21 papers · ranked by Valyu relevance
Tzahi Noiman, Chaim Kahana
Gene knockout technologies have contributed fundamentally to our understanding of the cellular functions of various genes. Two prevalent systems used for the efficient elimination of the expression of specific genes are the Cre-LoxP system and the CRISPR-Cas9 system. Here we present a simple method that combines the…
Liangliang Chen, Ying Ye, Hongxia Dai, Heyao Zhang + 6 more
'Qiang Wu' 'Zhexin Zhu' 'Rapolas Spalinskas' 'Wenyan Ren' 'Wensheng Zhang'] Loss-of-function studies are critically important in gene functional analysis of model organisms and cells. However, conditional gene inactivation in diploid cells is difficult to achieve, as it involves laborious vector construction, multifold…
Szu-Hsien Sam Wu, Heetak Lee, Réka Szép-Bakonyi, Gabriele Colozza + 12 more
'Ayse Boese' 'Krista R. Gert' 'Natalia Hallay' 'Ji-Hyun Lee' 'Jihoon Kim' 'Yi Zhu' 'Margot M. Linssen' 'Sandra Pilat-Carotta' 'Peter Hohenstein' 'Hans-Christian Theussl' 'Andrea Pauli' 'Bon-Kyoung Koo'] The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short…
Szu-Hsien Sam Wu, Réka Szép-Bakonyi, Heetak Lee, Gabriele Colozza + 9 more
The generation of conditional alleles using CRISPR technology is still challenging. Here, we introduce a Short Conditional intrON (SCON, 189 bp) that enables rapid generation of conditional alleles via one-step zygote injection. SCON has conditional intronic function in various vertebrate species and its target…
Takuro Horii, Sumiyo Morita, Mika Kimura, Naomi Terawaki + 2 more
'Mihiro Shibutani' 'Izuho Hatada'] Conditional knockout using Cre/lox is essential for functional analysis of genes. CRISPR/Cas in combination with two sets of guide RNAs and a single-stranded oligonucleotide enables simultaneous insertion of two lox sequences. However, this method induces double-strand breaks at two…
Bei Wang, Zishi Wang, Daqi Wang, Baolong Zhang + 4 more
'Mingqing Li' 'Wenqiang Yu' 'Yongming Wang'] Title: Abstracts Background CRISPR/Cas9 system is a powerful tool for knocking out genes in cells. However, genes essential for cell survival cannot be directly knocked out. Traditionally, generation of conditional knockout cells requires multiple steps. Results In this…
Teruhiko Suzuki, Satoko Takagi, Takahiko Hara
Mouse embryonic stem cells (ESCs) are powerful tools for functional analysis of stem cell-related genes; however, complex gene manipulations, such as locus-targeted introduction of multiple genes and conditional gene knockout conditional knockout, are technically difficult. Here, we review recent advances in…
Wenyuan Li, Yage Zhang, Bingzhou Han, Lianyan Li + 11 more
'Xiaochan Lu' 'Cheng Chen' 'Mengjia Lu' 'Yujie Zhang' 'Xuefeng Jia' 'Zuoyan Zhu' 'Xiangjun Tong' 'Bo Zhang' 'Didier Y Stainier' 'Darius Balciunas'] CRISPR/Cas systems are widely used to knock out genes by inducing indel mutations, which are prone to genetic compensation. Complex genome modifications such as knockin…
Kohei Nishimura, Ryotaro Yamada, Shinya Hagihara, Rie Iwasaki + 5 more
Auxin-Inducible Degron (AID) technology enables conditional depletion of targeted proteins. However, the applicability of the AID in vertebrate cells has been limited due to cytotoxicity caused by high auxin concentrations. Here, we establish an improved AID system using an engineered orthogonal auxin-TIR1 pair, which…
Gregg E. Homanics, Susanne Hiller-Sturmhöfel
Recently developed approaches to creating genetically engineered animals have expanded researchers’ repertoire of methods to investigate the roles of individual genes in the development of certain behaviors and diseases, including alcoholism. For example, knockout mice, in which single mouse genes have been…
Quanjiang Ji, Hongyuan Zhang, Yifei Zhang, Wei-Xiao Wang + 4 more
