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2023
1 Al-jibury, Ediem; King, James W. D.; Guo, Ya; Lenhard, Boris; Fisher, Amanda G.; Merkenschlager, Matthias; Rueckert, Daniel.
A deep learning method for replicate-based analysis of chromosome conformation contacts using Siamese neural networks. Nature Communications 2023 ;Volume 14.(1) p. -
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2 Rauluseviciute, Ieva; Launay, Timothée; Barzaghi, Guido; Nikumbh, Sarvesh; Lenhard, Boris; Krebs, Arnaud Regis; Castro Mondragon, Jaime Abraham; Mathelier, Anthony.
Identification of transcription factor co-binding patterns with non-negative matrix factorization. bioRxiv 2023
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3 Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Castro Mondragon, Jaime Abraham; Ferenc, Katalin Terezia; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jeremy; Cheneby, Jeanne; Baranasic, Damir; Khan, Aziz; Fornes, Oriol; Gundersen, Sveinung; Johansen, Morten; Hovig, Eivind; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W.; Parcy, François; Mathelier, Anthony.
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2023 ;Volume 52.(D1) p. D174-D182
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2022
4 Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé; Menichelli, Christophe; Ramilowski, Jordan A.; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyama, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin C.; Abugessaisa, Imad; Aitken, Stuart; Aken, Bronwen L.; Alam, Intikhab; Alam, Tanvir; Alasiri, Rami; Alhendi, Ahmad M. N.; Alinejad-Rokny, Hamid; Alvarez, Mariano J.; Andersson, Robin; Arakawa, Takahiro; Araki, Marito; Arbel, Taly; Archer, John; Archibald, Alan L.; Arner, Erik; Arner, Peter; Asai, Kiyoshi; Ashoor, Haitham; Astrom, Gaby; Babina, Magda; Baillie, J. Kenneth; Bajic, Vladimir B.; Bajpai, Archana; Baker, Sarah; Baldarelli, Richard M.; Balic, Adam; Bansal, Mukesh; Batagov, Arsen O.; Batzoglou, Serafim; Beckhouse, Anthony G.; Beltrami, Antonio P.; Beltrami, Carlo A.; Bertin, Nicolas; Bhattacharya, Sharmodeep; Bickel, Peter J.; Blake, Judith A.; Blanchette, Mathieu; Bodega, Beatrice; Bonetti, Alessandro; Bono, Hidemasa; Bornholdt, Jette; Bttcher, Michael; Bougouffa, Salim; Boyd, Mette; Breda, Jeremie; Brombacher, Frank; Brown, James B.; Bult, Carol J.; Burroughs, A. Maxwell; Burt, Dave W.; Busch, Annika; Caglio, Giulia; Califano, Andrea; Cameron, Christopher J.; Cannistraci, Carlo V.; Carbone, Alessandra; Carlisle, Ailsa J.; Carninci, Piero; Carter, Kim W.; Cesselli, Daniela; Chang, Jen-Chien; Chen, Julie C.; Chen, Yun; Chierici, Marco; Christodoulou, John; Ciani, Yari; Clark, Emily L.; Coskun, Mehmet; Dalby, Maria; Dalla, Emiliano; Daub, Carsten O.; Davis, Carrie A.; de Hoon, Michiel J. L.; de Rie, Derek; Denisenko, Elena; Deplancke, Bart; Detmar, Michael; Deviatiiarov, Ruslan; Di Bernardo, Diego; Diehl, Alexander D.; Dieterich, Lothar C.; Dimont, Emmanuel; Djebali, Sarah; Dohi, Taeko; Dostie, Jose; Drabløs, Finn; Edge, Albert S. B.; Edinger, Matthias; Ehrlund, Anna; Ekwall, Karl; Elofsson, Arne; Endoh, Mitsuhiro; Enomoto, Hideki; Enomoto, Saaya; Faghihi, Mohammad; Fagiolini, Michela; Farach-Carson, Mary C.; Faulkner, Geoffrey