; Loewer A.; Daughdrill G.W.
Disorder and residual helicity alter p53-Mdm2 binding affinity and signaling in cells
Nature Chemical Biology 10 (12): 1000-1002 (2014-12)



Rybak-Wolf A.; Jens M.; Murakawa Y.; Herzog M.; Landthaler M.; Rajewsky N.
A variety of dicer substrates in human and C. elegans
Cell 159 (5): 1153-1167 (2014-11-20)



Gonzalez E.; Rother M.; Kerr M.C.; Al-Zeer M.A.; Abu-Lubad M.; Kessler M.; Brinkmann V.; Loewer A.; Meyer T.F.
Chlamydia infection depends on a functional MDM2-p53 axis
Nature Communications 5: 5201 (2014-11-13)



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)



Gustafsson M.; Nestor C.E.; Zhang H.; Barabasi A.L.; Baranzini S.; Brunak S.; Chung K.F.; Federoff H.J.; Gavin A.C.; Meehan R.R.; Picotti P.; Pujana M.A.; Rajewsky N.; Smith K.G.C.; Sterk P.J.; Villoslada P.; Benson M.
Modules, networks and systems medicine for understanding disease and aiding diagnosis
Genome Medicine 6 (10): 82 (2014-10-17)



Peter S.; Borkowska E.; Drayton R.M.; Rakhit C.P.; Noon A.P.; Chen W.; Catto J.W.F.
Identification of differentially expressed long noncoding RNAs in bladder cancer
Clinical Cancer Research 20 (20): 5311-5321 (2014-10-15)



Ashwal-Fluss R.; Meyer M.; Pamudurti N.R.; Ivanov A.; Bartok O.; Hanan M.; Evantal N.; Memczak S.; Rajewsky N.; Kadener S.
circRNA biogenesis competes with pre-mRNA splicing
Molecular Cell 56 (1): 55-66 (2014-10-02)



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)



Stoeckius M.; Gruen D.; Kirchner M.; Ayoub S.; Torti F.; Piano F.; Herzog M.; Selbach M.; Rajewsky N.
Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism
EMBO Journal 33 (16): 1751-1766 (2014-08-18)



Stoeckius M.; Gruen D.; Rajewsky N.
Paternal RNA contributions in the Caenorhabditis elegans zygote
EMBO Journal 33 (16): 1740-1750 (2014-08-18)



Libri V.; Yandim C.; Athanasopoulos S.; Loyse N.; Natisvili T.; Law P.P.; Chan P.K.; Mohammad T.; Mauri M.; Tam K.T.; Leiper J.; Piper S.; Ramesh A.; Parkinson M.H.; Huson L.; Giunti P.; Festenstein R.
Epigenetic and neurological effects and safety of high-dose nicotinamide in patients with Friedreich's ataxia: an exploratory, open-label, dose-escalation study
Lancet 384 (9942): 504-513 (2014-08-09)



Maatz H.; Jens M.; Liss M.; Schafer S.; Heinig M.; Kirchner M.; Adami E.; Rintisch C.; Dauksaite V.; Radke M.H.; Selbach M.; Barton P.J.R.; Cook S.A.; Rajewsky N.; Gotthardt M.; Landthaler M.; Hubner N.
RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing
Journal of Clinical Investigation 124 (8): 3419-3430 (2014-08-01)



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)



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)



Grosswendt S.; Filipchyk A.; Manzano M.; Klironomos F.; Schilling M.; Herzog M.; Gottwein E.; Rajewsky N.
Unambiguous identification of miRNA:target site interactions by different types of ligation reactions
Molecular Cell 54 (6): 1042-1054 (2014-06-19)



Benitah S.A.; Bracken A.; Dou Y.; Huangfu D.; Ivanova N.; Koseki H.; Laurent L.; Lim D.A.; Meshorer E.; Pombo A.; Sander M.; Xu G.L.
Stem cell epigenetics: looking forward
Cell Stem Cell 14 (6): 706-709 (2014-06-05)



