Aivia KI-Bildanalysesoftware

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Publications 2022

Glycine-induced NMDA receptor internalization provides neuroprotection and preserves vasculature following ischemic stroke
J Cappelli, P Khacho, B Wang, A Sokolovski, W Bakkar, S Raymond, N Ahlskog, J Pitney, J Wu, P Chudalayandi, AYC Wong, R Bergeron
iScience
2022 25(2)

Imaging mitosis with lattice lightsheet
A Barazia, C Monks
Mitosis
2022 10

Deletion of ABCB10 in beta-cells protects from high-fat diet induced insulin resistance
M Shum, M Segawa, R Gharakhanian, A Viñuela, M Wortham, S Baghdasarian, DM Wolf, SB Sereda, L Nocito, L Stiles, Z Zhou, V Gutierrez, M Sander, OS Shirihai, M Liesa
Molecular Metabolism
2022 55

Morphological heterogeneity description enabled early and parallel non-invasion prediction of T-cell proliferation inhibitory potency and growth rate for facilitating donor selection of human mesenchymal stem cells
Y Imai, K Kanie, R Kato
Inflammation and Regneration
2022 42

A female in vivo haploid-induction system via mutagenesis of egg cell-speciic peptidases
X Zhang, C Shi, S Li, B Zhang, T Dresselhaus, MX Sun
Research Square
2022 Preprint

Abscisic acid drives stomatal closure through increases in hydrogen peroxide in distinct subcellular compartments including mitochondria
AE Postiglione, GK Muday
BioRxiv
2022 Preprint

In vivo simultaneous nonlinear absorption Raman and fluorescence (SNARF) imaging of mouse brain cortical structures
AT Francis, B Manifold, EC Thomas, R Hu, AH Hill, S Men, D Fu
Communications Biology
2022 5

Traip controls mushroom body size by supressing mitotic defects
RS O'Neill, NM Rusan
Development
2022 149(7)

Expansion of fibroblast cell sheets using a modified MEEK micrografting technique for wound healing applications
K Benchaprathanphom, P Sakulaue, W Siriwatwechakul, P Muangman, K Chinaroonchai, N Namviriyachote, K Viravaidya-Pasuwat
Research Square
2022 Preprint

Myc supports self-renewal of basal cells in the esophageal epithelium
T Hishida, E Vazquez-Ferrer, Y Hishida-Nozaki, Y Takemoto, F Hatanaka, K Yoshida, J Prieto, SK Sahu, Y Takahashi, P Reddy, DD O'Keefe, CR Esteban, PS Knoepfler, EN Delicado, A Castells, JM Campistol, R Kato, H Nakagawa, JCI Belmonte
Frontiers in Cell and Developmental Biology
2022

Automated stain-free histomorphometry of peripheral nerve by contrast-enhancing techniques and artificial intelligence
IC Hernández, S Mohan, N Jowett
Journal of Neuroscience Methods
2022 375

Nutritional control of thyroid morphogenesis through gastrointestinal hormones
M Takagishi, BM Aleogho, M Okamura, K Ushida, Y Yamada, Y Seino, S Fujimura, K Nakashima, A Shindo
Current Biology
2022 32(7)

3D cell cultures toward quantitative high-throughput drug screening
Y Wang, H Jeon
Trends in Pharmacological Sciences
2022 Preprint

Uninterrupted CAG repeat drives striatum-selective transcriptionopathy and nuclear pathogenesis in human Huntingtin BAC mice
X Gu, J Richman, P Langfelder, N Wang, S Zhang, M Bañez-Coronel, HB Wang, L Yang, L Ramanathan, L Deng, CS Park, CR Choi, JP Cantle, F Gao, M Gray, G Coppola, GP Bates, LPW Ranum, S Horvath, CS Colwell, XW Yang
Neuron
2022 110(7)

Deep learning - promises for 3D nuclear imaging: a guide for biologists
G Mougeot, T Dubos, F Chausse, E Péry, K Graumann, C Tatout, DE Evans, S Desset
Journal of Cell Science
2022 135(7)

Aspirin-triggered resolvin D1 reduces chronic dust-induced lung pathology without altering susceptibility to dust-enhanced carcinogenesis
EC Dominguez, R Phandthong, M Nguyen, A Ulu, S Guardado, S Sveiven, P Talbot, TM Nordgren
Cancers
2022 14(8)

A brain-penetrant stearoyl-CoA desaturase inhibitor reverses α-synuclein toxicity
S Nuber, CY Chung, DF Tardiff, PA Bechade, TD McCaffery, K Shimanaka, J Choi, B Chang, W Raja, E Neve, C Burke, X Jiang, P Xu, K Khurana, U Dettmer, S Fanning, KJ Rhodes, DJ Selkoe, RH Scannevin
Neurotherapeutics
2022

Identification of embryonic RNA granules that act as sites of mRNA translation after changing their physical properties
K Sato, M Sakai, A Ishii, K Maehata, Y Takada, K Yasuda, T Kotani
iScience
2022 Preprint

Mitapivat increases ATP and decreases oxidative stress and erythrocyte mitochondria retention in a SCD mouse model
ZMN Quezado, S Kamimura, M Smith, X Wang, MR Heaven, S Jana, S Vogel, P Zeras, CA Combs, LEF Almeida, Q Li, M Quezado, I Horkayne-Szakaly, PA Kosinski, S Yu, U Kapadnis, C Kung, L Dang, P Wakim, WA Eaton, AI Alayash, SL Thein
Blood Cells, Molecules, and Diseases
2022 95

Publications 2021

Super-resolved fluorescence imaging of peripheral nerve
IC Hernández, S Mohan, N Jowett
Research Square
2021 Preprint

Oxidation shuts down an auto-inhibitory mechanism of von Willebrand Factor
R Tsai, G Interlandi
Proteins
2021 89(6)

Two-photon excitation fluorescent spectral and decay properties of retrograde neuronal tracer fluoro-gold
MQ Miller, IC Hernández, JV Chacko, S Minderler, N Jowett
Research Square
2021 Preprint

Harnessing non-destructive 3D pathology
JTC Liu, AK Glaser, K Bera, LD True, NP Reder, KW Eliceiri, A Madabhushi
Nature Biomedical Engineering
2021 5

Detecting cells in intravital video microscopy using a deep convolutional neural network
BCG da Silva, R Tam, RJ Ferrari
Computers in Biology and Medicine
2021 129

Controlled activation of cortical astrocytes can reverse neuropathic chronic pain
I Takeda, K Yoshihara, D Cheung, M Agetsuma, M Tsuda, K Eto, A Moorhouse, J Nabekura
Research Square
2021 Preprint

Predicting quality decay in continuously passaged mesenchymal stem cell by detecting morphological anomalies
Y Takemoto, Y Imai, K Kanie, R Kato
Journal of Bioscience and Bioengineering
2021 131(2)

Construction and evaluation of osteochondral-like tissue using chondrocyte sheet and cancellous bone
S Wongin, R Narkbunnam, S Waikakul, P Chotiyarnwong, T Aresanasuwan, S Roytrakul, K Viravaidya-Pasuwat
Tissue Engineering, Part A
2021 27(3-4)

p53 is a central regulator driving neurodegeneration caused by C9orf72 poly(PR)
M Maor-Nof, Z Shipony, R Lopez-Gonzalez, L Nakayama, YJ Zhang, J Couthouis, JA Blum, PA Castruita, GR Linares, K Ruan, G Ramaswami, DJ Simon, A Nof, M Santana, K Han, N Sinnott-Armstrong, MC Bassic, DH Geschwind, M Tessier-Lavigne, LD Attardi, TE Lloyd, JK Ichida, FB Gao, WJ Greenleaf, JS Yokoyama, L Petrucelli, AD Gitler
Cell
2021 184(3)

Exploring rare cellular activity in more than one million cells by a trans-scale-scope
T Ichimura, T Kakizuka, K Horikawa, K Seiriki, A Kasai, H Hashimoto, K Fujita, TM Watanabe, T Nagai
BioRxiv
2021 Preprint

Capase-2 regulates S-phase cell cycle events to protect from DNA damage accumulation independent of apoptosis
A Boice, RK Pandita, K Lopez, MJ Parsons, CI Charendoff, V Charaka, AF Carisey, TK Pandita, L Bouchier-Hayes
BioRxiv
2021 Preprint

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells
J Brown, C Barry, MT Schmitz, C Argus, JM Bolin, MP Schwartz, A Van Aartsen, J Steill, S Swanson, R Stewart, JA Thompson, C Kendziorski
PLoS Computational Biology
2021 17(3)

NLRP3 inflammasome and bruton tyrosine kinase inhibition interferes with upregulated platelet aggregation and in vitro thrombus formation in sickle cell mice
S Vogel, S Kamimura, T Arora, ML Smith, LEF Almeida, CA Combs, SL Thein, ZMN Quezado
Biochemical and Biophysical Research Communications
2021 555

Arginine vasopressin-containing neurons of the suprachiasmatic nucleus project to CSF
A Taub, Y Carbajal, K Rimu, R Holt, Y Yao, AL Hernanadez, J LeSauter, R Silver
eNeuro
2021 8(2)

Connectivity characerization of the mouse basolateral amygdalar complex
H Hintiryan, I Bowman, DL Johnson, L Korobkova, M Zhu, N Khanjani, L Gou, L Gao, S Yamashita, MS Bienkowski, L Garcia, NN Foster, NL Benavidez, MY Song, D Lo, K Cotter, M Becerra, S Aquino, C Cao, R Cabeen, J Stanis, M Fayzullina, S Ustrell, T Boesen, ZG Zhang, MS Fanselow, P Golshani, JD Hahn, IR Wickersham, GA Ascoli, LI Zhang, HW Dong
Nature Communications
2021 12

Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes
J Chen, H Sasaki, H Lai, Y Su, J Liu, Y Wu, A Zhovmer, CA Combs, I Rey-Suarez, H Chang, CC Huang, X Li, M Guo, S Nizambad, A Upadhyaya, SJJ Lee, LAG Lucas, H Shroff
Nature Methods
2021 18

3D visualization of immune cell populations in HIV-infected tissues via clearing, immunostaining, confocal, and light sheet fluorescence microscopy
T Zhang, A Gupta, D Frederick, L Layman, DM Smith, S Gianella, C Kieffer
JoVE
2021 171

Effect of sex chromosomes versus hormones in neonatal lung injury
SL Grimm, X Dong, Y Zhang, AF Carisey, AP Arnold, B Moorthy, C Coarfa, K Lingappan
JCI Insight
2021 6(13)

Organization of the inputs and outputs of the mouse superior colliculus
NL Benavidez, MS Bienkowski, M Zhu, LH Garcia, M Fayzullina, L Gao, I Bowman, L Gou, N Khanjani, KR Cotter, L Korobkova, M Becerra, C Cao, MY Song, B Zhang, S Yamashita, AJ Tugangui, B Zingg, K Rose, D Lo, NN Foster, T Boesen, HS Mun, S Aquino, IR Wickersham, GA Ascoli, H Hintiryan, HW Dong
Nature Communications
2021 12

Capturing human trophoblast development with naive pluripotent stem cells in vitro
S Io, M Kabata, Y Iemura, K Semi, N Morone, A Minagawa, B Wang, I Okamoto, T Nakamura, Y Kojima, C Iwatani, H Tsuchiya, B Kaswandy, E Kondoh, S Kaneko, K Woltjen, M Saitou, T Yamamoto, M Mandai, Y Takashima
Cell Stem Cell
2021 28(6)

Efficient targeted transgene delivery to injured lower motor neurons
M Miller, I Hernandez, S Minderler, J Nammour, C Ng, C Maguire, N Jowett
Research Square
2021 Preprint

Tissue clearing to examine tumour complexity in three dimensions
J Almagro, HA Messal, MZ Thin, J van Rheenen, A Behrens
Nature Reviews Cancer
2021 21

Two-photon exictation fluorescent spectral and decay properties of retrograde neuronal tracer Fluoro-Gold
MQ Miller, IC Hernández, JV Chacko, S Minderler, N Jowett
Scientific Reports
2021 11:18053

Metal-nano-ink coating for monitoring and quantification of cotyledon epidermal cell morphogenesis
K Kikukawa, K Yoshimura, A Watanabe, T Higaki
Frontiers in Plant Science
2021 12:745980

Protocol for tissue clearing and 3D analysis of dopamine neurons in the developing mouse midbrain
Y Adolfs, DDA Raj, s Brignani, RJ Pasterkamp
STAR Protocols
2021 2(3)

Video bioinformatics analysis of human pluripotent stem cell morphology, quality, and cellular dynamics
SC Lin, A Loza, L Antrim, P Talbot
Stem Cells Translational Medicine
2021 10(9)

Genetically variant human pluripotent stem cells selectively eliminate wild-type counterparts through YAP-mediated cell competition
CJ Price, D Stavish, PJ Gokhale, BA Stevenson, S Sargeant, J Lacey, TA Rodriguez, I Barbaric
Developmental Cell
2021 56(17)

Cellular anatomy of the mouse primary motor cortex
R Muñoz-Castañeda, B Zingg, KS Matho, Q Wang, X Chen, NN Foster, A Narasimhan, A Li, KE Hirokawa, B Huo, S Bannerjee, L Korobkova, CS Park, YG Park, MS Bienkowski, U Chon, DW Wheeler, Xi Li, Y Wang, K Kelly, X An, SM Attili, I Bowman, A Bludova, A Cetin, L Ding, R Drewes, F d'Orazi, C Elowsky, S Fischer, W Galbavy, L Gao, J Gillis, PA Groblewski, L Gou, JD Hahn, JT Hatfield, H Hintiryan, J Huang, H Kondo, X Kuang, P Lesnar, Xu Li, Y Li, M Lin, L Liu, D Lo, J Mizrachi, S Mok, M Naeemi, PR Nicovich, R Palaniswamy, J Palmer, X Qi, E Shen, YC Sun, H Tao, W Wakeman, Y Wang, P Xie, S Yao, J Yuan, M Zhu, L Ng, LI Zhang, BK Lim, M Hawrylycz, H Gong, JC Gee, Y Kim, H Peng, K Chuang, XW Yang, Q Luo, PP Mitra, AM Zador, H Zeng, GA Ascoli, ZJ Huang, P Osten, JA Harris, HW Dong
Nature
2021 598

The mouse cortico-basal ganglia-thalamic network
NN Foster, L Korobkova, L Garcia, L Gao, M Becerra, Y Sherafat, B Peng, X Li, JH Choi, L Gou, B Zingg, S Azam, D Lo, N Khanjani, B Zhang, J Stanis, I Bowman, K Cotter, C Cao, S Yamashita, A Tugangui, A Li, T Jiang, X Jia, Z Feng, S Aquino, G Dan, M Fayzullina, HS Mun, S Ustrell, T Boesen, A Santarelli, M Zhu, NL Benavidez, M Song, DL Johnson, H Xu, HS Bienkowski, XW Yang, H Gong, I Wickersham, Q Luo, BK Lim, LI Zhang, H Hintiryan, H Dong
Nature
2021 598

Deep learning to analyse microscopy images
G Jacquemet
The Biochemist
2021 43(5)

miR-1 sustains muscle physiology by controlling V-ATPase compex assembly
P Gutiérrez-Pérez, EM Santillán, T Lendl, J Wang, A Schrempf, TL Steinacker, M Asparuhov, M Brandstetter, D Haselbach, L Cochella
Science Advances
2021 7

PUCHI regulates giant cell morphology during root-knot nematode infection in Arabidopsis thaliana
R Suzuki, M Yamada, T Higaki, M Aida, M Kubo, AYL Tsai, S Sawa
Frontiers in Plant Science
2021 12:755610

Tutorial: methods for three-dimensional visualization of archival tissue material
TS Haddad, P Friedl, N Farahani, D Treanor, I Zlobec, I Nagtegaal
Nature Protocols
2021 16

Imaging in focus: an introduction to denoising bioimages in the era of deep learning
RF Laine, G Jacquemet, A Krull
International Journal of Biochemistry and Cell Biology
2021 140

Anti-Siglec-15 antibody suppresses bone resorption by inhibiting osteoclast multinucleation without attenuating bone formation
H Tsukazaki, J Kikuta, T Ao, A Morimoto, C Fukuda, E Tsuda, M Minoshima, K Kikuchi, T Kaito, M Ishii
Bone
2021 152

Navigating the light-sheet image analysis software landscape: concepts for driving cohesion from data acquisition to analysis
HC Gibbs, SM Mota, NA Hart, SW Min, AO Vernino, AL Pritchard, A Sen, S Vitha, S Sarasamma, AL McIntosh, AT Yeh, AC Lekven, DA McCreedy, KC Maitland, LM Perez
Frontiers in Cell and Developmental Biology
2021 9

High concentration of extracellular nucleotides suppresses cell growth via delayed cell cycle progression in cancer and noncancer cell lines
C Sawa, S Yofu, K Kiriyama, K Sutoh, T Saito, S Kishi, M Gunji, Y Inoue, M Sugi, S Shioda, K Honda
Heliyon
2021 7(11)

Tissue clearing
DS Richardson, W Guan, K Matsumoto, C Pan, K Chung, A Ertürk, HR Ueda, JW Lichtman
Nature Reviews Methods Primers
2021 1

Generative adversarial networks for morphological-temporal classification of stem cell images
A Witmer, B Bhanu
Sensors
2021 22(1)

Next-generation imaging: new insights from multicolor microscopy in liver biology and disease
F Heymann, A Guillot, M Peiseler, F Tacke
Engineering
2021 Preprint

Publications 2020

Tutorial: guidance for quantitative confocal microscopy
J Jonkman, CM Brown, CD Wright, KI Anderson, AJ North
Nature Protocols
2020 15

N-terminal amino acids determine KLF4 protein stability in 2A peptide-linked polycistronic reprogramming constructs
A Reinhardt, H Kagawa, K Woltjen
Stem Cell Reports
2020 14(3)

Menthol in electronic cigarettes: a contributor to respiratory disease?
V Nair, M Tran, RZ Behar, S Zhai, X Cui, R Phandthong, Y Wang, S Pan, W Luo, JF Pankow, DC Volz, P Talbot
BioRxiv
2020 Preprint

In vivo dynamic analysis of BMP-2-induced ectopic bone formation
K Hashimoto, T Kaito, M Furuya, S Seno, D Okuzaki, J Kikuta, H Tsukazaki, H Matsuda, H Yoshikawa, M Ishii
Scientific Reports
2020 10

Anisotropic stiffness gradient-regulated mechanical guidance drives directional migration of cancer cells
H Zhang, F Lin, J Huang, C Xiong
Acta Biomaterialia
2020 106

Imaging flowers, a guide to current microscopy and tomography techniques to study flower development
N Prunet, K Duncan
Journal of Experimental Botany
2020 71(10)

3D particle tracking for noninvasive in vivo analysis of synaptic microtubule dynamics in dendrites and neuromuscular junctions of drosophila
VT Chou, HG Yesilyurt, H Lai, JB Long, M Arnes, K Obbad, M Jones, H Sasaki, LAG Lucas, S Alworth, JS Lee, D Van Vactor
JoVE
2020 159

Cellular logics bring the symmetry breaking in spiral nucleation reveled by trans-scale imaging
T Kakizuka, Y Hara, Y Ohta, A Mukai, A Ichiraku, Y Arai, T Ichimura, T Nagai, K Horikawa
BioRxiv
2020 Preprint

The importance of scoring recognition fitness in spheroid morphological analysis for robust label-free quality evaluation
K Shirai, H Kato, Y Imai, M Shibuta, K Kanie, R Kato
Regenerative Therapy
2020 14

Generation of inner ear hair cells by direct lineage conversion of primary somatic cells
L Menendez, T Trecek, S Gopalakrishnan, L Tao, AL Markowitz, HV Yu, X Wang, J Llamas, C Huang, J Lee, R Kalluri, J Ichida, N Segil
eLife
2020 9:e55249

Label-free histomorphometry of peripheral nerve by stimulated Raman spectroscopy
IC Hernández, W Yang, S Mohan, N Jowett
Muscle and Nerve
2020 62(1)

Insulin and Leptin/Upd2 exert opposing influences on synapse number in fat-sensing neurons
AE Brent, A Rajan
Cell Metabolism
2020 15(8)

Four-dimensional imaging with virtual reality to quantitatively explore jigsaw puzzle-like morphogenesis of Arabidopsis cotyledon pavement cells
T Higaki, H Mizuno
Plant Biotechnology
2020 15(8)

Reproducible production and image-based quality evaluation of retinal pigment epithelium sheets from human induced pluripotent stem cells
K Ye, Y Takemoto, A Ito, M Onda, N Morimoto, M Mandai, M Takahashi, R Kato, F Osakada
Scientific Reports
2020 10:14387

Construction and evaluation of osteochondral-like tissue using chondrocyte sheet and cancellous bone
S Wongin, R Narkbunnam, S Waikakul, P Chotiyarnwong, T Aresanasuwan, S Roytrakul, K Viravaidya-Pasuwat
Tissue Engineering, Part A
2020 Preprint

Quantitative neurotoxicology: potential role of artificial intelligence / deep learning approach
A Srivastava, JP Hanig
Journal of Applied Toxicology
2020

The Allen cell and structure segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
J Chen, L Ding, MP Viana, HW Lee, MF Sluezwski, B Morris, MC Hendershott, R Yang, IA Mueller, SM Rafelski
BioRxiv
2020 Preprint

Publications 2019

OVOL1 influences the determination and expansion of iPSC reprogramming intermediates
H Kagawa, R Shimamoto, SI Kim, F Oceguera-Yanez, T Yamamoto, T Schroeder, K Woltjen
Stem Cell Reports
2019 12(2)

Mitochondria stress response in neural stem cells exposed to electronic cigarettes
A Zahedi, R Phandthong, A Chaili, S Leung, E Omaiye, P Talbot
iScience
2019 16

Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues
AK Glaser, NP Reder, Y Chen, C Yin, L Wei, S Kang, LA Barner, W Xie, EF McCarty, C Mao, AR Halpern, CR Stoltzfus, JS Daniels, MY Gerner, PR Nicovich, JC Vaughan, LD True, JTC Liu
Nature Communications
2019 10

The rBC2LCN-postiive subpopulation of PC-3 cells exhibits cancer stem-like properties
S Mawaribuchi, Y Onuma, Y Aiki, Y Kuriyama, M Mutoh, G Fujii, Y Ito
Biochemical and Biophysical Research Communications
2019 515(1)

Time-course colony tracking analysis for evaluating induced pluripotent stem cell culture processes
K Yoshida, M Okada, R Nagasaka, H Sasaki, M Okada, K Kanie, R Kato
Journal of Bioscience and Bioengineering
2019 128(2)

Segmentation and modelling of the nuclear envelope of HeLa cells imaged with serial block face scanning electron microscopy
C Karabağ, ML Jones, CJ Peddie, AE Weston, LM Collinson, CC Reyes-Aldasoro
Journal of Imaging
2019 5(9)

Constitutive expression of a fluorescent protein reports the size of live human cells
DF Berenson, E Zatulovskiy, S Xie, JM Skotheim
Molecular Biology of the Cell
2019 30(24)

C. elegans pronuclei fuse after fertilization through a novel membrane structure
M Rahman, IY Chang, A Harned, R Maheshwari, K Amoateng, K Narayan, O Cohen-Fix
Journal of Cell Biology
2019 219(2)

Effect of mechanical vibration stress in cell culture on human induced pluripotent stem cells
K Kanie, T Sakai, Y Imai, K Yoshida, A Sugimoto, H Makino, H Kubo, R Kato
Regenerative Therapy
2019 12

Publications 2018

Direct cell-cell contact between mature osteoblasts and osteoclasts dynamically controls their functions in vivo
M Furuya, J Kikuta, S Fujimori, S Seno, H Maeda, M Shirazaki, M Uenaka, H Mizuno, Y Iwamoto, A Morimoto, K Hashimoto, T Ito, Y Isogai, M Kashii, T Kaito, S Ohba, UI Chung, AC Lichtler, K Kikuchi, H Matsuda, H Yoshikawa, M Ishii
Nature Communications
2018 9

Size matters: measurement of capsule diameter in Cryptococcus neoformans
T Guess, H Lai, SE Smith, L Sircy, K Cunningham, DE Nelson, EE McClelland
JoVE
2018 132

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons
Y Shi, S Lin, KA Staats, Y Li, WH Chang, ST Hung, E Hendricks, GR Linares, Y Wang, EY Son, X Wen, K Kisler, B Wilkinson, L Menendez, T Sugawara, P Woolwine, M Huang, MJ Cowan, B Ge, N Koutsodendris, KP Sandor, J Komberg, VR Vangoor, K Senthilkumar, V Hennes, C Seah, AR Nelson, TY Cheng, SJJ Lee, PR August, JA Chen, N Wisniewski, V Hanson-Smith, TG Belgard, A Zhang, M Coba, C Brunseich, ME Ward, LH van den Berg, RJ Pasterkamp, D Trotti, BV Zlokovic, JK Ichida
Nature Medicine
2018 24

CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat protein toxicity
NJ Kramer, MS Haney, DW Morgens, A Jovičić, J Couthouis, A Li, J Ousey, R Ma, G Bieri, CK Tsui, Y Shi, NT Hertz, M Tessier-Lavigne, JK Ichida, MC Bassik, AD Gitler
Nature Genetics
2018 50

The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation
AJ McKenzie, SR Hicks, KV Svec, H Naughton, ZL Edmunds, AK Howe
Scientific Reports
2018 8

Using automated live cell imaging to reveal early changes during human motor neuron degeneration
HY Shin, KL Pfaff, LS Davidow, C Sun, T Uozumi, F Yanagawa, Y Yamazaki, Y Kiyota, LL Rubin
eNeuro
2018 5(3)

NeuroMorphoVis: a collaborative framework for analysis and visualization of neuronal morphology skeletons reconstructed from microscopy stacks
M Abdellah, J Hernando, S Eilemann, S Lapere, N Antille, H Markram, F Schürmann
Bioinformatics
2018 34(13)

Metformin treatment ameliorates diabetes-associated decline in hippocampal neurogenesis and memory via phosphorylation of insulin receptor substrate 1
D Tanokashira, E Kurata, W Fukuokaya, K Kawabe, M Kashiwada, H Takeuchi, M Nakazato, A Taguchi
FEBS Open Bio
2018 8(7)

Epithelial-to-mesenchymal transition of A549 lung cancer cells exposed to electronic cigarettes
A Zahedi, R Phandthong, A Chaili, G Remark, P Talbot
Lung Cancer
2018 122

Morphology-based analysis of myoblasts for prediction of myotube formation
K Ishikawa, K Yoshida, K Kanie, K Omori, R Kato
SLAS Discovery
2018 24(1)

Modeling sporadic ALS in iPSC-derived motor neurons identifies a potential therapeutic agent
K Fujimori, M Ishikawa, A Otomo, N Atsuta, R Nakamura, T Akiyama, S Hadano, M Aoki, H Saya, G Sobue, H Okano
Nature Medicine
2018 24

Expression of the alternative oxidase influences Jun N-terminal kinase signaling and cell migration
A Andjelković, A Mordas, L Bruinsma, A Ketola, G Cannino, L Giordano, PK Dhandapani, M Szibor, E Dufour, HT Jacobs
Molecular and Cellular Biology
2018 38(24)

Targeting peroxiredoxin 1 impairs growth of breast cancer cells and potently sensitises these cells to prooxidant agents
M Bajor, AO Zych, A Graczyk-Jarzynka, A Muchowicz, M Firczuk, L Trzeciak, P Gaj, A Domagala, M Siernicka, A Zagozdzon, P Siedlecki, M Kniotek, PC O'Leary, J Golab, R Zagozdzon
British Journal of Cancer
2018 119

Viscoelastic properties of microgel thin films control fibroblast modes of migration and pro-fibrotic responses
D Chester, R Kathard, J Nortey, K Nellenbach, AC Brown
Biomaterials
2018 185

U-Net: deep learning for cell counting, detection and morphometry
T Falk, D Mai, R Bensch, Ö Çiçek, A Abdulkadir, Y Marrakchi, A Böhm, J Deubner, Z Jäckel, K Seiwald, A Dovzhenko, O Tietz, C Dal Bosco, S Walsh, D Saltukoglu, TL Tay, M Prinz, K Palme, M Simons, I Diester, T Brox, O Ronneberger
Nature
2018 16

The Allen Cell Structure Segmenter: a new open source toolkit for segmenting 3D intracellular structures in fluorescence microscopy images
J Chen, L Ding, MP Viana, MC Hendershott, R Yang, IA Mueller, SM Rafelski
BioRxiv
2018 Preprint

In-process evaluation of culture errors using morphology-based image analysis
Y Imai, K Yoshida, M Matsumoto, M Okada, K Kanie, K Shimizu, H Honda, R Kato
Regenerative Therapy
2018 9

Publications 2017

SOX10-nano-lantern reporter human iPS cells; a versatile tool for neural crest research
T Horikiri, H Ohi, M Shibata, M Ikeya, M Ueno, C Sotozono, S Kinoshita, T Sato
PLoS One
2017 12(1)

A xenogeneic-free system generating functional human gut organoids from pluripotent stem cells
H Uchida, M Machida, T Miura, T Kawasaki, T Okazaki, K Sasaki, S Sakamoto, N Ohuchi, M Kasahara, A Umezawa, H Akutsu
JCI Insight
2017 2(1)

Making the cut: innovative methods for optimizing perfusion-based migration assays
AW Holt, WE Howard, ET Ables, SM George, CA Kukoly, JE Rabidou, JT Francisco, AN Chukwu, DA Tulis
Cytometry A
2017 91(3)

Image-based cell quality evaluation to detect irregularities under same culture process of human induced pluripotent stem cells
R Nagasaka, Y Gotou, K Yoshida, K Kanie, K Shimizu, H Honda, R Kato
Journal of Bioscience and Bioengineering
2017 123(5)

Visualization of morphological categories of colonies for monitoring of effect on induced pluripotent stem cell culture status
R Nagasaka, M Matsumoto, M Okada, H Sasaki, K Kanie, H Kii, T Uozumi, Y Kiyota, H Honda, R Kato
Regenerative Therapy
2017 6

Fibroblast-led cancer cell invasion is activated by epithelial-mesenchymal transition through platelet-derived growth factor BB secretion of lung adenocarcinoma
S Neri, T Miyashita, H Hashimoto, Y Suda, M Ishibashi, H Kii, H Watanabe, T Kuwata, M Tsuboi, K Goto, T Menju, M Sonobe, H Date, A Ochiai, G Ishii
Cancer Letters
2017 395

COE inhibits vasculogenic mimicry in hepatocellular carcinoma via suppressing Notch1 signaling
C Jue, Z Min, Z Zhisheng, C Lin, Q Yayun, W Xuanyi, J Feng, W Haibo, S Youyang, H Tadashi, I Shintaro, G Shiyu, L Yanqing
Journal of Ethnopharmacology
2017 208

Morphology-based non-invasive quantitative prediction of the differentiation status of neural stem cells
M Fujitani, NS Huddin, S Kawai, K Kanie, Y Kiyota, K Shimizu, H Honda, R Kato
Journal of Bioscience and Bioengineering
2017 124(3)

Specific electrostatic interactions between charged amino acid residues regulate binding of von Willebrand factor to blood platelets
G Interlandi, O Yakovenko, AY Tu, J Harris, J Le, J Chen, JA López, WE Thomas
Journal of Biological Chemistry
2017 292(45)

3D high-content screening of organioids for drug discovery
L Li, DV LaBarbera
Comprehensive medicinal chemistry III
2017 8()

Publications 2016

Cancer cell invasion driven by extracellular matrix remodeling is dependent on the properties of cancer-associated fibroblasts
S Neri, H Hashimoto, H Kii, H Watanabe, K Masutomi, T Kuwata, H Date, M Tsuboi, K Goto, A Ochiai, G Ishii
Journal of Cancer Research and Clinical Oncology
2016 142(2)

Evaluating cell processes, quality, and biomarkers in pluripotent stem cells using video bioinformatics
A Zahedi, V On, SC Lin, BC Bays, E Omaiye, B Bhanu, P Talbot
PLoS One
2016 11(2)

Differential surface activation of the A1 domain of von Willebrand factor
EH Tronic, O Yakovenko, T Weidner
Biointerphases
2016 11(2)

Cytotoxicity of thirdhand smoke and identification of acrolein as a volatile thirdhand smoke chemical that inhibits cell proliferation
V Bahl, NJH Weng, SF Schick, M Sleiman, J Whitehead, A Ibarra, P Talbot
Toxicological Sciences
2016 150(1)

Morphological evaluation of nonlabeled cells to detect stimulation of nerve growth factor expression by lyconadin B
S Kawai, H Sasaki, N Okada, K Kanie, S Yokoshima, T Fukyama, H Honda, R Kato
Journal of Biomolecular Screening
2016 21(8)

Thirdhand smoke: chemical dynamics cytotoxicity, and genotoxicity in outdoor and indoor environments
V Bahl, HJ Shim, P Jacob, K Dias, SF Schick, P Talbot
Toxicology in Vitro
2016 32

Cell line with endogenous EGFR-VIII expression is a suitable model for research and drug development purposes
WJ Stec, K Rosiak, P Siejka, J Peciak, M Popeda, M Banaszczyk, R Pawlowska, C Treda, K Hulas-Bigoszewska, S Piaskowski, E Stoczynska-Fidelus, P Rieske
Oncotarget
2016 7(22)

Soluble guanylyl cyclase-activated cyclic GMP-dependent protein kinase inhibits arterial smooth muscle cell migration independent of VASP-serine 239 phosphorylation
AW Holt, DN Martin, PR Shaver, SP Adderley, JD Stone, CN Joshi, JT Francisco, RM Lust, DA Weidner, BM Shewchuk, DA Tulis
Cellular Signaling
2016 28(9)

Parameteric analysis of colony morphology of non-labelled live human pluripotent stem cells for cell quality control
R Kato, M Matsumoto, H Sasaki, R Joto, M Okada, Y Ikeda, K Kanie, M Suga, M Kinehara, K Yanagihara, Y Liu, K Uchio-Yamada, T Fukuda, H Kii, T Uozumi, H Honda, Y Kiyota, MK Furue
Scientific Reports
2016 6

Thirdhand cigarette smoke causes stress-induced mitochondrial hyperfusion and alters the transcriptional profile of stem cells
V Bahl, K Johnson, R Phandthong, A Zahedi, SF Schick, P Talbot
Toxicological Sciences
2016 153(1)

Screening of human cDNA library reveals two differentiation-related genes, HHEX and HLX, as promoters of early phase reprogramming toward pluripotency
T Yamakawa, Y Sato, Y Matsumura, Y Kobayashi, Y Kawamura, N Goshima, S Yamanaka, K Okita
Stem Cells
2016 34(11)

Chapter 2 - Imaging GPCRs trafficking and signaling with total internal reflection fluorescence microscopy in cultured neurons
F Delgado-Peraza, C Nogueras-Ortiz, AMA Canabal, C Roman-Vendrell, GA Yudowski
Methods in Cell Biology
2016 132

