Article
Biochemistry & Molecular Biology
Hun-Goo Lee, Sachiko Imaichi, Elizabeth Kraeutler, Rodrigo Aguilar, Yong-Woo Lee, Steven D. Sheridan, Jeannie T. Lee
Summary: In this article, we describe an approach to correct the genetic defect in fragile X syndrome (FXS) through the recruitment of endogenous repair mechanisms. By investigating conditions favorable to FMR1 reactivation, we identify MEK and BRAF inhibitors that induce a strong repeat contraction and full FMR1 reactivation in cellular models. This study reveals a potential method of treating FXS in the future by recruiting endogenous DNA repair mechanisms.
Article
Computer Science, Interdisciplinary Applications
Oli D. Johannsson, Thomas Mejer Hansen
Summary: The paper introduces an MPS estimation algorithm to directly compute and store parameter-wise conditional statistics for potentially faster and more accurate estimation. The method is demonstrated on two types of MPS algorithms and compared with sequential simulation and estimation methods.
COMPUTERS & GEOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Xuqing Liu, Yubang Gao, Jiakai Liao, Miao Miao, Kai Chen, Feihu Xi, Wentao Wei, Huihui Wang, Yongsheng Wang, Xi Xu, Anireddy S. N. Reddy, Lianfeng Gu
Summary: This study identified a large number of circRNAs and R-loops in the stem-differentiating xylem of Populus trichocarpa, and investigated their roles in modulating alternative splicing (AS). The results showed that they may play crucial roles in regulating AS in the xylem.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Ausra Domanska, Sergey Guryanov, Sarah J. Butcher
Summary: Parechoviruses are non-enveloped icosahedral viruses with a single-stranded RNA genome, infecting humans and causing a range of illnesses. There are currently no approved antivirals for treating parechovirus infections.
Article
Computer Science, Artificial Intelligence
Manisha Sawant, Kishor M. Bhurchandi
Summary: Human age estimation from facial images is a hot research topic in computer vision. This paper proposes a discriminative manifold learning method based on hidden factor analysis (HFA) model, which can effectively extract aging patterns from facial features and achieve high accuracy in age estimation.
Article
Cell Biology
Beata E. Jady, Amandine Ketele, Dylan Moulis, Tamas Kiss
Summary: This study demonstrates that at least four human H/ACA RNAs have dual pseudouridylation loops, supporting the synthesis of two consecutive pseudouridines in specific human RNAs. The dual guide loops form alternative base-pairing interactions with their target RNAs, allowing the positioning of two substrate Us for pseudouridylation. This structural flexibility provides versatility for RNA-directed pseudouridylation without compromising efficiency and accuracy.
GENES & DEVELOPMENT
(2022)
Article
Multidisciplinary Sciences
Chou-Wei Chang, Anup Kumar Singh, Min Li, Li Guan, Nhung Le, Kenneth Omabe, Feng Liang, Yilun Liu
Summary: BRCA1 BRCT plays a role in suppressing ribosomal R-loops formation, in addition to its role in DNA repair.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Megumi Shigematsu, Yohei Kirino
Summary: RNA-seq is a common tool for characterizing RNA expression profiles and regulations in physiological processes and diseases. Specific RNA-seq methods have been developed to characterize the expression profiles of sncRNAs with various terminal formations, shedding light on previously unrecognized sncRNAs.
Editorial Material
Cell Biology
Jenna M. Frame, Trista E. North
Summary: This study uncovers that loss of DEAD-box helicase Ddx41 triggers an inflammatory cascade mediated by R-loop during embryonic development, promoting HSPC production. Human studies suggest conservation of this inflammatory mechanism in DDX41-associated hematologic diseases, providing a potential avenue for future therapeutic interventions.
DEVELOPMENTAL CELL
(2021)
Article
Computer Science, Information Systems
Jiun-Kai You, Chen-Chien James Hsu, Wei-Yen Wang, Shao-Kang Huang
Summary: In this paper, a new method is proposed to address the issues in 3D object pose estimation, including the use of a projection loss function and refinement network to correct pose predictions. Experimental results show that this method outperforms existing techniques in terms of accuracy and practicality.