Nicodemi M.; Pombo A.
Models of chromosome structure
Current Opinion in Cell Biology 28: 90-95 (2014-06-01)



Rintisch C.; Heinig M.; Bauerfeind A.; Schafer S.; Mieth C.; Patone G.; Hummel O.; Chen W.; Cook S.; Cuppen E.; Colome-Tatche M.; Johannes F.; Jansen R.C.; Neil H.; Werner M.; Pravenec M.; Vingron M.; Hubner N.
Natural variation of histone modification and its impact on gene expression in the rat genome
Genome Research 24 (6): 942-953 (2014-06)



Gregersen L.H.; Schueler M.; Munschauer M.; Mastrobuoni G.; Chen W.; Kempa S.; Dieterich C.; Landthaler M.
MOV10 is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs
Molecular Cell 54 (4): 573-585 (2014-05-22)



Bazzini A.A.; Johnstone T.G.; Christiano R.; Mackowiak S.D.; Obermayer B.; Fleming E.S.; Vejnar C.E.; Lee M.T.; Rajewsky N.; Walther T.C.; Giraldez A.J.
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
EMBO Journal 33 (9): 981-993 (2014-05-02)



Michalik K.M.; You X.; Manavski Y.; Doddaballapur A.; Zoernig M.; Braun T.; John D.; Ponomareva Y.; Chen W.; Uchida S.; Boon R.A.; Dimmeler S.
Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth
Circulation Research 114 (9): 1389-1397 (2014-04-25)



Roedelsperger C.; Neher R.A.; Weller A.M.; Eberhardt G.; Witte H.; Mayer W.E.; Dieterich C.; Sommer R.J.
Characterization of genetic diversity in the nematode pristionchus pacificus from population-scale resequencing data
Genetics 196 (4): 1153-1165 (2014-04)



Gruen D.; Kirchner M.; Thierfelder N.; Stoeckius M.; Selbach M.; Rajewsky N.
Conservation of mRNA and protein expression during development of C. elegans
Cell Reports 6 (3): 565-577 (2014-02-13)



Schueler M.; Munschauer M.; Gregersen L.H.; Finzel A.; Loewer A.; Chen W.; Landthaler M.; Dieterich C.
Differential protein occupancy profiling of the mRNA transcriptome
Genome Biology 15 (1): R15 (2014-01-13)



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)



Tattikota S.G.; Rathjen T.; McAnulty S.J.; Wessels H.H.; Akerman I.; van de Bunt M.; Hausser J.; Esguerra J.L.S.; Musahl A.; Pandey A.K.; You X.; Chen W.; Herrera P.L.; Johnson P.R.; O'Carroll D.; Eliasson L.; Zavolan M.; Gloyn A.L.; Ferrer J.; Shalom-Feuerstein R.; Aberdam D.; Poy M.N.
Argonaute2 mediates compensatory expansion of the pancreatic {beta} cell
Cell Metabolism 19 (1): 122-134 (2014-01-07)



Kuehnen P.; Turan S.; Froehler S.; Gueran T.; Abali S.; Biebermann H.; Bereket A.; Grueters A.; Chen W.; Krude H.
Identification of PENDRIN (SLC26A4) mutations in patients with congenital hypothyroidism and "apparent" thyroid dysgenesis
Journal of Clinical Endocrinology and Metabolism 99 (1): E169-E176 (2014-01)



Cochella L.; Tursun B.; Hsieh Y.W.; Galindo S.; Johnston R.J.; Chuang C.F.; Hobert O.
Two distinct types of neuronal asymmetries are controlled by the Caenorhabditis elegans zinc finger transcription factor die-1
Genes & Development 28 (1): 34-43 (2014-01-01)



2013

Cevik S.; Sanders A.A.W.M.; Van Wijk E.; Boldt K.; Clarke L.; van Reeuwijk J.; Hori Y.; Horn N.; Hetterschijt L.; Wdowicz A.; Mullins A.; Kida K.; Kaplan O.I.; van Beersum S.E.C.; Man Wu K.; Letteboer S.J.F.; Mans D.A.; Katada T.; Kontani K.; Ueffing M.; Roepman R.; Kremer H.; Blacque O.E.
Active transport and diffusion barriers restrict Joubert Syndrome-associated ARL13B/ARL-13 to an Inv-like ciliary membrane subdomain
PLoS Genetics 9 (12): e1003977 (2013-12)



Solana J.; Gamberi C.; Mihaylova Y.; Grosswendt S.; Chen C.; Lasko P.; Rajewsky N.; Aboobaker A.A.
The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation
PLoS Genetics 9 (12): e1004003 (2013-12)



Loewer A.; Karanam K.; Mock C.; Lahav G.
The p53 response in single cells is linearly correlated to the number of DNA breaks without a distinct threshold
BMC Biology 11 (1): 114 (2013-11-19)



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)



Doerr J.R.; Yu Y.; Milanovic M.; Beuster G.; Zasada C.; Daebritz J.H.M.; Lisec J.; Lenze D.; Gerhardt A.; Schleicher K.; Kratzat S.; Purfuerst B.; Walenta S.; Mueller-Klieser W.; Graeler M.; Hummel M.; Keller U.; Buck A.K.; Doerken B.; Willmitzer L.; Reimann M.; Kempa S.; Lee S.; Schmitt C.A.
Synthetic lethal metabolic targeting of cellular senescence in cancer therapy
Nature 501 (7467): 421-425 (2013-09-19)



Sebinger D.D.; Ofenbauer A.; Gruber P.; Malik S.; Werner C.
ECM modulated early kidney development in embryonic organ culture
Biomaterials 34 (28): 6670-6682 (2013-09)



Rodriguez-Seguel E.; Mah N.; Naumann H.; Pongrac I.M.; Cerda-Esteban N.; Fontaine J.F.; Wang Y.; Chen W.; Andrade-Navarro M.A.; Spagnoli F.M.
Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence
Genes & Development 27 (17): 1932-1946 (2013-09-01)



Wang Y.; Gogol-Doering A.; Hu H.; Froehler S.; Ma Y.; Jens M.; Maaskola J.; Murakawa Y.; Quedenau C.; Landthaler M.; Kalscheuer V.; Wieczorek D.; Wang Y.; Hu Y.; Chen W.
Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation
EMBO Molecular Medicine 5 (9): 1431-1442 (2013-09)



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)



Rohwer N.; Zasada C.; Kempa S.; Cramer T.
The growing complexity of HIF-1{alpha}'s role in tumorigenesis: DNA repair and beyond
Oncogene 32 (31): 3569-3576 (2013-08-01)



Atanur S.S.; Diaz A.G.; Maratou K.; Sarkis A.; Rotival M.; Game L.; Tschannen M.R.; Kaisaki P.J.; Otto G.W.; John Ma M.C.; Keane T.M.; Hummel O.; Saar K.; Chen W.; Guryev V.; Gopalakrishnan K.; Garrett M.R.; Joe B.; Citterio L.; Bianchi G.; McBride M.; Dominiczak A.; Adams D.J.; Serikawa T.; Flicek P.; Cuppen E.; Hubner N.; Petretto E.; Gauguier D.; Kwitek A.; Jacob H.; Aitman T.J.
Genome sequencing reveals loci under artificial selection that underlie disease phenotypes in the laboratory rat
Cell 154 (3): 691-703 (2013-08-01)



Sun W.; You X.; Gogol-Doering A.; He H.; Kise Y.; Sohn M.; Chen T.; Klebes A.; Schmucker D.; Chen W.
Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing
EMBO Journal 32 (14): 2029-2038 (2013-07-17)



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)



Pham T.H.; Minderjahn J.; Schmidl C.; Hoffmeister H.; Schmidhofer S.; Chen W.; Laengst G.; Benner C.; Rehli M.
Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1
Nucleic Acids Research 41 (13): 6391-6402 (2013-07)



Graf R.; Munschauer M.; Mastrobuoni G.; Mayr F.; Heinemann U.; Kempa S.; Rajewsky N.; Landthaler M.
Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation
RNA Biology 10 (7): 1146-1159 (2013-07-01)