J.; Favorov, Alexander; Fernandes, Ana Miguel; Ferrai, Carmelo; Forrest, Alistair R. R.; Forrester, Lesley M.; Forsberg, Mattias; Fort, Alexandre; Francescatto, Margherita; Freeman, Tom C.; Frith, Martin; Fukuda, Shinji; Funayama, Manabu; Furlanello, Cesare; Furuno, Masaaki; Furusawa, Chikara; Gao, Hui; Gazova, Iveta; Gebhard, Claudia; Geier, Florian; Geijtenbeek, Teunis B. H.; Ghosh, Samik; Ghosheh, Yanal; Gingeras, Thomas R.; Gojobori, Takashi; Goldberg, Tatyana; Goldowitz, Daniel; Gough, Julian; Greco, Dario; Gruber, Andreas J.; Guhl, Sven; Guigo, Roderic; Guler, Reto; Gusev, Oleg; Gustincich, Stefano; Ha, Thomas J.; Haberle, Vanja; Hale, Paul; Hallstrom, Bjrn M.; Hamada, Michiaki; Handoko, Lusy; Hara, Mitsuko; Harbers, Matthias; Harrow, Jennifer; Harshbarger, Jayson; Hase, Takeshi; Hasegawa, Akira; Hashimoto, Kosuke; Hatano, Taku; Hattori, Nobutaka; Hayashi, Ryuhei; Hayashizaki, Yoshihide; Herlyn, Meenhard; Heutink, Peter; Hide, Winston; Hitchens, Kelly J.; Sui, Shannon Ho; ’t Hoen, Peter A. C.; Hon, Chung Chau; Hori, Fumi; Horie, Masafumi; Horimoto, Katsuhisa; Horton, Paul; Hou, Rui; Huang, Edward; Huang, Yi; Hugues, Richard; Hume, David; Ienasescu, Hans; Iida, Kei; Ikawa, Tomokatsu; Ikemura, Toshimichi; Ikeo, Kazuho; Inoue, Norihiko; Ishizu, Yuri; Ito, Yosuke; Itoh, Masayoshi; Ivshina, Anna V.; Jankovic, Boris R.; Jenjaroenpun, Piroon; Johnson, Rory; Jorgensen, Mette; Jorjani, Hadi; Joshi, Anagha; Jurman, Giuseppe; Kaczkowski, Bogumil; Kai, Chieko; Kaida, Kaoru; Kajiyama, Kazuhiro; Kaliyaperumal, Rajaram; Kaminuma, Eli; Kanaya, Takashi; Kaneda, Hiroshi; Kapranov, Philip; Kasianov, Artem S.; Kasukawa, Takeya; Katayama, Toshiaki; Kato, Sachi; Kawaguchi, Shuji; Kawai, Jun; Kawaji, Hideya; Kawamoto, Hiroshi; Kawamura, Yuki I.; Kawasaki, Satoshi; Kawashima, Tsugumi; Kempfle, Judith S.; Kenna, Tony J.; Kere, Juha; Khachigian, Levon; Kiryu, Hisanori; Kishima, Mami; Kitajima, Hiroyuki; Kitamura, Toshio; Kitano, Hiroaki; Klaric, Enio; Klepper, Kjetil; Klinken, S. Peter; Kloppmann, Edda; Knox, Alan J.; Kodama, Yuichi; Kogo, Yasushi; Kojima, Miki; Kojima, Soichi; Komatsu, Norio; Komiyama, Hiromitsu; Kono, Tsukasa; Koseki, Haruhiko; Koyasu, Shigeo; Kratz, Anton; Kukalev, Alexander; Kulakovskiy, Ivan; Kundaje, Anshul; Kunikata, Hiroshi; Kuo, Richard; Kuo, Tony; Kuraku, Shigehiro; Kuznetsov, Vladimir A.; Kwon, Tae Jun; Larouche, Matt; Lassmann, Timo; Law, Andy; Le-Cao, Kim-Anh; Lecellier, Charles-Henri; Lee, Weonju; Lenhard, Boris; Lennartsson, Andreas; Li, Kang; Li, Ruohan; Lilje, Berit; Lipovich, Leonard; Lizio, Marina; Lopez, Gonzalo; Magi, Shigeyuki; Mak, Gloria K.; Makeev, Vsevolod; Manabe, Riichiro; Mandai, Michiko; Mar, Jessica; Maruyama, Kazuichi; Maruyama, Taeko; Mason, Elizabeth; Matsuda, Hideo; Medvedeva, Yulia A.; Meehan, Terrence F.; Mejhert, Niklas; Meynert, Alison; Mikami, Norihisa; Minoda, Akiko; Miura, Hisashi; Miyagi, Yohei; Miyawaki, Atsushi; Mizuno, Yosuke; Morikawa, Hiromasa; Morimoto, Mitsuru; Morioka, Masaki; Morishita, Soji; Moro, Kazuyo; Motakis, Efthymios; Motohashi, Hozumi; Mukarram, Abdul Kadir; Mummery, Christine L.; Mungall, Christopher J.; Murakawa, Yasuhiro; Muramatsu, Masami; Murata, Mitsuyoshi; Nagasaka, Kazunori; Nagase, Takahide; Nakachi, Yutaka; Nakahara, Fumio; Nakai, Kenta; Nakamura, Kumi; Nakamura, Yasukazu; Nakamura, Yukio; Nakazawa, Toru; Nason, Guy