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Targeted H3K9 acetylation at lncSox1 promoter by cell type-specific epigenome editing promotes intermediate progenitor proliferation in developing mouse cortex.
Sokpor, Godwin, Ulmke, P.A., Nguyen, H.D., Pham, L., Kakani, P., Chu, V.T., Arnold, S.J., Brand-Saberi, B., Nguyen, H.P. and Tuoc, T.
bioRxiv : 2024.11.05.621758. 5 November 2024

Targeted disruption of linkage-specific ubiquitylation reveals a key role of K29-linked ubiquitylation in epigenome integrity.
Arroyo-Gomez, J., Wang, J., Guérillon, C., Isaakova, E., Reverón-Gómez, N., Koutrouli, M., Rahmanto, A.S., Mitrofanov, K., Ingham, A., Schovsbo, S., Weischenfeldt, K., Coscia, F., Typas, D., Völker-Albert, M., Solis, V., Jensen, L.J., Groth, A., Mund, A., Beli, P., Shearer, R.F. and Mailand, N.
bioRxiv : 2024.10.29.620783. 2 November 2024

The STRIPAK complex is required for radial sorting and laminin receptor expression in Schwann cells.
Weaver, M.R., Shkoruta, D., Pellegatta, M.R., Berti, C., Palmisano, M., Ferguson, S., Hurley, E., French, J., Patel, S., Belin, S., Selbach, M., Paul, F.E., Sim, F., Poitelon, Y. and Feltri, M.L.
bioRxiv : 2024.10.30.620661v1. 31 October 2024

The functional impact of LGI1 autoantibodies on human CA3 pyramidal neurons.
Monni, L., Kornau, H.C., Podestà, A., Stumpf, A., Kalbhenn, T., Simon, M., Sauvigny, T., Onken, J., Prüss, H., Alle, H., Geiger, J.R.P., Holtkamp, M., Schmitz, D. and Fidzinski, P.
bioRxiv : 2024.10.28.620296v1. 28 October 2024

An integrated view of the structure and function of the human 4D nucleome.
Dekker, J., Oksuz, B.A., Zhang, Y., Wang, Y., Minsk, M.K., Kuang, S., Yang, L., Gibcus, J.H., Krietenstein, N., Rando, O., Xu, J., Janssens, D.H., Henikoff, S., Kukalev, A., Willemin, A., Winick-Ng, W., Kempfer, R., Pombo, A., Yu, M., Kumar, P., Zhang, L., Belmont, A.S., Sasaki, T., van Schaik, T., Brueckner, L., Peric-Hupkes, D., van Steensel, B., Wang, P., Chai, H., Kim, M., Ruan, Y., Zhang, R., Quinodoz, S.A., Bhat, P., Guttman, M., Zhao, W., Chien, S., Liu, Y., Venev, S.V., Plewczynski, D., Irastorza Azcarate, I., Szabo, D., Thieme, C.J., Szczepinska, T., Chilinski, M., Sengupta, K., Conte, M., Esposito, A., Abraham, A., Zhang, R., Wang, Y., Wen, X., Wu, Q., Yang, Y., Liu, J., Boninsegna, L., Yildirim, A., Zhan, Y., Chiariello, A.M., Bianco, S., Lee, L., Hu, M., Li, Y., Barnett, R.., Cook, A.L., Emerson, D.J., Marchal, C., Zhao, P., Park, P., Alver, B.H., Schroeder, A., Navelkar, R., Bakker, C., Ronchetti, W., Ehmsen, S., Veit, A., Gehlenborg, N., Wang, T., Li, D., Wang, X., Nicodemi, M., Ren, B., Zhong, S., Phillips-Cremins, J.E., Gilbert, D.M., Pollard, K.S., Alber, F., Ma, J., Noble, W.S. and Yue, F.
bioRxiv : 2024.09.17.613111v2. 27 October 2024

Rewired type I IFN signaling is linked to age-dependent differences in COVID-19.
Petrov, L., Brumhard, S., Wisniewski, S., Georg, P., Hillus, D., Hiller, A., Astaburuaga-García, R., Blüthgen, N., Wyler, E., Vogt, K., Dey, H.P., von Stillfried, S., Iwert, C., Bülow, R.D., Märkl, B., Maas, L., Langner, C., Meyer, T., Loske, J., Eils, R., Lehmann, I., Ondruschka, B., Ralser, M., Trimpert, J., Boor, P., Bedoui, S., Meisel, C., Mall, M.A., Corman, V.M., Sander, L.E., Röhmel, J. and Sawitzki, B.
bioRxiv : 2024.10.23.619479. 23 October 2024

Systemic effects of cystic fibrosis transmembrane conductance regulator (CFTR) modulators on the blood proteome.
Fentker, K., Kirchner, M., Ziehm, M., Niquet, S., Popp, O., Duerr, J., Schaupp, L., Roehmel, J., Thee, S., Haemmerling, S., Sommerburg, O., Stahl, M., Graeber, S.Y., Mall, M.A. and Mertins, P.
bioRxiv : 2024.10.18.619058. 18 October 2024

Mapping DHPS evolvability: identification of novel evolutionarily critical sub-structure through evolutionary and structural analyses of DHPS.
Sanyal, D., Shivram, A., Banerjee, S., Uversky, V.N., Chivukula, A., Chattopadhyay, K. and Chowdhury, S.
bioRxiv : 2024.10.16.618629. 18 October 2024

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development.
Schindler, M., Feregrino, C., Aldrovandi, S., Lo, B.W., Monaco, A.A., Ringel, A.R., Morales, A., Zehnder, T., Behncke, R.Y., Glaser, J., Barclay, A., Andrey, G., Kragesteen, B.K., Hägerling, R., Haas, S., Vingron, M., Ulitsky, I., Marti-Renom, M., Hechavarria, J., Fasel, N., Hiller, M., Lupianez, D.G., Mundlos, S. and Real, F.M.
bioRxiv : 2024.10.10.617585. 13 October 2024

TENM4 is an essential transduction component for touch and pain.
Khallaf, M.A., Huang, A.T.L., Dalmasso, L., Chakrabarti, S., Groeneveld, R., Sierra, Y.A.B., Garcia-Contreras, J.A., Schutz, A., Bégay, V., Hedtrich, S., Zhong, W., Popp, O., Mertins, P. and Lewin, G.R.
bioRxiv : 2024.10.10.617546. 12 October 2024

Endogenous tagging of Munc13-1 with a SNAP tag as a tool for monitoring synapse nanoarchitecture.
Kowald, M., Bachollet, S.P.J.T., Benseler, F., Steinecker, M., Kaushik, S., Soykan, T., Siqi, S., Birke, R., Ilic, D., Brose, N., Hörnberg, H., Lehmann, M., Rizzoli, S.O., Broichhagen, J. and Lipstein, N.
bioRxiv : 2024.10.08.617143. 10 October 2024

Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference.
Lareau, C.A., Chapman, M.S., Penter, L., Nawy, T., Pe’er, D. and Ludwig, L.S.
bioRxiv : 2024.07.28.605517v2. 5 October 2024

Sociality shapes mitochondrial adaptations supporting hypoxia tolerance.
Rossi, A., Ruwolt, M., Kakouri, P., Kosten, T., Kunz, S., Puchkov, D., Reznick, J., Purfürst, B., Omerbašić, D., Méndez Aranda, D., Carai, G., Mastrobuoni, G., Hart, D.W., Carraro, M., Tommasin, L., Bennett, N.C., Bégay, V., Faelber, K., Daumke, O., Bernardi, P., Park, T.J., Kempa, S., Liu, F. and Lewin, G.R.
bioRxiv : 2024.09.30.615914. 2 October 2024

Activation mapping in multi-center rat sensory-evoked functional MRI datasets using a unified pipeline.
Galteau, M.E., Broadwater, M., Chen, Y., Desrosiers-Gregoire, G., Gil, R., Kaesser, J., Kim, E., Kiryagdi, P., Lambers, H., Liu, Y.Y., Lopez-Gil, X., MacNicol, E., Mohebkhodaei, P., De Oliveira, R.X.N., Pereira, C.A., Reimann, H.M., Rivera-Olvera, Al., Selingue, E., Sirmpilatze, N., Strobelt, S., Sumiyoshi, A., Tham, C., Tudela, R., Vrooman, R.M., Wank, I., Zhang, Y., van Engelenburg, W.A., Baudewig, J., Boretius, S., Cash, D., Chakravarty, M.M., Chuang, K.H., Ciobanu, L., Devenyi, G.A., Faber, C., Hess, A., Homberg, J.R., Jelescu, I.O., Justicia, C., Kawashima, R., Niendorf, T., Scheenen, T.W.J., Shemesh, N., Soria, G., Todd, N., Wachsmuth, L., Yu, X., Zhang, B.B., Shih, Y.Y.I., Lee, S.H. and Grandjean, J.
bioRxiv : 2024.09.27.615384. 30 September 2024

Enhancing biomarker-based oncology trial matching using large language models.
Al Khoury, N., Shaik, M., Wurmus, R. and Akalin, A.
bioRxiv : 2024.09.13.612922. 19 September 2024

Autophagy acts as a brake on obesity-related fibrosis by controlling purine nucleoside signalling.
Piletic, K., Kayvanjoo, A.H., Richter, F.C., Borsa, M., Lechuga-Vieco, A.V., Popp, O., Grenet, S., Ko, J.K.L., Zec, K., Kyriazi, M., Koneva, L., Sansom, S., Mertins, P., Powrie, F., Alsaleh, G. and Simon, A.K.
bioRxiv : 2024.09.17.613382. 17 September 2024

YAP/TAZ signaling in allantois-derived cells is required for placental vascularization.
Gao, S., Thillaikumaran, T., Dominguez, M.H., Giang, W., Hayes, K., Chen, X., Pace, J., Bockman, J., Jathan, D., Sung, D., Narayan, S., Frankfurter, M., Mericko-Ishizuka, P., Yang, J., Castro, M., Potente, M. and Kahn, M.L.
bioRxiv : 2024.09.15.613151. 16 September 2024

Bimodal dendritic processing in basket cells drives distinct memory-related oscillations.
Tzilivaki, A., Larkum, M.E. and Schmitz, D.
bioRxiv : 2024.09.11.612262. 14 September 2024

Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation.
Vučićević, D., Hsu, C.W., Lopez Zepeda, L.S., Burkert, M., Hirsekorn, A., Bilić, I., Kastelić, N., Landthaler, M., Lacadie, S.A. and Ohler, U.
bioRxiv : 2024.09.12.612198. 12 September 2024

IGF1R is protective in pneumococcal pneumonia.
Felten, M., Teixeira Alves, L.G., Letsiou, E., Arnedo, E.A., Piñeiro-Hermida, S., López, I.P., Dietert, K., Firsching, T., Gruber, A.D., Fatykhova, D., Hocke, A., Lingscheid, T., Lienau, J., Rohde, G., Pichel, J.G. and Witzenrath, M.
bioRxiv : 2024.09.11.612370. 11 September 2024

Single-stranded HDR templates with truncated Cas12a binding sequences improve knock-in efficiencies in primary human T cells.
Nitulescu, A.M., Du, W., Glaser, V., Kath, J., Greensmith, R., Mikkelsen, N.S., Stein, M., Bak, R., Kaminski, M.M. and Wagner, D.L.
bioRxiv : 2024.09.11.608426. 11 September 2024

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.
Deutsch, Eric W, Kok, Leron W, Mudge, Jonathan M, Ruiz-Orera, J., Fierro-Monti, Ivo, Sun, Zhi, Abelin, Jennifer G, Alba, M Mar, Aspden, Julie L, Bazzini, Ariel A, Bruford, Elspeth, Brunet, Marie A, Calviello, L., Carr, Steven A, Carvunis, Anne-Ruxandra, Chothani, Sonia, Clauwaert, Jim, Dean, Kellie, Faridi, Pouya, Frankish, Adam, Hubner, N., Ingolia, Nicholas, Magrane, Michele, Martin, Maria Jesus, Martinez, Thomas F, Menschaert, Gerben, Ohler, U., Orchard, Sandra, Rackham, Owen, Roucou, Xavier, Slavoff, Sarah A, Valen, Eivind, Wacholder, Aaron C, Weissman, Jonathan S., Wu, Wei, Xie, Zhi, Choudhary, Jyoti, Bassani-Sternberg, Michal, Vizcaino, Juan Antonio, Ternette, Nicola, Moritz, Robert L., Prensner, John and van Heesch, S.
bioRxiv : 2024.09.09.612016. 9 September 2024

Cell-mechanical parameter estimation from 1D cell trajectories using simulation-based inference.
Heyn, J., Atienza Juanatey, M., Falcke, M. and Raedler, J.
bioRxiv : 2024.09.06.611766. 8 September 2024

Neuromuscular dysfunction in patient-derived FUS(R244RR)-ALS iPSC model via axonal downregulation of neuromuscular junction proteins.
von Kuegelgen, N., Ludwik, K., Mendonsa, S., Roemer, C., Becher, E., Breimann, L., Strauch, M., Mari, T., Mongellaz, S., Zuckerman, B., Grexa, N., Oliveras-Martinez, A., Woehler, A., Selbach, M., La Bella, V., Ulitsky, I. and Chekulaeva, M.
bioRxiv : 2024.08.17.607965. 17 August 2024

Refined enterotyping reveals dysbiosis in global fecal metagenomes.
Keller, M.I., Nishijima, S., Podlesny, D., Kim, C.Y., Robbani, S.M., Schudoma, C., Fullam, A., Richter, J., Letunic, I., Akanni, W., Orakov, A., Schmidt, T.S., Marotta, F., Trebicka, J., Kuhn, M., Van Rossum, T. and Bork, P.
bioRxiv : 2024.08.13.607711v2. 14 August 2024

Do transformers and CNNs learn different concepts of brain age?
Siegel, N.T., Kainmueller, D., Deniz, F., Ritter, K. and Schulz, M.A.
bioRxiv : 2024.08.09.607321. 9 August 2024

Touch inhibits cold: non-contact cooling reveals a novel thermotactile gating mechanism.
Ezquerra-Romano, I., Chowdhury, M. and Haggard, P.
bioRxiv : 2024.08.06.606653. 8 August 2024

Insights into therapeutic discovery through the Kelch domain structure of Keap1 at ambient temperature.
Yilmaz, M., Sever, B., Kutlu, Y., Gul, M., Okuducu, C., Tavli, S., Otsuka, M., Fujita, M., Haliloglu, T., Ciftci, H. and DeMirci, H.
bioRxiv : 2024.07.30.605796. 2 August 2024

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond.
Uyar, B., Savchyn, T., Wurmus, R., Sarigun, A., Shaik, M.M., Franke, V. and Akalin, A.
bioRxiv : 2024.07.16.603606. 18 July 2024

Oncogene inactivation-induced senescence facilitates tumor relapse.
Schmitt, P., Hönig, K., Milojkovic, A., Anders, K., Schröck, E., Sauer, S., Uyar, B., Akalin, A., Martínez-Reyes, I. and Blankenstein, T.
bioRxiv : 2024.07.13.603369. 17 July 2024

Denoising, deblurring, and optical deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR.
Li, R., Yushkevich, A., Chu, X., Kudryashev, M. and Yakimovich, A.
bioRxiv : 2024.07.12.603278. 16 July 2024

Ultraslow serotonin oscillations in the hippocampus delineate substates across NREM and waking.
Cooper, C., Parthier, D., Sibille, J., Tukker, J.J., Tritsch, N.X. and Schmitz, D.
bioRxiv : 2024.07.09.602643. 13 July 2024

Reporter-based screening identifies RAS-RAF mutations as drivers of resistance to active-state RAS inhibition in colorectal cancer.
Aust, O., Blanc, E., Lüthen, M., Hollek, V., Astaburuaga-García, R., Klinger, B., Trinks, A., Beule, D., Papke, B., Horst, D., Blüthgen, N., Sers, C., Der, C.J. and Morkel, M.
bioRxiv : 2024.07.01.601542v2. 12 July 2024

Mechanosensitive PIEZO2 channels shape coronary artery development.
Pampols-Perez, M., Fürst, C., Sánchez-Carranza, O., Cano, E., Raimundo, S., Lindberg, E.L., Taube, M., Heuser, A., Sporbert, A., Hübner, N., Gerhardt, H., Lewin, G.R. and Hammes, A.
bioRxiv : 2024.07.08.602502. 11 July 2024

Pial collaterals develop through mosaic colonization of capillaries by arterial and microvascular endothelial cells.
Perovic, T., Hollfinger, I., Mayer, S., Lips, J., Dopatka, M., Harms, C. and Gerhardt, H.
bioRxiv : 2023.10.09.561542v3. 7 February 2024

Cytokines as potential novel therapeutic targets in severe inflammatory cardiomyopathy.
Suwalski, P., Golpour, A., Weiner, J., Musigk, N., Balzer, F., Giesa, N., Amr, A., Trebing, J., Sedaghat, F., Meder, B., Beule, D., Landmesser, U. and Heidecker, B.
bioRxiv : 2023.07.27.23293253. 4 August 2023

RIF1 acts as a gatekeeper of B cell identity during late differentiation.
Rahjouei, A., Kabrani, E., Berruezo-Llacuna, M., Altwasser, R., Delgado-Benito, V., Pavri, R. and Di Virgilio, M.
bioRxiv : 2023.07.18.549543v2. 20 July 2023

Cellular and synaptic diversity of layer 2-3 pyramidal neurons in human individuals.
Planert, H., Mittermaier, F.X., Grosser, S., Fidzinski, P., Schneider, U.C., Radbruch, H., Onken, J., Holtkamp, M., Schmitz, D., Alle, H., Vida, I., Geiger, J.R.P. and Peng, Y.
bioRxiv : 2021.11.08.467668. 24 January 2023

Replicative aging impedes stress-induced assembly of a key human protein disaggregase.
Mathangasinghe, Y., Alberts, N., Rosado, C.J., Cox, D., Payne, N.L., Ormsby, A.R., Alp, K.M., Sakson, R., Uthishtran, S., Ruppert, T., Arumugam, S., Hatters, D.M., Kampinga, H.H. and Nillegoda, N.B.
bioRxiv : 2022.06.25.497591. 8 January 2023

The lncRNA landscape of cardiac resident macrophages and identification of Schlafenlnc as a regulator of macrophage migratory function.
Dueck, A., Althaus, L., Heise, K., Esfandyari, D., Bayguen, S., Brandes, R.P., Gagneur, J., Jae, N., Knolle, P., Leisegang, M.S., Maegdefessel, L., Meitinger, T., Petzold, N., Ramanujam, D., Sager, H., Schulz, C., Theodorakis, E., Uzonyi, A., Weinberger, T., Bader, M., Schmidt-Supprian, M. and Engelhardt, S.
bioRxiv : 2022.11.30.518576. 22 December 2022

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in severe COVID-19.
Essex, M., Pascual-Leone, B.M., Löber, U., Kuhring, M., Zhang, B., Bruening, U., Fritsche-Guenther, R., Krzanowski, M., Vernengo, F.F., Brumhard, S., Röwekamp, I., Bielecka, A.A., Lesker, T.R., Wyler, E., Landthaler, M., Mantei, A., Meisel, C., Caesar, S., Thiebeault, C., Corman, V., Marko, L., Suttorp, N., Strowig, T., Kurth, F., Sander, L.E., Li, Y., Kirwan, J.A., Forslund, S.K. and Opitz, B.
bioRxiv : 2022.12.02.518860. 2 December 2022

Therapy-induced senescence upregulates antigen presentation machinery and triggers anti-tumor immunity in Acute Myeloid Leukemia.
Gilioli, D., Fusco, S., Tavella, T., Giannetti, K., Conti, A., Santoro, A., Carsana, E., Beretta, S., Schönlein, M., Gambacorta, V., Aletti, F.M., Carraba, M.G., Bonini, C., Ciceri, F., Merelli, I., Vago, L., Schmitt, C.A. and Di Micco, R.
bioRxiv : 2022.11.17.515658. 17 November 2022

Autophagy limits inflammatory gene expression through targeting of nuclear p65/RelA by LC3 and p62 for lysosomal degradation.
Brischetto, C., Mucka, P., Kaergel, E. and Scheidereit, C.
bioRxiv : 2022.11.02.514846. 2 November 2022

Engineered vasculature induces functional maturation of pluripotent stem cell-derived islet organoids.
Nguyen-Ngoc, K.V., Jun, Y., Sai, S., Bender, R.H.F., Kravets, V., Zhu, H., Hatch, C.J., Schlichting, M., Gaetani, R., Mallick, M., Hachey, S.J., Christman, K.L., George, S.C., Hughes, C.C.W. and Sander, M.
bioRxiv : 2022.10.28.513298. 30 October 2022

3D genome topologies distinguish pluripotent epiblast and primitive endoderm cells in the mouse blastocyst.
Loof, G., Szabo, D., Garg, V., Kukalev, A., Zea-Redondo, L., Kempfer, R., Sparks, T.M., Zhang, Yi., Thieme, C.J., Carvalho, S., Weise, A., Balachandran, M., Liehr, T., Welch, L.R., Hadjantonakis, A.K. and Pombo, A.
bioRxiv : 2022.10.19.512781. 20 October 2022

The molecular mechanism and physiological role of silent nociceptor activation.
Nees, T.A., Wang, N., Adamek, P., Verkest, C., Schaefer, I., Virnich, J., Balkaya, S., Prato, V., Morelli, C., Zeitzschel, N., Begay, V., Lee, Y.J., Lewin, G.R., Heppenstall, P.A., Taberner, F.J. and Lechner, S.G.
bioRxiv : 2022.04.07.486730. 19 October 2022

The little skate genome and the evolutionary emergence of wing-like fin appendages.
Marletaz, F., de la Calle-Mustienes, E., Acemel, R.D., Nakamura, T., Paliou, C., Naranjo, S., Martinez-Garcia, P.M., Cases, I., Sleight, V.A., Hirschberger, C., Marcet-Houben, M., Navon, D., Andrescavage, A., Skvortsova, K., Duckett, P.E., Gonzalez-Rajal, A., Bogdanovic, O., Gibcus, J.H., Yang, L., Gallardo-Fuentes, L., Sospedra, I., Lopez-Rios, J., Darbellay, F., Visel, A., Dekker, J., Shubin, N., Gabaldon, T., Tena, J.J., Lupianez, D.G., Rokhsar, D.S. and Gomez-Skarmeta, J.L.
bioRxiv : 2022.03.21.485123. 22 March 2022

One gene - two proteins: the C-terminus of the prototypical M2 muscarinic receptor localizes to the mitochondria.
Fasciani, I., Petragnano, F., Wang, Z., Edwards, R., Telugu, N., Pietrantoni, I., Zauber, H., Rossi, M., Zabel, U., Grieben, M., Terzenidou, M.E., Di Gregorio, J., Pellegrini, C., Santini, S., Taddei, A.R., Poehl, B., Aringhieri, S., Aloisi, G., Marampon, F., Roman, A., Diecke, S., Flati, V., Giorgi, F., Amicarelli, F., Tobin, A.B., Scarselli, M., Tokatlidis, K., Lohse, M.J., Maggio, R. and Annibale, P.
bioRxiv : 2021.04.13.438299. 26 February 2022