Tattikota S.G.; Sury M.D.; Rathjen T.; Wessels H.H.; Pandey A.K.; You X.; Becker C.; Chen W.; Selbach M.; Poy M.N.
Argonaute2 regulates the pancreatic {beta}-cell secretome
Molecular & Cellular Proteomics 12 (5): 1214-1225 (2013-05)



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



Memczak S.; Jens M.; Elefsinioti A.; Torti F.; Krueger J.; Rybak A.; Maier L.; Mackowiak S.D.; Gregersen L.H.; Munschauer M.; Loewer A.; Ziebold U.; Landthaler M.; Kocks C.; le Noble F.; Rajewsky N.
Circular RNAs are a large class of animal RNAs with regulatory potency
Nature 495 (7441): 333-338 (2013-03-21)



Carlo A.S.; Gustafsen C.; Mastrobuoni G.; Nielsen M.S.; Burgert T.; Hartl D.; Rohe M.; Nykjaer A.; Herz J.; Heeren J.; Kempa S.; Petersen C.M.; Willnow T.E.
The pro-neurotrophin receptor sortilin is a major neuronal apolipoprotein E receptor for catabolism of amyloid-beta peptide in the brain
Journal of Neuroscience 33 (1): 358-370 (2013-01-02)



Mazin P.; Xiong J.; Liu X.; Yan Z.; Zhang X.; Li M.; He L.; Somel M.; Yuan Y.; Chen Y.P.P.; Li N.; Hu Y.; Fu N.; Ning Z.; Zeng R.; Yang H.; Chen W.; Gelfand M.; Khaitovich P.
Widespread splicing changes in human brain development and aging
Molecular Systems Biology 9: 633 (2013)



Dieterich C.; Stadler P.F.
Computational biology of RNA interactions
Wiley Interdisciplinary Reviews: RNA 4 (1): 107-120 (2013-01)



Liu Y.; Hu W.; Murakawa Y.; Yin J.; Wang G.; Landthaler M.; Yan J.
Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation
Scientific Reports 3: 2054 (2013)



2012

Marguerat S.; Schmidt A.; Codlin S.; Chen W.; Aebersold R.; Baehler J.
Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells
Cell 151 (3): 671-683 (2012-10-26)



Voigt K.; Gogol-Doering A.; Miskey C.; Chen W.; Cathomen T.; Izsvak Z.; Ivics Z.
Retargeting Sleeping Beauty transposon insertions by engineered zinc finger DNA-binding domains
Molecular Therapy 20 (10): 1852-1862 (2012-10)



Tursun B.
Cellular reprogramming processes in Drosophila and C. elegans
Current Opinion in Genetics & Development 22 (5): 475-484 (2012-10)



Peng C.; Li N.; Ng Y.K.; Zhang J.; Meier F.; Theis F.J.; Merkenschlager M.; Chen W.; Wurst W.; Prakash N.
A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation
Journal of Neuroscience 32 (38): 13292-13308 (2012-09-19)



Ammar I.; Gogol-Doering A.; Miskey C.; Chen W.; Cathomen T.; Izsvak Z.; Ivics Z.
Retargeting transposon insertions by the adeno-associated virus Rep protein
Nucleic Acids Research 40 (14): 6693-6712 (2012-08-01)



Pham T.H.; Benner C.; Lichtinger M.; Schwarzfischer L.; Hu Y.; Andreesen R.; Chen W.; Rehli M.
Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states
Blood 119 (24): e161-e171 (2012-06-14)



Baltz A.G.; Munschauer M.; Schwanhaeusser B.; Vasile A.; Murakawa Y.; Schueler M.; Youngs N.; Penfold-Brown D.; Drew K.; Milek M.; Wyler E.; Bonneau R.; Selbach M.; Dieterich C.; Landthaler M.
The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts
Molecular Cell 46 (5): 674-690 (2012-06-08)