P.; Nepal, Chirag; Nguyen, Quan Hoang; Nielsen, Lars K.; Nishida, Kohji; Nishiguchi, Koji M.; Nishiyori, Hiromi; Nitta, Kazuhiro; Noguchi, Shuhei; Noma, Shohei; Notredame, Cedric; Ogishima, Soichi; Ohkura, Naganari; Ohno, Hiroshi; Ohshima, Mitsuhiro; Ohtsu, Takashi; Okada, Yukinori; Okada-Hatakeyama, Mariko; Okazaki, Yasushi; Oksvold, Per; Orlando, Valerio; Ow, Ghim Sion; Ozturk, Mumin; Pachkov, Mikhail; Paparountas, Triantafyllos; Parihar, Suraj P.; Park, Sung-Joon; Pascarella, Giovanni; Passier, Robert; Persson, Helena; Philippens, Ingrid H.; Piazza, Silvano; Plessy, Charles; Pombo, Ana; Ponten, Fredrik; Poulain, Stéphane; Poulsen, Thomas M.; Pradhan, Swati; Prezioso, Carolina; Pridans, Clare; Qin, Xiang-Yang; Quackenbush, John; Rackham, Owen; Ramilowski, Jordan; Ravasi, Timothy; Rehli, Michael; Rennie, Sarah; Rito, Tiago; Rizzu, Patrizia; Robert, Christelle; Roos, Marco; Rost, Burkhard; Roudnicky, Filip; Roy, Riti; Rye, Morten Beck; Sachenkova, Oxana; Sætrom, Pål; Sai, Hyonmi; Saiki, Shinji; Saito, Mitsue; Saito, Akira; Sakaguchi, Shimon; Sakai, Mizuho; Sakaue, Saori; Sakaue-Sawano, Asako; Sandelin, Albin; Sano, Hiromi; Sasamoto, Yuzuru; Sato, Hiroki; Saxena, Alka; Saya, Hideyuki; Schafferhans, Andrea; Schmeier, Sebastian; Schmidl, Christian; Schmocker, Daniel; Schneider, Claudio; Schueler, Marcus; Schultes, Erik A.; Schulze-Tanzil, Gundula; Semple, Colin A.; Seno, Shigeto; Seo, Wooseok; Sese, Jun; Severin, Jessica; Sheng, Guojun; Shi, Jiantao; Shimoni, Yishai; Shin, Jay W.; SimonSanchez, Javier; Sivertsson, Asa; Sjostedt, Evelina; Soderhall, Cilla; Laurent, Georges St; Stoiber, Marcus H.; Sugiyama, Daisuke; Summers, Kim M.; Suzuki, Ana Maria; Suzuki, Harukazu; Suzuki, Kenji; Suzuki, Mikiko; Suzuki, Naoko; Suzuki, Takahiro; Swanson, Douglas J.; Swoboda, Rolf K.; Tagami, Michihira; Taguchi, Ayumi; Takahashi, Hazuki; Takahashi, Masayo; Takamochi, Kazuya; Takeda, Satoru; Takenaka, Yoichi; Tam, Kin Tung; Tanaka, Hiroshi; Tanaka, Rica; Tanaka, Yuji; Tang, Dave; Taniuchi, Ichiro; Tanzer, Andrea; Tarui, Hiroshi; Taylor, Martin S.; Terada, Aika; Terao, Yasuhisa; Testa, Alison C.; Thomas, Mark; Thongjuea, Supat; Tomii, Kentaro; Triglia, Elena Torlai; Toyoda, Hiroo; Tsang, H. Gwen; Tsujikawa, Motokazu; Uhlén, Mathias; Valen, Eivind Dale; van de Wetering, Marc; van Nimwegen, Erik; Velmeshev, Dmitry; Verardo, Roberto; Vitezic, Morana; Vitting-Seerup, Kristoffer; von Feilitzen, Kalle; Voolstra, Christian R.; Vorontsov, Ilya E.; Wahlestedt, Claes; Wasserman, Wyeth W.; Watanabe, Kazuhide; Watanabe, Shoko; Wells, Christine A.; Winteringham, Louise N.; Wolvetang, Ernst; Yabukami, Haruka; Yagi, Ken; Yamada, Takuji; Yamaguchi, Yoko; Yamamoto, Masayuki; Yamamoto, Yasutomo; Yamamoto, Yumiko; Yamanaka, Yasunari; Yano, Kojiro; Yasuzawa, Kayoko; Yatsuka, Yukiko; Yo, Masahiro; Yokokura, Shunji; Yoneda, Misako; Yoshida, Emiko; Yoshida, Yuki; Yoshihara, Masahito; Young, Rachel; Young, Robert S.; Yu, Nancy Y.; Yumoto, Noriko; Zabierowski, Susan E.; Zhang, Peter G.; Zucchelli, Silvia; Zwahlen, Martin; Chatelain, Clément; Carninci, Piero; de Hoon, Michiel J. L.; Wasserman, Wyeth W.; Bréhélin, Laurent; Lecellier, Charles-Henri.
