Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression

by Grinchuk, O.V, Motakis, E, Kuznetsov, V.A
Published 2020

How to discriminate between potentially novel and considered biomarkers within molecular signature?

by Ow, G.S., Jenjaroenpun, P., Thiery, J.P., Kuznetsov, V.A.
Published 2014

Meta-analysis of transcriptome reveals let-7b as an unfavorable prognostic biomarker and predicts molecular and clinical subclasses in high-grade serous ovarian carcinoma

by Tang, Z., Ow, G.S., Thiery, J.P., Ivshina, A.V., Kuznetsov, V.A.
Published 2014

Genome and transcriptome delineation of two major oncogenic pathways governing invasive ductal breast cancer development

by Aswad, L, Yenamandra, S.P, Ow, G.S, Grinchuk, O, Ivshina, A.V, Kuznetsov, V.A
Published 2020

Benchmarking selected computational gene network growing tools in context of virus-host interactions

by Taye, B, Vaz, C, Tanavde, V, Kuznetsov, V.A, Eisenhaber, F, Sugrue, R.J, Maurer-Stroh, S
Published 2020

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

by Yarmishyn, A.A, Batagov, A.O, Tan, J.Z, Sundaram, G.M, Sampath, P, Kuznetsov, V.A, Kurochkin, I.V
Published 2020

Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients

by Wongsurawat, T, Woo, CC, Giannakakis, A, Lin, XY, Cheow, ESH, Lee, CN, Richards, M, Sze, SK, Nookaew, I, Kuznetsov, VA, Sorokin, V
Published 2022

Tumor-adjacent tissue co-expression profile analysis reveals pro-oncogenic ribosomal gene signature for prognosis of resectable hepatocellular carcinoma

by Grinchuk, O.V., Yenamandra, S.P., Iyer, R., Singh, M., Lee, H.K., Lim, K.H., Chow, P.K.-H., Kuznetsov, V.A.
Published 2022

Sense-antisense gene-pairs in breast cancer and associated pathological pathways

by Grinchuk, O.V, Motakis, E, Yenamandra, S.P, Ow, G.S, Jenjaroenpun, P, Tang, Z, Yarmishyn, A.A, Ivshina, A.V, Kuznetsov, V.A
Published 2020

Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients

by Wongsurawat, T., Woo, C.C., Giannakakis, A., Lin, X.Y., Cheow, E.S.H., Lee, C.N., Mark Richards, Sze, S.K., Nookaew, I., Kuznetsov, V.A., Sorokin, V.
Published 2022

Host gene expression profiling of dengue virus infection in cell lines and patients

by Fink J., Gu F., Ling L., Tolfvenstam T., Olfat F., Chin K.C., Aw P., George J., Kuznetsov V.A., Schreiber M., Vasudevan S.G., Hibberd M.L.
Published 2018

P53-Independent regulation of p21Waf1/Cip1 expression and senescence by PRMT6

by Phalke, S., Mzoughi, S., Bezzi, M., Jennifer, N., Mok, W.C., Low, D.H.P., Thike, A.A., Kuznetsov, V.A., Tan, P.H., Voorhoeve, P.M., Guccione, E.
Published 2014

Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer

by Ivshina, A.V., George, J., Senko, O., Mow, B., Putti, T.C., Smeds, J., Lindahl, T., Pawitan, Y., Hall, P., Nordgren, H., Wong, J.E.L., Liu, E.T., Bergh, J., Kuznetsov, V.A., Miller, L.D.
Published 2014

Whole-Genome Mapping of Histone H3 Lys4 and 27 Trimethylations Reveals Distinct Genomic Compartments in Human Embryonic Stem Cells

by Zhao, X.D., Han, X., Chew, J.L., Liu, J., Chiu, K.P., Choo, A., Orlov, Y.L., Sung, W.-K., Shahab, A., Kuznetsov, V.A., Bourque, G., Oh, S., Ruan, Y., Ng, H.-H., Wei, C.-L.
Published 2013

Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

by Giannakakis, A, Zhang, J, Jenjaroenpun, P, Nama, S, Zainolabidin, N, Aau, M.Y, Yarmishyn, A.A, Vaz, C, Ivshina, A.V, Grinchuk, O.V, Voorhoeve, M, Vardy, L.A, Sampath, P, Kuznetsov, V.A, Kurochkin, I.V, Guccione, E
Published 2020

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

by Ruan, Y., Hong, S.O., Siew, W.C., Kuo, P.C., Xiao, D.Z., Srinivasan, K.G., Yao, F., Chiou, Y.C., Liu, J., Ariyaratne, P., Bin, W.G.W., Kuznetsov, V.A., Shahab, A., Sung, W.-K., Bourque, G., Palanisamy, N., Wei, C.-L.
Published 2013

A global map of p53 transcription-factor binding sites in the human genome

by Wei, C.-L., Wu, Q., Vega, V.B., Chiu, K.P., Ng, P., Zhang, T., Shahab, A., Yong, H.C., Fu, Y., Weng, Z., Liu, J., Zhao, X.D., Chew, J.-L., Lee, Y.L., Kuznetsov, V.A., Sung, W.-K., Miller, L.D., Lim, B., Liu, E.T., Yu, Q., Ng, H.-H., Ruan, Y.
Published 2014

Whole-genome cartography of estrogen receptor α binding sites

by Lin, C.-Y., Vega, V.B., Thomsen, J.S., Zhang, T., Say, L.K., Xie, M., Kuo, P.C., Lipovich, L., Barnett, D.H., Stossi, F., Yeo, A., George, J., Kuznetsov, V.A., Yew, K.L., Tze, H.C., Palanisamy, N., Miller, L.D., Cheung, E., Katzenellenbogen, B.S., Ruan, Y., Bourque, G., Wei, C.-L., Liu, E.T.
Published 2015

The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

by Loh, Y.-H., Wu, Q., Chew, J.-L., Vega, V.B., Zhang, W., Chen, X., Bourque, G., George, J., Leong, B., Liu, J., Wong, K.-Y., Sung, K.W., Lee, C.W.H., Zhao, X.-D., Chiu, K.-P., Lipovich, L., Kuznetsov, V.A., Robson, P., Stanton, L.W., Wei, C.-L., Ruan, Y., Lim, B., Ng, H.-H.
Published 2014

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

by 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, M., Baillie, J.K., Bajic, V.B., Bajpai, A., Baker, S., Baldarelli, R.M., Balic, A., Bansal, M., Batagov, A.O., Batzoglou, S., Beckhouse, A.G., Beltrami, A.P., Beltrami, C.A., Bertin, Nicolas, Bhattacharya, S., Bickel, P.J., Blake, J.A., Blanchette, M., Bodega, B., Bonetti, A., Bono, H., Bornholdt, J., Bttcher, M., Bougouffa, S., Boyd, M., Breda, J., Brombacher, F., Brown, J.B., Bult, C.J., Burroughs, A.M., Burt, D.W., Busch, A., Caglio, G., Califano, A., Cameron, C.J., Cannistraci, C.V., Carbone, A., Carlisle, A.J., Carninci, Piero, Carter, K.W., Cesselli, D., Chang, J.-C., Chen, J.C., Chen, Y., Chierici, M., Christodoulou, J., Ciani, Y., Clark, E.L., Coskun, M., Dalby, M., Dalla, E., Daub, C.O., Davis, C.A., de Hoom, Michiel J. L., de Rie, D., Denisenko, E., Deplancke, B., Detmar, M., Deviatiiarov, R., Di Bernardo, D., Diehl, A.D., Dieterich, L.C., Dimont, E., Djebali, S., Dohi, T., Dostie, J., Drablos, F., Edge, A.S.B., Edinger, M., Ehrlund, A., Ekwall, K., Elofsson, A., Endoh, M., Enomoto, H., Enomoto, S., Faghihi, M., Fagiolini, M., Farach-Carson, M.C., Faulkner, G.J., Favorov, A., Fernandes, A.M., Ferrai, C., Forrest, A.R.R., Forrester, L.M., Forsberg, M., Fort, A., Francescatto, M., Freeman, T.C., Frith, Martin C., Fukuda, S., Funayama, M., Furlanello, C., Furuno, M., Furusawa, C., Gao, H., Gazova, I., Gebhard, C., Geier, F., Geijtenbeek, T.B.H., Ghosh, S., Ghosheh, Y., Gingeras, T.R., Gojobori, T., Goldberg, T., Goldowitz, D., Gough, J., Greco, D., Gruber, A.J., Guhl, S., Guigo, R., Guler, R., Gusev, O., Gustincich, S., Ha, T.J., Haberle, V., Hale, P., Hallstrom, B.M., Hamada, M., Handoko, L., Hara, M., Harbers, M., Harrow, J., Harshbarger, J., Hase, T., Hasegawa, Akira, Hashimoto, K., Hatano, T., Hattori, N., Hayashi, R., Hayashizaki, Yoshihide, Herlyn, M., Hettne, K., Heutink, P., Hide, W., Hitchens, K.J., Sui, S.H., ’t Hoen, P.A.C., Hon, C.C., Hori, F., Horie, M., Horimoto, K., Horton, P., Hou, R., Huang, E., Huang, Y., Hugues, R., Hume, D., Ienasescu, H., Iida, K., Ikawa, T., Ikemura, T., Ikeo, K., Inoue, N., Ishizu, Y., Ito, Y., Itoh, Masayoshi, Ivshina, A.V., Jankovic, B.R., Jenjaroenpun, P., Johnson, R., Jorgensen, M., Jorjani, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kajiyama, K., Kaliyaperumal, R., Kaminuma, E., Kanaya, T., Kaneda, H., Kapranov, P., Kasianov, A.S., Kasukawa, Takeya, Katayama, T., Kato, S., Kawaguchi, S., Kawai, J., Kawaji, H., Kawamoto, H., Kawamura, Y.I., Kawasaki, S., Kawashima, T., Kempfle, J.S., Kenna, T.J., Kere, J., Khachigian, L., Kiryu, H., Kishima, M., Kitajima, H., Kitamura, T., Kitano, H., Klaric, E., Klepper, K., Klinken, S.P., Kloppmann, E., Knox, A.J., Kodama, Y., Kogo, Y., Kojima, M., Kojima, S., Komatsu, N., Komiyama, H., Kono, T., Koseki, H., Koyasu, S., Kratz, A., Kukalev, A., Kulakovskiy, I., Kundaje, A., Kunikata, H., Kuo, R., Kuo, T., Kuraku, S., Kuznetsov, V.A., Kwon, T.J., Larouche, M., Lassmann, T., Law, A., Le-Cao, K.-A., Lecellier, C.-H., Lee, W., Lenhard, B., Lennartsson, A., Li, K., Li, R., Lilje, B., Lipovich, L., Lizio, M., Lopez, G., Magi, S., Mak, G.K., Makeev, V., Manabe, R., Mandai, M., Mar, J., Maruyama, K., Maruyama, T., Mason, E., Mathelier, A., Matsuda, H., Medvedeva, Y.A., Meehan, T.F., Mejhert, N., Meynert, A., Mikami, N., Minoda, A., Miura, H., Miyagi, Y., Miyawaki, A., Mizuno, Y., Morikawa, H., Morimoto, M., Morioka, M., Morishita, S., Moro, K., Motakis, E., Motohashi, H., Mukarram, A.K., Mummery, C.L., Mungall, C.J., Murakawa, Y., Muramatsu, M., Murata, Mitsuyoshi, Nagasaka, K., Nagase, T., Nakachi, Y., Nakahara, F., Nakai, K., Nakamura, K., Nakamura, Y., Nakamura, Y., Nakazawa, T., Nason, G.P., Nepal, C., Nguyen, Q.H., Nielsen, L.K., Nishida, K., Nishiguchi, K.M., Nishiyori, H., Nitta, K., Noguchi, Shuhei, Noma, Shohei, Notredame, C., Ogishima, S., Ohkura, N., Ohno, H., Ohshima, M., Ohtsu, T., Okada, Y., Okada-Hatakeyama, M., Okazaki, Y., Oksvold, P., Orlando, V., Ow, G.S., Ozturk, M., Pachkov, M., Paparountas, T., Parihar, S.P., Park, S.-J., Pascarella, G., Passier, R., Persson, H., Philippens, I.H., Piazza, S., Plessy, C., Pombo, A., Ponten, F., Poulain, S., Poulsen, T.M., Pradhan, S., Prezioso, C., Pridans, C., Qin, X.-Y., Quackenbush, J., Rackham, O., Ramilowski, Jordan A., Ravasi, T., Rehli, M., Rennie, S., Rito, T., Rizzu, P., Robert, C., Roos, M., Rost, B., Roudnicky, F., Roy, R., Rye, M.B., Sachenkova, O., Saetrom, P., Sai, H., Saiki, S., Saito, M., Saito, A., Sakaguchi, S., Sakai, M., Sakaue, S., Sakaue-Sawano, A., Sandelin, A., Sano, H., Sasamoto, Y., Sato, H., Saxena, A., Saya, H., Schafferhans, A., Schmeier, S., Schmidl, C., Schmocker, D., Schneider, C., Schueler, M., Schultes, E.A., Schulze-Tanzil, G., Semple, C.A., Seno, S., Seo, W., Sese, J., Severin, Jessica, Sheng, G., Shi, J., Shimoni, Y., Shin, J.W., SimonSanchez, J., Sivertsson, A., Sjostedt, E., Soderhall, C., Laurent, G.S., Stoiber, M.H., Sugiyama, D., Summers, K.M., Suzuki, A.M., Suzuki, Harukazu, Suzuki, K., Suzuki, M., Suzuki, N., Suzuki, T., Swanson, D.J., Swoboda, R.K., Tagami, Michihira, Taguchi, A., Takahashi, H., Takahashi, M., Takamochi, K., Takeda, S., Takenaka, Y., Tam, K.T., Tanaka, H., Tanaka, R., Tanaka, Y., Tang, D., Taniuchi, I., Tanzer, A., Tarui, H., Taylor, M.S., Terada, A., Terao, Y., Testa, A.C., Thomas, M., Thongjuea, S., Tomii, K., Triglia, E.T., Toyoda, H., Tsang, H.G., Tsujikawa, M., Uhlén, M., Valen, E., van de Wetering, M., van Nimwegen, E., Velmeshev, D., Verardo, R., Vitezic, M., Vitting-Seerup, K., von Feilitzen, K., Voolstra, C.R., Vorontsov, I.E., Wahlestedt, C., Wasserman, Wyeth W., Watanabe, K., Watanabe, S., Wells, C.A., Winteringham, L.N., Wolvetang, E., Yabukami, H., Yagi, K., Yamada, T., Yamaguchi, Y., Yamamoto, M., Yamamoto, Y., Yamamoto, Y., Yamanaka, Y., Yano, K., Yasuzawa, K., Yatsuka, Y., Yo, M., Yokokura, S., Yoneda, M., Yoshida, E., Yoshida, Y., Yoshihara, M., Young, R., Young, R.S., Yu, N.Y., Yumoto, N., Zabierowski, S.E., Zhang, P.G., Zucchelli, S., Zwahlen, M., Chatelain, Clement, Carninci, Piero, de Hoom, Michiel J. L., Wasserman, Wyeth W., Bréhélin, L., Lecellier, C.-H., FANTOM consortium.
Published 2022