Publications

Pramod Bharadwaj Chandrashekar, Sayali Alatkar, Jiebiao Wang, Gabriel E Hoffman, Chenfeng He, Ting Jin, Saniya Khullar, Jaroslav Bendl, John F Fullard, Panos Roussos, Daifeng Wang (2023). DeepGAMI: deep biologically guided auxiliary learning for multimodal integration and imputation to improve genotype–phenotype prediction. Genome Medicine.

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Kaiyi Zhu*, Jaroslav Bendl*, Samir Rahman, James M Vicari, Claire Coleman, Tereza Clarence, Ovaun Latouche, Nadejda M Tsankova, Aiqun Li, Kristen J Brennand, Donghoon Lee, Guo-Cheng Yuan, John F Fullard, Panos Roussos (2023). Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Nucleic Acids Research.

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Samir Rahman, Pengfei Dong, Pasha Apontes, Michael B Fernando, Roman Kosoy, Kayla G Townsley, Kiran Girdhar, Jaroslav Bendl, Zhiping Shao, Ruth Misir, Nadia Tsankova, Steven P Kleopoulos, Kristen J Brennand, John F Fullard, Panos Roussos (2023). Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome. Nucleic Acids Research.

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Mathilde Pruvost, Julia Patzig, Camila Yattah, Ipek Selcen, Marylens Hernandez, Hye-Jin Park, Sarah Moyon, Shibo Liu, Malia S Morioka, Lindsay Shopland, Osama Al-Dalahmah, Jaroslav Bendl, John F Fullard, Panos Roussos, James Goldman, Ye He, Jeffrey L Dupree, Patrizia Casaccia (2023). The stability of the myelinating oligodendrocyte transcriptome is regulated by the nuclear lamina. Cell Reports.

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Claire Coleman, Minghui Wang, Erming Wang, Courtney Micallef, Zhiping Shao, James M Vicari, Yuxin Li, Kaiwen Yu, Dongming Cai, Junmin Peng, Vahram Haroutunian, John F Fullard, Jaroslav Bendl, Bin Zhang, Panos Roussos (2023). Multi-omic atlas of the parahippocampal gyrus in Alzheimers disease. Scientific Data.

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David Burstein, Trevor C. Griffen, Karen Therrien, Jaroslav Bendl, Sanan Venkatesh, Pengfei Dong, Amirhossein Modabbernia, Biao Zeng, Deepika Mathur, Gabriel Hoffman, Robyn Sysko, Tom Hildebrandt, Georgios Voloudakis, Panos Roussos (2023). Genome-wide analysis of a model-derived binge eating disorder phenotype identifies risk loci and implicates iron metabolism. Nature Genetics.

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Yixuan Ma*, Jaroslav Bendl*, Brigham J Hartley, John F Fullard, Rawan Abdelaal, Seok-Man Ho, Roman Kosoy, Peter Gochman, Judith Rapoport, Gabriel E Hoffman, Kristen J Brennand, Panos Roussos (2023). Activity-Dependent Transcriptional Program in NGN2+ Neurons Enriched for Genetic Risk for Brain-Related Disorders. Biological Psychiatry.

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Erming Wang, Minghui Wang, Lei Guo, John F Fullard, Courtney Micallef, Jaroslav Bendl, Won-Min Song, Chen Ming, Yong Huang, Yuxin Li, Kaiwen Yu, Junmin Peng, David A Bennett, Philip L De Jager, Panos Roussos, Vahram Haroutunian, Bin Zhang (2023). Genome-wide methylomic regulation of multiscale gene networks in Alzheimers disease. Alzheimers & Dementia.

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Ditte Demontis, G Bragi Walters, Georgios Athanasiadis, Raymond Walters, Karen Therrien, Leila Farajzadeh, Georgios Voloudakis, Jaroslav Bendl, Biao Zeng, Wen Zhang, Jakob Grove, Thomas D Als, Jinjie Duan, F Kyle Satterstrom, Jonas Bybjerg-Grauholm, Marie Baekved-Hansen, Olafur O Gudmundsson, Sigurdur H Magnusson, Gisli Baldursson, Katrin Davidsdottir, Gyda S Haraldsdottir, Trine Tollerup Nielsen, Esben Agerbo, Gabriel E Hoffman, Soeren Dalsgaard, Joanna Martin, Marta Ribases, Dorret I Boomsma, Maria Soler Artigas, Nina Roth Mota, Daniel Howrigan, Sarah E Medland, Tetyana Zayats, Veera Manikandan, ADHD Working Group of the Psychiatric Genomics Consortium, iPSYCH-Broad Consortium, Merete Nordentoft, Ole Mors, David M Hougaard, Preben Bo Mortensen, Mark J Daly, Stephen V Faraone, Hreinn Stefansson, Panos Roussos, Barbara Franke, Thomas Werge, Benjamin M Neale, Kari Stefansson, Anders D Børglum (2023). Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains. Nature Genetics.

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Ditte Demontis, G Bragi Walters, Georgios Athanasiadis, Raymond Walters, Karen Therrien, Leila Farajzadeh, Georgios Voloudakis, Jaroslav Bendl, Biao Zeng, Wen Zhang, Jakob Grove, Thomas D Als, Jinjie Duan, F Kyle Satterstrom, Jonas Bybjerg-Grauholm, Marie Baekved-Hansen, Olafur O Gudmundsson, Sigurdur H Magnusson, Gisli Baldursson, Katrin Davidsdottir, Gyda S Haraldsdottir, Trine Tollerup Nielsen, Esben Agerbo, Gabriel E Hoffman, Soeren Dalsgaard, Joanna Martin, Marta Ribases, Dorret I Boomsma, Maria Soler Artigas, Nina Roth Mota, Daniel Howrigan, Sarah E Medland, Tetyana Zayats, Veera Manikandan, ADHD Working Group of the Psychiatric Genomics Consortium, iPSYCH-Broad Consortium, Merete Nordentoft, Ole Mors, David M Hougaard, Preben Bo Mortensen, Mark J Daly, Stephen V Faraone, Hreinn Stefansson, Panos Roussos, Barbara Franke, Thomas Werge, Benjamin M Neale, Kari Stefansson, Anders D Børglum (2023). Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains. Nature Genetics.

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Sasha L. Fulton, Wendy Wenderski, Ashley E. Lepack, Andrew L. Eagle, Tomas Fanutza, Ryan M. Bastle, Aarthi Ramakrishnan, Emma C. Hays, Arianna Neal, Jaroslav Bendl, Lorna A. Farrelly, Amni Al-Kachak, Yang Lyu, Bulent Cetin, Jennifer C. Chan, Tina N. Tran, Rachael L. Neve, Randall J. Roper, Kristen J. Brennand, Panos Roussos, John C. Schimenti, Allyson K. Friedman, Li Shen, Robert D. Blitzer, Alfred J. Robison, Gerald R. Crab, Ian Maze (2022). Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome. Nature Communications.

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Jaroslav Bendl*, Mads E. Hauberg*, Kiran Girdhar*, Eunju Im, James M. Vicari, Samir Rahman, Michael B. Fernando, Kayla G. Townsley, Pengfei Dong, Ruth Misir, Steven P. Kleopoulos, Sarah M. Reach, Pasha Apontes, Biao Zeng, Wen Zhang, Georgios Voloudakis, Kristen J. Brennand, Ralph A. Nixon, Vahram Haroutunian, Gabriel E. Hoffman, John F. Fullard, Panos Roussos (2022). The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease. Nature Neuroscience.

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Pengfei Dong, Gabriel E. Hoffman, Pasha Apontes, Jaroslav Bendl, Samir Rahman, Michael B. Fernando, Biao Zeng, James M. Vicari, Wen Zhang, Kiran Girdhar, Kayla G. Townsley, Ruth Misir, the CommonMind Consortium, Kristen J. Brennand, Vahram Haroutunian, Georgios Voloudakis, John F. Fullard, Panos Roussos (2022). Population-level variation in enhancer expression identifies disease mechanisms in the human brain. Nature Genetics.

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Manuel Mattheisen, Jakob Grove, Thomas D. Als, Joanna Martin, Georgios Voloudakis, Sandra Meier, Ditte Demontis, Jaroslav Bendl, Raymond Walters, Caitlin E. Carey, Anders Rosengren, Nora I. Strom, Mads Engel Hauberg, Biao Zeng, Gabriel Hoffman, Wen Zhang, Jonas Bybjerg-Grauholm, Marie Bækvad-Hansen, Esben Agerbo, Bru Cormand, Merete Nordentoft, Thomas Werge, Ole Mors, David M. Hougaard, Joseph D. Buxbaum, Stephen V. Faraone, Barbara Franke, Søren Dalsgaard, Preben B. Mortensen, Elise B. Robinson, Panos Roussos, Benjamin M. Neale, Mark J. Daly, Anders D. Børglum (2022). Identification of shared and differentiating genetic architecture for autism spectrum disorder, attention-deficit hyperactivity disorder and case subgroups. Nature Genetics.