Article
Engineering, Electrical & Electronic
Nir Shlezinger, Tirza Routtenberg
Summary: Inference tasks in signal processing often involve reliable statistical modeling with missing parameters. One approach is to estimate the missing parameters using data and then perform inference based on the estimated model. Alternatively, data can be used to directly learn the inference mapping in an end-to-end manner. These approaches are related to generative and discriminative models in machine learning literature, typically used in the context of classifiers.
IEEE SIGNAL PROCESSING MAGAZINE
(2023)
Article
Biochemistry & Molecular Biology
Phillip Wulfridge, Qingqing Yan, Nathaniel Rell, John Doherty, Skye Jacobson, Sarah Offley, Sandra Deliard, Kelly Feng, Jennifer E. Phillips-Cremins, Alessandro Gardini, Kavitha Sarma
Summary: CTCF is a critical regulator of genome architecture and gene expression. This study shows that R-loops and G-quadruplex structures facilitate CTCF binding and regulate chromatin organization. The stability of R-loops and G-quadruplex structures can affect CTCF occupancy and gene expression.
Article
Automation & Control Systems
Roy S. Smith, Bassam Bamieh
Summary: Introducing stochastic components in a feedback loop can result in state behaviors different from those observed in a deterministic system. Multiplicative stochastic signals can lead to a richer set of state behaviors. These phenomena are also present in more complex stochastic dynamical systems.
IEEE CONTROL SYSTEMS MAGAZINE
(2021)
Article
Astronomy & Astrophysics
Mingzhe Guo, Bo Li, Mijie Shi
Summary: Using ideal magnetohydrodynamics framework, this study found that oscillatory behavior similar to fast sausage modes (FSMs) can occur in solar coronal cylinders even with complex fine structures. The research indicated that density-enhanced equilibria do not necessarily need to be strictly axisymmetric to exhibit FSM-like motions, making FSMs still a candidate interpretation for rapid QPPs in solar flares.
ASTROPHYSICAL JOURNAL LETTERS
(2021)
Article
Cell Biology
Esther Marchena-Cruz, Lola P. Camino, Jay Bhandari, Sonia Silva, Jose Javier Marqueta-Gracia, Shahad A. Amdeen, Cristina Guillen-Mendoza, Maria L. Garcia-Rubio, Jose M. Calderon-Montano, Xiaoyu Xue, Rosa Luna, Andres Aguilera
Summary: Unscheduled R loops can lead to genome instability, a characteristic of cancer cells. By targeting activation-induced cytidine deaminase (AID), 59 potential candidates causing R loops were identified, which are enriched in factors involved in chromatin, transcription, RNA biogenesis, and other processes. The study suggests that various gene dysfunctions can affect R-loop homeostasis through different mechanisms, thereby altering cell physiology.
