Publications

Sasha L Fulton, Jaroslav Bendl, Giuseppina Di Salvo, John F Fullard, Amni Al-Kachak, Ashley E Lepack, Andrew F Stewart, Sumnima Singh, Wolfram F Poller, Ryan M Bastle, Mads E Hauberg, Amanda K Fakira, Vishwendra Patel, Min Chen, Romain Durand-de Cuttoli, Isabel Gameiro-Ros, Flurin Cathomas, Aarthi Ramakrishnan, Kelly Gleason, Li Shen, Carol A Tamminga, Ana Milosevic, Scott J Russo, Filip K Swirski, Paul A Slesinger, Ishmail Abdus-Saboor, Robert D Blitzer, Panos Roussos, Ian Maze (2025). Major-depressive-disorder-associated dysregulation of ZBTB7A in orbitofrontal cortex promotes astrocyte-mediated stress susceptibility. Neuron.

DOI

John F Fullard, Prashant NM, Donghoon Lee, Deepika Mathur, Karen Therrien, Aram Hong, Clara Casey, Zhiping Shao, Marcela Alvia, Stathis Argyriou, Tereza Clarence, David Burstein, Sanan Venkatesh, Pavan K Auluck, Lisa L Barnes, David A Bennett, Stefano Marenco, Kiran Girdhar, Vahram Haroutunian, Gabriel E Hoffman, Georgios Voloudakis, Jaroslav Bendl*, Panos Roussos* (2025). Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution. Scientific Data.

Code Dataset DOI

Tereza Clarence, Jaroslav Bendl, Xuan Cao, Xinyi Wang, Shiwei Zheng, Gabriel E Hoffman, Alexey Kozlenkov, Aram Hong, Marina Iskhakova, Manoj K Jaiswal, Sarah Murphy, Alexander Yu, Vahram Haroutunian, Stella Dracheva, Schahram Akbarian, John F Fullard, Guo-Cheng Yuan, Donghoon Lee, Panos Roussos (2025). Chromatin accessibility provides a window into the genetic etiology of human brain disease. Nature Genetics.

Code Dataset DOI

Jaroslav Bendl, John F. Fullard, Kiran Girdhar, Pengfei Dong, Roman Kosoy, Biao Zeng, Gabriel E. Hoffman, Panos Roussos (2025). Chromatin accessibility provides a window into the genetic etiology of human brain disease. Trends in Genetics.

DOI

Kevin S O Connell, Maria Koromina, Tracey van der Veen, Toni Boltz, Friederike S David, Jessica Mei Kay Yang, Keng-Han Lin, Xin Wang, Jonathan R I Coleman, Brittany L Mitchell, Caroline C McGrouther, Aaditya V Rangan, Penelope A Lind, Elise Koch, Arvid Harder, Nadine Parker, Jaroslav Bendl, …, Ole A Andreassen, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium (2025). A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping. Nature.

Dataset DOI

Prashant N. M., John F. Fullard, Tereza Clarence, Deepika Mathur, Clara Casey, Evelyn Hennigan, Marcela Alvia, Joana Krause-Massaguer, Ayled Barreda, David A. Davis, Regina T. Vontell, Susanna P. Garamszegi, Jeffery M. Vance, Lorelle Sang, Michael Chatigny, David Vismer, Barry Landin, David Burstein, Donghoon Lee, Georgios Voloudakis, Sabina Berretta, Vahram Haroutunian, William K. Scott, Jaroslav Bendl, Panos Roussos (2024). A multi-region single nucleus transcriptomic atlas of Parkinson's disease. Scientific Data.

Code Dataset DOI

Pengfei Dong, Liting Song, Jaroslav Bendl, Ruth Misir, Zhiping Shao, Jonathan Edelstien, David A. Davis, Vahram Haroutunian, William K. Scott, Susanne Acker, Nathan Lawless, Gabriel E. Hoffman, John F. Fullard, Panos Roussos (2024). A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping. Nature Communications.

Dataset DOI

Bo Zhou, Joseph G Arthur, Hanmin Guo, Taeyoung Kim, Yiling Huang, Reenal Pattni, Tao Wang, Soumya Kundu, Jay X J Luo, HoJoon Lee, Daniel C Nachun, Carolin Purmann, Emma M Monte, Annika K Weimer, Ping-Ping Qu, Minyi Shi, Lixia Jiang, Xinqiong Yang, John F Fullard, Jaroslav Bendl, Kiran Girdhar, Minsu Kim, Xi Chen, PsychENCODE Consortium, William J Greenleaf, Laramie Duncan, Hanlee P Ji, Xiang Zhu, Giltae Song, Stephen B Montgomery, Dean Palejev, Heinrich Zu Dohna, Panos Roussos, Anshul Kundaje, Joachim F Hallmayer, Michael P Snyder, Wing H Wong, Alexander E Urban (2024). Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell.

DOI

Qi Wang, Jerry Antone, Eric Alsop, Rebecca Reiman, Cory Funk, Jaroslav Bendl, Joel T Dudley, Winnie S Liang, Timothy L Karr, Panos Roussos, David A Bennett, Philip L De Jager, Geidy E Serrano, Thomas G Beach, Kendall Van Keuren-Jensen, Diego Mastroeni, Eric M Reiman, Benjamin P Readhead (2024). Single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease. Nature Communications.

Code Dataset DOI

Brad W. Ruzicka, Shahin Mohammadi, John F Fullard, Jose Davila-Velderrain, Sivan Subburaju, Daniel Reed Tso, Makayla Hourihan, Shan Jiang, Hao-Chih Lee, Jaroslav Bendl, PsychENCODE Consortium, Georgios Voloudakis, Vahram Haroutunian, Gabriel E Hoffman, Panos Roussos, Manolis Kellis (2024). Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science.

Dataset DOI

Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Pengyu Ni, Xiao Zhou, PsychENCODE Consortium, Trygve E Bakken, Jaroslav Bendl, Lucy Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panos Roussos, Nenad Sestan, Zhiping Weng, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel Geschwind, Mark Gerstein (2024). Single-cell genomics and regulatory networks for 388 human brains. Science.

Dataset DOI

Biao Zeng*, Jaroslav Bendl*, Chengyu Deng, Donghoon Lee, Ruth Misir, Sarah M Reach, Steven P Kleopoulos, Pavan Auluck, Stefano Marenco, David A Lewis, Vahram Haroutunian, Nadav Ahituv, John F Fullard, Gabriel E Hoffman, Panos Roussos (2024). Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology. Science.

Dataset DOI

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.

PDF DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

Dataset DOI

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.

PDF DOI

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.

PDF DOI

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.

PDF Dataset DOI

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.

PDF Code Dataset DOI

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.

PDF Code Dataset DOI

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.

PDF Dataset Slides DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

PDF Code Dataset DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

Code DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

PDF Dataset DOI

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.

PDF DOI

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

DOI

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.

PDF DOI

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.

PDF DOI

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.

PDF DOI

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.

DOI

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

DOI

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.

DOI

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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