Onal P.; Gruen D.; Adamidi C.; Rybak A.; Solana J.; Mastrobuoni G.; Wang Y.; Rahn H.P.; Chen W.; Kempa S.; Ziebold U.; Rajewsky N.
Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells
EMBO Journal 31 (12): 2755-2769 (2012-04-27)



Liu X.; Somel M.; Tang L.; Yan Z.; Jiang X.; Guo S.; Yuan Y.P.; He L.; Oleksiak A.; Zhang Y.; Li N.; Hu Y.; Chen W.; Qiu Z.; Paeaebo S.; Khaitovich P.
Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
Genome Research 22 (4): 611-622 (2012-04)



Milek M.; Wyler E.; Landthaler M.
Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing
Seminars in Cell & Developmental Biology 23 (2): 206-212 (2012-04)



Liu L.; Ulbrich J.; Mueller J.; Wuestefeld T.; Aeberhard L.; Kress T.R.; Muthalagu N.; Rycak L.; Rudalska R.; Moll R.; Kempa S.; Zender L.; Eilers M.; Murphy D.J.
Deregulated MYC expression induces dependence upon AMPK-related kinase 5
Nature 483 (7391): 608-612 (2012-03-29)



von Eyss B.; Maaskola J.; Memczak S.; Moellmann K.; Schuetz A.; Loddenkemper C.; Tanh M.D.; Otto A.; Muegge K.; Heinemann U.; Rajewsky N.; Ziebold U.
The SNF2-like helicase HELLS mediates E2F3-dependent transcription and cellular transformation
EMBO Journal 31 (4): 972-985 (2012-02-15)



Anders G.; Mackowiak S.D.; Jens M.; Maaskola J.; Kuntzagk A.; Rajewsky N.; Landthaler M.; Dieterich C.
doRiNA: a database of RNA interactions in post-transcriptional regulation
Nucleic Acids Research 40 (1): D180-D186 (2012-01)



Friedlaender M.R.; Mackowiak S.D.; Li N.; Chen W.; Rajewsky N.
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
Nucleic Acids Research 40 (1): 37-52 (2012-01-01)



2011

Jungkamp A.C.; Stoeckius M.; Mecenas D.; Gruen D.; Mastrobuoni G.; Kempa S.; Rajewsky N.
In vivo and transcriptome-wide identification of RNA binding protein target sites
Molecular Cell 44 (5): 828-840 (2011-12-09)



Loewer A.; Lahav G.
We are all individuals: causes and consequences of non-genetic heterogeneity in mammalian cells
Current opinion in genetics & development 21 (6): 753-758 (2011-12)



Somel M.; Liu X.; Tang L.; Yan Z.; Hu H.; Guo S.; Jiang X.; Zhang X.; Xu G.; Xie G.; Li N.; Hu Y.; Chen W.; Paeaebo S.; Khaitovich P.
MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates
PLoS Biology 9 (12): e1001214 (2011-12)



Najmabadi H.; Hu H.; Garshasbi M.; Zemojtel T.; Abedini S.S.; Chen W.; Hosseini M.; Behjati F.; Haas S.; Jamali P.; Zecha A.; Mohseni M.; Puettmann L.; Vahid L.N.; Jensen C.; Moheb L.A.; Bienek M.; Larti F.; Mueller I.; Weissmann R.; Darvish H.; Wrogemann K.; Hadavi V.; Lipkowitz B.; Esmaeeli-Nieh S.; Wieczorek D.; Kariminejad R.; Firouzabadi S.G.; Cohen M.; Fattahi Z.; Rost I.; Mojahedi F.; Hertzberg C.; Dehghan A.; Rajab A.; Banavandi M.J.S.; Hoffer J.; Falah M.; Musante L.; Kalscheuer V.; Ullmann R.; Kuss A.W.; Tzschach A.; Kahrizi K.; Ropers H.H.
Deep sequencing reveals 50 novel genes for recessive cognitive disorders
Nature 478 (7367): 57-63 (2011-10-06)



