Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects

por Naeem, Muhammad, Alkhnbashi, Omer S.
Publicado 2023

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

por Lange, Sita J., Alkhnbashi, Omer S., Rose, Dominic, Will, Sebastian, Backofen, Rolf
Publicado 2013

CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection

por Mitrofanov, Alexander, Ziemann, Marcus, Alkhnbashi, Omer S, Hess, Wolfgang R, Backofen, Rolf
Publicado 2022

CRISPRidentify: identification of CRISPR arrays using machine learning approach

por Mitrofanov, Alexander, Alkhnbashi, Omer S, Shmakov, Sergey A, Makarova, Kira S, Koonin, Eugene V, Backofen, Rolf
Publicado 2020

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

por Alkhnbashi, Omer S., Costa, Fabrizio, Shah, Shiraz A., Garrett, Roger A., Saunders, Sita J., Backofen, Rolf
Publicado 2014

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

por Reimann, Viktoria, Alkhnbashi, Omer S., Saunders, Sita J., Scholz, Ingeborg, Hein, Stephanie, Backofen, Rolf, Hess, Wolfgang R.
Publicado 2017

RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

por Gelhausen, Rick, Müller, Teresa, Svensson, Sarah L, Alkhnbashi, Omer S, Sharma, Cynthia M, Eggenhofer, Florian, Backofen, Rolf
Publicado 2022

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

por Padilha, Victor A, Alkhnbashi, Omer S, Shah, Shiraz A, de Carvalho, André C P L F, Backofen, Rolf
Publicado 2020

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

por Shah, Shiraz A., Alkhnbashi, Omer S., Behler, Juliane, Han, Wenyuan, She, Qunxin, Hess, Wolfgang R., Garrett, Roger A., Backofen, Rolf
Publicado 2018

Casboundary: automated definition of integral Cas cassettes

por Padilha, Victor A, Alkhnbashi, Omer S, Tran, Van Dinh, Shah, Shiraz A, Carvalho, André C P L F, Backofen, Rolf
Publicado 2020

Adaptation induced by self-targeting in a type I-B CRISPR-Cas system

por Stachler, Aris-Edda, Wörtz, Julia, Alkhnbashi, Omer S., Turgeman-Grott, Israela, Smith, Rachel, Allers, Thorsten, Backofen, Rolf, Gophna, Uri, Marchfelder, Anita
Publicado 2020

The role of Cas8 in type I CRISPR interference

por Cass, Simon D.B., Haas, Karina A., Stoll, Britta, Alkhnbashi, Omer S., Sharma, Kundan, Urlaub, Henning, Backofen, Rolf, Marchfelder, Anita, Bolt, Edward L.
Publicado 2015

CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii

por Liao, Yan, Vogel, Verena, Hauber, Sabine, Bartel, Jürgen, Alkhnbashi, Omer S., Maaß, Sandra, Schwarz, Thandi S., Backofen, Rolf, Becher, Dörte, Duggin, Iain G., Marchfelder, Anita
Publicado 2021

Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

por Liao, Chunyu, Sharma, Sahil, Svensson, Sarah L., Kibe, Anuja, Weinberg, Zasha, Alkhnbashi, Omer S., Bischler, Thorsten, Backofen, Rolf, Caliskan, Neva, Sharma, Cynthia M., Beisel, Chase L.
Publicado 2022

The nuts and bolts of the Haloferax CRISPR-Cas system I-B

por Maier, Lisa-Katharina, Stachler, Aris-Edda, Brendel, Jutta, Stoll, Britta, Fischer, Susan, Haas, Karina A., Schwarz, Thandi S., Alkhnbashi, Omer S., Sharma, Kundan, Urlaub, Henning, Backofen, Rolf, Gophna, Uri, Marchfelder, Anita
Publicado 2018

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry

por Hadjeras, Lydia, Bartel, Jürgen, Maier, Lisa-Katharina, Maaß, Sandra, Vogel, Verena, Svensson, Sarah L, Eggenhofer, Florian, Gelhausen, Rick, Müller, Teresa, Alkhnbashi, Omer S, Backofen, Rolf, Becher, Dörte, Sharma, Cynthia M, Marchfelder, Anita
Publicado 2023

CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems

por Alkhnbashi, Omer S, Mitrofanov, Alexander, Bonidia, Robson, Raden, Martin, Tran, Van Dinh, Eggenhofer, Florian, Shah, Shiraz A, Öztürk, Ekrem, Padilha, Victor A, Sanches, Danilo S, de Carvalho, André C P L F, Backofen, Rolf
Publicado 2021

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

por Raden, Martin, Ali, Syed M, Alkhnbashi, Omer S, Busch, Anke, Costa, Fabrizio, Davis, Jason A, Eggenhofer, Florian, Gelhausen, Rick, Georg, Jens, Heyne, Steffen, Hiller, Michael, Kundu, Kousik, Kleinkauf, Robert, Lott, Steffen C, Mohamed, Mostafa M, Mattheis, Alexander, Miladi, Milad, Richter, Andreas S, Will, Sebastian, Wolff, Joachim, Wright, Patrick R, Backofen, Rolf
Publicado 2018