Editorial Material
Statistics & Probability
Niels Richard Hansen, Peter Dalgaard
SCANDINAVIAN JOURNAL OF STATISTICS
(2016)
Article
Statistics & Probability
Adam Lund, Martin Vincent, Niels Richard Hansen
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2017)
Article
Oncology
Justin Guinney, Tao Wang, Teemu D. Laajala, Kimberly Kanigel Winner, J. Christopher Bare, Elias Chaibub Neto, Suleiman A. Khan, Gopal Peddinti, Antti Airola, Tapio Pahikkala, Tuomas Mirtti, Thomas Yu, Brian M. Bot, Liji Shen, Kald Abdallah, Thea Norman, Stephen Friend, Gustavo Stolovitzky, Howard Soule, Christopher J. Sweeney, Charles J. Ryan, Howard I. Scher, Oliver Sartor, Yang Xie, Tero Aittokallio, Fang Liz Zhou, James C. Costello, Kald Abdallah, Tero Aittokallio, Antti Airola, Catalina Anghel, Helia Azima, Robert Baertsch, Pedro J. Ballester, Chris Bare, Vinayak Bhandari, Brian M. Bot, Cuong C. Dang, Maria Bekker-Nielsen Dunba, Ann-Sophie Buchardt, Ljubomir Buturovic, Da Cao, Prabhakar Chalise, Junwoo Cho, Tzu-Ming Chu, R. Yates Coley, Sailesh Conjeti, Sara Correia, James C. Costello, Ziwei Dai, Junqiang Dai, Philip Dargatz, Sam Delavarkhan, Detian Deng, Ankur Dhanik, Yu Du, Aparna Elangovan, Shellie Ellis, Laura L. Elo, Shadrielle M. Espiritu, Fan Fan, Ashkan B. Farshi, Ana Freitas, Brooke Fridley, Stephen Friend, Christiane Fuchs, Eyal Gofer, Gopalacharyulu Peddinti, Stefan Graw, Russ Greiner, Yuanfang Guan, Justin Guinney, Jing Guo, Pankaj Gupta, Anna I. Guyer, Jiawei Han, Niels R. Hansen, Billy H. W. Chang, Outi Hirvonen, Barbara Huang, Chao Huang, Jinseub Hwang, Joseph G. Ibrahim, Vivek Jayaswal, Jouhyun Jeon, Zhicheng Ji, Deekshith Juvvadi, Sirkku Jyrkkio, Kimberly Kanigel-Winner, Amin Katouzian, Marat D. Kazanov, Suleiman A. Khan, Shahin Khayyer, Dalho Kim, Agnieszka K. Golinska, Devin Koestler, Fernanda Kokowicz, Ivan Kondofersky, Norbert Krautenbacher, Damjan Krstajic, Luke Kumar, Christoph Kurz, Matthew Kyan, Teemu D. Laajala, Michael Laimighofer, Eunjee Lee, Wojciech Lesinski, Miaozhu Li, Ye Li, Qiuyu Lian, Xiaotao Liang, Minseong Lim, Henry Lin, Xihui Lin, Jing Lu, Mehrad Mahmoudian, Roozbeh Manshaei, Richard Meier, Dejan Miljkovic, Tuomas Mirtti, Krzysztof Mnich, Nassir Navab, Elias C. Neto, Yulia Newton, Thea Norman, Tapio Pahikkala, Subhabrata Pal, Byeongju Park, Jaykumar Patel, Swetabh Pathak, Alejandrina Pattin, Donna P. Ankerst, Jian Peng, Anne H. Petersen, Robin Philip, Stephen R. Piccolo, Sebastian Poelsterl, Aneta Polewko-Klim, Karthik Rao, Xiang Ren, Miguel Rocha, Witold R. Rudnicki, Charles J. Ryan, Hyunnam Ryu, Oliver Sartor, Hagen Scherb, Raghav Sehgal, Fatemeh Seyednasrollah, Jingbo Shang, Bin Shao, Liji Shen, Howard Sher, Motoki Shiga, Artem Sokolov, Julia F. Soellner, Lei Song, Howard Soule, Gustavo Stolovitzky, Josh Stuart, Ren Sun, Christopher J. Sweeney, Nazanin Tahmasebi, Kar-Tong Tan, Lisbeth Tomaziu, Joseph Usset, Yeeleng S. Vang, Roberto Vega, Vitor Vieira, David Wang, Difei Wang, Junmei Wang, Lichao Wang, Sheng Wang, Tao Wang, Yue Wang, Russ Wolfinger, Chris Wong, Zhenke Wu, Jinfeng Xiao, Xiaohui Xie, Yang Xie, Doris Xin, Hojin Yang, Nancy Yu, Thomas Yu, Xiang Yu, Sulmaz Zahedi, Massimiliano Zanin, Chihao Zhang, Jingwen Zhang, Shihua Zhang, Yanchun Zhang, Fang Liz Zhou, Hongtu Zhu, Shanfeng Zhu, Yuxin Zhu
Article
Biochemistry & Molecular Biology
Constanze Pentzold, Shiraz Ali Shah, Niels Richard Hansen, Benoit Le Tallec, Andaine Seguin-Orlando, Michelle Debatisse, Michael Lisby, Vibe H. Oestergaard
NUCLEIC ACIDS RESEARCH
(2018)
Article
Statistics & Probability
Frederik Riis Mikkelsen, Niels Richard Hansen
ANNALES DE L INSTITUT HENRI POINCARE-PROBABILITES ET STATISTIQUES
(2018)
Article
Statistics & Probability
Niels Richard Hansen
STATISTICS & PROBABILITY LETTERS
(2018)
Article
Statistics & Probability
Adam Lund, Niels Richard Hansen
JOURNAL OF MULTIVARIATE ANALYSIS
(2019)
Article
Statistics & Probability
Soren Wengel Mogensen, Niels Richard Hansen
ANNALS OF STATISTICS
(2020)
Article
Statistics & Probability
Adam Lund, Soren Wengel Mogensen, Niels Richard Hansen
Summary: In this study, the problem of extracting a common signal from heterogeneous data is addressed through the introduction of the soft maximin estimation method. By establishing relevant theoretical properties, it is shown that the soft maximin method is statistically sensible and computationally attractive. Experimental results demonstrate that soft maximin estimation outperforms other methods in terms of predictive performance and computational complexity.
SCANDINAVIAN JOURNAL OF STATISTICS
(2022)
Article
Statistics & Probability
Soren Wengel Mogensen, Niels Richard Hansen
Summary: We examine a class of graphs that represent local independence structures in stochastic processes with correlated noise. We classify graphs that encode the same local independencies and show that determining Markov equivalence for this class of graphs is a complex task. Additionally, we prove the global Markov property for a specific multivariate process.
Proceedings Paper
Computer Science, Artificial Intelligence
Jeffrey Adams, Niels Richard Hansen, Kun Zhang
Summary: This paper explores the application of linear non-Gaussian acyclic models in partially observed linear models, introducing two graphical conditions necessary for identifying causal structure, closely related to the sparsity of causal edges. These new conditions can be met even when the number of latent variables is large.
ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 34 (NEURIPS 2021)
(2021)
Proceedings Paper
Computer Science, Artificial Intelligence
Gherardo Varando, Niels Richard Hansen
CONFERENCE ON UNCERTAINTY IN ARTIFICIAL INTELLIGENCE (UAI 2020)
(2020)
Proceedings Paper
Computer Science, Artificial Intelligence
Soren Wengel Mogensen, Daniel Malinsky, Niels Richard Hansen
UNCERTAINTY IN ARTIFICIAL INTELLIGENCE
(2018)
Article
Automation & Control Systems
Lasse Petersen, Niels Richard Hansen
Summary: This paper develops a nonparametric test for conditional independence by combining the partial copula with a quantile regression based method for estimating the nonparametric residuals. The resulting test is demonstrated to be sound under complicated data generating distributions and competitive to other state-of-the-art conditional independence tests, with superior power in cases with conditional variance heterogeneity of X and Y given Z.