Hu H.Y.; Guo S.; Xi J.; Yan Z.; Fu N.; Zhang X.; Menzel C.; Liang H.; Yang H.; Zhao M.; Zeng R.; Chen W.; Paeaebo S.; Khaitovich P.
MicroRNA expression and regulation in human, chimpanzee, and macaque brains
PLoS Genetics 7 (10): e1002327 (2011-10)



Lebedeva S.; Jens M.; Theil K.; Schwanhaeusser B.; Selbach M.; Landthaler M.; Rajewsky N.
Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR
Molecular Cell 43 (3): 340-352 (2011-08-05)



Yan Z.; Hu H.Y.; Jiang X.; Maierhofer V.; Neb E.; He L.; Hu Y.; Hu H.; Li N.; Chen W.; Khaitovich P.
Widespread expression of piRNA-like molecules in somatic tissues
Nucleic Acids Research 39 (15): 6596-6607 (2011-08-01)



Moldt B.; Miskey C.; Staunstrup N.H.; Gogol-Doering A.; Bak R.O.; Sharma N.; Mates L.; Izsvak Z.; Chen W.; Ivics Z.; Mikkelsen J.G.
Comparative genomic integration profiling of Sleeping Beauty transposons mobilized with high efficacy from integrase-defective lentiviral vectors in primary human cells
Molecular Therapy 19 (8): 1499-1510 (2011-08)



Adamidi C.; Wang Y.; Gruen D.; Mastrobuoni G.; You X.; Tolle D.; Dodt M.; Mackowiak S.D.; Gogol-Doering A.; Oenal P.; Rybak A.; Ross E.; Alvarado A.S.; Kempa S.; Dieterich C.; Rajewsky N.; Chen W.
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics
Genome Research 21 (7): 1193-1200 (2011-07)



Schwanhaeusser B.; Busse D.; Li N.; Dittmar G.; Schuchhardt J.; Wolf J.; Chen W.; Selbach M.
Global quantification of mammalian gene expression control
Nature 473 (7347): 337-342 (2011-05-19)



Ogawa A.; Bento G.; Bartelmes G.; Dieterich C.; Sommer R.J.
Pristionchus pacificus daf-16 is essential for dauer formation but dispensable for mouth form dimorphism
Development 138 (7): 1281-1284 (2011-04)



Leddin M.; Perrod C.; Hoogenkamp M.; Ghani S.; Assi S.; Heinz S.; Wilson N.K.; Follows G.; Schoenheit J.; Vockentanz L.; Mosamam A.; Chen W.; Tenen D.G.; Westhead D.R.; Goettgens B.; Bonifer C.; Rosenbauer F.
Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells
Blood 117 (10): 2827-2838 (2011-03-10)



2010

Gerstein M.B.; Lu Z.J.; Van Nostrand E.L.; Cheng C.; Arshinoff B.I.; Liu T.; Yip K.Y.; Robilotto R.; Rechtsteiner A.; Ikegami K.; Alves P.; Chateigner A.; Perry M.; Morris M.; Auerbach R.K.; Feng X.; Leng J.; Vielle A.; Niu W.; Rhrissorrakrai K.; Agarwal A.; Alexander R.P.; Barber G.; Brdlik C.M.; Brennan J.; Brouillet J.J.; Carr A.; Cheung M.S.; Clawson H.; Contrino S.; Dannenberg L.O.; Dernburg A.F.; Desai A.; Dick L.; Dose A.C.; Du J.; Egelhofer T.; Ercan S.; Euskirchen G.; Ewing B.; Feingold E.A.; Gassmann R.; Good P.J.; Green P.; Gullier F.; Gutwein M.; Guyer M.S.; Habegger L.; Han T.; Henikoff J.G.; Henz S.R.; Hinrichs A.; Holster H.; Hyman T.; Iniguez A.L.; Janette J.; Jensen M.; Kato M.; Kent W.J.; Kephart E.; Khivansara V.; Khurana E.; Kim J.K.; Kolasinska-Zwierz P.; Lai E.C.; Latorre I.; Leahey A.; Lewis S.; Lloyd P.; Lochovsky L.; Lowdon R.F.; Lubling Y.; Lyne R.; Maccoss M.; Mackowiak S.D.; Mangone M.; McKay S.; Mecenas D.; Merrihew G.; Miller D.M.; Muroyama A.; Murray J.I.; Ooi S.L.; Pham H.; Phippen T.; Preston E.A.; Rajewsky N.; Raetsch G.; Rosenbaum H.; Rozowsky J.; Rutherford K.; Ruzanov P.; Sarov M.; Sasidharan R.; Sboner A.; Scheid P.; Segal E.; Shin H.; Shou C.; Slack F.J.; Slightam C.; Smith R.; Spencer W.C.; Stinson E.O.; Taing S.; Takasaki T.; Vafeados D.; Voronina K.; Wang G.; Washington N.L.; Whittle C.M.; Wu B.; Yan K.K.; Zeller G.; Zha Z.; Zhong M.; Zhou X.; Ahringer J.; Strome S.; Gunsalus K.C.; Micklem G.; Liu X.S.; Reinke V.; Kim S.K.; Hillier L.W.; Henikoff S.; Piano F.; Snyder M.; Stein L.; Lieb J.D.; Waterston R.H.
Integrative analysis of the caenorhabditis elegans genome by the modENCODE project
Science 330 (6012): 1775-1787 (2010-12-24)