Publications 2015

KLF4 N-terminal variance modulates induced reprogramming to pluripotency
SI Kim, F Oceguera-Yanez, R Hirohata, S Linker, K Okita, Y Yamada, T Yamamoto, S Yamanaka, K Woltjen
Stem Cell Reports
2015 4

VISIONET: intuitive visualization of overlapping transcription factor networks, with applications in cardiogenic gene discovery
HT Nim, MB Furtado, MW Costa, NA Rosenthal, H Kitano, SE Boyd
BMC Bioinformatics
2015 16

Time-lapse imaging assay using the BioStation CT: a sensitive drug-screening method for three-dimensional cell culture
R Sakamoto, MM Rahman, M Shimomura, M Itoh, T Nakatsura
Cancer Science
2015 106(6)

Pluripotent stem cell growth by time-lapse image analysis
M Suga, H Kii, K Niikura, Y Kiyota, MK Furue
Stem Cells Translational Medicine
2015 4(7)

Evaluation of dynamic cell processes and behavior using video bioinformatics tools
SC Lin, H Yip, R Phandthong, B Davis, P Talbot
Video Bioinformatics
2015 10

Publications 2014

Protein kinase C-induced early growth response protein-1 binding to SNAIL promoter in epithelial mesenchymal transition of human embryonic stem cells
M Kinehara, S Kawamura, S Mimura, M Suga, A Hamada, M Wakabayashi, H Nikawa, MK Furue
Stem Cells and Development
2014 23(18)

NEIL2 protects against oxidative DNA damage induced by sidestream smoke in human cells
AH Sarker, A Chatterjee, M Williams, S Lin, C Havel, P Jacob, I Boldogh, TK Hazra, P Talbot, B Hang
PLoS One
2014 9(3)

Sphingosine 1-phosphate receptor-3 is potential mediator of renal fibrosis
S Shiohira, T Yoshida, H Sugiura, M Nishida, K Nitta, K Tsuchiya
Nephrology Dialysis Transplantation
2014 29(3)

Bio-driven cell region detection in human embryonic stem cell assay
BX Guan, B Bhanu, P Talbot, S Lin
IEEE Transactions on Computational Biology and Bioinformatics
2014 11(3)

MTCL1 crosslinks and stabilizes non-centrosomal microtubules on the Golgi membrane
Y Sato, K Hayashi, Y Amano, M Takahashi, S Yonemura, I Hayashi, H Hirose, S Ohno, A Suzuki
Nature Communications
2014 5

Publications 2013

Gastrointestinal hypomotility with loss of enteric nicotinic acetylcholine receptors: active immunization model in mice
JW Meeusen, KE Haselkorn, JP Fryer, TJ Kryzer, SJ Gibbons, Y Xiao, VA Lennon
Neurogastroenterology and Motility
2013 25(1)

Dynamic visualization of RANKL and Th17-mediated osteoclast function
J Kikuta, Y Wada, T Kowada, Z Wang, GH Sun-Wada, I Nishiyama, S Mizukami, N Maiya, H Yasuda, A Kumanogoh, K Kikuchi, RN Germain, M Ishii
Journal of Clinical Investigation
2013 123(2)

Protein kinase C regulates human pluripotent stem cell self-renewal
M Kinehara, S Kawamura, D Tateyama, M Suga, H Matsumura, S Mimura, N Hirayama, M Hirata, K Uchio-Yamada, A Kohara, K Yanagihara, MK Furue
PLoS One
2013 8(1)

Inhibition of mTORC2 but not mTORC1 up-regulates e-cadherin expression and inhibits cell motility by blocking HIF-2α expression in human renal cell carcinoma
S Maru, Y Ishigaki, N Shinohara, T Takata, N Tomosugi, K Nonomura
Journal of Urology
2013 189(5)

Direct induction of chondrogenic cells from human dermal fibroblast culture by defined factors
H Outani, M Okada, A Yamashita, K Nakagawa, H Yoshikawa, N Tsumaki
PLoS One
2013 8(10)

Publications 2012

Image-based cell quality assessment: modeling of cell morphology and quality for clinical cell therapy
H Sasaki, F Matsuoka, W Yamamoto, K Kojima, H Honda, R Kato
Computational Modeling in Tissue Engineering
2012 10

Publication 2010

Video bioinformatics analysis of human embryonic stem cell colony growth
S Lin, S Fonteno, S Satish, B Bhanu, P Talbot
JoVE
2010 39

Teachable, high-content analytics for live-cell, phase contrast movies
SV Alworth, H Watanabe, JS Lee
Journal of Biomolecular Screening
2010 15(8)

Comparison of the toxicity of smoke from conventional and harm reduction cigarettes using human embryonic stem cells
S Lin, S Fonteno, JH Weng, P Talbot
Toxicological Sciences
2010 118(1)

Publications 2007

Coordinate gene regulation during hematopoiesis is related to genomic organization
ST Kosak, D Scalzo, SV Alworth, F Li, S Palmer, T Enver, JS Lee, M Groudine
PLoS Biology
2007 5(11)