Applied Bioinformatics Laboratories Featured Publications

Applied Bioinformatics Laboratories Applied Bioinformatics Laboratories Featured Publications
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Applied Bioinformatics Laboratories Featured Publications

Faculty and staff of the Applied Bioinformatics Laboratories publish frequently in peer-reviewed journals. Here is a selection of their recent publications.

Cimmino L, Dolgalev I, Wang Y, Yoshimi A, Martin GH, Wang J, et al. Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell. 2017;170(6):1079-95.

Tetz GV, Ruggles KV, Zhou H, Heguy A, Tsirigos A, Tetz V. Bacteriophages as potential new mammalian pathogens. Sci Rep. 2017;7(1):7043.

Cerrone M, Montnach J, Lin X, Zhao YT, Zhang M, Agullo-Pascual E, et al. Plakophilin-2 is required for transcription of genes that control calcium cycling and cardiac rhythm. Nat Commun. 2017;8(1):106.

Gong Y, Huang HT, Liang Y, Trimarchi T, Aifantis I, Tsirigos A. lncRNA-screen: an interactive platform for computationally screening long non-coding RNAs in large genomics datasets. BMC Genomics. 2017;18(1):434.

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, et al. Methods, tools and current perspectives in proteogenomics. Mol Cell Proteomics. 2017;16(6):959-81.

Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, et al. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nat Commun. 2017;8:14864.

Koetz-Ploch L, Hanniford D, Dolgalev I, Sokolova E, Zhong J, Díaz-Martínez M, et al. MicroRNA-125a promotes resistance to BRAF inhibitors through suppression of the intrinsic apoptotic pathway. Pigment Cell Melanoma Res. 2017;30(3):328-38.

Coudray N, L Seyler S, Lasala R, Zhang Z, Clark KM, Dumont ME, et al. Structure of the SLC4 transporter Bor1p in an inward-facing conformation. Protein Sci. 2017;26(1):130-45.

Gutiérrez GD, Bender AS, Cirulli V, Mastracci TL, Kelly SM, Tsirigos A, et al. Pancreatic β cell identity requires continual repression of non-β cell programs. J Clin Invest. 2017;127(1):244-59.

Lazaris C, Kelly S, Ntziachristos P, Aifantis I, Tsirigos A. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics. 2017;18(1):22.

Cardiac arrhythmia and neuroexcitability gene variants in resected brain tissue from patients with sudden unexpected death in epilepsy (SUDEP)

Friedman, Daniel; Kannan, Kasthuri; Faustin, Arline; Shroff, Seema; Thomas, Cheddhi; Heguy, Adriana; Serrano, Jonathan; Snuderl, Matija; Devinsky, Orrin