Stittrich A.B.; Haftmann C.; Sgouroudis E.; Kuehl A.A.; Hegazy A.N.; Panse I.; Riedel R.; Flossdorf M.; Dong J.; Fuhrmann F.; Heinz G.A.; Fang Z.; Li N.; Bissels U.; Hatam F.; Jahn A.; Hammoud B.; Matz M.; Schulze F.M.; Baumgrass R.; Bosio A.; Mollenkopf H.J.; Gruen J.; Thiel A.; Chen W.; Hoefer T.; Loddenkemper C.; Loehning M.; Chang H.D.; Rajewsky N.; Radbruch A.; Mashreghi M.F.
The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes
Nature Immunology 11 (11): 1057-1062 (2010-11)



Somel M.; Guo S.; Fu N.; Yan Z.; Hu H.Y.; Xu Y.; Yuan Y.; Ning Z.; Hu Y.; Menzel C.; Hu H.; Lachmann M.; Zeng R.; Chen W.; Khaitovich P.
MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
Genome Research 20 (9): 1207-1218 (2010-09)



Landthaler M.
Chaperones get RISC loaded
Molecular Cell 39 (2): 161-162 (2010-07-30)



Mangone M.; Manoharan A.P.; Thierry-Mieg D.; Thierry-Mieg J.; Han T.; Mackowiak S.; Mis E.; Zegar C.; Gutwein M.R.; Khivansara V.; Attie O.; Chen K.; Salehi-Ashtiani K.; Vidal M.; Harkins T.T.; Bouffard P.; Suzuki Y.; Sugano S.; Kohara Y.; Rajewsky N.; Piano F.; Gunsalus K.C.; Kim J.K.
The Landscape of C. elegans 3'UTRs
Science 329 (5990): 432-435 (2010-07-23)



Xu A.G.; He L.; Li Z.; Xu Y.; Li M.; Fu X.; Yan Z.; Yuan Y.; Menzel C.; Li N.; Somel M.; Hu H.; Chen W.; Paeaebo S.; Khaitovich P.
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq
PLoS Computational Biology 6 (7): e1000843 (2010-07-01)



Borchert N.; Dieterich C.; Krug K.; Schuetz W.; Jung S.; Nordheim A.; Sommer R.J.; Macek B.
Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models
Genome Research 20 (6): 837-486 (2010-06)



Grabundzija I.; Irgang M.; Mates L.; Belay E.; Matrai J.; Gogol-Doering A.; Kawakami K.; Chen W.; Ruiz P.; Chuah M.K.; Vandendriessche T.; Izsvak Z.; Ivics Z.
Comparative analysis of transposable element vector systems in human cells
Molecular Therapy 18 (6): 1200-1209 (2010-06)