New therapeutic strategies for rapid and effective treatment of tuberculosis are highly desirable, and their development can be drastically accelerated by facile genetic manipulation methods in Mycobacterium tuberculosis. CRISPR base editors allow for rapid, robust, and programmed single base substitutions and gene…
J. E. Beasley
In this paper we consider a class of problems related to variable knockout. Given an optimisation problem formulated as an integer program the question we face in problems of this type is what might be an appropriate set of variables to delete, i.e. knockout of the problem, in order that the optimal solution to the…
Zixiang Xu
Gene knockout method has been used to improve the conversion ratio of industrial strains for many chemical products. There are a series of published algorithms to predict the targets for deletion. Based on metabolic networks, many of these algorithms are designed to predict the target of reaction or enzyme deletion.…
Kehinde Sowunmi, Victor Nnanna Nweze, Soyebo Titilayo Abiola, Okosesi Ebunoluwa Ajibike + 8 more
The development of precise DNA editing nucleases that induce double-strand breaks (DSBs) - including zinc finger nucleases, TALENs, and CRISPR/Cas systems - has revolutionized gene editing and genome engineering. Endogenous DNA DSB repair mechanisms are often leveraged to enhance editing efficiency and precision. While…
Georg Oberhofer, Tobin Ivy, Bruce A. Hay
One strategy for population suppression seeks to use gene drive to spread genes that confer conditional lethality or sterility, providing a way of combining population modification with suppression. Stimuli of potential interest could be introduced by humans, such as an otherwise benign virus or chemical, or occur…
Yuting Su, Zhenfeng Zou, Taizhong Hu
Negative dependence in tournaments has received attention in the literature. The property of negative orthant dependence (NOD) was proved for different tournament models with a special proof for each model. For general round-robin tournaments and knockout tournaments with random draws, Malinovsky and Rinott (2023)…
Duo Peng, Madhuri Vangipuram, Joan Wong, Manuel D. Leonetti
CRISPR/Cas9-mediated knock-in of DNA sequences enables precise genome engineering for research and therapeutic applications. However, designing effective guide RNAs (gRNAs) and homology-directed repair (HDR) donors remains a bottleneck. Here, we present protoSpaceJAM, an open-source algorithm to automate and optimize…
Frits Spieksma, Rudi Pendavingh, Roel Lambers
We investigate a new tournament format that consists of a series of individual knockout tournaments; we call this new format a Serial Knockout Competition (SKC). This format has recently been adopted by the Professional Darts Corporation. Depending on the seedings of the players used for each of the knockout…
Minh‐Hoang Nguyen, Batuhan K. Karaman, Heejong Kim, Alan Q. Wang + 2 more
'Fengbei Liu' 'Mert R. Sabuncu'] Deep learning models can extract predictive and actionable information from complex inputs. The richer the inputs, the better these models usually perform. However, models that leverage rich inputs (e.g., multi-modality) can be difficult to deploy widely, because some inputs may be…
Adam G. Bond, Miquel Muñoz i Ordoño, Celia M. Bisbach, Conner Craigon + 7 more
Proteolysis targeting chimera (PROTAC) degraders are typically bifunctional with one moiety of an E3 ligase ligand connected to one target protein ligand via a linker. While augmented valency has been shown with trivalent PROTACs targeting two binding sites within a given target protein, or used to recruit two…
Authors not listed
While virtual libraries of synthetically accessible compounds have exploded in size to many billions, our capacity to extract valuable drug leads from these vast databases remains limited by computational resources. To overcome this, we developed SLICE SMARTS and Logic In ChEmistry), a powerful new tool designed for…