JOURNAL OF MACHINE LEARNING RESEARCH
(2021)
Article
Oncology
Fatemeh Seyednasrollah, Devin C. Koestler, Tao Wang, Stephen R. Piccolo, Roberto Vega, Russell Greiner, Christiane Fuchs, Eyal Gofer, Luke Kumar, Russell D. Wolfinger, Kimberly Kanigel Winner, Chris Bare, Elias Chaibub Neto, Thomas Yu, Liji Shen, Kald Abdallah, Thea Norman, Gustavo Stolovitzky, Howard R. Soule, Christopher J. Sweeney, Charles J. Ryan, Howard Scher, Oliver Sartor, Laura L. Elo, Fang Liz Zhou, Justin Guinney, James C. Costello, Kald Abdallah, Antti Airola, Tero Aittokallio, Catalina Anghel, Donna P. Ankerst, Helia Azima, Robert Baertsch, Pedro J. Ballester, Chris Bare, Vinayak Bhandari, Brian M. Bot, Ann-Sophie Buchardt, Ljubomir Buturovic, Da Cao, Prabhakar Chalise, Billy H. W. Chang, Junwoo Cho, Tzu-Ming Chu, R. Yates Coley, Sailesh Conjeti, Sara Correia, James C. Costello, Ziwei Dai, Junqiang Dai, Cuong C. Dang, Philip Dargatz, Sam Delavarkhan, Detian Deng, Ankur Dhanik, Yu Du, Aparna Elangovan, Shellie Ellis, Laura L. Elo, Shadrielle M. Espiritu, Fan Fan, Ashkan B. Farshi, Ana Freitas, Brooke Fridley, Christiane Fuchs, Eyal Gofer, Agnieszka K. Golinska, Stefan Graw, Russ Greiner, Justin Guinney, Jing Guo, Pankaj Gupta, Anna Guyer, Jiawei Han, Niels R. Hansen, Outi Hirvonen, Barbara Huang, Chao Huang, Jinseub Hwang, Joseph G. Ibrahim, Vivek Jayaswal, Jouhyun Jeon, Zhicheng Ji, Deekshith Juvvadi, Sirkku Jyrkkio, Kimberly Kanigel-Winner, Amin Katouzian, Marat D. Kazanov, Suleiman A. Khan, Shahin Khayyer, Dalho Kim, Devin Koestler, Fernanda Kokowicz, Ivan Kondofersky, Damjan Krstajic, Luke Kumar, Christoph Kurz, Matthew Kyan, Teemu D. Laajala, Michael Laimighofer, Eunjee Lee, Wojciech Lesinski, Miaozhu Li, Ye Li, Qiuyu Lian, Xiaotao Liang, Minseong Lim, Henry Lin, Xihui Lin, Xihui Lin, Jing Lu, Mehrad Mahmoudian, Roozbeh Manshaei, Richard Meier, Dejan Miljkovic, Tuomas Mirtti, Krzysztof Mnich, Nassir Navab, Elias C. Neto, Yulia Newton, Thea Norman, Tapio Pahikkala, Subhabrata Pal, Byeongju Park, Jaykumar Patel, Swetabh Pathak, Alejandrin Pattin, Gopal Peddinti, Jian Peng, Anne H. Petersen, Robin Philip, Stephen R. Piccolo, Sebastian Poelsterl, Aneta Polewko-Klim, Karthik Rao, Xiang Ren, Miguel Rocha, Witold R. Rudnicki, Charles J. Ryan, Hyunnam Ryu, Oliver Sartor, Hagen Scherb, Raghav Sehgal, Fatemeh Seyednasrollah, Jingbo Shang, Bin Shao, Liji Shen, Howard Sher, Motoki Shiga, Artem Sokolov, Julia F. Soellner, Lei Song, Howard Soule, Gustavo Stolovitzky, Josh Stuart, Ren Sun, Christopher J. Sweeney, Nazanin Tahmasebi, Kar-Tong Tan, Lisbeth Tomaziu, Joseph Usset, Yeeleng S. Vang, Roberto Vega, Vitor vieira, David Wang, Difei Wang, Junmei Wang, Lichao Wang, Sheng Wang, Tao Wang, Yue Wang, Russ Wolfinger, Chris Wong, Zhenke Wu, Jinfeng Xiao, Xiaohui Xie, Doris Xin, Hojin Yang, Nancy Yu, Thomas Yu, Xiang Yu, Sulmaz Zahedi, Massimiliano Zanin, Chihao Zhang, Jingwen Zhang, Shihua Zhang, Yanchun Zhang, Fang Liz Zhou, Hongtu Zhu, Shanfeng Zhu, Yuxin Zhu
JCO CLINICAL CANCER INFORMATICS
(2017)