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (Nature Communications, (2021), 12, 1, (3297), 10.1038/s41467-021-23143-7). Nature Communications 2022 ;Volume 13.(1) p. -
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5 Guo, Ya; Al-Jibury, Ediem; Garcia-Millan, Rosalba; Ntagiantas, Konstantinos; King, James W.D.; Nash, Alex J.; Galjart, Niels; Lenhard, Boris; Rueckert, Daniel; Fisher, Amanda G.; Pruessner, Gunnar; Merkenschlager, Matthias.
Chromatin jets define the properties of cohesin-driven in vivo loop extrusion. Molecular Cell 2022 ;Volume 82.(20) p. 3769-3780.e5
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2021
6 Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alexander J.; Ghilotti, Marco; Cameron, Christopher J.  F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata, Samudyata; Luginbühl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Gonçalo; Orlando, Valerio; Carninci, Piero.
Author Correction: RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions (Nature Communications, (2020), 11, 1, (1018), 10.1038/s41467-020-14337-6). Nature Communications 2021 ;Volume 12.(1) p. -
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7 Martín-Durán, José M.; Vellutini, Bruno Cossermelli; Marlétaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon Raymond; Grau-Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel Marc; Gómez-Skarmeta, Jose Luis; Irimia, Manuel; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas.
Publisher Correction: Conservative route to genome compaction in a miniature annelid (Nature Ecology & Evolution, (2021), 5, 2, (231-242), 10.1038/s41559-020-01327-6). Nature Ecology and Evolution 2021 ;Volume 5.(2) p. 262-
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8 Weiss, Felix D.; Calderon, Lesly; Wang, Yi-Fang; Georgieva, Radina; Guo, Ya; Cvetesic, Nevena; Kaur, Maninder; Dharmalingam, Gopuraja; Krantz, Ian D.; Lenhard, Boris; Fisher, Amanda G.; Merkenschlager, Matthias.
Neuronal genes deregulated in Cornelia de Lange Syndrome respond to removal and re-expression of cohesin. Nature Communications 2021 ;Volume 12.(1) p. -
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9 Zeisig, Bernd B; Fung, Tsz Kan; Zarowiecki, Magdalena; Tsai, Chiou-Tsun; Luo, Huacheng; Stanojevic, Boban; Lynn, Claire; Leung, Anskar Y.H.; Zuna, Jan; Zaliova, Marketa; Bornhauser, Martin; von Bonin, Malte; Lenhard, Boris; Huang, Suming; Mufti, Ghulam J.; Eric So, Chi Wai.
Functional reconstruction of human AML reveals stem cell origin and vulnerability of treatment-resistant MLL-rearranged leukemia. Science Translational Medicine 2021 ;Volume 13.(582) p. -
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2020
10 Bonetti, Alessandro; Agostini, Federico; Suzuki, Ana Maria; Hashimoto, Kosuke; Pascarella, Giovanni; Gimenez, Juliette; Roos, Leonie; Nash, Alex J.; Ghilotti, Marco; Cameron, Christopher J.  F.; Valentine, Matthew; Medvedeva, Yulia A.; Noguchi, Shuhei; Agirre, Eneritz; Kashi, Kaori; Samudyata, Samudyata; Luginbühl, Joachim; Cazzoli, Riccardo; Agrawal, Saumya; Luscombe, Nicholas M.; Blanchette, Mathieu; Kasukawa, Takeya; de Hoon, Michiel; Arner, Erik; Lenhard, Boris; Plessy, Charles; Castelo-Branco, Gonçalo; Orlando, Valerio; Carninci, Piero.
RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nature Communications 2020 ;Volume 11.(1018) p. -
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11 Lewis, Samuel H.; Ross, Laura; Bain, Stevie A.; Pahita, Eleni; Smith, Stephen A.; Cordaux, Richard; Miska, Eric A.; Lenhard, Boris; Jiggins, Francis M.; Sarkies, Peter.
Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods. PLoS Genetics 2020 ;Volume 6.(16) p. -
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12 Martin Duran, Jose Maria; Vellutini, Bruno Cossermelli; Marletaz, Ferdinand; Cetrangolo, Viviana; Cvetesic, Nevena; Thiel, Daniel; Henriet, Simon; Grau-Bové, Xavier; Carrillo-Baltodano, Allan M.; Gu, Wenjia; Kerbl, Alexandra; Marquez, Yamile; Bekkouche, Nicolas; Chourrout, Daniel; Gómez-Skarmeta, José Luis; Irimia, Manuel; Lenhard, Boris; Worsaae, Katrine; Hejnol, Andreas.