Qiu W.; Hu Y.; Andersen T.E.; Jafari A.; Li N.; Chen W.; Kassem M.
Tumor necrosis factor receptor superfamily member 19 (TNFRSF19) regulates differentiation fate of human mesenchymal (stromal) stem cells through canonical Wnt signaling and C/EBP
Journal of Biological Chemistry 285 (19): 14438-14449 (2010-05-07)



Peleg S.; Sananbenesi F.; Zovoilis A.; Burkhardt S.; Bahari-Javan S.; Agis-Balboa R.C.; Cota P.; Wittnam J.L.; Gogol-Doering A.; Opitz L.; Salinas-Riester G.; Dettenhofer M.; Kang H.; Farinelli L.; Chen W.; Fischer A.
Altered histone acetylation is associated with age-dependent memory impairment in mice
Science 328 (5979): 753-756 (2010-05-07)



2009

Stoeckius M.; Maaskola J.; Colombo T.; Rahn H.P.; Friedlaender M.R.; Li N.; Chen W.; Piano F.; Rajewsky N.
Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression
Nature Methods 6 (10): 745-751 (2009-10)



Friedlaender M.R.; Adamidi C.; Han T.; Lebedeva S.; Isenbarger T.A.; Hirst M.; Marra M.; Nusbaum C.; Lee W.L.; Jenkin J.C.; Alvarado A.S.; Kim J.K.; Rajewsky N.
High-resolution profiling and discovery of planarian small RNAs
Proceedings of the National Academy of Sciences of the United States of America 106 (28): 11546-11551 (2009-07-14)



2008

Ender C.; Krek A.; Friedlaender M.R.; Beitzinger M.; Weinmann L.; Chen W.; Pfeffer S.; Rajewsky N.; Meister G.
A human snoRNA with microRNA-like functions
Molecular Cell 32 (4): 519-528 (2008-11-21)



Selbach M.; Schwanhaeusser B.; Thierfelder N.; Fang Z.; Khanin R.; Rajewsky N.
Widespread changes in protein synthesis induced by microRNAs
Nature 455 (7209): 58-63 (2008-09-04)



Friedlaender M.R.; Chen W.; Adamidi C.; Maaskola J.; Einspanier R.; Knespel S.; Rajewsky N.
Discovering microRNAs from deep sequencing data using miRDeep
Nature Biotechnology 26 (4): 407-415 (2008-04)



Koralov S.B.; Muljo S.A.; Galler G.R.; Krek A.; Chakraborty T.; Kanellopoulou C.; Jensen K.; Cobb B.S.; Merkenschlager M.; Rajewsky N.; Rajewsky K.
Dicer ablation affects antibody diversity and cell survival in the B lymphocyte lineage
Cell 132 (5): 860-874 (2008-03-07)



2007

Thai T.H.; Calado D.P.; Casola S.; Ansel K.M.; Xiao C.; Xue Y.; Murphy A.; Frendewey D.; Valenzuela D.; Kutok J.L.; Schmidt-Supprian M.; Rajewsky N.; Yancopoulos G.; Rao A.; Rajewsky K.
Regulation of the germinal center response by microRNA-155
Science 316 (5824): 604-608 (2007-04-27)



Chen K.; Rajewsky N.
The evolution of gene regulation by transcription factors and microRNAs
Nature Reviews Genetics 8 (2): 93-103 (2007-02)



Gruen D.; Rajewsky N.
Computational prediction of microRNA targets in vertebrates, fruitflies and nematodes
MicroRNAs: From Basic Science to Disease Biology : 172-186 (2007)



2006

Chen K.; Rajewsky N.
Natural selection on human microRNA binding sites inferred from SNP data
Nature Genetics 38 (12): 1452-1456 (2006-12-01)



Rajewsky N.
L(ou)sy miRNA targets?
Nature Structural & Molecular Biology 13 (9): 754-755 (2006-09)



Chen K.; Rajewsky N.
Deep conservation of microRNA-target relationships and 3'UTR motifs in vertebrates, flies, and nematodes
Cold Spring Harbor Symposia on Quantitative Biology 71: 149-156 (2006)