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Dongxin Liu, Amy Zinski, Akanksha Mishra, Haneul Noh, Gun-Hoo Park, Yiren Qin, Oshoname Olorife, James M. Park, Chiderah P. Abani, Joy S. Park, Janice Fung, Farah Sawaqed, Joseph T. Coyle, Eli Stahl, Jaroslav Bendl, John F. Fullard, Panos Roussos, Xiaolei Zhang, Patric K. Stanton, Changhong Yin, Weihua Huang, Hae-Young Kim, Hyejung Won, Jun-Hyeong Cho, Sangmi Chung (2022). Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development. Molecular Psychiatry.

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Kiran Girdhar, Gabriel E. Hoffman, Jaroslav Bendl, Samir Rahman, Pengfei Dong, Will Liao, Mads E. Hauberg, Laura Sloofman, Leanne Brown, Olivia Devillers, Bibi S. Kassim, Jennifer R. Wiseman, Royce Park, Elizabeth Zharovsky, Rivky Jacobov, Elie Flatow, Alexey Kozlenkov, Thomas Gilgenast, Jessica S. Johnson, Lizette Couto, Mette A. Peters, Jennifer E. Phillips-Cremins, Chang-Gyu Hahn, Raquel E. Gur, Carol A. Tamminga, David A. Lewis, Vahram Haroutunian, PsychENCODE Consortium, Stella Dracheva, Barbara K. Lipska, Stefano Marenco, Marija Kundakovic, John F. Fullard, Yan Jiang, Panos Roussos, Schahram Akbarian (2022). Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains. Nature Neuroscience.

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Bingxin Zhao, Tengfei Li, Stephen M. Smith, Di Xiong, Xifeng Wang, Yue Yang, Tianyou Luo, Ziliang Zhu, Yue Shan, Nana Matoba, Quan Sun, Yuchen Yang, Mads E. Hauberg, Jaroslav Bendl, John F. Fullard, Panagiotis Roussos, Weili Lin, Yun Li, Jason L. Stein, Hongtu Zhu (2022). Common variants contribute to intrinsic human brain functional networks. Nature Genetics.

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Biao Zeng, Jaroslav Bendl, Roman Kosoy, John F. Fullard, Gabriel E. Hoffman, Panos Roussos (2022). Identification of shared and differentiating genetic architecture for autism spectrum disorder, attention-deficit hyperactivity disorder and case subgroups. Nature Genetics.

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Maria-Daniela Cirnaru, Sicheng Song, Kizito-Tshitoko Tshilenge, Chuhyon Corwin, Justyna Mleczko, Carlos Galicia Aguirre, Houda Benlhabib, Jaroslav Bendl, Pasha Apontes, John Fullard, Jordi Creus-Muncunill, Azadeh Reyahi, Ali M Nik, Peter Carlsson, Panos Roussos, Sean D Mooney, Lisa M Ellerby, Michelle E Ehrlich (2021). Unbiased identification of novel transcription factors in striatal compartmentation and striosome maturation. eLife.

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John F Fullard*, Jaroslav Bendl*, Panos Roussos (2021). ATAC-seq and psychiatric disorders. Epigenetics in Psychiatry.

DOI

Roman Kosoy*, John F. Fullard*, Biao Zeng*, Jaroslav Bendl*, Pengfei Dong, Samir Rahman, Steven P. Kleopoulos, Zhiping Shao, Kiran Girdhar, Jack Humphrey, Katia de Paiva Lopes, Alexander W. Charney, Brian H. Kopell, Towfique Raj, David Bennett, Christopher P. Kellner, Vahram Haroutunian, Gabriel E. Hoffman, Panos Roussos (2021). Genetics of the human microglia regulome refines Alzheimer’s disease risk loci. Nature Genetics.

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Gabriel E. Hoffman*, Yixuan Ma*, Kelsey S. Montgomery, Jaroslav Bendl, Manoj Kumar Jaiswal, Alex Kozlenkov, Mette A. Peters, Stella Dracheva, John F. Fullard, Andrew Chess, Bernie Devlin, Solveig K. Sieberts, Panos Roussos (2021). Sex Differences in the Human Brain Transcriptome of Cases With Schizophrenia. Biological Psychiatry.

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Gloriia Novikova, Manav Kapoor, Julia TCW, Edsel M. Abud, Anastasia G. Efthymiou, Steven X. Chen, Haoxiang Cheng, John F. Fullard, Jaroslav Bendl, Yiyuan Liu, Panos Roussos, Johan LM Björkegren, Yunlong Liu, Wayne W. Poon, Ke Hao, Edoardo Marcora, Alison M. Goate (2021). Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes. Nature Communications.

