Batch Effects are Causal Effects: Applications in Human Connectomics

Kavli Affiliate: Brian Caffo, Joshua Vogelstein | Authors: Eric W. Bridgeford, Michael Powell, Gregory Kiar, Stephanie Noble, Jaewon Chung, Sambit Panda, Ross Lawrence, Ting Xu, Michael Milham, Brian Caffo and Joshua T. Vogelstein | Summary: Batch effects, undesirable sources of variance across multiple experiments, present a substantial hurdle for scientific and clinical discoveries. Specifically, the […]


Continue.. Batch Effects are Causal Effects: Applications in Human Connectomics

Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions

Kavli Affiliate: Michael Beer | Authors: Renhe Luo, Jielin Yan, Jin Woo Oh, Wang Xi, Dustin Shigaki, Wilfred Wong, Hyunwoo Cho, Dylan Murphy, Ronald Cutler, Bess P. Rosen, Julian Pulecio, Dapeng Yang, Rachel Glenn, Tingxu Chen, Qing V. Li, Thomas Vierbuchen, Simone Sidoli, Effie Apostolou, Danwei Huangfu and Michael A. Beer | Summary: Comprehensive enhancer […]


Continue.. Dynamic network-guided CRISPRi screen reveals CTCF loop-constrained nonlinear enhancer-gene regulatory activity in cell state transitions

BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

Kavli Affiliate: Michael Miller, Joshua Vogelstein | Authors: Thomas Athey, Matthew Wright, Marija Pavlovic, Vikram Chandrashekhar, Karl Deisseroth, Michael Miller and Joshua Vogelstein | Summary: Whole-brain fluorescence images require several stages of computational processing to fully reveal the neuron morphology and connectivity information they contain. However, these computational tools are rarely part of an integrated […]


Continue.. BrainLine: An Open Pipeline for Connectivity Analysis of Heterogeneous Whole-Brain Fluorescence Volumes

Early retinal deprivation crossmodally alters nascent subplate circuits and activity in the auditory cortex during the precritical period

Kavli Affiliate: Patrick Kanold | Authors: Didhiti Mukherjee, Binghan Xue, Chih-Ting Chen, Minzi Chang, Joseph P-Y. Kao and Patrick O. Kanold | Summary: Sensory perturbation in one modality results in adaptive reorganization of neural pathways within the spared modalities, a phenomenon known as “crossmodal plasticity”, which has been examined during or after the classic ‘critical […]


Continue.. Early retinal deprivation crossmodally alters nascent subplate circuits and activity in the auditory cortex during the precritical period

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

Kavli Affiliate: Keri Martinowich | Authors: Louise A. Huuki-Myers, Abby Spangler, Nicholas J. Eagles, Kelsey D. Montgomery, Sang Ho Kwon, Boyi Guo, Melissa Grant-Peters, Heena R. Divecha, Madhavi Tippani, Chaichontat Sriworarat, Annie B. Nguyen, Prashanthi Ravichandran, Matthew N. Tran, Arta Seyedian, PsychENCODE Consortium, Thomas M. Hyde, Joel E. Kleinman, Alexis Battle, Stephanie C. Page, Mina […]


Continue.. Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

Mapping Neurophysiological Subtypes of Major Depressive Disorder Using Normative Models of the Functional Connectome

Kavli Affiliate: Xiaoqin Wang | Authors: Xiaoyi Sun, Jin Liu, Qing Ma, Xiaoqin Wang, Dongtao Wei, Yuan Chen, Bangshan Liu, Chu-Chung Huang, Yanting Zheng, Yankun Wu, Taolin Chen, Yuqi Cheng, Xiufeng Xu, Qiyong Gong, Tianmei Si, Shijun Qiu, Ching-Po Lin, Jingliang Cheng, Yanqing Tang, Fei Wang, Jiang Qiu, Peng Xie, Lingjiang Li, Wenxu Wang, Yong […]


Continue.. Mapping Neurophysiological Subtypes of Major Depressive Disorder Using Normative Models of the Functional Connectome

MISPEL: A deep learning approach for harmonizing multi-scanner matched neuroimaging data

Kavli Affiliate: Ciprian Crainiceanu | Authors: Mahbaneh Eshaghzadeh Torbati, Davneet S Minhas, Charles M Laymon, Pauline Maillard, James D Wilson, Chang-Le Chen, Ciprian M Crainiceanu, Charles S DeCarli, Seong Jae Hwang and Dana L Tudorascu | Summary: Abstract Large-scale data obtained from aggregation of already collected multi-site neuroimaging datasets has been brought benefits such as […]


Continue.. MISPEL: A deep learning approach for harmonizing multi-scanner matched neuroimaging data

Auditory memory of complex sounds in sparsely distributed, highly correlated neurons in the auditory cortex

Kavli Affiliate: Patrick Kanold | Authors: HiJee Kang and Patrick O Kanold | Summary: Listening in complex sound environments requires rapid segregation of different sound sources e.g., speakers from each other, speakers from other sounds, or different instruments in an orchestra, and also adjust auditory processing on the prevailing sound conditions. Thus, fast encoding of […]


Continue.. Auditory memory of complex sounds in sparsely distributed, highly correlated neurons in the auditory cortex

Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Kavli Affiliate: Keri Martinowich | Authors: Chaichontat Sriworarat, Annie B. Nguyen, Nicholas J. Eagles, Leonardo Collado-Torres, Keri Martinowich, Kristen R. Maynard and Stephanie C. Hicks | Summary: High-resolution and multiplexed imaging techniques are giving us an increasingly detailed observation of a biological system. However, sharing, exploring, and customizing the visualization of large multidimensional images can […]


Continue.. Performant web-based interactive visualization tool for spatially-resolved transcriptomics experiments

Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions

Kavli Affiliate: Denis Wirtz | Authors: Alicia M Braxton, Ashley L Kiemen, Mia P Grahn, Andre Forjaz, Jaanvi Mahesh Babu, Lily Zheng, Liping Jiang, Haixia Cheng, Qianqian Song, Rebecca Reichel, Sarah Graham, Alexander I Damanakis, Catherine G Fischer, Stephanie Mou, Cameron Metz, Julie Granger, Xiao-Ding Liu, Niklas Bachmann, Cristina Almagro-Perez, Ann Chenyu Jiang, Jeonghyun Yoo, […]


Continue.. Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions