Publications

Fazal S, Danzi MC, Xu I, Kobren SNadimpalli, Sunyaev S, Reuter C, Marwaha S, Wheeler M, Dolzhenko E, Lucas F et al..  2024.  RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci.. Genome Biol. 25(1):39.

Talarico M, de Bellescize J, De Wachter M, Le Guillou X, Le Meur G, Egloff M, Isidor B, Cogné B, Beysen D, Rollier P et al..  2024.  RORA-neurodevelopmental disorder: a unique triad of developmental disability, cerebellar anomalies, and myoclonic seizures.. Genet Med. :101347.

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJune, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K et al..  2024.  Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.. Nat Biotechnol.

Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJune, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K et al..  2024.  Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.. Nat Biotechnol.

Stankovic I, Notaras M, Wolujewicz P, Lu T, Lis R, M Ross E, Colak D.  2024.  Schizophrenia endothelial cells exhibit higher permeability and altered angiogenesis patterns in patient-derived organoids.. Transl Psychiatry. 14(1):53.

Peter CJ, Agarwal A, Watanabe R, Kassim BS, Wang X, Lambert TY, Javidfar B, Evans V, Dawson T, Fridrikh M et al..  2024.  Single chromatin fiber profiling and nucleosome position mapping in the human brain.. Cell Rep Methods. 4(12):100911.

Peter CJ, Agarwal A, Watanabe R, Kassim BS, Wang X, Lambert TY, Javidfar B, Evans V, Dawson T, Fridrikh M et al..  2024.  Single chromatin fiber profiling and nucleosome position mapping in the human brain.. Cell Rep Methods. 4(12):100911.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G et al..  2024.  Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.. Nat Methods. 21(7):1349-1363.

Lopez-Lee C, Kodama L, Fan L, Zhu D, Zhu J, Wong MYing, Ye P, Norman K, Foxe NR, Ijaz L et al..  2024.  Tlr7 drives sex differences in age- and Alzheimer's disease-related demyelination.. Science. 386(6725):eadk7844.

Larrea D, Tamucci KA, Kabra K, Velasco KR, Yun TD, Pera M, Montesinos J, Agrawal RR, Paradas C, Smerdon JW et al..  2025.  Altered mitochondria-associated ER membrane (MAM) function shifts mitochondrial metabolism in amyotrophic lateral sclerosis (ALS).. Nat Commun. 16(1):379.

Barbier M, Rajamani KThirtamara, Netser S, Wagner S, Harony-Nicolas H.  2025.  Altered Neural Activity in the Mesoaccumbens Pathway Underlies Impaired Social Reward Processing in Shank3-Deficient Rats.. Adv Sci (Weinh). :e2414813.

Zheng H, Feng Y, Tang J, Yu F, Wang Z, Xu J, Hai C, Jiang M, Cheng Y, Shao Z et al..  2025.  Astrocyte-secreted cues promote neural maturation and augment activity in human forebrain organoids.. Nat Commun. 16(1):2845.

Li D, Li J, Johann DJ, Butler D, Chen G, Foox J, Gong B, Jones W, Kreil DP, Kusko R et al..  2025.  Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations.. NPJ Precis Oncol. 9(1):182.

Carnevale D, Iadecola C, Wardlaw J.  2025.  Beat strong, think fast: how brain and heart keep each other in check.. Cardiovasc Res. 120(18):2323-2324.

Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor AL, Brittain D et al..  2025.  Connectomics of predicted Sst transcriptomic types in mouse visual cortex.. Nature. 640(8058):497-505.

Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor AL, Brittain D et al..  2025.  Connectomics of predicted Sst transcriptomic types in mouse visual cortex.. Nature. 640(8058):497-505.

Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor AL, Brittain D et al..  2025.  Connectomics of predicted Sst transcriptomic types in mouse visual cortex.. Nature. 640(8058):497-505.

Chen H, Fan L, Guo Q, Wong MYing, Zhu J, Foxe N, Wang W, Nessim A, Carling G, Liu B et al..  2025.  DAP12 deletion reduces neuronal SLIT2 and demyelination and enhances brain resilience in female tauopathy mice.. Mol Neurodegener. 20(1):124.

Chen H, Fan L, Guo Q, Wong MYing, Zhu J, Foxe N, Wang W, Nessim A, Carling G, Liu B et al..  2025.  DAP12 deletion reduces neuronal SLIT2 and demyelination and enhances brain resilience in female tauopathy mice.. Mol Neurodegener. 20(1):124.

Arora J, Ossowski A, Patchell A, Jamison KW, Kuceyeski A, Singh J, Garetti J, Cappillo M, Hamill L, Blunt E et al..  2025.  Depression Symptoms Associated With Clinical Symptoms, Disability, and Functional Connectivity After Traumatic Brain Injury.. J Neuropsychiatry Clin Neurosci. :appineuropsych20240262.