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Bingxin Zhao, Tengfei Li, Yue Yang, Xifeng Wang, Tianyou Luo, Yue Shan, Ziliang Zhu, Di Xiong, Mads E. Hauberg, Jaroslav Bendl, John F. Fullard, Panagiotis Roussos, Yun Li, Jason L. Stein, Hongtu Zhu (2021). Common genetic variation influencing human white matter microstructure. Science.

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Mads E. Hauberg*, Jordi Creus-Muncunill*, Jaroslav Bendl*, Alexey Kozlenkov, Biao Zeng, Chuhyon Corwin, Sarah Chowdhury, Harald Kranz, Yasmin L. Hurd, Michael Wegner, Anders D. Børglum, Stella Dracheva, Michelle E. Ehrlich, John F. Fullard, Panos Roussos (2020). Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons. Nature Communications.

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Sergio Espeso-Gil, Tobias Halene, Jaroslav Bendl, Bibi Kassim, Gabriella Ben Hutta, Marina Iskhakova, Neda Shokrian, Pavan Auluck, Behnam Javidfar, Prashanth Rajarajan, Sandhya Chandrasekaran, Cyril J. Peter, Alanna Cote, Rebecca Birnbaum, Will Liao, Tyler Borrman, Jennifer Wiseman, Aaron Bell, Michael J. Bannon, Panagiotis Roussos, John F. Crary, Zhiping Weng, Stefano Marenco, Barbara Lipska, Nadejda M. Tsankova, Laura Huckins, Yan Jiang, Schahram Akbarian (2020). A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome Medicine.

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Gabriel E Hoffman, Jaroslav Bendl, Kiran Girdhar, Panos Roussos (2020). decorate: Differential Epigenetic Correlation Test. Bioinformatics.

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Gabriel E Hoffman, Jaroslav Bendl, Kiran Girdhar, Eric E Schadt, Panos Roussos (2019). Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification. ChemBioChem.

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Gabriel E Hoffman, Jaroslav Bendl, Georgios Voloudakis, Kelsey S Montgomery, Laura Sloofman, Ying-Chih Wang, Hardik R Shah, Mads E Hauberg, Jessica S Johnson, Kiran Girdhar, Lingyun Song, John F Fullard, Robin Kramer, Chang-Gyu Hahn, Raquel Gur, Stefano Marenco, Barbara K Lipska, David A Lewis, Vahram Haroutunian, Scott Hemby, Patrick Sullivan, Schahram Akbarian, Andrew Chess, Joseph D Buxbaum, Greg E Crawford, Enrico Domenici, Bernie Devlin, Solveig K Sieberts, Mette A Peters, Panos Roussos (2019). CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder. Scientific Data.

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Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chen Ming, Ryan Neff, Weiping Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Allan I. Levey, Joseph D. Buxbaum, Michelle Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric Schadt, Bin Zhang (2018). The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease. Scientific Data.

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John F. Fullard*, Mads E. Hauberg*, Jaroslav Bendl, Gabor Egervari, Maria-Daniela Cirnaru, Sarah M. Reach, Jan Motl, Michelle E. Ehrlich, Yasmin L. Hurd, Panos Roussos (2018). An atlas of chromatin accessibility in the adult human brain. Genome Research.

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Andreas Schwarte, Maika Genz, Lilly Skalden, Alberto Nobili, Clare Vickers, Okke Melse, Remko Kuipers, Henk-Jan Joosten, Jan Stourac, Jaroslav Bendl, Jon Black, Peter Haase, Coos Baakman, Jiri Damborsky, Uwe Bornscheuer, Gert Vriend, Hanka Venselaar (2017). NewProt - a protein engineering portal . Protein Engineering, Design and Selection.

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Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomas Martinek, David Bednar, Jiri Damborsky (2017). FireProt: web server for automated design of thermostable proteins. Nucleic Acids Research.

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Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jiri Damborsky, Jan Brezovsky (2016). PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS computational biology.

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Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jiri Damborsky, Jan Brezovsky, Jiri Damborsky (2016). HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Research.

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David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jiri Damborsky (2015). FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS computational biology.

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Pavel Dvorak, Nagendra Prasad Kurumbang, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jiri Damborsky (2014). Maximizing the efficiency of multienzyme process by stoichiometry optimization. ChemBioChem.

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Eva Sebestova, Jaroslav Bendl, Jan Brezovsky, Jiri Damborsky (2014). Computational tools for designing smart libraries. Directed Evolution Library Creation.

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Nagendra Prasad Kurumbang, Pavel Dvorak, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jiri Damborsky (2014). Computer-assisted engineering of the synthetic pathway for biodegradation of a toxic persistent pollutant. ACS Synthetic Biology.

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Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky (2014). PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations. PLoS computational biology.

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