Publications by authors named "Jordan A Ramilowski"

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connectomeDB2025: a rigorously curated, multi-species resource of experimentally supported ligand-receptor interactions.
Peiwen Liu, Sakura Eri B Maezono, Weitao Lin, Yen Yeow, Ya-Yu Liu, Jordan A Ramilowski

Nucleic Acids Res· October 2025

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Annotation of nuclear lncRNAs based on chromatin interactions.
Saumya Agrawal, Andrey Buyan, Jessica Severin, Masaru Koido, Tanvir Alam, Jordan A Ramilowski

PLoS One· May 2024

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Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation.
Takaya Yamasaki, Akira Nishiyama, Nagomi Kurogi, Koutarou Nishimura, Shion Nishida, Jordan A Ramilowski

Cell Rep· April 2024

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ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data.
Jessica Severin, Saumya Agrawal, Jordan A Ramilowski, Ruslan Deviatiiarov, Jay W Shin

NAR Genom Bioinform· September 2023

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Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting.
Yoshihiro Aizawa, Kentaro Takada, Jun Aoyama, Daisuke Sano, Shoji Yamanaka, Jordan A Ramilowski

Cell Oncol (Dordr)· April 2023

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Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.
Chi Wai Yip, Chung-Chau Hon, Kayoko Yasuzawa, Divya M Sivaraman, Jordan A Ramilowski

Cell Rep· December 2022

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Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers.
Ryosuke Jikuya, Koichi Murakami, Akira Nishiyama, Ikuma Kato, Mitsuko Furuya, Jordan A Ramilowski

iScience· June 2022

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Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski

Nat Commun· March 2022

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Low Quantity Single Strand CAGE (LQ-ssCAGE) Maps Regulatory Enhancers and Promoters.
Hazuki Takahashi, Hiromi Nishiyori-Sueki, Jordan A Ramilowski, Masayoshi Itoh, Piero Carninci

Methods Mol Biol· September 2021

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The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.
Luca Ducoli, Saumya Agrawal, Chung-Chau Hon, Jordan A Ramilowski, Eliane Sibler

BMC Genom Data· September 2021

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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski

Nat Commun· June 2021

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Combined inhibition of XIAP and BCL2 drives maximal therapeutic efficacy in genetically diverse aggressive acute myeloid leukemia.
Mari Hashimoto, Yoriko Saito, Ryo Nakagawa, Ikuko Ogahara, Shinsuke Takagi, Jordan A Ramilowski

Nat Cancer· March 2021

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FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.
Imad Abugessaisa, Jordan A Ramilowski, Marina Lizio, Jesicca Severin, Akira Hasegawa

Nucleic Acids Res· January 2021

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Predicting cell-to-cell communication networks using NATMI.
Rui Hou, Elena Denisenko, Huan Ting Ong, Jordan A Ramilowski, Alistair R R Forrest

Nat Commun· October 2020

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Comparative transcriptomics of primary cells in vertebrates.
Tanvir Alam, Saumya Agrawal, Jessica Severin, Robert S Young, Robin Andersson, Jordan A Ramilowski

Genome Res· July 2020

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Functional annotation of human long noncoding RNAs via molecular phenotyping.
Jordan A Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani

Genome Res· July 2020

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Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.
Michal Pawlak, Katarzyna Z Kedzierska, Maciej Migdal, Abu Nahia Karim, Jordan A Ramilowski

Genome Res· March 2019

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An atlas of human long non-coding RNAs with accurate 5' ends.
Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J L Rackham

Nature· March 2017

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Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.
Marina Lizio, Jayson Harshbarger, Imad Abugessaisa, Shuei Noguchi, Atsushi Kondo, Jordan A Ramilowski

Nucleic Acids Res· January 2017

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Corrigendum: A draft network of ligand-receptor-mediated multicellular signalling in human.
Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppmann, Marina Lizio

Nat Commun· February 2016

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Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals distinct gene expression profiles.
Helena Persson, Andrew T Kwon, Jordan A Ramilowski, Gilad Silberberg, Cilla Söderhäll

J Allergy Clin Immunol· September 2015

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A draft network of ligand-receptor-mediated multicellular signalling in human.
Jordan A Ramilowski, Tatyana Goldberg, Jayson Harshbarger, Edda Kloppmann, Marina Lizio

Nat Commun· July 2015

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A promoter-level mammalian expression atlas.

Nature· March 2014

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Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.
Jordan A Ramilowski, Satoru Sawai, Hikaru Seki, Keiichi Mochida, Takuhiro Yoshida

Plant Cell Physiol· May 2013

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Fixed node diffusion Monte Carlo using a genetic algorithm: a study of the CO-(4)He(N) complex, N = 1…10.
Jordan A Ramilowski, David Farrelly

Phys Chem Chem Phys· June 2012

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