C. difficile is overdiagnosed in adults and a commensal in infants.
Ferretti, P., Wirbel, J., Maistrenko, O.M., Van Rossum, T., Alves, R., Fullam, A., Akanni, W., Schudoma, C., Schwarz, A., Thielemann, R., Thomas, L., Kuhn, M., Zeller, G., Schmidt, T.S.B. and Bork, P.
bioRxiv : 2022.02.16.480740v1. 18 February 2022

Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I., Emmenegger, L., Zappulo, A., Wurmus, R., Oliveras Martinez, A., Cerda Jara, C., Boltengagen, A., Hessler, T., Mastrobuoni, G., Rybak-Wolf, A., Kempa, S., Zinzen, R.P., Woehler, A. and Rajewsky, N.
bioRxiv : 2021.09.26.461850v3. 9 February 2022

Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging.
Freitag, K., Eede, P., Ivanov, A., Schneeberger, S., Borodina, T., Sauer, S., Beule, D. and Heppner, F.L.
bioRxiv : 2021.08.02.454573v1. 28 November 2021

Drivers and determinants of strain dynamics following faecal microbiota transplantation.
Schmidt, T.S.B., Li, S.S., Maistrenko, O.M., Akanni, W., Coelho, L.P., Dolai, S., Fullam, A., Glazek, A.M., Hercog, R., Herrema, H., Jung, F., Kandels, S., Orakov, A., Van Rossum, T., Benes, V., Borody, T.J., de Vos, W.M., Ponsioen, C.Y., Nieuwdorp, M. and Bork, P.
bioRxiv : 2021.09.30.462010. 30 September 2021

PatchPerPixMatch for automated 3d search of neuronal morphologies in light microscopy.
Mais, L., Hirsch, P., Managan, C., Wang, K., Rokicki, K., Svirskas, R.R., Dickson, B.J., Korff, W., Rubin, G.M., Ihrke, G., Meissner, G.W. and Kainmueller, D.
bioRxiv : 2021.07.23.453511. 26 July 2021

UPF3A and UPF3B are redundant and modular activators of nonsense-mediated mRNA decay in human cells.
Wallmeroth, D., Boehm, V., Lackmann, J.W., Altmüller, J., Dieterich, C. and Gehring, N.H.
bioRxiv : 2021.07.07.451444. 13 July 2021

An executive center for the intake of liquids.
Dempsey, B., Sungeelee, S., Bokiniec, P., Chettouh, Z., Diem, S., Autran, S., Harrell, E.R., Poulet, J.F.A., Birchmeier, C., Carrey, H., Genovesio, A., McMullan, S., Goridis, C., Fortin, G. and Brunet, J.F.
bioRxiv : 2021.07.02.450862. 4 July 2021

Insulin mRNA is stored in RNA granules in resting beta cells.
Vasiljević, J., Vasiljević, D., Ganß, K., Sönmez, A., Wegbrod, C., Quezada, E., Münster, C., Schöniger, E., Friedland, D., Kipke, N., Distler, M., Selbach, M. and Solimena, M.
bioRxiv : 2021.05.07.443159. 29 June 2021

Timed global reorganization of protein synthesis during neocortex neurogenesis at codon resolution.
Harnett, D., Ambrozkiewicz, M.C., Zinnall, U., Borisova, E., Rusanova, A., Dannenberg, R., Imami, K., Münster-Wandowski, A., Fauler, B., Mielke, T., Selbach, M., Landthaler, M., Spahn, C.M.T., Tarabykin, V., Ohler, U. and Kraushar, M.L.
bioRxiv : 2021.06.23.449626. 24 June 2021

Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers.
Lange, J.T., Chen, C.Y., Pichugin, Y., Xie, L., Tang, J., Hung, K.L., Yost, K.E., Shi, Q., Erb, M.L., Rajkumar, U., Wu, S., Swanton, C., Liu, Z., Huang, W., Chang, H.Y., Bafna, V., Henssen, A.G., Werner, B. and Mischel, P.S.
bioRxiv : 10.1101/2021.06.11.447968. 11 June 2021

Emerging single cell endothelial heterogeneity supports sprouting tumour angiogenesis and growth.
Matsumoto, K., Rambow, F., Stanchi, F., Mathivet, T., Qian, J., Giese, W., He, L., Lambrechts, D., Zhou, B., Betsholtz, C., Marine, J.C. and Gerhardt, H.
bioRxiv : 2021.06.09.447719. 11 June 2021

Single-cell transcriptomic analysis of antiviral responses and viral antagonism in Chikungunya virus-infected synovial fibroblasts.
Pott, F., Postmus, D., Brown, R.J.P., Wyler, E., Neumann, E., Landthaler, M. and Goffinet, C.
bioRxiv : 2020.06.07.138610. 11 June 2021

Investigating the concept of accessibility for predicting novel RNA-RNA interactions.
Reißer, S. and Meyer, I.M.
bioRxiv : 2021.06.03.446902. 3 June 2021

The neuroinflammatory interleukin-12 signaling pathway drives Alzheimer's disease-like pathology by perturbing oligodendrocyte survival and neuronal homeostasis.
Schneeberger, S., Kim, S.J., Eede, P., Boltengagen, A., Braeuning, C., Andreadou, M., Becher, B., Karaiskos, N., Kocks, C., Rajewsky, N. and Heppner, F.L.
bioRxiv : 2021.04.25.441313. 27 April 2021

Dual-function RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes.
Schneider-Lunitz, V., Ruiz-Orera, J., Hubner, N. and van Heesch, S.
bioRxiv : 2021.04.13.439465. 13 April 2021

Expression of a modified astrocytic glutamate transporter alleviates Huntington’s hypokinesia, promotes synaptic glutamate clearance and counteracts potentially adverse EAAT2 interactions.
Hirschberg, S., Dvorzhak, A., Rasooli-Nejad, S.M.A., Angelov, S., Kirchner, M., Mertins, P., Lättig-Tünnemann, G., Harms, C., Schmitz, D. and Grantyn, R.
bioRxiv : 2020.09.17.302158. 26 March 2021

Uncharted biosynthetic potential of the ocean microbiome.
Paoli, L., Ruscheweyh, H.J., Forneris, C.C., Kautsar, S., Clayssen, Q., Salazar, G., Milanese, A., Gehrig, D., Larralde, M., Carroll, L.M., Sánchez, P., Zayed, A.A., Cronin, D.R., Acinas, S.G., Bork, P., Bowler, C., Delmont, T.O., Sullivan, M.B., Wincker, P., Zeller, G., Robinson, S.L., Piel, J. and Sunagawa, S.
bioRxiv : 2021.03.24.436479. 24 March 2021

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression.
Walter, S., Franke, V., Drayman, N., Wyler, E., Tay, S., Landthaler, M., Akalin, A., Ensser, A. and Full, F.
bioRxiv : 2021.03.24.436599. 24 March 2021

N-myristoyltransferase inhibition is synthetic lethal in MYC-deregulated cancers.
Lueg, G.A., Faronato, M., Gorelik, A., Grocin, A.G., Caamano-Gutierrez, E., Falciani, F., Solari, R., Carr, R., Bell, A.S., Bartlett, E., Hutton, J.A., Llorian-Sopena, M., Chakravarty, P., Brzezicha, B., Janz, M., Garnett, M.J., Calado, D.P. and Tate, E.W.
bioRxiv : 2021.03.20.436222. 20 March 2021

Neurodegeneration in human brain organoids infected with herpes simplex virus type 1.
Rybak-Wolf, A., Wyler, E., Legnini, I., Loewa, A., Glažar, P., Kim, S.J., Pentimalli, T.M., Oliveras Martinez, A., Beyersdorf, B., Woehler, A., Landthaler, M. and Rajewsky, N.
bioRxiv : 2021.03.05.434122. 7 March 2021