NPJ genomic medicine. 2018 Mar 27; 3:9-9

DNA methylation-based classification of central nervous system tumours

Capper, David; Jones, David T W; Sill, Martin; Hovestadt, Volker; Schrimpf, Daniel; Sturm, Dominik; Koelsche, Christian; Sahm, Felix; Chavez, Lukas; Reuss, David E; Kratz, Annekathrin; Wefers, Annika K; Huang, Kristin; Pajtler, Kristian W; Schweizer, Leonille; Stichel, Damian; Olar, Adriana; Engel, Nils W; Lindenberg, Kerstin; Harter, Patrick N; Braczynski, Anne K; Plate, Karl H; Dohmen, Hildegard; Garvalov, Boyan K; Coras, Roland; Hölsken, Annett; Hewer, Ekkehard; Bewerunge-Hudler, Melanie; Schick, Matthias; Fischer, Roger; Beschorner, Rudi; Schittenhelm, Jens; Staszewski, Ori; Wani, Khalida; Varlet, Pascale; Pages, Melanie; Temming, Petra; Lohmann, Dietmar; Selt, Florian; Witt, Hendrik; Milde, Till; Witt, Olaf; Aronica, Eleonora; Giangaspero, Felice; Rushing, Elisabeth; Scheurlen, Wolfram; Geisenberger, Christoph; Rodriguez, Fausto J; Becker, Albert; Preusser, Matthias; Haberler, Christine; Bjerkvig, Rolf; Cryan, Jane; Farrell, Michael; Deckert, Martina; Hench, Jürgen; Frank, Stephan; Serrano, Jonathan; Kannan, Kasthuri; Tsirigos, Aristotelis; Brück, Wolfgang; Hofer, Silvia; Brehmer, Stefanie; Seiz-Rosenhagen, Marcel; Hänggi, Daniel; Hans, Volkmar; Rozsnoki, Stephanie; Hansford, Jordan R; Kohlhof, Patricia; Kristensen, Bjarne W; Lechner, Matt; Lopes, Beatriz; Mawrin, Christian; Ketter, Ralf; Kulozik, Andreas; Khatib, Ziad; Heppner, Frank; Koch, Arend; Jouvet, Anne; Keohane, Catherine; Mühleisen, Helmut; Mueller, Wolf; Pohl, Ute; Prinz, Marco; Benner, Axel; Zapatka, Marc; Gottardo, Nicholas G; Driever, Pablo Hernáiz; Kramm, Christof M; Müller, Hermann L; Rutkowski, Stefan; von Hoff, Katja; Frühwald, Michael C; Gnekow, Astrid; Fleischhack, Gudrun; Tippelt, Stephan; Calaminus, Gabriele; Monoranu, Camelia-Maria; Perry, Arie; Jones, Chris; Jacques, Thomas S; Radlwimmer, Bernhard; Gessi, Marco; Pietsch, Torsten; Schramm, Johannes; Schackert, Gabriele; Westphal, Manfred; Reifenberger, Guido; Wesseling, Pieter; Weller, Michael; Collins, Vincent Peter; Blümcke, Ingmar; Bendszus, Martin; Debus, Jürgen; Huang, Annie; Jabado, Nada; Northcott, Paul A; Paulus, Werner; Gajjar, Amar; Robinson, Giles W; Taylor, Michael D; Jaunmuktane, Zane; Ryzhova, Marina; Platten, Michael; Unterberg, Andreas; Wick, Wolfgang; Karajannis, Matthias A; Mittelbronn, Michel; Acker, Till; Hartmann, Christian; Aldape, Kenneth; Schüller, Ulrich; Buslei, Rolf; Lichter, Peter; Kool, Marcel; Herold-Mende, Christel; Ellison, David W; Hasselblatt, Martin; Snuderl, Matija; Brandner, Sebastian; Korshunov, Andrey; von Deimling, Andreas; Pfister, Stefan M

Nature. 2018 Mar 22; 555:469-474

Data Science in the Research Domain Criteria Era: Relevance of Machine Learning to the Study of Stress Pathology, Recovery, and Resilience

Galatzer-Levy, Isaac R; Ruggles, Kelly; Chen, Zhe

Chronic stress. 2018 Mar 17; 2:

Atrx inactivation drives disease-defining phenotypes in glioma cells of origin through global epigenomic remodeling

Danussi, Carla; Bose, Promita; Parthasarathy, Prasanna T; Silberman, Pedro C; Van Arnam, John S; Vitucci, Mark; Tang, Oliver Y; Heguy, Adriana; Wang, Yuxiang; Chan, Timothy A; Riggins, Gregory J; Sulman, Erik P; Lang, Frederick; Creighton, Chad J; Deneen, Benjamin; Miller, C Ryan; Picketts, David J; Kannan, Kasthuri; Huse, Jason T

Nature communications. 2018 Mar 13; 9:1057-1057

Mass spectrometry-based proteomics reveals potential roles of NEK9 and MAP2K4 in resistance to PI3K inhibitors in triple negative breast cancers

Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V; Mooradian, Arshag D; Mertins, Philipp; Gillette, Michael A; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D R; Clauser, Karl R; Gao, Feng; Luo, Jingqin; Davies, Sherri R; Johnson, Gary L; Huang, Kuan-Lin; Yoon, Christopher J; Ding, Li; Fenyö, David; Ellis, Matthew J; Townsend, R Reid; Held, Jason M; Carr, Steven A; Ma, Cynthia X

Cancer research. 2018 Feb 22;

The Ancient Origins of Neural Substrates for Land Walking

Jung, Heekyung; Baek, Myungin; D'Elia, Kristen P; Boisvert, Catherine; Currie, Peter D; Tay, Boon-Hui; Venkatesh, Byrappa; Brown, Stuart M; Heguy, Adriana; Schoppik, David; Dasen, Jeremy S

Cell. 2018 Feb 08; 172:667-682.e15

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

Gong, Yixiao; Lazaris, Charalampos; Sakellaropoulos, Theodore; Lozano, Aurelie; Kambadur, Prabhanjan; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis

Nature communications. 2018 Feb 07; 9:542-542

Hacking macrophage-associated immunosuppression for regulating glioblastoma angiogenesis

Cui, Xin; Morales, Renee-Tyler Tan; Qian, Weiyi; Wang, Haoyu; Gagner, Jean-Pierre; Dolgalev, Igor; Placantonakis, Dimitris; Zagzag, David; Cimmino, Luisa; Snuderl, Matija; Lam, Raymond H W; Chen, Weiqiang

Biomaterials. 2018 Feb 02; 161:164-178