Items where Author is "Pachkov, Mikhail"

Article

Baranasic, Damir and Hörtenhuber, Matthias and Balwierz, Piotr J. and Zehnder, Tobias and Mukarram, Abdul Kadir and Nepal, Chirag and Várnai, Csilla and Hadzhiev, Yavor and Jimenez-Gonzalez, Ada and Li, Nan and Wragg, Joseph and D'Orazio, Fabio M. and Relic, Dorde and Pachkov, Mikhail and Díaz, Noelia and Hernández-Rodríguez, Benjamín and Chen, Zelin and Stoiber, Marcus and Dong, Michaël and Stevens, Irene and Ross, Samuel E. and Eagle, Anne and Martin, Ryan and Obasaju, Oluwapelumi and Rastegar, Sepand and McGarvey, Alison C. and Kopp, Wolfgang and Chambers, Emily and Wang, Dennis and Kim, Hyejeong R. and Acemel, Rafael D. and Naranjo, Silvia and Łapiński, Maciej and Chong, Vanessa and Mathavan, Sinnakaruppan and Peers, Bernard and Sauka-Spengler, Tatjana and Vingron, Martin and Carninci, Piero and Ohler, Uwe and Lacadie, Scott Allen and Burgess, Shawn M. and Winata, Cecilia and van Eeden, Freek and Vaquerizas, Juan M. and Gómez-Skarmeta, José Luis and Onichtchouk, Daria and Brown, Ben James and Bogdanovic, Ozren and van Nimwegen, Erik and Westerfield, Monte and Wardle, Fiona C. and Daub, Carsten O. and Lenhard, Boris and Müller, Ferenc. (2022) Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nature Genetics, 54 (7). pp. 1037-1050.

Mukhtar, Tanzila and Breda, Jeremie and Adam, Manal A. and Boareto, Marcelo and Grobecker, Pascal and Karimaddini, Zahra and Grison, Alice and Eschbach, Katja and Chandrasekhar, Ramakrishnan and Vermeul, Swen and Okoniewski, Michal and Pachkov, Mikhail and Harwell, Corey C. and Atanasoski, Suzana and Beisel, Christian and Iber, Dagmar and van Nimwegen, Erik and Taylor, Verdon. (2022) Temporal and sequential transcriptional dynamics define lineage shifts in corticogenesis. The EMBO Journal. e111132.

Berger, Severin and Pachkov, Mikhail and Arnold, Phil and Omidi, Saeed and Kelley, Nicholas and Salatino, Silvia and van Nimwegen, Erik. (2019) Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs. Genome Research, 29 (7). pp. 1164-1177.

Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176.

Artimo, Panu and Duvaud, Séverine and Pachkov, Mikhail and Ioannidis, Vassilios and van Nimwegen, Erik and Stockinger, Heinz. (2016) The ISMARA client. F1000Research, 5 (Elixir). p. 2851.

Pemberton-Ross, Peter J. and Pachkov, Mikhail and van Nimwegen, Erik. (2015) ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data. Methods, Vol. 85. pp. 62-74.

Bertels, Frederic and Silander, Olin K. and Pachkov, Mikhail and Rainey, Paul B. and van Nimwegen, Erik. (2014) Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular biology and evolution, Vol. 31, no. 5. pp. 1077-1088.

Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326.

Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884.

Tiwari, Neha and Meyer-Schaller, Nathalie and Arnold, Phil and Antoniadis, Helena and Pachkov, Mikhail and van Nimwegen, Erik and Christofori, Gerhard. (2013) Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8). PLoS ONE, Vol. 8, H. 10 , nn.

Arnold, Phil and Schöler, Anne and Pachkov, Mikhail and Balwierz, Piotr J. and Jørgensen, Helle and Stadler, Michael B. and van Nimwegen, Erik and Schübeler, Dirk. (2013) Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting. Genome research, Vol. 23. pp. 60-73.

Arner, Erik and Mejhert, Niklas and Kulyté, Agné and Balwierz, Piotr J. and Pachkov, Mikhail and Cormont, Mireille and Lorente-Cebrián, Silvia and Ehrlund, Anna and Laurencikiene, Jurga and Hedén, Per and Dahlman-Wright, Karin and Tanti, Jean-François and Hayashizaki, Yoshihide and Rydén, Mikael and Dahlman, Ingrid and van Nimwegen, Erik and Daub, Carsten O. and Arner, Peter. (2012) Adipose tissue microRNAs as regulators of CCL2 production in human obesity. Diabetes, Vol. 61, H. 8. pp. 1986-1993.

Arnold, Phil and Erb, Ionas and Pachkov, Mikhail and Molina, Nacho and van Nimwegen, Erik. (2012) MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, Vol. 28, H. 4. pp. 487-494.

Pachkov, Mikhail and Balwierz, Piotr J. and Arnold, Phil and Ozonov, Evgeniy and van Nimwegen, Erik. (2012) SwissRegulon : a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Research, 41 (D1). D214-D220.

Aceto, Nicola and Sausgruber, Nina and Brinkhaus, Heike and Gaidatzis, Dimos and Martiny-Baron, Georg and Mazzarol, Giovanni and Confalonieri, Stefano and Quarto, Micaela and Hu, Guang and Balwierz, Piotr J. and Pachkov, Mikhail and Elledge, Stephen J. and van Nimwegen, Erik and Stadler, Michael B. and Bentires-Alj, Mohamed. (2012) Tyrosine phosphatase SHP2 promotes breast cancer progression and maintains tumor-initiating cells via activation of key transcription factors and a positive feedback signaling loop. Nature medicine, Vol. 18, H. 4. pp. 529-537.