Conservative route to genome compaction in a miniature annelid. Nature Ecology and Evolution 2020 ;Volume 5. p. 231-242
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13 Nepal, Chirag; Taranta, Andrzej; Hadzhiev, Yavor; Pundhir, Sachin; Mydel, Piotr Mateusz; Lenhard, Boris; Müller, Ferenc; Andersen, Jesper B..
Ancestrally Duplicated Conserved Noncoding Element Suggests Dual Regulatory Roles of HOTAIR in cis and trans. iScience 2020 ;Volume 23.(4) p. -
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14 Ramilowski, Jordan; Yip, Chiu Wai Mickey; Agrawal, Saumya; Chang, Jen-Chien; Ciani, Yari; Kulakovskiy, Ivan; Mendez, Mickaël; Ching Ooi, Jasmine Li; Ouyang, John F; Parkinson, Nick; Petri, Andreas; Roos, Leonie; Severin, Jessica; Yasuzawa, Kayoko; Abugessaisa, Imad; Akalin, Altuna; Antonov, Ivan V.; Arner, Erik; Bonetti, Alessandro; Bono, Hidemasa; Borsari, Beatrice; Kasukawa, Takeya; Kauppinen, Sakari; Kere, Juha; Lenhard, Boris; Schneider, Claudio; Suzuki, Harukazu; Yagi, Ken; De Hoon, Michiel J L; Shin, Jay W; Piero, Carninci.
Functional annotation of human long noncoding RNAs via molecular phenotyping. Genome Research 2020 ;Volume 30. p. 1060-1072
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2019
15 Barešić, Anja; Nash, Alexander Jolyon; Dahoun, Tarik; Howes, Oliver; Lenhard, Boris.
Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks. Molecular Psychiatry 2019 p. 1-13
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16 Borlin, Christoph S; Cvetesic, Nevena; Holland, Petter; Bergenholm, David; Siewers, Verena; Lenhard, Boris; Nielsen, Jens.
Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions. FEMS Yeast Research 2019 ;Volume 19.(2) p. 1-10
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17 Cvetesic, Nevena; Pahita, Elena; Lenhard, Boris.
Transcription start site mapping using super-low input carrier-CAGE. Journal of Visualized Experiments 2019 ;Volume 2019.(148)
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18 Ferreirós-Vidal, Isabel; Carroll, Thomas; Zhang, Tianyi; Lagani, Vincenzo; Ramirez, Ricardo N; Ing-Simmons, Elizabeth; Gómez-Valadés, Alicia G.; Cooper, Lee; Liang, Ziwei; Papoutsoglou, Georgios; Dharmalingam, Gopuraja; Guo, Ya; Tarazona, Sonia; Fernandes, Sunjay J.; Noori, Peri; Silberberg, Gilad; Fisher, Amanda G.; Tsamardinos, Ioannis; Mortazavi, Ali; Lenhard, Boris; Conesa, Ana; Tegnér, Jesper; Merkenschlager, Matthias; Gomez-Cabrero, David.
Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation. PLoS Biology 2019 ;Volume 17:e2006506.(4) p. 1-28
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19 Fornes, Oriol; Castro Mondragón, Jaime Abraham; Khan, Aziz; Robin van der, Lee; Zhang, Xi; A. Richmond, Phillip; P. Modi, Bhavi; Correard, Solenne; Gheorghe, Marius; Baranasic, Damir; Santana-Garcia, Walter; Tan, Ge; Cheneby, Jeanne; Ballester, Benoit; Parcy, François; Sandelin, Albin; Lenhard, Boris; Wasserman, Wyeth W.; Mathelier, Anthony.
JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2019 ;Volume 48. p. 87-92
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20 Nash, Alexander J.; Lenhard, Boris.
A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates. Bioinformatics 2019 ;Volume 35.(14) p. 2354-2361
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21 Newton, Matthew D; Taylor, Benjamin; Driessen, Rosalie P C; Roos, Leonie; Cvetesic, Nevena; Allyjaun, Shenaz; Lenhard, Boris; Cuomo, Maria Emanuela; Rueda, David S.
DNA stretching induces Cas9 off-target activity. Nature Structural & Molecular Biology 2019 ;Volume 26.(3) p. 185-192
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22 Tan, Ge; Polychronopoulos, Dimitris; Lenhard, Boris.
CNEr: A toolkit for exploring extreme noncoding conservation. PLoS Computational Biology 2019 ;Volume 15.(8) p. 1-16
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2018
23 Cvetešić, Nevena; Leitch, Harry G.; Borkowska, Malgorzata; Müller, Ference; Carninci, Piero; Hájková, Petra; Lenhard, Boris.
SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Genome Research 2018 ;Volume 28.(12) p. 1943-1956
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24 Danks, Gemma Barbara; Navratilova, Pavla; Lenhard, Boris; Thompson, Eric.
Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. BMC Genomics 2018 ;Volume 19.(164) p. -
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25 Li, Caí; Lenhard, Boris; Luscombe, Nicholas M.
Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Genome Research 2018 ;Volume 28.(5) p. 676-688
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26 Marletaz, Ferdinand; Firbas, Panos N.; Maeso, Ignacio; Tena, Juan J.; Bogdanovic, Ozren; Perry, Malcolm; Wyatt, Christopher D.R.; de la Calle-Mustienes, Elisa; Bertrand, Stephanie; Burguera, Demian; Acemel, Rafael D.; van Heeringen, Simon J.; Naranjo, Silvia; Herrera-Ubeda, Carlos; Skvortsova, Ksenia; Jimenez-Gancedo, Sandra; Aldea, Daniel; Marquez, Yamile; Buono, Lorena; Kozmikova, Iryna; Permanyer, Jon; Louis, Alexandra; Albuixech-Crespo, Beatriz; Le Petillon, Yann; Leon, Anthony; Subirana, Lucie; Balwierz, Piotr J.; Duckett, Paul Edward; Farahani, Ensieh; Aury, Jean-Marc; Mangenot, Sophie; Wincker, Patrick; Albalat, Ricard; Benito-Gutiérrez, Èlia; Cañestro, Cristian; Castro, Filipe; D'Aniello, Salvatore; Ferrier, David E.K.; Huang, Shengfeng; Laudet, Vincent; Marais, Gabriel A.B.; Pontarotti, Pierre; Schubert, Michael; Seitz, Hervé; Somorjai, Ildiko; Takahashi, Tokiharu; Mirabeau, Olivier; Xu, Anlong; Yu, Jr-Kai; Carninci, Piero; Martinez-Morales, Juan Ramon; Crollius, Hugues Roest; Kozmik, Zbynek; Weirauch, Matthew T.; Garcia-Fernàndez, Jordi; Lister, Ryan; Lenhard, Boris; Holland, Peter W.H.; Escriva, Hector; Gómez-Skarmeta, José Lúis; Irimia, Manuel.
Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 2018 ;Volume 564.(7734) p. 64-70
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2017
27 Harmston, Nathan; Ing-Simmons, Elizabeth; Tan, Ge; Perry, Malcolm; Merkenschlager, Matthias; Lenhard, Boris.
Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation. Nature Communications 2017 ;Volume 8:441. p. 1-13
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28 Polychronopoulos, Dimitris; King, James W.D.; Nash, Alexander J.; Tan, Ge; Lenhard, Boris.
Conserved non-coding elements: Developmental gene regulation meets genome organization. Nucleic Acids Research (NAR) 2017 ;Volume 45.(22) p. 12611-12624
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29 Siriboonpiputtana, Teerapong; Zeisig, Bernd B; Zarowiecki, Magdalena; Fung, Tsz Kan; Mallardo, Maria; Tsai, Chiou-Tsun; Lau, Priscilla Nga Ieng; Hoang, Quoc Chinh; Veiga, Pedro; Barnes, Jo; Lynn, Claire; Wilson, Amanda; Lenhard, Boris; So, Chi Wai Eric.
Transcriptional memory of cells of origin overrides β‐catenin requirement of MLL cancer stem cells. EMBO Journal 2017 ;Volume 36.(21) p. 3139-3155
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2016
30 Haberle, Vanja; Lenhard, Boris.
Promoter architectures and developmental gene regulation. Seminars in Cell and Developmental Biology 2016 ;Volume 57. p. 11-23
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31 Sharma, Yogita.
Nuclear Receptor Genes - Regulation and Evolution. : University of Bergen 2016 (ISBN 978-82-308-3372-8)
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2015
32 Bryne, Jan Christian.
Determining the regulatory roles of transcription factor complexes by analysis of high throughput sequencing data. Development of analysis methods and their application. : University of Bergen 2015 (ISBN 978-82-308-2612-6)
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33 Danks, Gemma Barbara; Raasholm, Martina; Campsteijn, Coen; Long, Abby M.; Manak, J Robert; Lenhard, Boris; Thompson, Eric.
Trans-splicing and operons in metazoans: Translational control in maternally regulated development and recovery from growth arrest. Molecular Biology and Evolution (MBE) 2015 ;Volume 32.(3) p. 585-599
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34 Haberle, Vanja; Forrest, Alistair R.R.; Hayashizaki, Yoshihide; Carninci, Piero; Lenhard, Boris.