Optogenetic silencing of neurotransmitter release with a naturally occurring invertebrate rhodopsin.
Mahn, M., Saraf-Sinik, I., Patil, P., Pulin, M., Bitton, E., Karalis, N., Bruentgens, F., Palgi, S., Gat, A., Dine, J., Wietek, J., Davidi, I., Levy, R., Litvin, A., Zhou, F., Sauter, K., Soba, P., Schmitz, D., Luthi, A., Rost, B.R., Wiegert, J.S. and Yizhar, O.
bioRxiv : 2021.02.18.431673. 18 February 2021

Rabies anterograde monosynaptic tracing reveals organization of spinal sensory circuits.
Pimpinella, S. and Zampieri, N.
bioRxiv : 429920. 11 February 2021

On the distribution of spinal premotor interneurons.
Ronzano, R., Skarlatou, S., Bannatyne, B.A., Bhumbra, G.S., Foster, J.D., Lancelin, C., Pocratsky, A., Ozyurt, M.G., Smith, C.C., Todd, A.J., Maxwell, D.J., Murray, A.J., Brownstone, R.M., Zampieri, N. and Beato, M.
bioRxiv : 2021.02.10.430608. 11 February 2021

AI-driven Deep Visual Proteomics defines cell identity and heterogeneity.
Mund, A., Coscia, F., Hollandi, R., Kovács, F., Kriston, A., Brunner, A.D., Bzorek, M., Naimy, S., Rahbek Gjerdrum, L.M., Dyring-Andersen, B., Bulkescher, J., Lukas, C., Gnann, C., Lundberg, E., Horvath, P. and Mann, M.
bioRxiv : 2021.01.25.427969. 27 January 2021

Fructose 1,6-bisphosphate sensing by pyruvate kinase isozymes M2 (PKM2) controls MyoD stability and myogenic differentiation.
Kim, M., Zhang, Y. and Birchmeier, C.
bioRxiv : 2020.12.22.424062. 22 December 2020

Local microcircuitry of parasubiculum shows distinct and common features of excitatory and inhibitory connectivity.
Sammons, R.P., Tzilivaki, A. and Schmitz, D.
bioRxiv : 2020.12.18.423400. 19 December 2020

IFT88 transports Gucy2d, a guanylyl cyclase, to maintain sensory cilia function in Drosophila.
Werner, S., Zitouni, S., Okenve-Ramos, P., Mendonça, S., Sporbert, A., Spalthoff, C., Göpfert, M.C., Jana, S.C. and Bettencourt-Dias, M.
bioRxiv : 2020.12.15.417840. 15 December 2020

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes.
Garipler, G., Lu, C., Morrissey, A., Lopez-Zepeda, L.S., Vidal, S.E., Aydin, B., Stadtfeld, M., Ohler, U., Mahony, S., Sanjana, N.E. and Mazzoni, E.O.
bioRxiv : 2020.11.23.391771. 23 November 2020

LoopDetect: comprehensive feedback loop detection in ordinary differential equation models.
Baum, K. and Wolf, J.
bioRxiv : 2020.11.15.383703. 17 November 2020

The mechanotransduction protein STOML3 is required for functional plasticity following peripheral nerve regeneration.
Haseleu, J., Walcher, J. and Lewin, G.R.
bioRxiv : 2020.11.10.367748. 10 November 2020

Diverse chemotypes drive biased signaling by cannabinoid receptors.
Miljuš, T., Heydenreich, F.M., Gazzi, T., Kimbara, A., Rogers-Evans, M., Nettekoven, M., Zirwes, E., Osterwald, A., Rufer, A.C., Ullmer, C., Guba, W., Le Gouill, C., Fingerle, J., Nazaré, M., Grether, U., Bouvier, M. and Veprintsev, D.B.
bioRxiv : 2020.11.09.375162. 10 November 2020

Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity.
Hall, G.R., Boehm-Sturm, P., Dirnagl, U., Finke, C., Foddis, M., Harms, C., Koch, S.P., Kuchling, J., Madan, C.R., Mueller, S., Sassi, C., Sotiropoulos, S.N., Trueman, R.C., Wallis, M., Yildirim, F. and Farr, T.D.
bioRxiv : 2020.11.04.366294. 5 November 2020

Olig3 acts as a master regulator of cerebellar development.
Lowenstein, E.D., Rusanova, A., Stelzer, J., Hernaiz-Llorens, M., Schroer, A.E., Epifanova, E., Bladt, F., Isik, E.G., Jia, S., Tarabykin, V. and Hernandez-Miranda, L.R.
bioRxiv : 2020.10.10.334615. 10 October 2020

Morphine alleviates pain after heart cryoinjury in zebrafish without impeding regeneration.
Lelek, S., Simões, M., Hu, B., Alameldeen, A.M.A., Czajkowski, M.T., Meyer, A.M., Ferrara, F., Junker, J.P. and Panáková, D.
bioRxiv : 2020.10.01.322560. 2 October 2020

RBM20 phosphorylation on serine/arginine domain is crucial to regulate pre-mRNA splicing and protein shuttling in the heart.
Sun, M., Jin, Y., Zhu, C., Zhang, Y., Liss, M., Gotthardt, M., Ren, J., Ge, Y. and Guo, W.
bioRxiv : 2020.09.15.297002. 15 September 2020

Myogenic vasoconstriction requires canonical Gq/11 signaling of the angiotensin II type 1a receptor in the murine vasculature.
Cui, Y., Kassmann, M., Nickel, S., Zhang, C., Alenina, N., Anistan, Y.M., Schleifenbaum, J., Bader, M., Welsh, D.G., Huang, Y. and Gollasch, M.
bioRxiv : 2020.09.09.289280. 11 September 2020

Mechanistic basis for motor-driven membrane constriction by dynamin.
Ganichkin, O., Vancraenenbroeck, R., Rosenblum, G., Hofmann, H., Mikhailov, A.S., Daumke, O. and Noel, J.K.
bioRxiv : 2020.09.10.289546. 11 September 2020

The CONDOR pipeline for simultaneous knockdown of multiple genes identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans.
Kazmierczak, M., Díaz, C.F., Ofenbauer, A. and Tursun, B.
bioRxiv : 2020.09.01.276972. 1 September 2020

Increased and synchronous recruitment of release sites underlies hippocampal mossy fiber presynaptic potentiation.
Orlando, M., Dvorzhak, A., Bruentgens, F., Maglione, M., Rost, B.R., Sigrist, S.J., Breustedt, Jm and Schmitz, D.
bioRxiv : 2020.08.21.260638. 21 August 2020

A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model.
Kreye, J., Reincke, S.M., Kornau, H.C., Sanchez-Sendin, E., Corman, V.M., Liu, H., Yuan, M., Wu, N.C., Zhu, X., Lee, C.C.D., Trimpert, J., Hoeltje, M., Dietert, K., Stoeffler, L., von Wardenburg, N., van Hoof, S., Homeyer, M.A., Hoffmann, J., Abdelgawad, A., Gruber, A.D., Bertzbach, L.D., Vladimirova, D., Li, L.Y., Barthel, P.C., Skriner, K., Hocke, A.C., Hippenstiel, S., Witzenrath, M., Suttorp, N., Kurth, F., Franke, C., Endres, M., Schmitz, D., Jeworowski, L.M., Richter, A., Schmidt, M.L., Schwarz, T., Mueller, M.A., Drosten, C., Wendisch, D., Sander, L.E., Osterrieder, N., Wilson, I.A. and Pruess, H.
bioRxiv : 2020.08.15.252320. 16 August 2020

CD40 provides immune privilege to the bone marrow hematopoietic niche.
Bassani, B., Gulino, A., Portararo, P., Botti, L., Cappetti, B., Chiodoni, C., Bolli, N., Ciciarello, M., Joehrens, K., Anagnostopoulos, I., Na, I.K., Curti, A., Tripodo, C., Colombo, M.P. and Sangaletti, S.
bioRxiv : 2020.08.10.243691. 10 August 2020