CAGEr: Precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. Nucleic Acids Research (NAR) 2015 ;Volume 43.(8:e51)
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35 Ishibashi, Minaka; Manning, Elizabeth; Shoubridge, Cheryl; Krecsmarik, Monika; Hawkins, Thomas A.; Giacomotto, Jean; Zhao, Ting; Mueller, Thomas; Bader, Patricia I.; Cheung, Sau W.; Stankiewicz, Pawel; Bain, Nicole L.; Hackett, Anna; Chilamakuri, Chandra Sekhar Reddy; Mechaly, Alejandro S.; Peers, Bernard; Wilson, Stephen W.; Lenhard, Boris; Bally-Cuif, Laure; Gecz, Jozef; Becker, Thomas S.; Rinkwitz, Silke.
Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene. Human Genetics 2015 ;Volume 134.(11-12) p. 1163-1182
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36 Naville, Magali; Ishibashi, Minaka; Ferg, Marco; Bengani, Hemant; Rinkwitz, Silke; Krecsmarik, Monika; Hawkins, Thomas A.; Wilson, Stephen W.; Manning, Elizabeth; Chilamakuri, Chandra Sekhar Reddy; Wilson, David I.; Louis, Alexandra; Raymond, F. Lucy; Rastegar, Sepand; Strähle, Uwe; Lenhard, Boris; Bally-Cuif, Laure; van Heyningen, Veronica; Fitzpatrick, David R.; Becker, Thomas S.; Crollius, Hugues Roest.
Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome. Nature Communications 2015 ;Volume 6:6904.
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37 Nepal, Chirag; Coolen, Marion; Hadzhiev, Yavor; Cussigh, Delphine; Mydel, Piotr Mateusz; Steen, Vidar Martin; Carninci, Piero; Andersen, Jesper B.; Bally-Cuif, Laure; Müller, Ferenc; Lenhard, Boris.
Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs.. Nucleic Acids Research (NAR) 2015 ;Volume 44.(7) p. 3070-3081
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38 Stadhouders, Ralph; Cico, Alba; Stephen, Tharshana; Thongjuea, Supat; Kolovos, Petros; Baymaz, H. Irem; Yu, Xiao; Demmers, Jeroen; Bezstarosti, Karel; Maas, Alex; Barroca, Vilma; Kockx, Christel; Ozgur, Zeliha; Van Ijcken, Wilfred; Arcangeli, Marie-Laure; Andrieu-Soler, Charlotte; Lenhard, Boris; Grosveld, Frank; Soler, Eric.
Control of developmentally primed erythroid genes by combinatorial co-repressor actions. Nature Communications 2015 ;Volume 6. p. -
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2014
39 Sharma, Yogita; Chilamakuri, Chandra Sekhar Reddy; Bakke, Marit; Lenhard, Boris.
Computational characterization of modes of transcriptional regulation of nuclear receptor genes. PLOS ONE 2014 ;Volume 9.(2:e88880)
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40 Forest, Alistair R.R.; Kawaji, Hideya; Rehli, Michael; Baillie, John Kenneth; de Hoon, Michiel; Haberle, Vanja; Lassmann, Timo; Kulakovskiy, Ivan; Lizio, Marina; Itoh, Masayoshi; Andersson, Robin; Mungall, Christopher; Meehan, Terrence; Schmeier, Sebastian; Bertin, Nicolas; Jørgensen, Mette Kristine; Dimont, Emmanuel; Arner, Erik; Schmidl, Christian; Schaefer, Ulf; Medvedeva, Yulia; Plessy, Charles; Vitezic, Morana; Severin, Jessica; Semple, Colin; Ishizu, Yuri; Young, Robert; Francescatto, Margherita; Altschuler, Intikhab Alam; Albanese, Davide; Altschule, Gabriel M.; Arakawa, Takahiro; Archer, John; Arner, Peter; Babina, Magda; Rennie, Sarah; Balwierz, Piotr J.; Beckhouse, Anthony G.; Pradhan-Bhatt, Swati; Blake, Judith; Blumenthal, Antje; Bodega, Beatrice; Bonetti, Alessandro; Briggs, James A.; Brombacher, Frank; Burroughs, Alexander Maxwell; Califano, Andrea C.; Lenhard, Boris; Rye, Morten Beck; Drabløs, Finn; Consortium, FANTOM.
A promoter-level mammalian expression atlas. Nature 2014 ;Volume 507.(7493) p. 462-470
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41 Haberle, Vanja; Li, Nan; Hadzhiev, Yavor; Plessy, Charles; Previti, A. Christopher; Nepal, Chirag; Gehrig, Jochen; Dong, Xianjun; Akalin, Altuna; Suzuki, Ana Maria; van IJcken, Wilfred F.J.; Armant, Olivier; Ferg, Marco; Strähle, Uwe; Carninci, Piero; Müller, Ferenc; Lenhard, Boris.
Two independent transcription initiation codes overlap on vertebrate core promoters. Nature 2014 ;Volume 507.(7492) p. 381-385
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42 Haberle, Vanja; Li, Nan; Hadzhiev, Yavor; Plessy, Charles; Previti, Christopher; Nepal, Chirag; Gehrig, Jochen; Dong, Xianjun; Akalin, Altuna; Suzuki, Ana Maria; van Ijcken, Wilfred; Armant, Olivier; Ferg, Marco; Strähle, Uwe; Carninci, Piero; Müller, Ferenc; Lenhard, Boris.
High-resolution promoterome mining and differential transcription start site usage analysis reveal unexpected features of vertebrate promoters. The Biology of Genomes; 2014-05-06 - 2014-05-10
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43 Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W..
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Research (NAR) 2014 ;Volume 42.(1) p. D142-D147
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44 Pascarella, Giovanni; Lazarevic, Dejan; Plessy, Charles; Bertin, Nicolas; Akalin, Altuna; Vlachouli, Christina; Simone, Roberto; Faulkner, Geoffrey J.; Zucchelli, Silvia; Kawai, Jun; Daub, Carsten O.; Hayashizaki, Yoshihide; Lenhard, Boris; Carninci, Piero; Gustincich, Stefano.
NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience 2014 ;Volume 8:41.
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45 Plessy, Charles; Pascarella, Giovanni; Bertin, Nicolas; Akalin, Altuna; Carrieri, Claudia; Vassalli, Anne; Lazarevic, Dejan; Severin, Jessica; Vlachouli, Christina; Simone, Roberto; Faulkner, Geoffrey J.; Kawai, Jun; Daub, Carsten Olivier; Zucchelli, Silvia; Hayashizaki, Yoshihide; Mombaerts, Peter; Lenhard, Boris; Gustincich, Stefano; Carninci, Piero.
Promoter architecture of mouse olfactory receptor genes. Chemical Senses 2014 ;Volume 39.(1) p. 79-79
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46 Stadhouders, Ralph; Aktuna, Suleyman; Thongjuea, Supat; Aghajanirefah, Ali; Pourfarzad, Farzin; van IJcken, Wilfred F.J.; Lenhard, Boris; Rooks, Helen; Best, Steve; Menzel, Stephan; Grosveld, Frank G.; Thein, Swee Lay; Soler, Eric.
HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers. Journal of Clinical Investigation 2014 ;Volume 124.(4) p. 1699-1710
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47 Zuin, Jessica; Franke, Vedran; van IJcken, Wilfred F.J.; van der Sloot, Antoine; Krantz, Ian D.; van der Reijden, Michael .I.J.A.; Nakato, Ryuichiro; Lenhard, Boris; Wendt, Kerstin S..
A cohesin-independent role for NIPBL at promoters provides insights in CdLS. PLoS Genetics 2014 ;Volume 10.(2:e1004153)
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2013
48 Carvalho, Rejane H.; Hou, Jun; Haberle, Vanja; Aerts, Joachim; Grosveld, Frank; Lenhard, Boris; Philipsen, Sjaak.
Genomewide DNA Methylation Analysis Identifies Novel Methylated Genes in Non-Small-Cell Lung Carcinomas. Journal of Thoracic Oncology 2013 ;Volume 8.(5) p. 562-573
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49 Nepal, Chirag; Hadzhiev, Yavor; Previti, A. Christopher; Haberle, Vanja; Li, Nan; Takahashi, Hazuki; Suzuki, Ana Maria; Sheng, Ying; Abdelhamid, Rehab; Anand, Santosh; Gehrig, Jochen; Akalin, Altuna; Kockx, Christel E.M.; van der Sloot, Antoine A.J.; van IJcken, Wilfred F.J.; Armant, Olivier; Rastegar, Sepand; Watson, Craig; Strähle, Uwe; Stupka, Elia; Carninci, Piero; Lenhard, Boris; Müller, Ferenc.
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Research 2013 ;Volume 23.(11) p. 1938-1950
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50 Armant, Olivier; März, Martin; Schmidt, Rebecca; Ferg, Marco; Diotel, Nicolas; Ertzer, Raymond; Bryne, Jan Christian; Yang, Lixin; Baader, Isabelle; Reischl, Markus; Legradi, Jessica; Mikut, Ralf; Stemple, Derek; van Ijcken, Wilfred; van der Sloot, Antoine; Lenhard, Boris; Strähle, Uwe; Rastegar, Sepand.
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Developmental Biology 2013 ;Volume 380.(2) p. 351-362
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