A semi-automated intestinal organoid screening method demonstrates epigenetic control of epithelial maturation.
Ostrop, J., Zwiggelaar, R., Pedersen, M.T., Gerbe, F., Bösl, K., Lindholm, H.T., Díez-Sánchez, Al., Parmar, N., Radetzki, S., von Kries, J.P., Jay, P., Jensen, K.B., Arrowsmith, C. and Oudhoff, M.J.
bioRxiv : 2020.07.23.217414. 24 July 2020

Open Source ImmGen: network perspective on metabolic diversity among mononuclear phagocytes.
Gainullina, A., Huang, L.H., Todorov, H., Kim, K., Yng, L.S., Kent, A., Jia, B., Seddu, K., Krchma, K., Wu, J., Crozat, K., Tomasello, E., Narang, V., Dress, R., See, P., Scott, C., Gibbings, S., Bajpai, G., Desai, J.V., Maier, B., This, S., Wang, P., Aguilar, S.V., Poupel, L., Dussaud, S., Zhou, T.A., Angeli, V., Blander, J.M., Choi, K., Dalod, M., Dzhagalov, I., Gautier, E.L., Jakubzick, C., Lavine, K., Lionakis, M.S., Paidassi, H., Sieweke, M.H., Ginhoux, Fl., Guilliams, M., Benoist, C., Merad, M., Randolph, G.J., Sergushichev, A. and Artyomov, M.N.
bioRxiv : 2020.07.15.204388. 16 July 2020

CTCF mediates dosage and sequence-context-dependent transcriptional insulation through formation of local chromatin domains.
Huang, H., Zhu, Q., Jussila, A., Han, Y., Bintu, B., Kern, C., Conte, M., Zhang, Y., Bianco, S., Chiariello, A.M., Yu, M., Hu, R., Juric, I., Hu, M., Nicodemi, M., Zhuang, X. and Ren, B.
bioRxiv : 2020.07.07.192526. 8 July 2020

Regional expression profiles of risk genes for depression are associated with brain activation patterns in emotion and reward tasks.
Komorowski, A., Vidal, R., Singh, A., Murgaš, M., Pena-Centeno, T., Gryglewski, G., Kasper, S., Wiltfang, J., Lanzenberger, R. and Goya-Maldonado, R.
bioRxiv : 2020.06.27.175257. 27 June 2020

Deciphering the regulatory logic of a Drosophila enhancer through systematic sequence mutagenesis and quantitative image analysis.
Le Poul, Y., Xin, Y., Ling, L., Mühling, B., Jaenichen, R., Hörl, D., Bunk, D., Harz, H., Leonhardt, H., Wang, Y., Osipova, E., Museridze, M., Dharmadhikari, D., Murphy, E., Rohs, R., Preibisch, S., Prud'homme, B. and Gompel, N.
bioRxiv : 2020.06.24.169748. 25 June 2020

Rub1/NEDD8, a ubiquitin-like modifier, is also a ubiquitin modifier.
Zerath Gurevich, S., Sinha, A., Longworth, J., Singh, R.K., Lemma, B.E., Thakur, A., Popp, O., Kornitzer, D., Reis, N., Scheffner, M., Dittmar, G., Pick, E., Fushman, D. and Glickman, M.H.
bioRxiv : 2020.06.18.159145. 19 June 2020

HMGXB4 targets Sleeping Beauty transposition to vertebrate germinal stem sells.
Devaraj, A., Singh, M., Narayanavari, S., Yong, G., Wang, J., Wang, J., Becker, M., Walisko, O., Schorn, A., Cseresznyés, Z., Grzela, D., Raskó, T., Selbach, M., Ivics, Z. and Izsvák, Z.
bioRxiv : 2020.06.15.145656. 15 June 2020

YAP and β-catenin co-operate to drive oncogenesis in basal breast cancer.
Quinn, H., Koren, E., Vogel, R., Popp, O., Mertins, P., Messerschmidt, C., Marangoni, E., Fuchs, Y. and Birchmeier, W.
bioRxiv : 2020.06.05.115881. 6 June 2020

Serotonin suppresses slow oscillations by activating somatostatin interneurons via the 5-HT(2A) receptor.
de Filippo, R., Rost, B., Stumpf, A., Cooper, C., Tukker, J.J., Harms, C., Beed, P. and Schmitz, D.
bioRxiv : 2020.05.26.113373. 26 May 2020

Dissecting HSV-1-induced host shut-off at RNA level.
Friedel, C.C., Whisnant, A.W., Djakovic, L., Rutkowski, A.J., Friedl, M.S., Kluge, M., Williamson, J.C., Sai, S., Oliveira Vidal, R., Sauer, S., Hennig, T., Prusty, B., Lehner, P.J., Matheson, N.J., Erhard, F. and Dölken, L.
bioRxiv : 2020.05.20.106039. 20 May 2020

Host genetic and environmental factors shape the human gut resistome.
Le Roy, C.I., Bowyer, R.C.E., Carr, V.R., Costeira, R., Castillo-Fernandez, J.E.R., Martin, T.C., Spector, T., Steves, C., Moyes, D., Forslund, S.K. and Bell, J.T.
bioRxiv : 2020.05.18.092973. 20 May 2020

Single cell RNA-sequencing-based analysis of CD4(+) T-cell subset-specific susceptibility to transcriptional modulation by HIV-1 latency-reversing agents.
Kazmierski, J., Postmus, D., Wyler, E., Fischer, C., Jansen, J., Meixenberger, K., Vitcetz, S.N., Sohn, M., Sauer, S., Bannert, N., Landthaler, M. and Goffinet, C.
bioRxiv : 2020.05.04.075119. 5 May 2020

Cdon mutation and fetal alcohol converge on nodal signaling in a gene-environment interaction model of holoprosencephaly.
Hong, M., Christ, A., Christa, A., Willnow, T.E. and Krauss, R.S.
bioRxiv : 2020.04.30.070870. 1 May 2020

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells.
Muus, C., Luecken, M.D., Eraslan, G., Waghray, A., Heimberg, G., Sikkema, L., Kobayashi, Y., Vaishnav, E.D., Subramanian, A., Smilie, C., Jagadeesh, K., Thu Duong, E., Fiskin, E., Torlai Triglia, E., Ansari, M., Cai, P., Lin, B., Buchanan, J., Chen, S., Shu, J., Haber, A.L., Chung, H., Montoro, D.T., Adams, T., Aliee, H., Allon, S.J., Andrusivova, A.Z., Angelidis, I., Ashenberg, O., Bassler, K., Bécavin, C., Benhar, I., Bergenstråhle, J., Bergenstråhle, L., Bolt, L., Braun, E., Bui, L.T., Chaffin, M., Chichelnitskiy, E., Chiou, J., Conlon, T.M., Cuoco, M.S., Deprez, M., Fischer, D.S., Gillich, A., Gould, J., Guo, M., Gutierrez, A.J., Habermann, A.C., Harvey, T., He, P., Hou, X., Hu, L., Jaiswal, A., Jiang, P., Kapellos, T., Kuo, C.S., Larsson, L., Leney-Greene, M.A., Lim, K., Litviňuková, M., Lu, J., Ludwig, L.S., Luo, W., Maatz, H., Madissoon, E., Mamanova, L., Manakongtreecheep, K., Marquette, C.H., Mbano, I., McAdams, A.M., Metzger, R.J., Nabhan, A.N., Nyquist, S.K., Penland, L., Poirion, O.B., Poli, S., Qi, C.C., Queen, R., Reichart, D., Rosas, I., Schupp, J., Sinha, R., Sit, R.V., Slowikowski, K., Slyper, M., Smith, N., Sountoulidis, A., Strunz, M., Sun, D., Talavera-López, C., Tan, P., Tantivit, J., Travaglini, K.J., Tucker, N.R., Vernon, K., Wadsworth, M.H., Waldman, J., Wang, X., Yan, W., Zhao, W. and Ziegler, C.G.K.
bioRxiv : 2020.04.19.049254. 21 April 2020

A CRISPR-Cas9-engineered mouse model for GPI anchor deficiency mirrors human phenotype and shows hippocampal synaptic dysfunctions.
Rodríguez de los Santos, M., Rivalan, M., David, F.S., Knaus, A., Stumpf, A., Velasquez, L.M., Voigt, A., Mattei, D., Long, M., Vogt, G., Wittler, L., Timmermann, B., Robinson, P.N., Horn, D., Mundlos, S., Kornak, U., Schmitz, D., Winter, Y. and Krawitz, P.M.
bioRxiv : 2020.04.20.050591. 21 April 2020

Co-activation of NF-κB and MYC renders cancer cells addicted to IL6 for survival and phenotypic stability.
Barbosa, R.R., Xu, A.Q., D'Andrea, D., Copley, F., Patel, H., Chakravarty, P., Clear, A., Calaminici, M., Janz, M., Zhang, B., Schmidt-Supprian, M., Wang, J., Gribben, J.G., Tooze, R., Fitzgibbon, J., Franzoso, G., Rajewsky, K. and Calado, D.P.
bioRxiv : 2020.04.12.038414. 13 April 2020

Mapping the unique and shared functions of oncogenic KRAS and RIT1 with proteome and transcriptome profiling.
Lo, A., Holmes, K., Mundt, F., Moorthi, S., Fung, I., Fereshetian, S., Watson, J., Carr, S.A., Mertins, P. and Berger, A.H.
bioRxiv : 2020.04.10.030460. 11 April 2020

Cells and gene expression programs in the adult human heart.
Litviňuková, M., Talavera-López, C., Maatz, H., Reichart, D., Worth, C.L., Lindberg, E.L., Kanda, M., Polanski, K., Fasouli, E.S., Samari, S., Roberts, K., Tuck, L., Heinig, M., DeLaughter, D.M., McDonough, B., Wakimoto, H., Gorham, J.M., Nadelmann, E.R., Mahbubani, K.T., Saeb-Parsy, K., Patone, G., Boyle, J.J., Zhang, H., Zhang, H., Viveiros, A., Oudit, G.Y., Bayraktar, O., Seidman, J.G., Seidman, C., Noseda, M., Hübner, N. and Teichmann, S.A.
bioRxiv : 2020.04.03.024075. 10 April 2020

Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping.
Welch, L.R., Baugher, C., Zhang, Y., Davis, T., Marzluff, W.F., Welch, J.D. and Pombo, A.
bioRxiv : 2020.02.10.941047. 13 February 2020

VarFish - Collaborative and comprehensive variant analysis for diagnosis and research.
Holtgrewe, M., Stolpe, O., Nieminen, M., Mundlos, S., Knaus, A., Kornak, U., Seelow, D., Segebrecht, L., Spielmann, M., Fischer-Zirnsak, B., Boschann, F., Scholl, U., Ehmke, N. and Beule, D.
bioRxiv : 2020.01.27.921965. 31 January 2020

A census of cell types and paracrine interactions in colorectal cancer.
Uhlitz, F., Bischoff, P., Sieber, A., Obermayer, B., Blanc, E., Lüthen, M., Sawitzki, B., Kamphues, C., Beule, D., Sers, C., Horst, D., Blüthgen, N. and Morkel, M.
bioRxiv : 2020.01.10.901579. 11 January 2020

Exploiting a PAX3-FOXO1-induced synthetic lethal ATR dependency for rhabdomyosarcoma therapy.
García, H.D., Bei, Y., von Stebut, J., Ibáñez, G., Imami, K., Gürgen, D., Rolff, J., Helmsauer, K., Timme, N., Bardinet, V., Chamorro González, R., MacArthur, I.C., Pusch, F.F., Chen, C.Y., Schulz, J., Wengner, A.M., Furth, C., Lala, B., Eggert, A., Seifert, G., Hundsoerfer, P., Kirchner, M., Mertins, P., Selbach, M., Lissat, A., Schulte, J.H., Haase, K., Scheer, M., Ortiz, M.V. and Henssen, A.G.
bioRxiv : 2020.12.04.411413. 2020

Microbiome determinants and physiological effects of the benzoate-hippurate microbial-host co-metabolic pathway.
Brial, F., Chilloux, J., Nielsen, T., Vieira-Silva, S., Falony, G., Hoyles, L., Neves, A.L., Rodriguez-Martinez, A., Mouawad, G.I., Pons, N., Forslund, S., Le Chatelier, E., Le Lay, A.M., Nicholson, J.K., Hansen, T., Clément, K., Bork, P., Ehrlich, S.D., Raes, J., Pedersen, O., Gauguier, D. and Dumas, M.E.
bioRxiv : 2019.12.15.876672. 16 December 2019

Chloroplast cold-resistance is mediated by the acidic domain of the RNA binding protein CP31A.
Okuzaki, A., Lehniger, M.K., Muino, J.M., Lenzen, B., Rühe, Thilo, Leister, D., Ohler, U. and Schmitz-Linneweber, C.
bioRxiv : 832337. 5 December 2019

LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes.
Piazza, I., Beaton, N., Bruderer, R., Knobloch, T., Barbisan, C., Siepe, I., Rinner, O., de Souza, N., Picotti, P. and Reiter, L.
bioRxiv : 860072. 1 December 2019

A fully phased accurate assembly of an individual human genome.
Porubsky, D., Ebert, P., Audano, P.A., Vollger, M.R., Harvey, W.T., Munson, K.M., Sorensen, M., Sulovari, A., Haukness, M., Ghareghani, M., Lansdorp, P.M., Paten, B., Devine, S.E., Sanders, A.D., Lee, C., Chaisson, M.J.P., Korbel, J.O., Eichler, E.E. and Marschall, T.
bioRxiv : 855049. 26 November 2019

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes.
Sanders, A.D., Meiers, S., Ghareghani, M., Porubsky, D., Jeong, H., van Vliet, M.A.C.C., Rausch, T., Richter-Pechańska, P., Kunz, J.B., Jenni, S., Raeder, B., Kinanen, V., Zimmermann, J., Benes, V., Schrappe, M., Mardin, B.R., Kulozik, A., Bornhauser, B., Bourquin, J.P., Marschall, T. and Korbel, J.O.
bioRxiv : 849604. 21 November 2019

Wnt11/Fzd7 signaling compartmentalizes AKAP2/PKA to regulate L-type Ca(2+) channel.
Csalyi, K.D., Rharass, T., Schulz, M., Phan, M.H.Q., Wakula, P., Mhatre, K.N., Plotnick, D., Werdich, A.A., Zauber, H., Sury, M.D., Selbach, M., Heinzel, F.R., Klussmann, E. and Panakova, D.
bioRxiv : 741637. 20 August 2019

SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud.
Obermayer, B., Holtgrewe, M., Nieminen, M., Messerschmidt, C. and Beule, D.
bioRxiv : 713008. 24 July 2019

Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data.
Calviello, L., Sydow, D., Harnett, D. and Ohler, U.
bioRxiv : 601468. 8 April 2019

The Tug1 locus is essential for male fertility.
Lewandowski, J.P., Dumbović, G., Watson, A.R., Hwang, T., Jacobs-Palmer, E., Chang, N., Much, C., Turner, K., Kirby, C., Schulz, J.F., Müller, C.L., Rubinstein, N.D., Groff, A.F., Liapis, S.C., Gerhardinger, C., Hubner, N., van Heesch, S., Hoekstra, H.E., Sauvageau, M. and Rinn, J.L.
bioRxiv : 562066. 28 February 2019

BIQ: A method for searching circular RNAs in transcriptome databases by indexing backsplice junctions.
Menzel, P. and Meyer, I.M.
bioRxiv : 556993. 25 February 2019

Crowdfunded whole-genome sequencing of the celebrity cat Lil BUB identifies causal mutations for her osteopetrosis and polydactyly.
Bridavsky, M., Kuhl, H., Woodruf, A., Kornak, U., Timmermann, B., Mages, N., Lupiáñez, D.G., Symmons, O. and Ibrahim, D.M.
bioRxiv : 556761. 22 February 2019

Splicing factor Rbm10 facilitates heterochromatin assembly in fission yeast.
Weigt, M., Gao, Q., Ban, H., He, H., Mastrobuoni, G., Kempa, S., Chen, W. and Li, F.
bioRxiv : 518936. 11 January 2019

Glutamate uptake and release at single adult corticostriatal synapses of normal and Huntington mice.
Dvorzhak, A., Helassa, N., Torok, K., Schmitz, D. and Grantyn, R.
bioRxiv : 455758. 30 October 2018

Emergence of robust nucleosome patterns from an interplay of positioning mechanisms.
Nuebler, J., Wolff, M., Obermayer, B., Mobius, W. and Gerland, U.
bioRxiv : 431445. 1 October 2018

Mutant screen reveals the Piccolo's control over depression and brain-gonad crosstalk.
Medrano, G.A., Singh, M., Plautz, E.J., Good, L.B., Chapman, K.M., Chaudhary, J., Jaichander, P., Powell, H.M., Pudasaini, A., Shelton, J.M., Richardson, J.A., Xie, X.J., Ivics, Z., Braun, C., Ackermann, F., Garner, C.C., Izsvak, Z. and Hamra, F.K.
bioRxiv : 405985. 31 August 2018

Loss of the Wnt/β-catenin pathway in microglia of the developing brain drives pro-inflammatory activation leading to white matter injury.
Van Steenwinckel, J., Schang, A.L., Krishnan, M.L., Degos, V., Delahaye-Duriez, A., Bokobza, C., Verdonk, F., Montane, A., Sigaut, S., Hennebert, O., Lebon, S., Schwendimann, L., Le Charpentier, T., Hassan-Abdi, R., Ball, G., Aljabar, P., Saxena, A., Holloway, R.K., Birchmeier, W., Miron, V., Rowitch, D., Chretien, F., Leconte, C., Besson, V.C., Petretto, E.G., Edwards, A.D., Hagberg, H., Soussi-Yanicostas, N., Fleiss, B. and Gressens, P.
bioRxiv : 334359. 31 May 2018

The phylogenetically distinct early human embryo.
Singh, M., Widmann, T.J., Cortes, J.L., Schumann, G.G., Wunderlich, S., Martin, U., Garcia-Perez, J.L., Hurst, L.D. and Izsvak, Z.
bioRxiv : 318329. 18 May 2018

Quantifying multi-layered expression regulation in response to stress of the endoplasmic reticulum.
Rendleman, J., Cheng, Z., Maity, S., Kastelic, N., Munschauer, M., Allgoewer, K., Teo, G., Zhang, Y.B., Lei, A., Parker, B., Landthaler, M., Freeberg, L., Kuersten, S., Choi, H. and Vogel, C.
bioRxiv : 308379. 25 April 2018

Cumulative regulatory potential of clustered methyl-arginine protein modifications.
Woodsmith, J., Casado-Medrano, V., Benlasfer, N., Eccles, R.L., Hutten, S., Heine, C., Thormann, V., Abou-Ajram, C., Rocks, O., Dormann, D. and Stelzl, U.
bioRxiv : 289041. 26 March 2018

Mutant Plasticity Related Gene 1 (PRG1) acts as a potential modifier in SCN1A related epilepsy.
Knierim, E., Vogt, J., Kintscher, M., Ponomarenko, A., Baumgart, J., Sanker Beed, P., Korotkova, T., Trimbuch, T., Panzer, A., Stephani, U., Escayg, A., Lerche, H., Nitsch, R., Schmitz, D. and Schuelke, M.
bioRxiv : 282871. 15 March 2018

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types.
Calabrese, C., Davidson, N.R., Fonseca, N.A., He, Y., Kahles, A., Lehmann, K.V., Liu, F., Shiraishi, Y., Soulette, C.M., Urban, L., Demircioğlu, D., Greger, L., Li, S., Liu, D., Perry, M.D., Xiang, L., Zhang, F., Zhang, J., Bailey, P., Erkek, S., Hoadley, K.A., Hou, Y., Kilpinen, H., Korbel, J.O., Marin, M.G., Markowski, J., Nandi, T., Pan-Hammarström, Q., Pedamallu, C.S., Siebert, R., Stark, S.G., Su, H., Tan, P., Waszak, S.M., Yung, C., Zhu, S., Awadalla, P., Creighton, C.J., Meyerson, M., Ouellette, B.F.F., Wu, K., Yang, H., Brazma, A., Brooks, A.N., Göke, J., Rätsch, G., Schwarz, R.F., Stegle, O. and Zhang, Z.
bioRxiv : 183889. 12 March 2018

Non-canonical HIF-1 stabilization is essential for intestinal tumorigenesis.
Rohwer, N., Jumpertz, S., Erdem, M., Egners, A., Warzecha, K.T., Fragoulis, A., Kuehl, A.A., Kramann, R., Neuss, S., Rudolph, I., Endermann, T., Zasada, C., Apostolova, I., Gerling, M., Kempa, S., Hughes, R., Lewis, C.E., Brenner, W., Malinowski, M.B., Stockmann, M., Schomburg, L., Faller, W., Sansom, O.J., Tacke, F., Morkel, M. and Cramer, T.
bioRxiv : 273045. 28 February 2018

An eicosanoid protects from statin-induced myopathic changes in primary human cells.
Grunwald, S.A., Popp, O., Haafke, S., Jedraszczak, N., Grieben, U., Saar, K., Patone, G., Kress, W., Steinhagen-Thiessen, E., Dittmar, G. and Spuler, S.
bioRxiv : 271932. 26 February 2018

Visualization of class A GPCR oligomerization by image-based fluorescence fluctuation spectroscopy.
Isbilir, A., Moeller, J., Bock, A., Zabel, U., Annibale, P. and Lohse, M.J.
bioRxiv : 240903. 29 December 2017

Assessing the gene regulatory landscape in 1,188 human tumors.
Calabrese, C., Lehmann, K.V., Urban, L., Liu, F., Erkek, S., Fonseca, N., Kahles, A., Kilpinen-Barrett, L.H., Markowski, J., Waszak, S., Korbel, J., Zhang, Z., Brazma, A., Raetsch, G., Schwarz, R. and Stegle, O.
bioRxiv : 225441. 29 November 2017

No major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data".
Lippert, C., Sabatini, R., Maher, M.C., Kang, E.Y., Lee, S., Arikan, O., Harley, A., Bernal, A., Garst, P., Lavrenko, V., Yocum, K., Wong, T.M., Zhu, M., Yang, W.Y.n, Chang, C., Hicks, B., Ramakrishnan, S., Tang, H., Xie, C., Brewerton, S., Turpaz, Y., Telenti, A., Roby, R.K., Och, F. and Venter, J.C.
bioRxiv : 187542. 19 October 2017

GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data.
Beagrie, R.A. and Schueler, M.
bioRxiv : 114710. 20 March 2017

Massively parallel clonal analysis using CRISPR/Cas9 induced genetic scars.
Junker, J.P., Spanjaard, B., Peterson-Maduro, J., Alemany, A., Hu, B., Florescu, M. and van Oudenaarden, A.
bioRxiv : 056499. 4 January 2017

LIMIX: genetic analysis of multiple traits.
Lippert, C., Casale, F.P., Rakitsch, B. and Stegle, O.
bioRxiv : 003905. 22 May 2014